references.bib

@dataset{abarenkov2023,
  type = {application/gzip},
  title = {{{UNITE}} General {{FASTA}} Release for {{Fungi}} 2},
  author = {Abarenkov, Kessy and Zirk, Allan and Piirmann, Timo and Pöhönen, Raivo and Ivanov, Filipp and Nilsson, R. Henrik and Kõljalg, Urmas},
  date = {2023-07-18},
  publisher = {UNITE Community},
  doi = {10.15156/BIO/2938068},
  url = {https://doi.plutof.ut.ee/doi/10.15156/BIO/2938068},
  urldate = {2024-02-04},
  abstract = {This release consists of a single FASTA file: the RepS/RefS of all SHs, adopting the dynamically use of clustering thresholds whenever available. Includes global and 97\% singletons.}
}

@dataset{abarenkov2023a,
  type = {application/gzip},
  title = {{{UNITE}} General {{FASTA}} Release for {{Fungi}}},
  author = {Abarenkov, Kessy and Zirk, Allan and Piirmann, Timo and Pöhönen, Raivo and Ivanov, Filipp and Nilsson, R. Henrik and Kõljalg, Urmas},
  date = {2023-07-18},
  publisher = {UNITE Community},
  doi = {10.15156/BIO/2938067},
  url = {https://doi.plutof.ut.ee/doi/10.15156/BIO/2938067},
  urldate = {2024-02-04},
  abstract = {This release consists of a single FASTA file: the RepS/RefS of all SHs, adopting the dynamically use of clustering thresholds whenever available.}
}

@incollection{adams2002,
  title = {Symbiotic {{Interactions}}},
  booktitle = {The {{Ecology}} of {{Cyanobacteria}}},
  author = {Adams, David G.},
  editor = {Whitton, Brian A. and Potts, Malcolm},
  date = {2002},
  pages = {523--561},
  publisher = {Kluwer Academic Publishers},
  location = {Dordrecht},
  doi = {10.1007/0-306-46855-7_19},
  url = {http://link.springer.com/10.1007/0-306-46855-7_19},
  urldate = {2024-05-02},
  isbn = {978-0-7923-4735-4},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Adams - 2002 - Symbiotic Interactions.pdf}
}

@article{aimone2023,
  title = {Fungal {{Symbionts Generate Water-Saver}} and {{Water-Spender Plant Drought Strategies}} via {{Diverse Effects}} on {{Host Gene Expression}}},
  author = {Aimone, Catherine D. and Giauque, Hannah and Hawkes, Christine V.},
  date = {2023-09},
  journaltitle = {Phytobiomes Journal},
  shortjournal = {Phytobiomes Journal},
  volume = {7},
  number = {2},
  pages = {172--183},
  issn = {2471-2906},
  doi = {10.1094/PBIOMES-01-22-0006-FI},
  url = {https://apsjournals.apsnet.org/doi/10.1094/PBIOMES-01-22-0006-FI},
  urldate = {2024-04-08},
  abstract = {Foliar fungal endophytes are known to alter plant physiology but the mechanisms by which they do so remain poorly understood. We focused on how plant gene expression was altered by six fungal strains that generated “water-saver” and “water-spender” drought physiologies in a C4 grass, Panicum hallii. Water-saver physiologies have lower plant water loss, improved wilt resistance, and higher survival compared with water-spender strategies. We expected that fungi within each functional group would have similar effects on P. hallii, and this was largely true for plant physiology but not for plant gene expression. When we focused only on genes that were differentially expressed relative to fungus-free controls, we found surprisingly little overlap in plant differentially expressed genes or gene regulatory pathways across the fungal treatments, including within and between the water-saver and water-spender strategies. Nevertheless, using lasso regression, we identified a small subset of genes that predicted 39 and 53\% of the variation in plant wilt resistance and water loss, respectively. These results suggest that fungal effects on plant transcription may identify how they extend the plant phenotype, and the comparison across multiple fungi allows us to differentiate broadly fungal-responsive plant genes versus those plant genes that respond only to single fungal taxa. The genes identified here could be targeted for future study to understand their function and, ultimately, represent candidates for precision breeding efforts to increase plant drought tolerance.             [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Aimone et al. - 2023 - Fungal Symbionts Generate Water-Saver and Water-Sp.pdf}
}

@article{albrectsen2010,
  title = {Endophytic Fungi in {{European}} Aspen ({{Populus}} Tremula) Leaves—Diversity, Detection, and a Suggested Correlation with Herbivory Resistance},
  author = {Albrectsen, Benedicte R. and Björkén, Lars and Varad, Akkamahadevi and Hagner, Åsa and Wedin, Mats and Karlsson, Jan and Jansson, Stefan},
  date = {2010-03},
  journaltitle = {Fungal Diversity},
  shortjournal = {Fungal Diversity},
  volume = {41},
  number = {1},
  pages = {17--28},
  issn = {1560-2745, 1878-9129},
  doi = {10.1007/s13225-009-0011-y},
  url = {http://link.springer.com/10.1007/s13225-009-0011-y},
  urldate = {2024-04-14},
  langid = {english}
}

@article{ali2016,
  title = {{{RAD Capture}} ({{Rapture}}): {{Flexible}} and {{Efficient Sequence-Based Genotyping}}},
  shorttitle = {{{RAD Capture}} ({{Rapture}})},
  author = {Ali, Omar A and O’Rourke, Sean M and Amish, Stephen J and Meek, Mariah H and Luikart, Gordon and Jeffres, Carson and Miller, Michael R},
  date = {2016-02-01},
  journaltitle = {Genetics},
  volume = {202},
  number = {2},
  pages = {389--400},
  issn = {1943-2631},
  doi = {10.1534/genetics.115.183665},
  url = {https://academic.oup.com/genetics/article/202/2/389/5930231},
  urldate = {2024-04-07},
  abstract = {Abstract             Massively parallel sequencing has revolutionized many areas of biology, but sequencing large amounts of DNA in many individuals is cost-prohibitive and unnecessary for many studies. Genomic complexity reduction techniques such as sequence capture and restriction enzyme-based methods enable the analysis of many more individuals per unit cost. Despite their utility, current complexity reduction methods have limitations, especially when large numbers of individuals are analyzed. Here we develop a much improved restriction site-associated DNA (RAD) sequencing protocol and a new method called Rapture (RAD capture). The new RAD protocol improves versatility by separating RAD tag isolation and sequencing library preparation into two distinct steps. This protocol also recovers more unique (nonclonal) RAD fragments, which improves both standard RAD and Rapture analysis. Rapture then uses an in-solution capture of chosen RAD tags to target sequencing reads to desired loci. Rapture combines the benefits of both RAD and sequence capture, i.e., very inexpensive and rapid library preparation for many individuals as well as high specificity in the number and location of genomic loci analyzed. Our results demonstrate that Rapture is a rapid and flexible technology capable of analyzing a very large number of individuals with minimal sequencing and library preparation cost. The methods presented here should improve the efficiency of genetic analysis for many aspects of agricultural, environmental, and biomedical science.},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Ali et al. - 2016 - RAD Capture (Rapture) Flexible and Efficient Sequ.pdf}
}

@incollection{anderson2017,
  title = {Permutational {{Multivariate Analysis}} of {{Variance}} ( {{PERMANOVA}} )},
  booktitle = {Wiley {{StatsRef}}: {{Statistics Reference Online}}},
  author = {Anderson, Marti J.},
  date = {2017-11-15},
  pages = {1--15},
  publisher = {Wiley},
  doi = {10.1002/9781118445112.stat07841},
  abstract = {PERMANOVA is a computer program for testing the simultaneous response of one or more variables to one or more factors in an ANOVA experimental design on the basis of any distance measure, using permutation methods. These notes for users assume knowledge of multi-factorial ANOVA, which has the same basic logic in multivariate as in univariate analysis, and an understanding of what it means to test a multivariate hypothesis. A more complete description of the method is given in Anderson (2001a) and McArdle \& Anderson (2001). The program includes: choice of appropriate transformation and/or standardization of the data; choice of 19 distance (or dissimilarity) measures to use as the basis of the analysis; option to rank the distances in the distance matrix before the analysis; analysis and partitioning of the total sum of squares according to the full model, including appropriate treatment of factors that are fixed or random, crossed (orthogonal) or nested (hierarchical), and all interaction terms; correct calculation of an appropriate distance-based pseudo F-statistic for each term in the model, based on expected mean squares as in univariate ANOVA (Winer et al. 1991, Searle et al.1992); correct permutation procedures to obtain P-values for each term in the model, using the correct permutable units (Anderson \& ter Braak 2003); choice of permutation method: raw data units or residuals under either a reduced or a full model (Anderson 2001b, Anderson \& Legendre 1999, Anderson \& Robinson 2001); correct P-values also obtained through Monte Carlo random draws from the asymptotic permutation distribution (Anderson \& Robinson 2003); option to include one or more covariables (i.e., to perform ANCOVA or MANCOVA); pair-wise a posteriori comparisons of levels for single factors, including within individual levels of other factors in the case of significant interactions and the use of correct permutable units in each case.}
}

@software{andrews2010,
  title = {{{FastQC}}},
  author = {Andrews, Simon and Krueger, Felix and Segonds-Pichon, Anne and Biggins, Laura and Krueger, Christel and Wingett, Steven},
  date = {2010},
  location = {Babraham, UK},
  abstract = {FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.},
  copyright = {GPL v3},
  howpublished = {Babraham Institute},
  version = {0.12.1}
}

@article{apigo2022,
  title = {Plant Abundance, but Not Plant Evolutionary History, Shapes Patterns of Host Specificity in Foliar Fungal Endophytes},
  author = {Apigo, Austen and Oono, Ryoko},
  date = {2022-01},
  journaltitle = {Ecosphere},
  shortjournal = {Ecosphere},
  volume = {13},
  number = {1},
  pages = {e03879},
  issn = {2150-8925, 2150-8925},
  doi = {10.1002/ecs2.3879},
  url = {https://esajournals.onlinelibrary.wiley.com/doi/10.1002/ecs2.3879},
  urldate = {2024-03-08},
  abstract = {Abstract             Understanding the origins and maintenance of host specificity, or why horizontally‐acquired symbionts associate with some hosts but not others, remains elusive. In this study, we explored whether patterns of host specificity in foliar fungal endophytes, a guild of highly diverse fungi that occur within the photosynthetic tissues of all major plant lineages, were related to characteristics of the plant community. We comprehensively sampled all plant host species within a single community and tested the relationship between plant abundance or plant evolutionary relatedness and metrics of endophyte host specificity. We quantified host specificity with methods that considered the total endophyte community per plant host (i.e., multivariate methods) along with species‐based methods (i.e., univariate metrics) that considered host specificity from the perspective of each endophyte. Univariate host specificity metrics quantified plant alpha‐diversity (structural specificity), plant beta‐diversity (beta‐specificity), and plant phylogenetic diversity (phylogenetic specificity) per endophyte. We standardized the effect sizes of univariate host specificity metrics to randomized distributions to avoid spurious correlations between host specificity metrics and endophyte abundance. We found that more abundant plant species harbored endophytes that occupied fewer plant species (higher structural specificity) and were consistently found in the same plant species across the landscape (higher beta‐specificity). There was no relationship between plant phylogenetic distance and endophyte community dissimilarity. We still found that endophyte community composition significantly varied among plant species, families, and major groups, supporting a plant identity effect. In particular, endophytes in angiosperm lineages associated with narrower phylogenetic breadths of plants (higher phylogenetic specificity) compared to endophytes within conifer and fern lineages. Overall, an effect of plant species abundance may help explain why horizontally‐transmitted endophytes vary geographically within host species ranges.},
  langid = {english},
  file = {/home/baponte/Zotero/storage/NJP9H53K/Apigo and Oono - 2022 - Plant abundance, but not plant evolutionary histor.pdf}
}

@online{aponterolon2023,
  title = {High-{{Molecular-Weight SPRI-aided DNA}} Extraction from {{Mimulus}} ({{Phrymaceae}}) Leaf Tissue.},
  author = {Aponte Rolón, Bolívar},
  date = {2023},
  url = {dx.doi.org/10.17504/protocols.io.bp2l6xn8rlqe/v2}
}

@article{armstrong2022,
  title = {Applications and {{Comparison}} of {{Dimensionality Reduction Methods}} for {{Microbiome Data}}},
  author = {Armstrong, George and Rahman, Gibraan and Martino, Cameron and McDonald, Daniel and Gonzalez, Antonio and Mishne, Gal and Knight, Rob},
  date = {2022-02-24},
  journaltitle = {Frontiers in Bioinformatics},
  shortjournal = {Front. Bioinform.},
  volume = {2},
  pages = {821861},
  issn = {2673-7647},
  doi = {10.3389/fbinf.2022.821861},
  url = {https://www.frontiersin.org/articles/10.3389/fbinf.2022.821861/full},
  urldate = {2024-06-11},
  abstract = {Dimensionality reduction techniques are a key component of most microbiome studies, providing both the ability to tractably visualize complex microbiome datasets and the starting point for additional, more formal, statistical analyses. In this review, we discuss the motivation for applying dimensionality reduction techniques, the special characteristics of microbiome data such as sparsity and compositionality that make this difficult, the different categories of strategies that are available for dimensionality reduction, and examples from the literature of how they have been successfully applied (together with pitfalls to avoid). We conclude by describing the need for further development in the field, in particular combining the power of phylogenetic analysis with the ability to handle sparsity, compositionality, and non-normality, as well as discussing current techniques that should be applied more widely in future analyses.},
  file = {/home/baponte/Box/Dissertation/master_papers/Armstrong et al. - 2022 - Applications and Comparison of Dimensionality Redu.pdf}
}

@article{arnold2003,
  title = {Fungal Endophytes Limit Pathogen Damage in a Tropical Tree},
  author = {Arnold, A Elizabeth and Mejía, Luis Carlos and Kyllo, Damond and Rojas, Enith I and Maynard, Zuleyka and Robbins, Nancy and Herre, Edward Allen},
  date = {2003},
  journaltitle = {Proceedings of the National Academy of Sciences},
  volume = {100},
  number = {26},
  pages = {15649--15654},
  abstract = {Every plant species examined to date harbors endophytic fungi within its asymptomatic aerial tissues, such that endophytes rep-resent a ubiquitous, yet cryptic, component of terrestrial plant communities. Fungal endophytes associated with leaves of woody angiosperms are especially diverse; yet, fundamental aspects of their interactions with hosts are unknown. In contrast to the relatively species-poor endophytes that are vertically transmitted and act as defensive mutualists of some temperate grasses, the diverse, horizontally transmitted endophytes of woody angio-sperms are thought to contribute little to host defense. Here, we document high diversity, spatial structure, and host affinity among foliar endophytes associated with a tropical tree (Theobroma cacao, Malvaceae) across lowland Panama. We then show that inoculation of endophyte-free leaves with endophytes isolated frequently from naturally infected, asymptomatic hosts signifi-cantly decreases both leaf necrosis and leaf mortality when T. cacao seedlings are challenged with a major pathogen (Phytophthora sp.). In contrast to reports of fungal inoculation inducing systemic defense, we found that protection was primarily localized to endophyte-infected tissues. Further, endophyte-mediated protec-tion was greater in mature leaves, which bear less intrinsic defense against fungal pathogens than do young leaves. In vitro studies suggest that host affinity is mediated by leaf chemistry, and that protection may be mediated by direct interactions of endophytes with foliar pathogens. Together, these data demonstrate the capacity of diverse, horizontally transmitted endophytes of woody angiosperms to play an important but previously unappreciated role in host defense.}
}

@article{arnold2007,
  title = {Fungal Endophytes Nearly Double Minimum Leaf Conductance in Seedlings of a Neotropical Tree Species},
  author = {Arnold, A. Elizabeth and Engelbrecht, Bettina M. J.},
  date = {2007-05},
  journaltitle = {Journal of Tropical Ecology},
  shortjournal = {J. Trop. Ecol.},
  volume = {23},
  number = {3},
  pages = {369--372},
  issn = {0266-4674, 1469-7831},
  doi = {10.1017/S0266467407004038},
  url = {https://www.cambridge.org/core/product/identifier/S0266467407004038/type/journal_article},
  urldate = {2024-01-20},
  abstract = {Drought strongly influences plant phenology, growth and mortality in tropical forests, thereby shaping plant performance, population dynamics and community structure (Bunker \& Carson 2005, Condit               et al.               1995). Microbial symbionts of plants profoundly influence host water relations (Lösch \& Gansert 2002), but are rarely considered in studies of tropical plant physiology. In particular, plant–fungus associations, which are ubiquitous in plant communities and especially common in tropical forests, play important and varied roles in plant water status. Fungal pathogens associated with roots, vascular tissue and foliage may interfere with water uptake and transport, increase rates of foliar transpiration, and induce xylem embolism and tissue death (Agrios 1997). In contrast, rhizosphere mutualists such as ecto- and arbuscular mycorrhizal fungi may benefit hosts by increasing surface area for water uptake, enhancing stomatal regulation of water loss, and increasing root hydraulic conductivity (Auge 2001, Lösch \& Gansert 2002).},
  langid = {english}
}

@article{arnold2019,
  title = {How to Analyse Plant Phenotypic Plasticity in Response to a Changing Climate},
  author = {Arnold, Pieter A. and Kruuk, Loeske E. B. and Nicotra, Adrienne B.},
  date = {2019-05},
  journaltitle = {New Phytologist},
  shortjournal = {New Phytologist},
  volume = {222},
  number = {3},
  pages = {1235--1241},
  issn = {0028-646X, 1469-8137},
  doi = {10.1111/nph.15656},
  url = {https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.15656},
  urldate = {2024-05-10},
  abstract = {Summary               Plant biology is experiencing a renewed interest in the mechanistic underpinnings and evolution of phenotypic plasticity that calls for a re‐evaluation of how we analyse phenotypic responses to a rapidly changing climate. We suggest that dissecting plant plasticity in response to increasing temperature needs an approach that can represent plasticity over multiple environments, and considers both population‐level responses and the variation between genotypes in their response. Here, we outline how a random regression mixed model framework can be applied to plastic traits that show linear or nonlinear responses to temperature. Random regressions provide a powerful and efficient means of characterising plasticity and its variation. Although they have been used widely in other fields, they have only recently been implemented in plant evolutionary ecology. We outline their structure and provide an example tutorial of their implementation.},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Arnold et al. - 2019 - How to analyse plant phenotypic plasticity in resp.pdf}
}

@article{arya.hoffmann2011,
  title = {Climate Change and Evolutionary Adaptation},
  author = {{Ary A. Hoffmann} and Hoffmann, Ary A. and {Carla M. Sgrò} and Sgrò, Carla M.},
  date = {2011-02-24},
  journaltitle = {Nature},
  volume = {470},
  number = {7335},
  eprint = {21350480},
  eprinttype = {pmid},
  pages = {479--485},
  doi = {10.1038/nature09670},
  abstract = {Evolutionary adaptation can be rapid and potentially help species counter stressful conditions or realize ecological opportunities arising from climate change. The challenges are to understand when evolution will occur and to identify potential evolutionary winners as well as losers, such as species lacking adaptive capacity living near physiological limits. Evolutionary processes also need to be incorporated into management programmes designed to minimize biodiversity loss under rapid climate change. These challenges can be met through realistic models of evolutionary change linked to experimental data across a range of taxa.},
  annotation = {MAG ID: 2008951609}
}

@manual{barton2023,
  type = {manual},
  title = {{{MuMIn}}: {{Multi-model}} Inference},
  author = {Bartoń, Kamil},
  date = {2023},
  url = {https://CRAN.R-project.org/package=MuMIn}
}

@article{belisle2012,
  title = {Flowers as {{Islands}}: {{Spatial Distribution}} of {{Nectar-Inhabiting Microfungi}} among {{Plants}} of {{Mimulus}} Aurantiacus, a {{Hummingbird-Pollinated Shrub}}},
  shorttitle = {Flowers as {{Islands}}},
  author = {Belisle, Melinda and Peay, Kabir G. and Fukami, Tadashi},
  date = {2012-05},
  journaltitle = {Microbial Ecology},
  shortjournal = {Microb Ecol},
  volume = {63},
  number = {4},
  pages = {711--718},
  issn = {0095-3628, 1432-184X},
  doi = {10.1007/s00248-011-9975-8},
  url = {http://link.springer.com/10.1007/s00248-011-9975-8},
  urldate = {2024-06-13},
  langid = {english},
  file = {/home/baponte/Box/Dissertation/master_papers/Belisle et al. - 2012 - Flowers as Islands Spatial Distribution of Nectar.pdf}
}

@article{benjamini1995,
  title = {Controlling the {{False Discovery Rate}}: {{A Practical}} and {{Powerful Approach}} to {{Multiple Testing}}},
  shorttitle = {Controlling the {{False Discovery Rate}}},
  author = {Benjamini, Yoav and Hochberg, Yosef},
  date = {1995-01},
  journaltitle = {Journal of the Royal Statistical Society: Series B (Methodological)},
  shortjournal = {Journal of the Royal Statistical Society: Series B (Methodological)},
  volume = {57},
  number = {1},
  pages = {289--300},
  issn = {0035-9246, 2517-6161},
  doi = {10.1111/j.2517-6161.1995.tb02031.x},
  url = {https://rss.onlinelibrary.wiley.com/doi/10.1111/j.2517-6161.1995.tb02031.x},
  urldate = {2024-01-14},
  abstract = {SUMMARY The common approach to the multiplicity problem calls for controlling the familywise error rate (FWER). This approach, though, has faults, and we point out a few. A different approach to problems of multiple significance testing is presented. It calls for controlling the expected proportion of falsely rejected hypotheses — the false discovery rate. This error rate is equivalent to the FWER when all hypotheses are true but is smaller otherwise. Therefore, in problems where the control of the false discovery rate rather than that of the FWER is desired, there is potential for a gain in power. A simple sequential Bonferronitype procedure is proved to control the false discovery rate for independent test statistics, and a simulation study shows that the gain in power is substantial. The use of the new procedure and the appropriateness of the criterion are illustrated with examples.},
  langid = {english}
}

@article{bergelson2021,
  title = {Assessing the Potential to Harness the Microbiome through Plant Genetics},
  author = {Bergelson, Joy and Brachi, Benjamin and Roux, Fabrice and Vailleau, Fabienne},
  date = {2021-08},
  journaltitle = {Current Opinion in Biotechnology},
  shortjournal = {Current Opinion in Biotechnology},
  volume = {70},
  pages = {167--173},
  issn = {09581669},
  doi = {10.1016/j.copbio.2021.05.007},
  url = {https://linkinghub.elsevier.com/retrieve/pii/S0958166921000744},
  urldate = {2024-04-10},
  langid = {english}
}

@article{beslile2012,
  title = {Flowers as Islands: {{Spatial}} Distribution of Nectar-Inhabiting Microfungi among Plants of {{{\emph{Mimulus}}}}{\emph{ Aurantiacus}}, a Hummingbird-Pollinated Shrub},
  author = {Beslile, Melinda and Peay, Kabir G. and Fukami, Tadashi},
  date = {2012},
  journaltitle = {Microbial Ecology},
  volume = {63},
  number = {4},
  pages = {711--718},
  doi = {10.1007/s00248-011-9975-8.Flowers},
  keywords = {dispersal limitation,floral nectar,metschnikowia reukaufii,microbial distribution,nectar yeast}
}

@article{blanchet2008,
  title = {{{FORWARD SELECTION OF EXPLANATORY VARIABLES}}},
  author = {Blanchet, F. Guillaume and Legendre, Pierre and Borcard, Daniel},
  date = {2008-09},
  journaltitle = {Ecology},
  shortjournal = {Ecology},
  volume = {89},
  number = {9},
  pages = {2623--2632},
  issn = {0012-9658, 1939-9170},
  doi = {10.1890/07-0986.1},
  url = {https://esajournals.onlinelibrary.wiley.com/doi/10.1890/07-0986.1},
  urldate = {2024-01-14},
  abstract = {This paper proposes a new way of using forward selection of explanatory variables in regression or canonical redundancy analysis. The classical forward selection method presents two problems: a highly inflated Type I error and an overestimation of the amount of explained variance. Correcting these problems will greatly improve the performance of this very useful method in ecological modeling. To prevent the first problem, we propose a two‐step procedure. First, a global test using all explanatory variables is carried out. If, and only if, the global test is significant, one can proceed with forward selection. To prevent overestimation of the explained variance, the forward selection has to be carried out with two stopping criteria: (1) the usual alpha significance level and (2) the adjusted coefficient of multiple determination (                                                              ) calculated using all explanatory variables. When forward selection identifies a variable that brings one or the other criterion over the fixed threshold, that variable is rejected, and the procedure is stopped. This improved method is validated by simulations involving univariate and multivariate response data. An ecological example is presented using data from the Bryce Canyon National Park, Utah, USA.},
  langid = {english}
}

@article{bodenhausen2014,
  title = {A {{Synthetic Community Approach Reveals Plant Genotypes Affecting}} the {{Phyllosphere Microbiota}}},
  author = {Bodenhausen, Natacha and Bortfeld-Miller, Miriam and Ackermann, Martin and Vorholt, Julia A.},
  date = {2014-04-17},
  journaltitle = {PLOS Genetics},
  volume = {10},
  number = {4},
  eprint = {24743269},
  eprinttype = {pmid},
  doi = {10.1371/journal.pgen.1004283},
  abstract = {The identity of plant host genetic factors controlling the composition of the plant microbiota and the extent to which plant genes affect associated microbial populations is currently unknown. Here, we use a candidate gene approach to investigate host effects on the phyllosphere community composition and abundance. To reduce the environmental factors that might mask genetic factors, the model plant Arabidopsis thaliana was used in a gnotobiotic system and inoculated with a reduced complexity synthetic bacterial community composed of seven strains representing the most abundant phyla in the phyllosphere. From a panel of 55 plant mutants with alterations in the surface structure, cell wall, defense signaling, secondary metabolism, and pathogen recognition, a small number of single host mutations displayed an altered microbiota composition and/or abundance. Host alleles that resulted in the strongest perturbation of the microbiota relative to the wild-type were lacs2 and pec1. These mutants affect cuticle formation and led to changes in community composition and an increased bacterial abundance relative to the wild-type plants, suggesting that different bacteria can benefit from a modified cuticle to different extents. Moreover, we identified ein2, which is involved in ethylene signaling, as a host factor modulating the community's composition. Finally, we found that different Arabidopsis accessions exhibited different communities, indicating that plant host genetic factors shape the associated microbiota, thus harboring significant potential for the identification of novel plant factors affecting the microbiota of the communities.},
  pmcid = {3990490},
  annotation = {MAG ID: 1990582630},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Bodenhausen et al. - 2014 - A Synthetic Community Approach Reveals Plant Genot.pdf}
}

@article{bowman2021,
  title = {Drivers and Implications of Distance Decay Differ for Ectomycorrhizal and Foliar Endophytic Fungi across an Anciently Fragmented Landscape},
  author = {Bowman, Elizabeth A. and Arnold, A. Elizabeth},
  date = {2021-12},
  journaltitle = {The ISME Journal},
  shortjournal = {ISME J},
  volume = {15},
  number = {12},
  pages = {3437--3454},
  issn = {1751-7362, 1751-7370},
  doi = {10.1038/s41396-021-01006-9},
  url = {https://www.nature.com/articles/s41396-021-01006-9},
  urldate = {2023-11-16},
  abstract = {Fungal communities associated with plants often decrease in similarity as the distance between sampling sites increases (i.e., they demonstrate distance decay). In the southwestern USA, forests occur in highlands separated from one another by warmer, drier biomes with plant and fungal communities that differ from those at higher elevations. These disjunct forests are broadly similar in climate to one another, offering an opportunity to examine drivers of distance decay in plant-associated fungi across multiple ecologically similar yet geographically disparate landscapes. We examined ectomycorrhizal and foliar endophytic fungi associated with a dominant forest tree (Pinus ponderosa) in forests across ca. 550 km of geographic distance from northwestern to southeastern Arizona (USA). Both guilds of fungi showed distance decay, but drivers differed for each: ectomycorrhizal fungi are constrained primarily by dispersal limitation, whereas foliar endophytes are constrained by specific environmental conditions. Most ectomycorrhizal fungi were found in only a single forested area, as were many endophytic fungi. Such regional-scale perspectives are needed for baseline estimates of fungal diversity associated with forest trees at a landscape scale, with attention to the sensitivity of different guilds of fungal symbionts to decreasing areas of suitable habitat, increasing disturbance, and related impacts of climate change.},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Bowman and Arnold - 2021 - Drivers and implications of distance decay differ .pdf}
}

@article{bowsher2020,
  title = {Locally {{Adapted}} {{{\emph{Mimulus}}}} {{Ecotypes Differentially Impact Rhizosphere Bacterial}} and {{Archaeal Communities}} in an {{Environment-Dependent Manner}}},
  author = {Bowsher, Alan W. and Kearns, Patrick J. and Popovic, Damian and Lowry, David B. and Shade, Ashley},
  date = {2020-01},
  journaltitle = {Phytobiomes Journal},
  shortjournal = {Phytobiomes Journal},
  volume = {4},
  number = {1},
  pages = {53--63},
  issn = {2471-2906, 2471-2906},
  doi = {10.1094/PBIOMES-05-19-0026-R},
  url = {https://apsjournals.apsnet.org/doi/10.1094/PBIOMES-05-19-0026-R},
  urldate = {2024-04-08},
  abstract = {Plant root−microbe interactions influence plant productivity, health, and resistance to stress. Although there is evidence that plant species and even genotypes can alter soil microbial community structure, environmental conditions can potentially outweigh plant genetic effects. Here, we used a reciprocal transplant experiment to understand the contributions of the environment and the host plant to rhizosphere microbiome composition in locally adapted ecotypes of Mimulus guttatus (syn. Erythranthe guttata). Two genotypes of a coastal ecotype and two genotypes of an inland ecotype were planted at coastal and inland sites. After 3 months, we collected rhizosphere and bulk soil and assessed microbial communities by 16S rRNA gene sequencing. We found that local environment (coastal versus inland site) strongly influenced rhizosphere communities, at least in part due to distinct local microbial species pools. Host identity played a smaller role: at each site, the ecotypes exhibited remarkably similar composition of microbial communities at the class level, indicating that divergent M. guttatus ecotypes recruit phylogenetically similar rhizosphere communities, even in environments to which they are maladapted. Nevertheless, the two ecotypes significantly differed in community composition at both sites due, in part, to an exclusive set of taxa associated with each ecotype. They also differed in alpha diversity at the inland site. Although this indicates that locally adapted M. guttatus ecotypes are genetically diverged in factors shaping rhizosphere communities, our findings highlight the context-specific interactions between host identity and local environment that shape those communities.             [Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Bowsher et al. - 2020 - Locally Adapted Mimulus Ecotypes Differenti.pdf}
}

@article{brachi2022,
  title = {Plant Genetic Effects on Microbial Hubs Impact Host Fitness in Repeated Field Trials},
  author = {Brachi, Benjamin and Filiault, Daniele and Whitehurst, Hannah and Darme, Paul and Le Gars, Pierre and Le Mentec, Marine and Morton, Timothy C. and Kerdaffrec, Envel and Rabanal, Fernando and Anastasio, Alison and Box, Mathew S. and Duncan, Susan and Huang, Feng and Leff, Riley and Novikova, Polina and Perisin, Matthew and Tsuchimatsu, Takashi and Woolley, Roderick and Dean, Caroline and Nordborg, Magnus and Holm, Svante and Bergelson, Joy},
  date = {2022-07-26},
  journaltitle = {Proceedings of the National Academy of Sciences},
  shortjournal = {Proc. Natl. Acad. Sci. U.S.A.},
  volume = {119},
  number = {30},
  pages = {e2201285119},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.2201285119},
  url = {https://pnas.org/doi/full/10.1073/pnas.2201285119},
  urldate = {2024-04-10},
  abstract = {Although complex interactions between hosts and microbial associates are increasingly well documented, we still know little about how and why hosts shape microbial communities in nature. In addition, host genetic effects on microbial communities vary widely depending on the environment, obscuring conclusions about which microbes are impacted and which plant functions are important. We characterized the leaf microbiota of 200               Arabidopsis thaliana               genotypes in eight field experiments and detected consistent host effects on specific, broadly distributed microbial species (operational taxonomic unit [OTUs]). Host genetic effects disproportionately influenced central ecological hubs, with heritability of particular OTUs declining with their distance from the nearest hub within the microbial network. These host effects could reflect either OTUs preferentially associating with specific genotypes or differential microbial success within them. Host genetics associated with microbial hubs explained over 10\% of the variation in lifetime seed production among host genotypes across sites and years. We successfully cultured one of these microbial hubs and demonstrated its growth-promoting effects on plants in sterile conditions. Finally, genome-wide association mapping identified many putatively causal genes with small effects on the relative abundance of microbial hubs across sites and years, and these genes were enriched for those involved in the synthesis of specialized metabolites, auxins, and the immune system. Using untargeted metabolomics, we corroborate the consistent association between variation in specialized metabolites and microbial hubs across field sites. Together, our results reveal that host genetic variation impacts the microbial communities in consistent ways across environments and that these effects contribute to fitness variation among host genotypes.},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Brachi et al. - 2022 - Plant genetic effects on microbial hubs impact hos.pdf}
}

@article{brandvain2014,
  title = {Speciation and {{Introgression Between}} {{{\emph{Mimulus}}}}{\emph{ Nasutus}} and {{{\emph{Mimulus}}}}{\emph{ Guttatus}}},
  author = {Brandvain, Yaniv and Kenney, Amanda M. and Flagel, Lex and Coop, Graham and Sweigart, Andrea L.},
  editor = {Jiggins, Chris D.},
  date = {2014-06-26},
  journaltitle = {PLoS Genetics},
  shortjournal = {PLoS Genet},
  volume = {10},
  number = {6},
  pages = {e1004410},
  issn = {1553-7404},
  doi = {10.1371/journal.pgen.1004410},
  url = {https://dx.plos.org/10.1371/journal.pgen.1004410},
  urldate = {2024-07-13},
  langid = {english},
  file = {/home/baponte/Box/Dissertation/master_papers/Brandvain et al. - 2014 - Speciation and Introgression between Mimulus nasut.pdf}
}

@article{busby2016,
  title = {Fungal Endophytes: Modifiers of Plant Disease},
  shorttitle = {Fungal Endophytes},
  author = {Busby, Posy E. and Ridout, Mary and Newcombe, George},
  date = {2016-04},
  journaltitle = {Plant Molecular Biology},
  shortjournal = {Plant Mol Biol},
  volume = {90},
  number = {6},
  pages = {645--655},
  issn = {0167-4412, 1573-5028},
  doi = {10.1007/s11103-015-0412-0},
  url = {http://link.springer.com/10.1007/s11103-015-0412-0},
  urldate = {2024-04-08},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Busby et al. - 2016 - Fungal endophytes modifiers of plant disease.pdf}
}

@article{buzzini2018,
  title = {Extremophilic Yeasts: The Toughest Yeasts Around?},
  shorttitle = {Extremophilic Yeasts},
  author = {Buzzini, Pietro and Turchetti, Benedetta and Yurkov, Andrey},
  date = {2018-08},
  journaltitle = {Yeast},
  shortjournal = {Yeast},
  volume = {35},
  number = {8},
  pages = {487--497},
  issn = {0749-503X, 1097-0061},
  doi = {10.1002/yea.3314},
  url = {https://onlinelibrary.wiley.com/doi/10.1002/yea.3314},
  urldate = {2024-03-20},
  abstract = {Abstract             Microorganisms are widely distributed in a multitude of environments including ecosystems that show challenging features to most life forms. The combination of extreme physical and chemical factors contributes to the definition of extreme habitats although the definition of extreme environments changes depending on one's point of view: anthropocentric, microbial‐centric or zymo‐centric. Microorganisms that live under conditions that cause hard survival are called extremophiles. In particular organisms that require extreme conditions are called true extremophiles while organisms that tolerate them to some extent are termed extremotolerant. Deviation of temperature, pH, osmotic stress, pressure and radiation from the common range delineates extreme environments. Yeasts are versatile eukaryotic organisms that are not frequently considered the toughest microorganisms in comparison with prokaryotes. Nevertheless extremophilic or extremotolerant species are present also within this group. Here a brief description is provided of the main extreme habitats and the metabolic and physiological modifications adopted by yeasts depending on their adverse conditions. Additionally the main extremophilic and extremotolerant yeast species associated with a few extreme habitats are listed.},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Buzzini et al. - 2018 - Extremophilic yeasts the toughest yeasts around.pdf}
}

@article{byrne2022,
  title = {Plant Development: {{Elementary}} Changes Determine Leaf Shape Complexity},
  shorttitle = {Plant Development},
  author = {Byrne, Mary E.},
  date = {2022-09},
  journaltitle = {Current Biology},
  shortjournal = {Current Biology},
  volume = {32},
  number = {17},
  pages = {R912-R914},
  issn = {09609822},
  doi = {10.1016/j.cub.2022.07.013},
  url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982222011149},
  urldate = {2024-05-13},
  langid = {english},
  file = {/home/baponte/Zotero/storage/A9BUM9TS/Byrne - 2022 - Plant development Elementary changes determine le.pdf}
}

@article{callahan2016,
  title = {{{DADA2}}: {{High-resolution}} Sample Inference from {{Illumina}} Amplicon Data},
  shorttitle = {{{DADA2}}},
  author = {Callahan, Benjamin J and McMurdie, Paul J and Rosen, Michael J and Han, Andrew W and Johnson, Amy Jo A and Holmes, Susan P},
  date = {2016-07},
  journaltitle = {Nature Methods},
  shortjournal = {Nat Methods},
  volume = {13},
  number = {7},
  pages = {581--583},
  issn = {1548-7091, 1548-7105},
  doi = {10.1038/nmeth.3869},
  url = {https://www.nature.com/articles/nmeth.3869},
  urldate = {2023-09-26},
  langid = {english}
}

@article{cameron2021,
  title = {Enhancing Diversity Analysis by Repeatedly Rarefying next Generation Sequencing Data Describing Microbial Communities},
  author = {Cameron, Ellen and Schmidt, Philip and Tremblay, Benjamin and Emelko, Monica and Müller, Kirsten},
  date = {2021-11},
  journaltitle = {Scientific Reports},
  volume = {11},
  pages = {22302},
  doi = {10.1038/s41598-021-01636-1},
  file = {/home/baponte/Boxx/Dissertation/master_papers/41598_2021_1636_MOESM1_ESM.docx;/home/baponte/Boxx/Dissertation/master_papers/Cameron et al. - 2021 - Enhancing diversity analysis by repeatedly rarefyi.pdf}
}

@article{chao2014,
  title = {Unifying {{Species Diversity}}, {{Phylogenetic Diversity}}, {{Functional Diversity}}, and {{Related Similarity}} and {{Differentiation Measures Through Hill Numbers}}},
  author = {Chao, Anne and Chiu, Chun-Huo and Jost, Lou},
  date = {2014-11-23},
  journaltitle = {Annual Review of Ecology, Evolution, and Systematics},
  shortjournal = {Annu. Rev. Ecol. Evol. Syst.},
  volume = {45},
  number = {1},
  pages = {297--324},
  issn = {1543-592X, 1545-2069},
  doi = {10.1146/annurev-ecolsys-120213-091540},
  url = {https://www.annualreviews.org/doi/10.1146/annurev-ecolsys-120213-091540},
  urldate = {2024-02-17},
  abstract = {Hill numbers or the effective number of species are increasingly used to quantify species diversity of an assemblage. Hill numbers were recently extended to phylogenetic diversity, which incorporates species evolutionary history, as well as to functional diversity, which considers the differences among species traits. We review these extensions and integrate them into a framework of attribute diversity (the effective number of entities or total attribute value) based on Hill numbers of taxonomic entities (species), phylogenetic entities (branches of unit-length), or functional entities (species-pairs with unit-distance between species). This framework unifies ecologists' measures of species diversity, phylogenetic diversity, and distance-based functional diversity. It also provides a unified method of decomposing these diversities and constructing normalized taxonomic, phylogenetic, and functional similarity and differentiation measures, including N-assemblage phylogenetic or functional generalizations of the classic Jaccard, Sørensen, Horn, and Morisita-Horn indexes. A real example shows how this framework extracts ecological meaning from complex data.},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Chao et al. - 2014 - Unifying Species Diversity, Phylogenetic Diversity.pdf}
}

@article{chao2014a,
  title = {Rarefaction and Extrapolation with {{Hill}} Numbers: A Framework for Sampling and Estimation in Species Diversity Studies},
  shorttitle = {Rarefaction and Extrapolation with {{Hill}} Numbers},
  author = {Chao, Anne and Gotelli, Nicholas J. and Hsieh, T. C. and Sander, Elizabeth L. and Ma, K. H. and Colwell, Robert K. and Ellison, Aaron M.},
  date = {2014-02},
  journaltitle = {Ecological Monographs},
  shortjournal = {Ecological Monographs},
  volume = {84},
  number = {1},
  pages = {45--67},
  issn = {0012-9615, 1557-7015},
  doi = {10.1890/13-0133.1},
  url = {https://esajournals.onlinelibrary.wiley.com/doi/10.1890/13-0133.1},
  urldate = {2024-04-11},
  abstract = {Quantifying and assessing changes in biological diversity are central aspects of many ecological studies, yet accurate methods of estimating biological diversity from sampling data have been elusive. Hill numbers, or the effective number of species, are increasingly used to characterize the taxonomic, phylogenetic, or functional diversity of an assemblage. However, empirical estimates of Hill numbers, including species richness, tend to be an increasing function of sampling effort and, thus, tend to increase with sample completeness. Integrated curves based on sampling theory that smoothly link rarefaction (interpolation) and prediction (extrapolation) standardize samples on the basis of sample size or sample completeness and facilitate the comparison of biodiversity data. Here we extended previous rarefaction and extrapolation models for species richness (Hill number                                q                 D                              , where               q               = 0) to measures of taxon diversity incorporating relative abundance (i.e., for any Hill number                                q                 D                              ,               q               {$>$} 0) and present a unified approach for both individual‐based (abundance) data and sample‐based (incidence) data. Using this unified sampling framework, we derive both theoretical formulas and analytic estimators for seamless rarefaction and extrapolation based on Hill numbers. Detailed examples are provided for the first three Hill numbers:               q               = 0 (species richness),               q               = 1 (the exponential of Shannon's entropy index), and               q               = 2 (the inverse of Simpson's concentration index). We developed a bootstrap method for constructing confidence intervals around Hill numbers, facilitating the comparison of multiple assemblages of both rarefied and extrapolated samples. The proposed estimators are accurate for both rarefaction and short‐range extrapolation. For long‐range extrapolation, the performance of the estimators depends on both the value of               q               and on the extrapolation range. We tested our methods on simulated data generated from species abundance models and on data from large species inventories. We also illustrate the formulas and estimators using empirical data sets from biodiversity surveys of temperate forest spiders and tropical ants.},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Chao et al. - 2014 - Rarefaction and extrapolation with Hill numbers a.pdf}
}

@article{christianeroscher2012,
  title = {Using {{Plant Functional Traits}} to {{Explain Diversity}}–{{Productivity Relationships}}},
  author = {{Christiane Roscher} and Roscher, Christiane and {Jens Schumacher} and Schumacher, Jens and {Marlén Gubsch} and Gubsch, Marlén and {Annett Lipowsky} and Lipowsky, Annett and {Alexandra Weigelt} and Weigelt, Alexandra and {Nina Buchmann} and Buchmann, Nina and {Bernhard Schmid} and Schmid, Bernhard and {Ernst Detlef Schulze} and Schulze, Ernst Detlef},
  date = {2012-05-18},
  journaltitle = {PLOS ONE},
  volume = {7},
  number = {5},
  eprint = {22623961},
  eprinttype = {pmid},
  doi = {10.1371/journal.pone.0036760},
  abstract = {Background  The different hypotheses proposed to explain positive species richness–productivity relationships, i.e. selection effect and complementarity effect, imply that plant functional characteristics are at the core of a mechanistic understanding of biodiversity effects. Methodology/Principal Findings  We used two community-wide measures of plant functional composition, (1) community-weighted means of trait values (CWM) and (2) functional trait diversity based on Rao’s quadratic diversity (FDQ) to predict biomass production and measures of biodiversity effects in experimental grasslands (Jena Experiment) with different species richness (2, 4, 8, 16 and 60) and different functional group number and composition (1 to 4; legumes, grasses, small herbs, tall herbs) four years after establishment. Functional trait composition had a larger predictive power for community biomass and measures of biodiversitity effects (40–82\% of explained variation) than species richness per se ({$<$}1–13\% of explained variation). CWM explained a larger amount of variation in community biomass (80\%) and net biodiversity effects (70\%) than FDQ (36 and 38\% of explained variation respectively). FDQ explained similar proportions of variation in complementarity effects (24\%, positive relationship) and selection effects (28\%, negative relationship) as CWM (27\% of explained variation for both complementarity and selection effects), but for all response variables the combination of CWM and FDQ led to significant model improvement compared to a separate consideration of different components of functional trait composition. Effects of FDQ were mainly attributable to diversity in nutrient acquisition and life-history strategies. The large spectrum of traits contributing to positive effects of CWM on biomass production and net biodiversity effects indicated that effects of dominant species were associated with different trait combinations. Conclusions/Significance  Our results suggest that the identification of relevant traits and the relative impacts of functional identity of dominant species and functional diversity are essential for a mechanistic understanding of the role of plant diversity for ecosystem processes such as aboveground biomass production.},
  pmcid = {3356333},
  annotation = {MAG ID: 2043985004}
}

@article{clay1996,
  title = {Interactions among Fungal Endophytes, Grasses and Herbivores},
  author = {Clay, Keith},
  date = {1996-12},
  journaltitle = {Population Ecology},
  shortjournal = {Population Ecology},
  volume = {38},
  number = {2},
  pages = {191--201},
  issn = {1438-3896, 1438-390X},
  doi = {10.1007/BF02515727},
  url = {https://esj-journals.onlinelibrary.wiley.com/doi/10.1007/BF02515727},
  urldate = {2024-04-08},
  abstract = {Abstract                            The interaction between two species often depends on the presence or absence of a third species. One widespread three‐species interaction involves fungal endophytes infecting grasses and the herbivores that feed upon them. The endophytes are allied with the fungal family Clavicipitaceae and grow systemically in intercellular spaces in above‐ground plant tissues including seeds. Like related               Claviceps               species, the endophytes produce a variety of alkaloids that make the host plants toxic or distasteful to herbivores. A large number of grass species are infected, especially cool‐season grasses in temperate areas. Field and laboratory studies have shown that herbivores avoid infected plants in choice trials and suffer increased mortality and decreased growth on infected grasses in feeding experiments. Resistance to herbivores may provide a selective advantage to infected plants in competitive interactions with noninfected plants. Recent studies have shown that differential herbivory can reverse competitive hierarchies among plant species. Both endophyte‐infected and noninfected tall fescue grass (               Festuca arundinacea               ) are outcompeted by orchardgrass (               Dactylis glomerata               ) in the absence of insect herbivory. However, when herbivores are present infected tall fescue outcompetes orchardgrass. These results suggest that the frequency of infection in grass species and grassland communities will increase over time. Several studies are reviewed illustrating increases in infection frequency within grass populations subject to herbivore pressure. Endophytic fungi may be important regulators of plant‐herbivore interactions and so indirectly affect the structure and dynamics of plant communities.},
  langid = {english}
}

@article{coince2014,
  title = {Leaf and {{Root-Associated Fungal Assemblages Do Not Follow Similar Elevational Diversity Patterns}}},
  author = {Coince, Aurore and Cordier, Tristan and Lengellé, Juliette and Defossez, Emmanuel and Vacher, Corinne and Robin, Cécile and Buée, Marc and {Benoît Marçais}},
  date = {2014-06-27},
  journaltitle = {PLOS ONE},
  volume = {9},
  number = {6},
  eprint = {24971637},
  eprinttype = {pmid},
  doi = {10.1371/journal.pone.0100668},
  abstract = {The diversity of fungi along environmental gradients has been little explored in contrast to plants and animals. Consequently, environmental factors influencing the composition of fungal assemblages are poorly understood. The aim of this study was to determine whether the diversity and composition of leaf and root-associated fungal assemblages vary with elevation and to investigate potential explanatory variables. High-throughput sequencing of the Internal Transcribed Spacer 1 region was used to explore fungal assemblages along three elevation gradients, located in French mountainous regions. Beech forest was selected as a study system to minimise the host effect. The variation in species richness and specific composition was investigated for ascomycetes and basidiomycetes assemblages with a particular focus on root-associated ectomycorrhizal fungi. The richness of fungal communities associated with leaves or roots did not significantly relate to any of the tested environmental drivers, i.e. elevation, mean temperature, precipitation or edaphic variables such as soil pH or the ratio carbon∶nitrogen. Nevertheless, the ascomycete species richness peaked at mid-temperature, illustrating a mid-domain effect model. We found that leaf and root-associated fungal assemblages did not follow similar patterns of composition with elevation. While the composition of the leaf-associated fungal assemblage correlated primarily with the mean annual temperature, the composition of root-associated fungal assemblage was explained equally by soil pH and by temperature. The ectomycorrhizal composition was also related to these variables. Our results therefore suggest that above and below-ground fungal assemblages are not controlled by the same main environmental variables. This may be due to the larger amplitude of climatic variables in the tree foliage compared to the soil environment.},
  pmcid = {4074112},
  annotation = {MAG ID: 2054366720},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Coince et al. - 2014 - Leaf and Root-Associated Fungal Assemblages Do Not.pdf}
}

@article{cordier2012,
  title = {The Composition of Phyllosphere Fungal Assemblages of {{European}} Beech ({{Fagus}} Sylvatica) Varies Significantly along an Elevation Gradient},
  author = {Cordier, Tristan and Robin, Cécile and Capdevielle, Xavier and Fabreguettes, Olivier and Desprez-Loustau, Marie-Laure and Vacher, Corinne},
  date = {2012-10-01},
  journaltitle = {New Phytologist},
  volume = {196},
  number = {2},
  eprint = {22934891},
  eprinttype = {pmid},
  pages = {510--519},
  doi = {10.1111/j.1469-8137.2012.04284.x},
  abstract = {Summary Little is known about the potential effect of climate warming on phyllosphere fungi, despite their important impact on the dynamics and diversity of plant communities. The structure of phyllosphere fungal assemblages along elevation gradients may provide information about this potential effect, because elevation gradients correspond to temperature gradients over short geographic distances. We thus investigated variations in the composition of fungal assemblages inhabiting the phyllosphere of European beech (Fagus sylvatica) at four sites over a gradient of 1000m of elevation in the French Pyrenees Mountains, by using tag-encoded 454 pyrosequencing. Our results show that the composition of fungal assemblages varied significantly between elevation sites, in terms of both the relative abundance and the presence–absence of species, and that the variations in assemblage composition were well correlated with variations in the average temperatures. Our results therefore suggest that climate warming might alter both the incidence and the abundance of phyllosphere fungal species, including potential pathogens. For example, Mycosphaerella punctiformis, a causal agent of leaf spots, showed decreasing abundance with elevation and might therefore shift to higher elevations in response to warming.},
  annotation = {MAG ID: 2055789653\\
S2ID: 48f75945976c3051dc57bd57f9eecc78c510a780},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Cordier et al. - 2012 - The composition of phyllosphere fungal assemblages.pdf}
}

@article{cordovez2019,
  title = {Ecology and {{Evolution}} of {{Plant Microbiomes}}},
  author = {Cordovez, Viviane and Dini-Andreote, Francisco and Carrión, Víctor J and Raaijmakers, Jos M},
  date = {2019-05},
  journaltitle = {Annual Review of Microbiology},
  publisher = {Annual Reviews},
  doi = {10.1146/annurev-micro-090817-062524},
  url = {https://doi.org/10.1146/annurev-micro-090817-062524},
  abstract = {Microorganisms colonizing plant surfaces and internal tissues provide a number of life-support functions for their host. Despite increasing recognition of the vast functional capabilities of the plant microbiome, our understanding of the ecology and evolution of the taxonomically hyperdiverse microbial communities is limited. Here, we review current knowledge of plant genotypic and phenotypic traits as well as allogenic and autogenic factors that shape microbiome composition and functions. We give specific emphasis to the impact of plant domestication on microbiome assembly and how insights into microbiomes of wild plant relatives and native habitats can contribute to reinstate or enrich for microorganisms with beneficial effects on plant growth, development, and health. Finally, we introduce new concepts and perspectives in plant microbiome research, in particular how community ecology theory can provide a mechanistic framework to unravel the interplay of distinct ecological processes?i.e., selection, dispersal, drift, diversification?that structure the plant microbiome. Expected final online publication date for the Annual Review of Microbiology Volume 73 is September 9, 2019. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.}
}

@article{coughlan2019,
  title = {Patterns of Hybrid Seed Inviability in Perennials of the {{{\emph{Mimulus}}}}{\emph{ Guttatus}} Sp . {{Complex}} Reveal a Potential Role of Parental Conflict in Reproductive Isolation},
  author = {Coughlan, Jenn M and Brown, Maya Wilson and Willis, John H and Hill, Chapel},
  date = {2019},
  keywords = {arms race,bdmis,cryptic species,endosperm,hybrid seed inviability,parental conflict,running headline,speciation}
}

@article{coughlan2021,
  title = {The Genetic Architecture and Evolution of Life-History Divergence among Perennials in the {{{\emph{Mimulus}}}}{\emph{ Guttatus}} Species Complex},
  author = {Coughlan, Jenn M. and Brown, Maya Wilson and Willis, John H.},
  date = {2021-04-14},
  journaltitle = {Proceedings of the Royal Society B: Biological Sciences},
  shortjournal = {Proc. R. Soc. B.},
  volume = {288},
  number = {1948},
  pages = {rspb.2021.0077, 20210077},
  issn = {0962-8452, 1471-2954},
  doi = {10.1098/rspb.2021.0077},
  url = {https://royalsocietypublishing.org/doi/10.1098/rspb.2021.0077},
  urldate = {2024-04-08},
  abstract = {Ecological divergence is a fundamental source of phenotypic diversity between closely related species, yet the genetic architecture of most ecologically relevant traits is poorly understood. Differences in elevation can impose substantial divergent selection on both complex, correlated suites of traits (such as life-history), as well as novel adaptations. We use the               Mimulus guttatus               species complex to assess if the divergence in elevation is accompanied by trait divergence in a group of closely related perennials and determine the genetic architecture of this divergence. We find that divergence in elevation is associated with differences in life-history, as well as a unique trait, the production of rhizomes. The divergence between two perennials is largely explained by few mid-to-large effect quantitative trait loci (QTLs). However, the presence of QTLs with correlated, but opposing effects on multiple traits leads to some hybrids with transgressive trait combinations. Lastly, we find that the genetic architecture of the ability to produce rhizomes changes through development, wherein most hybrids produce rhizomes, but only later in development. Our results suggest that elevational differences may shape life-history divergence between perennials, but aspects of the genetic architecture of divergence may have implications for hybrid fitness in nature.},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Coughlan et al. - 2021 - The genetic architecture and evolution of life-his.pdf}
}

@article{daru2019,
  title = {A Novel Proof of Concept for Capturing the Diversity of Endophytic Fungi Preserved in Herbarium Specimens},
  author = {Daru, Barnabas H. and Bowman, Elizabeth A. and Pfister, Donald H. and Arnold, A. Elizabeth},
  date = {2019-01-07},
  journaltitle = {Philosophical Transactions of the Royal Society B: Biological Sciences},
  shortjournal = {Phil. Trans. R. Soc. B},
  volume = {374},
  number = {1763},
  pages = {20170395},
  issn = {0962-8436, 1471-2970},
  doi = {10.1098/rstb.2017.0395},
  url = {https://royalsocietypublishing.org/doi/10.1098/rstb.2017.0395},
  urldate = {2023-11-06},
  abstract = {Herbarium specimens represent important records of morphological and genetic diversity of plants that inform questions relevant to global change, including species distributions, phenology and functional traits. It is increasingly appreciated that plant microbiomes can influence these aspects of plant biology, but little is known regarding the historic distribution of microbes associated with plants collected in the pre-molecular age. If microbiomes can be observed reliably in herbarium specimens, researchers will gain a new lens with which to examine microbial ecology, evolution, species interactions. Here, we describe a method for accessing historical plant microbiomes from preserved herbarium specimens, providing a proof of concept using two plant taxa from the imperiled boreal biome (               Andromeda polifolia               and               Ledum palustre               subsp               . groenlandicum,               Ericaceae). We focus on fungal endophytes, which occur within symptomless plant tissues such as leaves. Through a three-part approach (i.e. culturing, cloning and next-generation amplicon sequencing via the Illumina MiSeq platform, with extensive controls), we examined endophyte communities in dried, pressed leaves that had been processed as regular herbarium specimens and stored at room temperature in a herbarium for four years               .               We retrieved only one endophyte in culture, but cloning and especially the MiSeq analysis revealed a rich community of foliar endophytes. The phylogenetic distribution and diversity of endophyte assemblages, especially among the Ascomycota, resemble endophyte communities from fresh plants collected in the boreal biome. We could distinguish communities of endophytes in each plant species and differentiate likely endophytes from fungi that could be surface contaminants. Taxa found by cloning were observed in the larger MiSeq dataset, but species richness was greater when subsets of the same tissues were evaluated with the MiSeq approach. Our findings provide a proof of concept for capturing endophyte DNA from herbarium specimens, supporting the importance of herbarium records as roadmaps for understanding the dynamics of plant-associated microbial biodiversity in the Anthropocene.                          This article is part of the theme issue ‘Biological collections for understanding biodiversity in the Anthropocene’.},
  langid = {english},
  file = {/home/baponte/Zotero/storage/BRD6TBAX/Daru et al. - 2019 - A novel proof of concept for capturing the diversi.pdf}
}

@article{davey2013,
  title = {Amplicon-Pyrosequencing-Based Detection of Compositional Shifts in Bryophyte-Associated Fungal Communities along an Elevation Gradient},
  author = {Davey, Marie L. and Heegaard, Einar and Halvorsen, Rune and Kauserud, Håvard and Ohlson, Mikael},
  date = {2013-01-01},
  journaltitle = {Molecular Ecology},
  volume = {22},
  number = {2},
  eprint = {23190367},
  eprinttype = {pmid},
  pages = {368--383},
  doi = {10.1111/mec.12122},
  abstract = {Although bryophytes are a dominant vegetation component of boreal and alpine ecosystems, little is known about their associated fungal communities. HPLC assays of ergosterol (fungal biomass) and amplicon pyrosequencing of the ITS2 region of rDNA were used to investigate how the fungal communities associated with four bryophyte species changed across an elevational gradient transitioning from conifer forest to the lowalpine. Fungal biomass and OTU richness associated with the four moss hosts did not vary significantly across the gradient (P {$>$} 0.05), and both were more strongly affected by host and tissue type. Despite largely constant levels of fungal biomass, distinct shifts in community composition of fungi associated with Hylocomium, Pleurozium and Polytrichum occurred between the elevation zones of the gradient. This likely is a result of influence on fungal communities by major environmental factors such as temperature, directly or indirectly mediated by, or interacting with, the response of other components of the vegetation (i.e. the dominant trees). Fungal communities associated with Dicranum were an exception, exhibiting spatial autocorrelation between plots, and no significant structuring by elevation. Nevertheless, the detection of distinct fungal assemblages associated with a single host growing in different elevation zones along an elevational gradient is of particular relevance in the light of the ongoing changes in vegetation patterns in boreal and alpine systems due to global climate warming.},
  annotation = {MAG ID: 2143365507},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Davey et al. - 2013 - Amplicon-pyrosequencing-based detection of composi.pdf}
}

@article{davis2018,
  title = {Simple Statistical Identification and Removal of Contaminant Sequences in Marker-Gene and Metagenomics Data},
  author = {Davis, Nicole M. and Proctor, Diana M. and Holmes, Susan P. and Relman, David A. and Callahan, Benjamin J.},
  date = {2018-12-17},
  journaltitle = {Microbiome},
  shortjournal = {Microbiome},
  volume = {6},
  number = {1},
  pages = {226},
  issn = {2049-2618},
  doi = {10.1186/s40168-018-0605-2},
  url = {https://doi.org/10.1186/s40168-018-0605-2},
  abstract = {The accuracy of microbial community surveys based on marker-gene and metagenomic sequencing (MGS) suffers from the presence of contaminants—DNA sequences not truly present in the sample. Contaminants come from various sources, including reagents. Appropriate laboratory practices can reduce contamination, but do not eliminate it. Here we introduce decontam (https://github.com/benjjneb/decontam), an open-source R package that implements a statistical classification procedure that identifies contaminants in MGS data based on two widely reproduced patterns: contaminants appear at higher frequencies in low-concentration samples and are often found in negative controls.}
}

@article{decaceres2009,
  title = {Associations between Species and Groups of Sites: Indices and Statistical Inference},
  author = {De Cáceres, Miquel and Legendre, Pierre},
  date = {2009},
  journaltitle = {Ecology},
  volume = {90},
  pages = {3566--3574},
  doi = {10.1890/08-1823.1}
}

@article{delaux2015,
  title = {Tracing the Evolutionary Path to Nitrogen-Fixing Crops},
  author = {Delaux, Pierre-Marc and Radhakrishnan, Guru and Oldroyd, Giles},
  date = {2015-08},
  journaltitle = {Current Opinion in Plant Biology},
  shortjournal = {Current Opinion in Plant Biology},
  volume = {26},
  pages = {95--99},
  issn = {13695266},
  doi = {10.1016/j.pbi.2015.06.003},
  url = {https://linkinghub.elsevier.com/retrieve/pii/S1369526615000874},
  urldate = {2024-05-02},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Delaux et al. - 2015 - Tracing the evolutionary path to nitrogen-fixing c.pdf}
}

@article{demenezes2019,
  title = {Diversity, {{Distribution}}, and {{Ecology}} of {{Fungi}} in the {{Seasonal Snow}} of {{Antarctica}}},
  author = {De Menezes, Graciéle C.A. and Amorim, Soraya S. and Gonçalves, Vívian N. and Godinho, Valéria M. and Simões, Jefferson C. and Rosa, Carlos A. and Rosa, Luiz H.},
  date = {2019-10-12},
  journaltitle = {Microorganisms},
  shortjournal = {Microorganisms},
  volume = {7},
  number = {10},
  pages = {445},
  issn = {2076-2607},
  doi = {10.3390/microorganisms7100445},
  url = {https://www.mdpi.com/2076-2607/7/10/445},
  urldate = {2024-03-20},
  abstract = {We characterized the fungal community found in the winter seasonal snow of the Antarctic Peninsula. From the samples of snow, 234 fungal isolates were obtained and could be assigned to 51 taxa of 26 genera. Eleven yeast species displayed the highest densities; among them, Phenoliferia glacialis showed a broad distribution and was detected at all sites that were sampled. Fungi known to be opportunistic in humans were subjected to antifungal minimal inhibition concentration. Debaryomyces hansenii, Rhodotorula mucilaginosa, Penicillium chrysogenum, Penicillium sp. 3, and Penicillium sp. 4 displayed resistance against the antifungals benomyl and fluconazole. Among them, R. mucilaginosa isolates were able to grow at 37 °C. Our results show that the winter seasonal snow of the Antarctic Peninsula contains a diverse fungal community dominated by cosmopolitan ubiquitous fungal species previously found in tropical, temperate, and polar ecosystems. The high densities of these cosmopolitan fungi suggest that they could be present in the air that arrives at the Antarctic Peninsula by air masses from outside Antarctica. Additionally, we detected environmental fungal isolates that were resistant to agricultural and clinical antifungals and able to grow at 37 °C. Further studies will be needed to characterize the virulence potential of these fungi in humans and animals.},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/De Menezes et al. - 2019 - Diversity, Distribution, and Ecology of Fungi in t.pdf}
}

@article{deng2021,
  title = {Genome Wide Association Study Reveals Plant Loci Controlling Heritability of the Rhizosphere Microbiome},
  author = {Deng, Siwen and Caddell, Daniel F and Xu, Gen and Dahlen, Lindsay and Washington, Lorenzo and Yang, Jinliang and Coleman-Derr, Devin},
  date = {2021-11-01},
  journaltitle = {The ISME Journal},
  volume = {15},
  number = {11},
  pages = {3181--3194},
  issn = {1751-7362, 1751-7370},
  doi = {10.1038/s41396-021-00993-z},
  url = {https://academic.oup.com/ismej/article/15/11/3181-3194/7474377},
  urldate = {2024-04-10},
  abstract = {Abstract             Host genetics has recently been shown to be a driver of plant microbiome composition. However, identifying the underlying genetic loci controlling microbial selection remains challenging. Genome-wide association studies (GWAS) represent a potentially powerful, unbiased method to identify microbes sensitive to the host genotype and to connect them with the genetic loci that influence their colonization. Here, we conducted a population-level microbiome analysis of the rhizospheres of 200 sorghum genotypes. Using 16S rRNA amplicon sequencing, we identify rhizosphere-associated bacteria exhibiting heritable associations with plant genotype, and identify significant overlap between these lineages and heritable taxa recently identified in maize. Furthermore, we demonstrate that GWAS can identify host loci that correlate with the abundance of specific subsets of the rhizosphere microbiome. Finally, we demonstrate that these results can be used to predict rhizosphere microbiome structure for an independent panel of sorghum genotypes based solely on knowledge of host genotypic information.},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Deng et al. - 2021 - Genome wide association study reveals plant loci c.pdf}
}

@article{diemnguyen2015,
  title = {Effects of Tree Species Diversity on Foliar Fungal Distribution},
  author = {{Diem Nguyen} and Nguyen, Diem},
  date = {2015-01-01},
  abstract = {European forest ecosystems span many different ecological zones and are rich in tree species. The environment in which the trees grow similarly affects fungal communities that interact with these trees. Fungal pathogens can cause severe damage to trees and potentially impair forest stability. In particular, pathogens that damage the foliage will affect the tree’s photosynthetic ability, partly or completely. At the same time, pathogens can create niches for different plants by removing dominant species. The foliage community also comprises fungal species whose ecological functions are not entirely known and may either positively or negatively impact the tree’s health status. The aim of this thesis was to understand the effect of tree species diversity in mitigating fungal pathogen damage and in affecting the fungal community distribution. To achieve this, visual assessment of leaves for pathogen damages was carried out on 16 different tree species from six European forests. The fungal communities of Norway spruce needles from four European forests were studied by using next generation sequencing technology, and fungal communities of birch leaves by sequencing and morphological assessment. In this thesis, foliar fungal pathogen damages were positively correlated with tree species richness – latitude interaction, suggesting that tree species diversity may regulate pathogens but was dependent on the forest. Additionally, foliar fungal community composition was found to differ significantly in different forests, which may be attributable to local environmental effects or reflect the evolutionary history of the host tree, and thereby this study contributes to the understanding of biogeographic patterns of microorganisms. Finally, methods used to study fungal communities revealed that the sequencing-based method provided a richer picture of the fungal community than morphological assessment of fungal structures and symptoms, though neither method informed the distribution patterns as it relates to tree species diversity. Overall, impact of tree species diversity on foliar fungal distribution may not be strong, but it invites us to consider other factors that interact with fungal communities and how fungi may in turn shape their environment.},
  annotation = {MAG ID: 2175028890\\
S2ID: b4f66f117bf26cb9805cf5db31bf811e936b03f6}
}

@article{edgar2015,
  title = {Error Filtering, Pair Assembly and Error Correction for next-{{Generation}} Sequencing Reads},
  author = {Edgar, Robert C. and Flyvbjerg, Henrik},
  date = {2015-11-01},
  journaltitle = {Bioinformatics (Oxford, England)},
  shortjournal = {Bioinformatics},
  volume = {31},
  number = {21},
  pages = {3476--3482},
  issn = {1367-4811, 1367-4803},
  doi = {10.1093/bioinformatics/btv401},
  url = {https://academic.oup.com/bioinformatics/article/31/21/3476/194979},
  urldate = {2024-02-06},
  abstract = {Abstract Motivation: Next-generation sequencing produces vast amounts of data with errors that are difficult to distinguish from true biological variation when coverage is low. Results: We demonstrate large reductions in error frequencies, especially for high-error-rate reads, by three independent means: (i) filtering reads according to their expected number of errors, (ii) assembling overlapping read pairs and (iii) for amplicon reads, by exploiting unique sequence abundances to perform error correction. We also show that most published paired read assemblers calculate incorrect posterior quality scores. Availability and implementation: These methods are implemented in the USEARCH package. Binaries are freely available at http://drive5.com/usearch. Contact:  robert@drive5.com Supplementary information: Supplementary data are available at Bioinformatics online.},
  langid = {english},
  file = {/home/baponte/Zotero/storage/L8FRDCWQ/Edgar and Flyvbjerg - 2015 - Error filtering, pair assembly and error correctio.pdf}
}

@article{estrada2013,
  title = {Symbiotic Fungi Alter Plant Chemistry That Discourages Leaf-Cutting Ants},
  author = {Estrada, C. and Wcislo, William T. and Van Bael, Sunshine A.},
  date = {2013},
  journaltitle = {New Phytologist},
  volume = {198},
  number = {1},
  pages = {241--251},
  doi = {10.1111/nph.12140},
  abstract = {Fungal symbionts that live asymptomatically inside plant tissues (endophytes) can influence plant-insect interactions. Recent work has shown that damage by leaf-cutting ants, a major Neotropical defoliator, is reduced to almost half in plants with high densities of endophytes. We investigated changes in the phenotype of leaves that could influence ants' behavior to result in the reduction of foliar damage. We produced cucumber seedlings with high and low densities of one common endophyte species, Colletotrichum tropicale. We used the leaves in bioassays and to compare chemical and physical leaf characteristics important for ants' food selection. Ants cut about one-third more area of cucumber leaves with lower densities of endophytes and removed c. 20\% more paper disks impregnated with the extracts of those leaves compared with leaves and disks from plants hosting the fungus. Colletotrichum tropicale colonization did not cause detectable changes in the composition of volatile compounds, cuticular waxes, nutrients or leaf toughness. Our study shows that endophytes changed leaf chemistry and suggests that compounds with relative low volatility released after leaf wounding are a major factor influencing foraging decisions by ants when choosing between plants with low or high endophyte loads. © 2013 New Phytologist Trust.},
  keywords = {Atta colombica,Colletotrichum tropicale,Cucumis sativus,Endophytic fungi,Leaf-cutting ants,Plant defenses,Symbiosis}
}

@article{ewels2016,
  title = {{{MultiQC}}: {{Summarize}} Analysis Results for Multiple Tools and Samples in a Single Report},
  shorttitle = {{{MultiQC}}},
  author = {Ewels, Philip and Magnusson, Måns and Lundin, Sverker and Käller, Max},
  date = {2016-10-01},
  journaltitle = {Bioinformatics (Oxford, England)},
  shortjournal = {Bioinformatics},
  volume = {32},
  number = {19},
  pages = {3047--3048},
  issn = {1367-4811, 1367-4803},
  doi = {10.1093/bioinformatics/btw354},
  url = {https://academic.oup.com/bioinformatics/article/32/19/3047/2196507},
  urldate = {2024-02-10},
  abstract = {Abstract Motivation: Fast and accurate quality control is essential for studies involving next-generation sequencing data. Whilst numerous tools exist to quantify QC metrics, there is no common approach to flexibly integrate these across tools and large sample sets. Assessing analysis results across an entire project can be time consuming and error prone; batch effects and outlier samples can easily be missed in the early stages of analysis. Results: We present MultiQC, a tool to create a single report visualising output from multiple tools across many samples, enabling global trends and biases to be quickly identified. MultiQC can plot data from many common bioinformatics tools and is built to allow easy extension and customization. Availability and implementation: MultiQC is available with an GNU GPLv3 license on GitHub, the Python Package Index and Bioconda. Documentation and example reports are available at http://multiqc.info Contact:  phil.ewels@scilifelab.se},
  langid = {english},
  file = {/home/baponte/Zotero/storage/C62ZUX8V/Ewels et al. - 2016 - MultiQC summarize analysis results for multiple t.pdf}
}

@article{faris2020,
  title = {Plant Genes Hijacked by Necrotrophic Fungal Pathogens},
  author = {Faris, Justin D and Friesen, Timothy L},
  date = {2020-08},
  journaltitle = {Current Opinion in Plant Biology},
  shortjournal = {Current Opinion in Plant Biology},
  volume = {56},
  pages = {74--80},
  issn = {13695266},
  doi = {10.1016/j.pbi.2020.04.003},
  url = {https://linkinghub.elsevier.com/retrieve/pii/S1369526620300431},
  urldate = {2024-04-10},
  langid = {english}
}

@article{ferris2014,
  title = {Speciation on a Local Geographic Scale: {{The}} Evolution of a Rare Rock Outcrop Specialist in {{{\emph{Mimulus}}}}},
  author = {Ferris, Kathleen G. and Sexton, Jason P. and Willis, John H. and Ferris, Kathleen G.},
  date = {2014},
  journaltitle = {Philosophical Transactions of the Royal Society B: Biological Sciences},
  volume = {369},
  number = {1648},
  pages = {27--29},
  doi = {10.1098/rstb.2014.0001},
  abstract = {Speciation can occur on both large and small geographical scales. In plants, local speciation, where small populations split off from a large-ranged progenitor species, is thought to be the dominant mode, yet there are still few examples to verify speciation has occurred in this manner. A recently described morphological species in the yellow monkey flowers, Mimulus filicifolius, is an excellent candidate for local speciation because of its highly restricted geographical range. Mimulus filicifolius was formerly identified as a population of M. laciniatus due to similar lobed leaf morphology and rocky outcrop habitat. To investigate whether M. filicifolius is genetically divergent and reproductively isolated from M. laciniatus, we examined patterns of genetic diversity in ten nuclear and eight microsatellite loci, and hybrid fertility in M. filicifolius and its purported close relatives: M. laciniatus, M. guttatus and M. nasutus. We found that M. filicifolius is genetically divergent from the other species and strongly reproductively isolated from M. laciniatus. We conclude that M. filicifolius is an independent rock outcrop specialist despite being morphologically and ecologically similar to M. laciniatus, and that its small geographical range nested within other wide-ranging members of the M. guttatus species complex is consistent with local speciation.},
  keywords = {genetics,Genetics,Local speciation,Mimulus filicifolius,Mimulus guttatus,Mimulus laciniatus,plant science,Rock outcrops}
}

@article{ferris2014a,
  title = {The {{Genetics}} of {{Adaptation}} to a {{Harsh Granite Outcrop Environment}} in {{{\emph{Mimulus}}}}},
  author = {Ferris, Kathleen Gray},
  date = {2014}
}

@article{ferris2015,
  title = {Leaf Shape Evolution Has a Similar Genetic Architecture in Three Edaphic Specialists within the {{{\emph{Mimulus}}}} {\emph{Guttatus}} Species Complex},
  author = {Ferris, Kathleen G. and Rushton, Tullia and Greenlee, Anna B. and Toll, Katherine and Blackman, Benjamin K. and Willis, John H.},
  date = {2015},
  journaltitle = {Annals of Botany},
  volume = {116},
  number = {2},
  pages = {213--223},
  doi = {10.1093/aob/mcv080},
  abstract = {Background and Aims The genetic basis of leaf shape has long interested botanists because leaf shape varies extensively across the plant kingdom and this variation is probably adaptive. However, knowledge of the genetic architecture of leaf shape variation in natural populations remains limited. This study examined the genetic architecture of leaf shape diversification among three edaphic specialists in the Mimulus guttatus species complex. Lobed and narrow leaves have evolved from the entire, round leaves of M. guttatus in M. laciniatus, M. nudatus and a polymorphic serpentine M. guttatus population (M2L). Methods Bulk segregant analysis and next-generation sequencing were used to map quantitative trait loci (QTLs) that underlie leaf shape in an M. laciniatus∈×∈M. guttatus F2 population. To determine whether the same QTLs contribute to leaf shape variation in M. nudatus and M2L, F2s from M. guttatus∈×∈M. nudatus and lobed M2L∈×∈unlobed M. guttatus crosses were genotyped at QTLs from the bulk segregant analysis. Key Results Narrow and lobed leaf shapes in M. laciniatus, M. nudatus and M. guttatus are controlled by overlapping genetic regions. Several promising leaf shape candidate genes were found under each QTL. Conclusions The evolution of divergent leaf shape has taken place multiple times in the M. guttatus species complex and is associated with the occupation of dry, rocky environments. The genetic architecture of elongated and lobed leaves is similar across three species in this group. This may indicate that parallel genetic evolution from standing variation or new mutations is responsible for the putatively adaptive leaf shape variation in Mimulus.},
  keywords = {bulk segregant analysis,edaphic specialists,genetic architecture,leaf boundary layer,Leaf shape,M. guttatus,M. laciniatus,M. nudatus,Mimulus guttatus species complex,parallel evolution,QTL mapping},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Ferris et al. - 2015 - Leaf shape evolution has a similar genetic archite.pdf}
}

@article{ferris2016,
  title = {A Hot Topic: {{The}} Genetics of Adaptation to Geothermal Vents in {{{\emph{Mimulus}}}} {\emph{Guttatus}}},
  author = {Ferris, Kathleen G.},
  date = {2016},
  journaltitle = {Molecular Ecology},
  volume = {25},
  number = {22},
  pages = {5605--5607},
  doi = {10.1111/mec.13869},
  abstract = {Identifying the individual loci and mutations that underlie adaptation to extreme environments has long been a goal of evolutionary biology. However, finding the genes that underlie adaptive traits is difficult for several reasons. First, because many traits and genes evolve simultaneously as populations diverge, it is difficult to disentangle adaptation from neutral demographic processes. Second, finding the individual loci involved in any trait is challenging given the respective limitations of quantitative and population genetic methods. In this issue of Molecular Ecology, Hendrick et al. (2016) overcome these difficulties and determine the genetic basis of microgeographic adaptation between geothermal vent and nonthermal populations of Mimulus guttatus in Yellowstone National Park. The authors accomplish this by combining population and quantitative genetic techniques, a powerful, but labour-intensive, strategy for identifying individual causative adaptive loci that few studies have used (Stinchcombe \& Hoekstra ). In a previous common garden experiment (Lekberg et al. 2012), thermal M. guttatus populations were found to differ from their closely related nonthermal neighbours in various adaptive phenotypes including trichome density. Hendrick et al. (2016) combine quantitative trait loci (QTL) mapping, population genomic scans for selection and admixture mapping to identify a single genetic locus underlying differences in trichome density between thermal and nonthermal M. guttatus. The candidate gene, R2R3 MYB, is homologous to genes involved in trichome development across flowering plants. The major trichome QTL, Tr14, is also involved in trichome density differences in an independent M. guttatus population comparison (Holeski et al. 2010) making this an example of parallel genetic evolution.},
  keywords = {Angiosperms,Ecological genetics,Genomics/proteomics,Population genetics - empirical,Quantitative genetics}
}

@article{ferris2017,
  title = {The Genetic Architecture of Local Adaptation and Reproductive Isolation in Sympatry within the {{{\emph{Mimulus}}}}{\emph{ Guttatus}} Species Complex},
  author = {Ferris, Kathleen G. and Barnett, Laryssa L. and Blackman, Benjamin K. and Willis, John H.},
  date = {2017},
  journaltitle = {Molecular Ecology},
  volume = {26},
  number = {1},
  pages = {208--224},
  doi = {10.1111/mec.13763},
  abstract = {The genetic architecture of local adaptation has been of central interest to evolutionary biologists since the modern synthesis. In addition to classic theory on the effect size of adaptive mutations by Fisher, Kimura and Orr, recent theory addresses the genetic architecture of local adaptation in the face of ongoing gene flow. This theory predicts that with substantial gene flow between populations local adaptation should proceed primarily through mutations of large effect or tightly linked clusters of smaller effect loci. In this study, we investigate the genetic architecture of divergence in flowering time, mating system-related traits, and leaf shape between Mimulus laciniatus and a sympatric population of its close relative M. guttatus. These three traits are probably involved in M. laciniatus' adaptation to a dry, exposed granite outcrop environment. Flowering time and mating system differences are also reproductive isolating barriers making them 'magic traits'. Phenotypic hybrids in this population provide evidence of recent gene flow. Using next-generation sequencing, we generate dense SNP markers across the genome and map quantitative trait loci (QTLs) involved in flowering time, flower size and leaf shape. We find that interspecific divergence in all three traits is due to few QTL of large effect including a highly pleiotropic QTL on chromosome 8. This QTL region contains the pleiotropic candidate gene TCP4 and is involved in ecologically important phenotypes in other Mimulus species. Our results are consistent with theory, indicating that local adaptation and reproductive isolation with gene flow should be due to few loci with large and pleiotropic effects.},
  keywords = {flowering time,gene flow,genetic architecture,local adaptation,mating system,Mimulus guttatus species complex}
}

@article{ferris2018,
  title = {Differential Adaptation to a Harsh Granite Outcrop Habitat between Sympatric {{{\emph{Mimulus}}}} Species},
  author = {Ferris, Kathleen G. and Willis, John H.},
  date = {2018},
  journaltitle = {Evolution; international journal of organic evolution},
  shortjournal = {Evolution},
  volume = {72},
  number = {6},
  pages = {1225--1241},
  doi = {10.1111/evo.13476},
  abstract = {Understanding which environmental variables and traits underlie adaptation to harsh environments is difficult because many traits evolve simultaneously as populations or species diverge. Here, we investigate the ecological variables and traits that underlie Mimulus laciniatus’ adaptation to granite outcrops compared to its sympatric, mesic-adapted progenitor, Mimulus guttatus. We use fine-scale measurements of soil moisture and herbivory to examine differences in selective forces between the species’ habitats, and measure selection on flowering time, flower size, plant height, and leaf shape in a reciprocal transplant using M. laciniatus × M. guttatus F4 hybrids. We find that differences in drought and herbivory drive survival differences between habitats, that M. laciniatus and M. guttatus are each better adapted to their native habitat, and differential habitat selection on flowering time, plant stature, and leaf shape. Although early flowering time, small stature, and lobed leaf shape underlie plant fitness in M. laciniatus’ seasonally dry environment, increased plant size is advantageous in a competitive mesic environment replete with herbivores like M. guttatus’. Given that we observed divergent selection between habitats in the direction of species differences, we conclude that adaptation to different microhabitats is an important component of reproductive isolation in this sympatric species pair.},
  keywords = {Differential adaptation,drought,flowering time,Mimulus,phenotypic selection,plasticity}
}

@article{field2015,
  title = {Symbiotic Options for the Conquest of Land},
  author = {Field, Katie J. and Pressel, Silvia and Duckett, Jeffrey G. and Rimington, William R. and Bidartondo, Martin I.},
  date = {2015-08},
  journaltitle = {Trends in Ecology \& Evolution},
  shortjournal = {Trends in Ecology \& Evolution},
  volume = {30},
  number = {8},
  pages = {477--486},
  issn = {01695347},
  doi = {10.1016/j.tree.2015.05.007},
  url = {https://linkinghub.elsevier.com/retrieve/pii/S0169534715001366},
  urldate = {2024-05-02},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Field et al. - 2015 - images.pdf;/home/baponte/Boxx/Dissertation/master_papers/Field et al. - 2015 - Symbiotic options for the conquest of land.pdf}
}

@article{franks2014,
  title = {Evolutionary and Plastic Responses to Climate Change in Terrestrial Plant Populations},
  author = {Franks, Steven J. and Weber, Jennifer J. and Aitken, Sally N.},
  date = {2014-01},
  journaltitle = {Evolutionary Applications},
  shortjournal = {Evolutionary Applications},
  volume = {7},
  number = {1},
  pages = {123--139},
  issn = {1752-4571, 1752-4571},
  doi = {10.1111/eva.12112},
  url = {https://onlinelibrary.wiley.com/doi/10.1111/eva.12112},
  urldate = {2024-04-08},
  abstract = {Abstract             As climate change progresses, we are observing widespread changes in phenotypes in many plant populations. Whether these phenotypic changes are directly caused by climate change, and whether they result from phenotypic plasticity or evolution, are active areas of investigation. Here, we review terrestrial plant studies addressing these questions. Plastic and evolutionary responses to climate change are clearly occurring. Of the 38 studies that met our criteria for inclusion, all found plastic or evolutionary responses, with 26 studies showing both. These responses, however, may be insufficient to keep pace with climate change, as indicated by eight of 12 studies that examined this directly. There is also mixed evidence for whether evolutionary responses are adaptive, and whether they are directly caused by contemporary climatic changes. We discuss factors that will likely influence the extent of plastic and evolutionary responses, including patterns of environmental changes, species’ life history characteristics including generation time and breeding system, and degree and direction of gene flow. Future studies with standardized methodologies, especially those that use direct approaches assessing responses to climate change over time, and sharing of data through public databases, will facilitate better predictions of the capacity for plant populations to respond to rapid climate change.},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Franks et al. - 2014 - Evolutionary and plastic responses to climate chan.pdf}
}

@article{fritz2018,
  title = {Mechanisms {{Underlying}} the {{Environmentally Induced Plasticity}} of {{Leaf Morphology}}},
  author = {Fritz, Michael André and Rosa, Stefanie and Sicard, Adrien},
  date = {2018-10-24},
  journaltitle = {Frontiers in Genetics},
  shortjournal = {Front. Genet.},
  volume = {9},
  pages = {478},
  issn = {1664-8021},
  doi = {10.3389/fgene.2018.00478},
  url = {https://www.frontiersin.org/article/10.3389/fgene.2018.00478/full},
  urldate = {2024-05-07},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Fritz et al. - 2018 - Mechanisms Underlying the Environmentally Induced .pdf}
}

@article{gardes1993,
  title = {{{ITS}} Primers with Enhanced Specificity for Basidiomycetes ‐ Application to the Identification of Mycorrhizae and Rusts},
  author = {Gardes, M. and Bruns, T. D.},
  date = {1993-04},
  journaltitle = {Molecular Ecology},
  shortjournal = {Molecular Ecology},
  volume = {2},
  number = {2},
  pages = {113--118},
  issn = {0962-1083, 1365-294X},
  doi = {10.1111/j.1365-294X.1993.tb00005.x},
  url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1365-294X.1993.tb00005.x},
  urldate = {2024-02-10},
  abstract = {Abstract We have designed two taxon‐selective primers for the internal transcribed spacer (ITS) region in the nuclear ribosomal repeat unit. These primers, ITS1‐F and ITS4‐B, were intended to be specific to fungi and basidiomycetes, respectively. We have tested the specificity of these primers against 13 species of ascomycetes, 14 of basidiomycetes, and 15 of plants. Our results showed that ITS4‐B, when paired with either a ‘universal’ primer ITS1 or the fungal‐specific primer ITS1‐F, efficiently amplified DNA from all basidiomycetes and discriminated against ascomycete DNAs. The results with plants were not as clearcut. The ITS1‐F/ITS4‐B primer pair produced a small amount of PCR product for certain plant species, but the quantity was in most cases less than that produced by the ‘universal’ ITS primers. However, under conditions where both plant and fungal DNAs were present, the fungal DNA was amplified to the apparent exclusion of plant DNA. ITS1‐F/ITS4‐B preferential amplification was shown to be particularly useful for detection and analysis of the basidiomycete component in ectomycorrhizae and in rust‐infected tissues. These primers can be used to study the structure of ectomycorrhizal communities or the distribution of rusts on alternate hosts.},
  langid = {english}
}

@article{giauque2013,
  title = {Climate Affects Symbiotic Fungal Endophyte Diversity and Performance},
  author = {Giauque, Hannah and Hawkes, Christine V.},
  date = {2013-07},
  journaltitle = {American Journal of Botany},
  shortjournal = {American J of Botany},
  volume = {100},
  number = {7},
  pages = {1435--1444},
  issn = {0002-9122, 1537-2197},
  doi = {10.3732/ajb.1200568},
  url = {https://bsapubs.onlinelibrary.wiley.com/doi/10.3732/ajb.1200568},
  urldate = {2024-04-08},
  abstract = {•               Premise of the study:               Fungal endophytes are symbionts that inhabit aboveground tissues of most terrestrial plants and can affect plant physiology and growth under stressed conditions. In a future faced with substantial climate change, endophytes have the potential to play an important role in plant stress resistance. Understanding both the distributions of endophytes and their functioning in symbiosis with plants are key aspects of predicting their role in an altered climate.                                         •               Methods:               Here we characterized endophytes in grasses across a steep precipitation gradient to examine the relative importance of environmental and spatial factors in structuring endophyte communities. We also tested how 20 endophytes isolated from drier and wetter regions performed in symbiosis with grass seedlings under high and low soil moisture in the greenhouse.                                         •               Key results:               Environmental factors related to historical and current precipitation were the most important predictors of endophyte communities in the field. On average, endophytic fungi from western sites also reduced plant water loss in the greenhouse compared to fungi from eastern sites. However, there was substantial variability in how individual endophytic taxa affected plant traits under high and low water availability, with up to two orders of magnitude difference in the plasticity of plant traits conferred by the different fungal taxa.                                         •               Conclusions:               While species sorting appears to largely explain local endophyte community composition, their function in symbiosis is not predictable from local environmental conditions. The development of a predictive framework for endophyte function will require further study of individual fungal taxa and genotypes across environmental gradients.},
  langid = {english}
}

@article{giauque2016,
  title = {Historical and Current Climate Drive Spatial and Temporal Patterns in Fungal Endophyte Diversity},
  author = {Giauque, Hannah and Hawkes, Christine V},
  date = {2016-04},
  journaltitle = {FUNGAL ECOLOGY},
  volume = {20},
  pages = {108--114},
  publisher = {ELSEVIER SCI LTD},
  location = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND},
  doi = {10.1016/j.funeco.2015.12.005},
  abstract = {Horizontally-transmitted foliar endophytic fungi can moderate plant tolerance to abiotic and biotic stress. Previous studies have found correlations between climate and endophyte beta diversity, but were unable to clearly separate drivers related to long-term climate, annual weather, and host plants. To address this, we characterized endophyte communities in the perennial C-4 grass, Panicum hallii, across a precipitation gradient in central Texas over 3 years. A total of 65 unique leaf endophytes were isolated and identified based on ITS and LSU regions of rDNA. Mean annual rainfall and temperature were the primary drivers of endophyte richness and community composition, followed by annual weather conditions. In contrast, little explanatory value was provided by plant host traits, vegetation structure, or spatial factors. The importance of historical climate and annual weather in endophyte distributions suggests that species sort by environment and are likely to be affected by future climate change. (C) 2015 Elsevier Ltd and The British Mycological Society. All rights reserved.},
  keywords = {Ascomycota,Environmental filtering,Rainfall,Spe},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Giauque and Hawkes - 2016 - Historical and current climate drive spatial and t.pdf}
}

@article{giauque2019,
  title = {Endophyte Traits Relevant to Stress Tolerance, Resource Use and Habitat of Origin Predict Effects on Host Plants},
  author = {Giauque, Hannah and Connor, Elise W. and Hawkes, Christine V.},
  date = {2019-03},
  journaltitle = {New Phytologist},
  shortjournal = {New Phytologist},
  volume = {221},
  number = {4},
  pages = {2239--2249},
  issn = {0028-646X, 1469-8137},
  doi = {10.1111/nph.15504},
  url = {https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.15504},
  urldate = {2024-04-08},
  abstract = {Summary                                                                All terrestrial plants are colonized by foliar endophytic fungi that can affect plant growth and physiology, but the prediction of these effects on the plant host remains a challenge. Here, we examined three paradigms that potentially control how endophytes affect plant hosts: habitat adaptation, evolutionary history and functional traits.                                                                          We screened 35 plant–endophyte pairings in a microcosm experiment under well‐watered and drought conditions with                     Panicum virgatum                     as the host. We related the measured plant responses to fungal phylogenetic relatedness, characteristics of fungal habitats across a rainfall gradient and functional traits of the fungi related to stress tolerance and resource use.                                                                        The functional traits and habitat characteristics of the fungi predicted 26–53\% of endophyte‐mediated effects on measures of plant growth, physiology and survival. Overall, survival was higher for plants grown with more stress‐tolerant fungi, and aboveground biomass was enhanced by fungi from warmer and drier habitats. Plant growth and physiology were also dependent on fungal resource use indicators; however, specific predictors were dependent on water availability.                                                     Simple ecological traits of foliar endophytic fungi observed in culture can translate to symbiotic lifestyles. These findings offer new insights and key testable predictions for likely pathways by which endophytes benefit the plant host.},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Giauque et al. - 2019 - Endophyte traits relevant to stress tolerance, res.pdf}
}

@article{gibert2012,
  title = {A Fungal Endophyte Reinforces Population Adaptive Differentiation in Its Host Grass Species},
  author = {Gibert, Anaïs and Volaire, Florence and Barre, Philippe and Hazard, Laurent},
  date = {2012-04},
  journaltitle = {New Phytologist},
  shortjournal = {New Phytologist},
  volume = {194},
  number = {2},
  pages = {561--571},
  issn = {0028-646X, 1469-8137},
  doi = {10.1111/j.1469-8137.2012.04073.x},
  url = {https://nph.onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2012.04073.x},
  urldate = {2024-04-10},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Gibert et al. - 2012 - A fungal endophyte reinforces population adaptive .pdf}
}

@article{gonzalez-teuber2016,
  title = {The Defensive Role of Foliar Endophytic Fungi for a {{South American}} Tree},
  author = {González-Teuber, Marcia},
  date = {2016-01-01},
  journaltitle = {AoB PLANTS},
  volume = {8},
  pages = {plw050},
  issn = {2041-2851},
  doi = {10.1093/aobpla/plw050},
  url = {https://academic.oup.com/aobpla/article/doi/10.1093/aobpla/plw050/2609609},
  urldate = {2024-01-27},
  abstract = {Abstract             Fungal endophytes colonize living internal plant tissues without causing any visible symptoms of disease. Endophytic fungi associated with healthy leaves may play an important role in the protection of hosts against herbivores and pathogens. In this study, the diversity of foliar endophytic fungi (FEF) of the southern temperate tree Embothrium coccineum (Proteaceae), as well as their role in plant protection in nature was determined. Fungal endophytes were isolated from 40 asymptomatic leaves by the culture method for molecular identification of the 18S rRNA gene. A relationship between FEF frequency and plant protection was evaluated in juveniles of E. coccineum . Fungal endophyte frequency was estimated using real-time PCR analyses to determine endophyte DNA content per plant. A total of 178 fungal isolates were identified, with sequence data revealing 34 different operational taxonomic units (OTUs). A few common taxa dominated the fungal endophyte community, whereas most taxa qualified as rare. A significant positive correlation between plant protection (evaluated in terms of percentage of leaf damage) and FEF frequency was found. Furthermore, in vitro confrontation assays indicated that FEF were able to inhibit the growth of fungal pathogens. The data showed a relatively high diversity of fungal endophytes associated with leaves of E. coccineum , and suggest a positive relationship between fungal endophyte frequencies in leaves and host protection in nature.},
  langid = {english}
}

@article{gonzalez-teuber2020,
  title = {Leaf Resistance Traits Influence Endophytic Fungi Colonization and Community Composition in a {{South American}} Temperate Rainforest},
  author = {González‐Teuber, Marcia and Vilo, Claudia and Guevara‐Araya, María José and Salgado‐Luarte, Cristian and Gianoli, Ernesto},
  editor = {Züst, Tobias},
  date = {2020-05},
  journaltitle = {Journal of Ecology},
  shortjournal = {Journal of Ecology},
  volume = {108},
  number = {3},
  pages = {1019--1029},
  issn = {0022-0477, 1365-2745},
  doi = {10.1111/1365-2745.13314},
  url = {https://besjournals.onlinelibrary.wiley.com/doi/10.1111/1365-2745.13314},
  urldate = {2024-04-14},
  abstract = {Abstract                                                                Despite the ubiquitous presence of fungal endophytes in woody plants, mechanisms underlying variation in foliar fungal endophyte communities are poorly understood. Given that endophytes in woody plants are predominantly horizontally transmitted, fungal endophyte colonization of foliar tissues is likely to be influenced by plant resistance traits. Here, we evaluated the association between leaf resistance traits and colonization and community composition of horizontally transmitted endophytes (HTE) in 10 dominant trees species in a temperate rainforest in Southern Chile. Because resistance traits might restrict colonization of HTE, it was hypothesized that host trees with similar leaf resistance traits would show similar HTE communities.                                                     We measured leaf traits with reported roles in plant resistance against pathogens and/or herbivores: cell wall polysaccharides, leaf toughness, flavonoids, anthocyanins, terpenoids and chitinases. We also determined variation in fungal read counts, number of operational taxonomic units (OTUs), diversity and community structure across tree species. Foliar fungal endophyte communities were characterized using Illumina MiSeq sequencing of tagged amplicons of the ITS1 region.                                                                          Fungal read counts were significantly different among host trees, while number of OTUs and diversity were similar among them. Multivariate analyses showed that community composition of endophytic fungi significantly differed among hosts, and that variation in cell wall, flavonoids, anthocyanins and terpenoids was associated with differences in HTE communities. We found that host trees sharing leaf resistance traits harbour similar HTE communities. Fungal read counts decreased with increasing content of cell wall polysaccharides, while endophyte diversity decreased with increasing anthocyanin levels. Fungal read counts, in contrast, were positively associated with terpenoids. Additionally, culture‐based data indicated that some HTE strains inhibited the growth of the common fungal pathogen                     Botrytis cinerea                     .                                                                                             Synthesis                     . Overall, we found that leaf resistance traits may influence fungal endophyte colonization and community composition in tree species, likely through deterrent effects of structural and chemical traits. We suggest that endophytic fungi that overcome resistance traits might play a role in plant protection.},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/González‐Teuber et al. - 2020 - Leaf resistance traits influence endophytic fungi .pdf}
}

@article{gonzalez-teuber2021,
  title = {Roles of Leaf Functional Traits in Fungal Endophyte Colonization: {{Potential}} Implications for Host–Pathogen Interactions},
  shorttitle = {Roles of Leaf Functional Traits in Fungal Endophyte Colonization},
  author = {González‐Teuber, Marcia and Palma‐Onetto, Valeria and Aguilera‐Sammaritano, Juan and Mithöfer, Axel},
  date = {2021-12},
  journaltitle = {Journal of Ecology},
  shortjournal = {Journal of Ecology},
  volume = {109},
  number = {12},
  pages = {3972--3987},
  issn = {0022-0477, 1365-2745},
  doi = {10.1111/1365-2745.13678},
  url = {https://besjournals.onlinelibrary.wiley.com/doi/10.1111/1365-2745.13678},
  urldate = {2024-03-08},
  abstract = {Abstract                                                                Fungal endophytes (FE) are an important component of leaf microbial communities. They usually live asymptomatically within leaf tissues; however, FE can provide additional defensive features against microbial pathogens to the host. Leaf functional traits (LFTs) regulate FE entry, colonization and community composition in plants.                                                     There is evidence that thin leaves with less structural and chemical traits but high nutrient content are more prone to FE colonization than well‐defended thick leaves. This illustrates the relevance of trade‐offs (= an increase in a trait, with a decrease in another trait) in LFTs, suggesting that the leaf economics spectrum (LES, which describes relationships in a suite of leaf traits aligned from a resource‐acquisitive to a resource‐conservative ecological strategy) may be a predictor of FE colonization and community composition in plants.                                                     We hypothesize that LES‐modulated changes in the leaf internal environment (i.e. thin, low‐defended vs. thick, well‐defended leaves) will (a) have consequences for host resistance to pathogens due to changes in the FE colonization and diversity and, subsequently, in the foliar chemical profile and (b) may cause a switch in FE behaviour to a pathogenic lifestyle.                                                                          Synthesis                     . Still, our knowledge of how the coexistence between host plants and FE is regulated remains limited. LFTs may act as relevant ecological hub of FE colonization, community composition and life behaviour in natural ecosystems, with potential bottom‐up effects on other organisms, including pathogens. We highlight and discuss critical aspects in this topic and end by proposing new avenues of research in this emerging field.},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/González‐Teuber et al. - 2021 - Roles of leaf functional traits in fungal endophyt.pdf}
}

@article{gonzalo-turpin2010,
  title = {Co-Occurring Patterns of Endophyte Infection and Genetic Structure in the Alpine Grass, {{Festuca}} Eskia: Implications for Seed Sourcing in Ecological Restoration},
  shorttitle = {Co-Occurring Patterns of Endophyte Infection and Genetic Structure in the Alpine Grass, {{Festuca}} Eskia},
  author = {Gonzalo-Turpin, H. and Barre, P. and Gibert, A. and Grisard, A. and West, C. P. and Hazard, L.},
  date = {2010-06},
  journaltitle = {Conservation Genetics},
  shortjournal = {Conserv Genet},
  volume = {11},
  number = {3},
  pages = {877--887},
  issn = {1566-0621, 1572-9737},
  doi = {10.1007/s10592-009-9927-8},
  url = {http://link.springer.com/10.1007/s10592-009-9927-8},
  urldate = {2024-04-10},
  langid = {english}
}

@article{guo2023,
  title = {How Does Plant Sex Alter Microbiota Assembly in Dioecious Plants?},
  author = {{Guo, Qingxue} and {Zhu, Yu-Xian} and {Korpelainen, Helena} and {Niinemets, Ülo} and {Li, Chunyang}},
  date = {2023-09-01},
  volume = {31},
  number = {9},
  eprint = {37120361},
  eprinttype = {pmid},
  pages = {894--902},
  doi = {10.1016/j.tim.2023.03.014},
  abstract = {Plant microbiota can greatly impact plant growth, defense, and health in different environments. Thus, it might be evolutionarily beneficial for plants to be able to control processes related to microbiota assembly. Dioecious plant species display sexual dimorphism in morphology, physiology, and immunity. These differences imply that male and female individuals might differently regulate their microbiota, but the role of sex in microbiota assembly has been largely neglected so far. Here, we introduce the mechanism of how sex controls microbiota in plants analogically to the sex regulation of gut microbiota in animals, in particular in humans. We argue that plant sex imposes selective pressure on filtering and constructing microbiota in the rhizosphere, phyllosphere, and endosphere along the soil-plant continuum. Since male plants are more resistant than female plants to environmental stresses, we suggest that a male host forms more stable and resistant plant microbiota that cooperate more effectively with the host to resist stresses. Male and female plants can distinguish whether a plant is of the same or different sex, and males can alleviate stress-caused damage in females. The impact of a male host on microbiota would protect female plants from unfavorable environments.},
  annotation = {MAG ID: 4367322286}
}

@article{hall2006,
  title = {Divergent {{Selection}} on {{Flowering Time Contributes}} to {{Local Adaptation}} in {{Mimulus Guttatus Populations}}},
  author = {Hall, Megan C. and Willis, John H.},
  date = {2006},
  journaltitle = {Evolution; international journal of organic evolution},
  shortjournal = {EVOLUTION},
  volume = {60},
  number = {12},
  pages = {2466--2477}
}

@article{harrison2020,
  title = {The Diversity and Distribution of Endophytes across Biomes, Plant Phylogeny and Host Tissues: How Far Have We Come and Where Do We Go from Here?},
  shorttitle = {The Diversity and Distribution of Endophytes across Biomes, Plant Phylogeny and Host Tissues},
  author = {Harrison, Joshua G. and Griffin, Eric A.},
  date = {2020-06},
  journaltitle = {Environmental Microbiology},
  shortjournal = {Environmental Microbiology},
  volume = {22},
  number = {6},
  pages = {2107--2123},
  issn = {1462-2912, 1462-2920},
  doi = {10.1111/1462-2920.14968},
  url = {https://sfamjournals.onlinelibrary.wiley.com/doi/10.1111/1462-2920.14968},
  urldate = {2024-04-14},
  abstract = {Summary             The interiors of plants are colonized by diverse microorganisms that are referred to as endophytes. Endophytes have received much attention over the past few decades, yet many questions remain unanswered regarding patterns in their biodiversity at local to global scales. To characterize research effort to date, we synthesized results from \textasciitilde 600 published studies. Our survey revealed a global research interest and highlighted several gaps in knowledge. For instance, of the 17 biomes encompassed by our survey, 7 were understudied and together composed only 7\% of the studies that we considered. We found that fungal endophyte diversity has been characterized in at least one host from 30\% of embryophyte families, while bacterial endophytes have been surveyed in hosts from only 10.5\% of families. We complimented our survey with a vote counting procedure to determine endophyte richness patterns among plant tissue types. We found that variation in endophyte assemblages in above‐ground tissues varied with host growth habit. Stems were the richest tissue in woody plants, whereas roots were the richest tissue in graminoids. For forbs, we found no consistent differences in relative tissue richness among studies. We propose future directions to fill the gaps in knowledge we uncovered and inspire further research.},
  langid = {english},
  file = {/home/baponte/Zotero/storage/PLHI27QY/Harrison and Griffin - 2020 - The diversity and distribution of endophytes acros.pdf}
}

@article{hawkes2021,
  title = {Extension of {{Plant Phenotypes}} by the {{Foliar Microbiome}}},
  author = {Hawkes, Christine V. and Kjøller, Rasmus and Raaijmakers, Jos M. and Riber, Leise and Christensen, Svend and Rasmussen, Simon and Christensen, Jan H. and Dahl, Anders Bjorholm and Westergaard, Jesper Cairo and Nielsen, Mads and Brown-Guedira, Gina and Hestbjerg Hansen, Lars},
  date = {2021-06-17},
  journaltitle = {Annual Review of Plant Biology},
  shortjournal = {Annu. Rev. Plant Biol.},
  volume = {72},
  number = {1},
  pages = {823--846},
  issn = {1543-5008, 1545-2123},
  doi = {10.1146/annurev-arplant-080620-114342},
  url = {https://www.annualreviews.org/doi/10.1146/annurev-arplant-080620-114342},
  urldate = {2024-04-08},
  abstract = {The foliar microbiome can extend the host plant phenotype by expanding its genomic and metabolic capabilities. Despite increasing recognition of the importance of the foliar microbiome for plant fitness, stress physiology, and yield, the diversity, function, and contribution of foliar microbiomes to plant phenotypic traits remain largely elusive. The recent adoption of high-throughput technologies is helping to unravel the diversityand spatiotemporal dynamics of foliar microbiomes, but we have yet to resolve their functional importance for plant growth, development, and ecology. Here, we focus on the processes that govern the assembly of the foliar microbiome and the potential mechanisms involved in extended plant phenotypes. We highlight knowledge gaps and provide suggestions for new research directions that can propel the field forward. These efforts will be instrumental in maximizing the functional potential of the foliar microbiome for sustainable crop production.},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Hawkes et al. - 2021 - Extension of Plant Phenotypes by the Foliar Microb.pdf}
}

@book{hecht1978,
  title = {Evolutionary {{Biology}}},
  editor = {Hecht, Max K. and Steere, William C. and Wallace, Bruce},
  date = {1978},
  volume = {11},
  publisher = {Springer US},
  location = {Boston, MA},
  doi = {10.1007/978-1-4615-6956-5},
  url = {http://link.springer.com/10.1007/978-1-4615-6956-5},
  urldate = {2024-05-02},
  isbn = {978-1-4615-6958-9 978-1-4615-6956-5},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Hecht et al. - 1978 - Evolutionary Biology 2.pdf}
}

@article{henry2021,
  title = {The Microbiome Extends Host Evolutionary Potential},
  author = {Henry, Lucas P. and Bruijning, Marjolein and Forsberg, Simon K. G. and Ayroles, Julien F.},
  date = {2021-08-26},
  journaltitle = {Nature Communications},
  shortjournal = {Nat Commun},
  volume = {12},
  number = {1},
  pages = {5141},
  issn = {2041-1723},
  doi = {10.1038/s41467-021-25315-x},
  url = {https://www.nature.com/articles/s41467-021-25315-x},
  urldate = {2024-04-18},
  abstract = {Abstract             The microbiome shapes many host traits, yet the biology of microbiomes challenges traditional evolutionary models. Here, we illustrate how integrating the microbiome into quantitative genetics can help untangle complexities of host-microbiome evolution. We describe two general ways in which the microbiome may affect host evolutionary potential: by shifting the mean host phenotype and by changing the variance in host phenotype in the population. We synthesize the literature across diverse taxa and discuss how these scenarios could shape the host response to selection. We conclude by outlining key avenues of research to improve our understanding of the complex interplay between hosts and microbiomes.},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Henry et al. - 2021 - The microbiome extends host evolutionary potential.pdf}
}

@article{henry2023,
  title = {Evolutionary Implications of Host Genetic Control for Engineering Beneficial Microbiomes},
  author = {{Henry, Lucas P.} and {Bergelson, Joy}},
  date = {2023-06-01},
  volume = {34},
  eprint = {37287906},
  eprinttype = {pmid},
  pages = {100455--100455},
  doi = {10.1016/j.coisb.2023.100455},
  abstract = {Engineering new functions in the microbiome requires understanding how host genetic control and microbe-microbe interactions shape the microbiome. One key genetic mechanism underlying host control is the immune system. The immune system can promote stability in the composition of the microbiome by reshaping the ecological dynamics of its members, but the degree of stability will depend on the interplay between ecological context, immune system development, and higher-order microbe-microbe interactions. The eco-evolutionary interplay affecting composition and stability should inform the strategies used to engineer new functions in the microbiome. We conclude with recent methodological developments that provide an important path forward for both engineering new functionality in the microbiome and broadly understanding how ecological interactions shape evolutionary processes in complex biological systems.},
  annotation = {MAG ID: 4367186137}
}

@article{higgins2011,
  title = {Culturing and Direct {{PCR}} Suggest Prevalent Host Generalism among Diverse Fungal Endophytes of Tropical Forest Grasses},
  author = {Higgins, K. Lindsay and Coley, Phyllis D. and Kursar, Thomas A. and Arnold, A. Elizabeth},
  date = {2011},
  journaltitle = {Mycologia},
  volume = {103},
  number = {2},
  pages = {247--260},
  doi = {10.3852/09-158},
  abstract = {Most studies examining endophytic fungi associated with grasses (Poaceae) have focused on agronomically important species in managed ecosystems or on wild grasses in subtropical, temperate and boreal grasslands. However grasses first arose in tropical forests, where they remain a significant and diverse component of understory and forest-edge communities. To provide a broader context for understanding grass-endophyte associations we characterized fungal endophyte communities inhabiting foliage of 11 species of phylogenetically diverse C3 grasses in the understory of a lowland tropical forest at Barro Colorado Island, Panama. Our sample included members of early-arising subfamilies of Poaceae that are endemic to forests, as well as more recently arising subfamilies that transitioned to open environments. Isolation on culture media and direct PCR and cloning revealed that these grasses harbor species-rich and phylogenetically diverse communities that lack the endophytic Clavicipitaceae known from diverse woodland and pasture grasses in the temperate zone. Both the incidence and diversity of endophytes was consistent among grass species regardless of subfamily, clade affiliation or ancestral habitat use. Genotype and phylogenetic analyses suggest that these endophytic fungi are predominantly host generalists, shared not only among distinctive lineages of Poaceae but also with non-grass plants at the same site. © 2011 by The Mycological Society of America.},
  keywords = {Ascomycota,Barro colorado island,Diversity,Endophytes,Environmental sampling,Internal transcribed spacer,Poaceae,Tropical forest}
}

@article{higgins2014,
  title = {Communities of Fungal Endophytes in Tropical Forest Grasses: {{Highly}} Diverse Host- and Habitat Generalists Characterized by Strong Spatial Structure},
  author = {Higgins, K. Lindsay and Arnold, A. Elizabeth and Coley, Phyllis D. and Kursar, Thomas A.},
  date = {2014},
  journaltitle = {Fungal Ecology},
  volume = {8},
  number = {1},
  pages = {1--11},
  issn = {1754-5048},
  doi = {10.1016/j.funeco.2013.12.005},
  abstract = {Plant-symbiotic fungi influence the structure and function of all terrestrial ecosystems, but factors shaping their distributions in time and space are rarely well understood. Grasses (Poaceae), which first arose and diversified in tropical forests, harbor diverse but little-studied endophytes in the lowland forests of Panama. We used sequence data for 402 isolates from two sampling years, 11 host species, and 55 microsites at Barro Colorado Island, Panama to investigate the influence of host and habitat (soil type, forest age) in shaping endophyte diversity and composition. In contrast to previous studies, we found no evidence for host- or habitat specificity. Instead, endophytes demonstrated strong spatial structure consistent with dispersal limitation, with community similarity decaying markedly over a scale of hundreds of meters. Spatial structure that is independent of host species and habitat reveals remarkable heterogeneity of endophyte-host associations at small geographic scales and adds an important spatial component to extrapolative estimates of fungal diversity. © 2013 Elsevier Ltd and The British Mycological Society.},
  keywords = {Barro colorado island,Biodiversity,Community assembly,Fungal endophytes,Poaceae,Similarity,Tropical forest}
}

@software{hijmans2022,
  title = {Geosphere: {{Spherical}} Trigonometry},
  author = {Hijmans, Robert J.},
  date = {2022},
  version = {R package version 1.5-18}
}

@article{holeski2010,
  title = {The Genetics of Phenotypic Plasticity in Plant Defense: {{Trichome}} Production in {{{\emph{Mimulus}}}}{\emph{ Guttatus}}},
  author = {Holeski, Liza M and Chase-Alone, Ronnette and Kelly, John K},
  date = {2010},
  journaltitle = {American Naturalist},
  volume = {175},
  number = {4},
  pages = {391--400},
  issn = {1750451506},
  doi = {10.1086/651300},
  abstract = {Insect herbivory is a major driving force of plant evolution. Phenotypic plasticity and developmental variation provide a means for plants to cope with variable herbivory. We characterized the genetics of developmental variation and phenotypic plasticity in trichome density, a putative defensive trait of Mimulus guttatus (yellow monkeyflower). Our results are evaluated in relation to the optimal defense theory, which provides testable predictions for plastic and developmental patterns in defense traits. We found that both developmental stage and simulated insect damage affected trichome production, but in different ways. Plants were more likely to produce at least some trichomes on later leaves than on earlier leaves, regardless of damage. Damage did not affect the average probability of producing trichomes, but it did increase the density of hairs on trichome-positive plants. We mapped trichome quantitative trait loci (QTL) by selectively genotyping a large panel of recombinant inbred lines derived from two highly divergent populations. Several highly pleiotropic QTL influenced multiple aspects of the trichome phenotype (constitutive, developmental, and/or plastic responses). Only one of the QTL influenced trichome induction following damage. In a result that is consistent with a central prediction of optimal defense theory, the high allele at this location was from the ancestral population with low constitutive trichome production. © 2010 by The University of Chicago.},
  keywords = {Mimulus guttatus,Optimal defense theory,Phenotype plasticity,QTL,Trade-off,Trichomes},
  file = {/home/baponte/Zotero/storage/CL2I8KGA/Holeski_etal_2010_The_genetics_phenotypic_plasticity_of_Trichomes.pdf}
}

@article{hong2022,
  title = {To Rarefy or Not to Rarefy: Robustness and Efficiency Trade-Offs of Rarefying Microbiome Data},
  shorttitle = {To Rarefy or Not to Rarefy},
  author = {Hong, Johnny and Karaoz, Ulas and De Valpine, Perry and Fithian, William},
  editor = {Kelso, Janet},
  date = {2022-04-28},
  journaltitle = {Bioinformatics},
  volume = {38},
  number = {9},
  pages = {2389--2396},
  issn = {1367-4803, 1367-4811},
  doi = {10.1093/bioinformatics/btac127},
  url = {https://academic.oup.com/bioinformatics/article/38/9/2389/6536959},
  urldate = {2024-03-16},
  abstract = {Abstract                            Motivation               Microbiome datasets provide rich information about microbial communities. However, vast library size variations across samples present great challenges for proper statistical comparisons. To deal with these challenges, rarefaction is often used in practice as a normalization technique, although there has been debate whether rarefaction should ever be used. Conventional wisdom and previous work suggested that rarefaction should never be used in practice, arguing that rarefying microbiome data is statistically inadmissible. These discussions, however, have been confined to particular parametric models and simulation studies.                                         Results               We develop a semiparametric graphical model framework for grouped microbiome data and analyze in the context of differential abundance testing the statistical trade-offs of the rarefaction procedure, accounting for latent variations and measurement errors. Under the framework, it can be shown rarefaction guarantees that subsequent permutation tests properly control the Type I error. In addition, the loss in sensitivity from rarefaction is solely due to increased measurement error; if the underlying variation in microbial composition is large among samples, rarefaction might not hurt subsequent statistical inference much. We develop the rarefaction efficiency index (REI) as an indicator for efficiency loss and illustrate it with a dataset on the effect of storage conditions for microbiome data. Simulation studies based on real data demonstrate that the impact of rarefaction on sensitivity is negligible when overdispersion is prominent, while low REI corresponds to scenarios in which rarefying might substantially lower the statistical power. Whether to rarefy or not ultimately depends on assumptions of the data generating process and characteristics of the data.                                         Availability and implementation               Source codes are publicly available at https://github.com/jcyhong/rarefaction.                                         Supplementary information               Supplementary data are available at Bioinformatics online.},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Hong et al. - 2022 - To rarefy or not to rarefy robustness and efficie.pdf}
}

@article{hongqian2013,
  title = {Drivers of Β‐diversity along Latitudinal Gradients Revisited},
  author = {{Hong Qian} and Qian, Hong and {Shengbin Chen} and Chen, Shengbin and {Lingfeng Mao} and Mao, Lingfeng and {Zhiyun Ouyang} and Ouyang, Zhiyun},
  date = {2013-06-01},
  journaltitle = {Global Ecology and Biogeography},
  volume = {22},
  number = {6},
  pages = {659--670},
  doi = {10.1111/geb.12020},
  abstract = {Aim Ecologists have generally agreed that -diversity is driven at least in part by ecological processes and mechanisms of community assembly and is a key determinant of global patterns of species richness. This idea has been challenged by a recent study based on an individual-based null model approach, which aims to account for the species pool. The goal of the present study is twofold: (1) to analyse data sets from different parts of the world to determine whether there are significant latitude-diversity gradients after accounting for the species pool, and (2) to evaluate the validity of the null model. Location Global. Methods A total of 257 forest plots, each being 0.1 ha in size and having 10 0.01-ha subplots, were used. We conducted four sets of analyses. A modified version of Whittaker's -diversity index was used to quantify -diversity for each forest plot. A randomization procedure was used to determine expected -diversity. Results The number of individuals per species, which characterizes species abundance distribution, alone explains 56.884.2\% of the variation in observed -diversity. Species pool (-diversity) explained only an additional 2.615.2\% of the variation in observed -diversity. Latitude explains 18.6\% of the variation in raw deviation in Gentry's global data set, and explains 11.011.6\% of the variation in standardized deviation in the global and three regional analyses. Latitude explains 33.246.2\% of the variation in the number of individuals per species. Main conclusions Species abundance distribution, rather than species pool size, plays a key role in driving latitude-diversity gradients for -diversity in local forest communities. The individual-based null model is not a valid null model for investigating -diversity gradients driven by mechanisms of local community assembly because the null model incorporates species abundance distributions, which are driven by mechanisms of local community assembly and in turn generate -diversity gradients.},
  annotation = {MAG ID: 1583772763}
}

@article{horton2014,
  title = {Genome-Wide Association Study of {{{\emph{Arabidopsis}}}}{\emph{ Thaliana}} Leaf Microbial Community},
  author = {Horton, Matthew W. and Bodenhausen, Natacha and Beilsmith, Kathleen and Meng, Dazhe and Muegge, Brian D. and Subramanian, Sathish and Vetter, M. Madlen and Vilhjálmsson, Bjarni J. and Nordborg, Magnus and Gordon, Jeffrey I. and Bergelson, Joy},
  date = {2014},
  journaltitle = {Nature Communications},
  volume = {5},
  pages = {1--7},
  doi = {10.1038/ncomms6320},
  abstract = {Identifying the factors that influence the outcome of host-microbial interactions is critical to protecting biodiversity, minimizing agricultural losses and improving human health. A few genes that determine symbiosis or resistance to infectious disease have been identified in model species, but a comprehensive examination of how a host genotype influences the structure of its microbial community is lacking. Here we report the results of a field experiment with the model plant Arabidopsis thaliana to identify the fungi and bacteria that colonize its leaves and the host loci that influence the microbe numbers. The composition of this community differs among accessions of A. thaliana. Genome-wide association studies (GWAS) suggest that plant loci responsible for defense and cell wall integrity affect variation in this community. Furthermore, species richness in the bacterial community is shaped by host genetic variation, notably at loci that also influence the reproduction of viruses, trichome branching and morphogenesis.},
  issue = {May}
}

@article{hoysted2018,
  title = {A Mycorrhizal Revolution},
  author = {Hoysted, Grace A and Kowal, Jill and Jacob, Alison and Rimington, William R and Duckett, Jeffrey G and Pressel, Silvia and Orchard, Suzanne and Ryan, Megan H and Field, Katie J and Bidartondo, Martin I},
  date = {2018-08},
  journaltitle = {Current Opinion in Plant Biology},
  shortjournal = {Current Opinion in Plant Biology},
  volume = {44},
  pages = {1--6},
  issn = {13695266},
  doi = {10.1016/j.pbi.2017.12.004},
  url = {https://linkinghub.elsevier.com/retrieve/pii/S1369526617301280},
  urldate = {2024-05-02},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Hoysted et al. - 2018 - A mycorrhizal revolution.pdf}
}

@incollection{inbook,
  title = {White, {{T}}. {{J}}., {{T}}. {{D}}. {{Bruns}}, {{S}}. {{B}}. {{Lee}}, and {{J}}. {{W}}. {{Taylor}}. {{Amplification}} and Direct Sequencing of Fungal Ribosomal {{RNA}} Genes for Phylogenetics},
  author = {{White} and {Bruns} and {Tom} and Lee, Steven and Taylor, John},
  date = {1990-01},
  pages = {315--322},
  isbn = {0-12-372180-6}
}

@book{ipcc2023,
  title = {Climate {{Change}} 2021 – {{The Physical Science Basis}}: {{Working Group I Contribution}} to the {{Sixth Assessment Report}} of the {{Intergovernmental Panel}} on {{Climate Change}}},
  shorttitle = {Climate {{Change}} 2021 – {{The Physical Science Basis}}},
  author = {{Intergovernmental Panel omojican Climate Change}},
  date = {2023-07-06},
  edition = {1},
  publisher = {Cambridge University Press},
  doi = {10.1017/9781009157896},
  url = {https://www.cambridge.org/core/product/identifier/9781009157896/type/book},
  urldate = {2024-04-08},
  abstract = {The Working Group I contribution to the Sixth Assessment Report of the Intergovernmental Panel on Climate Change (IPCC) provides a comprehensive assessment of the physical science basis of climate change. It considers in situ and remote observations; paleoclimate information; understanding of climate drivers and physical, chemical, and biological processes and feedbacks; global and regional climate modelling; advances in methods of analyses; and insights from climate services. It assesses the current state of the climate; human influence on climate in all regions; future climate change including sea level rise; global warming effects including extremes; climate information for risk assessment and regional adaptation; limiting climate change by reaching net zero carbon dioxide emissions and reducing other greenhouse gas emissions; and benefits for air quality. The report serves policymakers, decision makers, stakeholders, and all interested parties with the latest policy-relevant information on climate change. Available as Open Access on Cambridge Core.},
  isbn = {978-1-00-915789-6},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Intergovernmental Panel On Climate Change - 2023 - Climate Change 2021 – The Physical Science Basis .pdf;/home/baponte/Zotero/storage/CWI567SJ/Intergovernmental Panel On Climate Change - 2023 - Climate Change 2021 – The Physical Science Basis .pdf}
}

@article{j.sebastiantello2015,
  title = {Elevational {{Gradients}} in β-{{Diversity Reflect Variation}} in the {{Strength}} of {{Local Community Assembly Mechanisms}} across {{Spatial Scales}}},
  author = {{J. Sebastián Tello} and Tello, J. Sebastián and {Jonathan A. Myers} and Myers, Jonathan and {Manuel J. Macía} and Macía, Manuel J. and {Alfredo F. Fuentes} and Fuentes, Alfredo F. and {Leslie Cayola} and Cayola, Leslie and {Gabriel Arellano} and Arellano, Gabriel and {M. Isabel Loza} and Loza, M. Isabel and {Vania Torrez} and Torrez, Vania and {Maritza Cornejo} and Cornejo, Maritza and {Tatiana B. Miranda} and Miranda, Tatiana and {Peter M. Jørgensen} and Jørgensen, Peter M.},
  date = {2015-03-24},
  journaltitle = {PLOS ONE},
  volume = {10},
  number = {3},
  eprint = {25803846},
  eprinttype = {pmid},
  pages = {1--17},
  doi = {10.1371/journal.pone.0121458},
  abstract = {Despite long-standing interest in elevational-diversity gradients, little is known about the processes that cause changes in the compositional variation of communities (β-diversity) across elevations. Recent studies have suggested that β-diversity gradients are driven by variation in species pools, rather than by variation in the strength of local community assembly mechanisms such as dispersal limitation, environmental filtering, or local biotic interactions. However, tests of this hypothesis have been limited to very small spatial scales that limit inferences about how the relative importance of assembly mechanisms may change across spatial scales. Here, we test the hypothesis that scale-dependent community assembly mechanisms shape biogeographic β-diversity gradients using one of the most well-characterized elevational gradients of tropical plant diversity. Using an extensive dataset on woody plant distributions along a 4,000-m elevational gradient in the Bolivian Andes, we compared observed patterns of β-diversity to null-model expectations. β-deviations (standardized differences from null values) were used to measure the relative effects of local community assembly mechanisms after removing sampling effects caused by variation in species pools. To test for scale-dependency, we compared elevational gradients at two contrasting spatial scales that differed in the size of local assemblages and regions by at least an order of magnitude. Elevational gradients in β-diversity persisted after accounting for regional variation in species pools. Moreover, the elevational gradient in β-deviations changed with spatial scale. At small scales, local assembly mechanisms were detectable, but variation in species pools accounted for most of the elevational gradient in β-diversity. At large spatial scales, in contrast, local assembly mechanisms were a dominant force driving changes in β-diversity. In contrast to the hypothesis that variation in species pools alone drives β-diversity gradients, we show that local community assembly mechanisms contribute strongly to systematic changes in β-diversity across elevations. We conclude that scale-dependent variation in community assembly mechanisms underlies these iconic gradients in global biodiversity.},
  pmcid = {4372560},
  annotation = {MAG ID: 2010362844}
}

@article{jimenez-hernandez2020,
  title = {Altitudinal Distribution of Alpha, Beta, and Gamma Diversity of Pseudoscorpions ({{Arachnida}}) in {{Oaxaca}}, {{Mexico}}},
  author = {Jiménez-Hernández, Violeta Saraí and Villegas-Guzmán, Gabriel Alfredo and Casasola-González, José Arturo and Vargas-Mendoza, Carlos Fabián},
  date = {2020-02},
  journaltitle = {Acta Oecologica},
  shortjournal = {Acta Oecologica},
  volume = {103},
  pages = {103525},
  issn = {1146609X},
  doi = {10.1016/j.actao.2020.103525},
  url = {https://linkinghub.elsevier.com/retrieve/pii/S1146609X20300175},
  urldate = {2024-03-20},
  langid = {english}
}

@article{jirongcao2020,
  title = {Functional Structure, Taxonomic Composition and the Dominant Assembly Processes of Soil Prokaryotic Community along an Altitudinal Gradient},
  author = {{Jirong Cao} and Cao, Jirong and Cao, Jirong and {Jirong Cao} and {Xiu Jia} and Jia, Xiu and {Shuang Pang} and Pang, Shuang and {Yecui Hu} and Hu, Yecui and {Yuncong Li} and Li, Yuncong and {Qibing Wang} and Wang, Qibing},
  date = {2020-11-01},
  journaltitle = {Applied Soil Ecology},
  volume = {155},
  pages = {103647},
  doi = {10.1016/j.apsoil.2020.103647},
  abstract = {Abstract   As more attentions have been paid to microbial taxonomic community structure along altitudinal gradients, the knowledge of the altitudinal variations in microbial functional structure in terrestrial ecosystems is limited. More importantly, the dominant assembly processes that drive altitudinal variations in both taxonomic composition and functional structure remain unclear. To fill the gaps, we integrated soil prokaryotic taxonomic community structure, functional community structure and community assembly processes along an altitudinal gradient into a comprehensive understanding. The results revealed that both taxonomic community structure and core functional community structure of soil prokaryotic microbes significantly differed across altitudes. We detected the core functional groups associated with the redox reactions essential for microbial metabolism and biogeochemical cycles across altitudes. Chemoheterotrophy and photoautotrophy were dominant in abundance, indicating the important roles of primary energy metabolism for soil prokaryotic community. The whole prokaryotic community taxonomic composition was dominantly shaped by dispersal limitation (governing 74\% of spatial turnover). The variation of functional structure was primarily caused by environmental selection, while the taxonomic variation within individual functional groups was weakly related to selection but mainly driven by drift. These results are critical for predicting the future dynamics of soil microbial community in the face of disturbances.},
  annotation = {MAG ID: 3024344364\\
S2ID: b797524a99254c79a6e4e7bbab63316c09614dbc}
}

@article{joos2020,
  title = {Daring to Be Differential: Metabarcoding Analysis of Soil and Plant-Related Microbial Communities Using Amplicon Sequence Variants and Operational Taxonomical Units},
  author = {Joos, Lisa and Beirinckx, Stien and Haegeman, Annelies and Debode, Jane and Vandecasteele, Bart and Baeyen, Steve and Goormachtig, Sofie and Clement, Lieven and De Tender, Caroline},
  date = {2020-10},
  journaltitle = {BMC Genomics},
  volume = {21},
  pages = {733},
  doi = {10.1186/s12864-020-07126-4}
}

@article{jost2006,
  title = {\emph{Entropy and Diversity}},
  author = {Jost, Lou},
  date = {2006-05},
  journaltitle = {Oikos},
  shortjournal = {Oikos},
  volume = {113},
  number = {2},
  pages = {363--375},
  issn = {0030-1299, 1600-0706},
  doi = {10.1111/j.2006.0030-1299.14714.x},
  url = {https://onlinelibrary.wiley.com/doi/10.1111/j.2006.0030-1299.14714.x},
  urldate = {2024-03-08},
  abstract = {Entropies such as the Shannon–Wiener and Gini–Simpson indices are not themselves diversities. Conversion of these to effective number of species is the key to a unified and intuitive interpretation of diversity. Effective numbers of species derived from standard diversity indices share a common set of intuitive mathematical properties and behave as one would expect of a diversity, while raw indices do not. Contrary to Keylock, the lack of concavity of effective numbers of species is irrelevant as long as they are used as transformations of concave alpha, beta, and gamma entropies. The practical importance of this transformation is demonstrated by applying it to a popular community similarity measure based on raw diversity indices or entropies. The standard similarity measure based on untransformed indices is shown to give misleading results, but transforming the indices or entropies to effective numbers of species produces a stable, easily interpreted, sensitive general similarity measure. General overlap measures derived from this transformed similarity measure yield the Jaccard index, Sørensen index, Horn index of overlap, and the Morisita–Horn index as special cases.},
  langid = {english}
}

@article{jump2005,
  title = {Running to Stand Still: {{Adaptation}} and the Response of Plants to Rapid Climate Change},
  author = {Jump, Alistair S. and Peñuelas, Josep},
  date = {2005},
  journaltitle = {Ecology Letters},
  volume = {8},
  number = {9},
  pages = {1010--1020},
  doi = {10.1111/j.1461-0248.2005.00796.x},
  abstract = {Climate is a potent selective force in natural populations, yet the importance of adaptation in the response of plant species to past climate change has been questioned. As many species are unlikely to migrate fast enough to track the rapidly changing climate of the future, adaptation must play an increasingly important role in their response. In this paper we review recent work that has documented climate-related genetic diversity within populations or on the microgeographical scale. We then describe studies that have looked at the potential evolutionary responses of plant populations to future climate change. We argue that in fragmented landscapes, rapid climate change has the potential to overwhelm the capacity for adaptation in many plant populations and dramatically alter their genetic composition. The consequences are likely to include unpredictable changes in the presence and abundance of species within communities and a reduction in their ability to resist and recover from further environmental perturbations, such as pest and disease outbreaks and extreme climatic events. Overall, a range-wide increase in extinction risk is likely to result. We call for further research into understanding the causes and consequences of the maintenance and loss of climate-related genetic diversity within populations. ©2005 Blackwell Publishing Ltd/CNRS.},
  keywords = {Adaptation,Climate change,Conservation,Decreased fitness,Extinction risk,Gene flow,Genetic diversity,Habitat fragmentation,Migration,Plant populations},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Jump and Peñuelas - 2005 - Running to stand still Adaptation and the respons.pdf}
}

@article{kaddes2019,
  title = {Endophytic {{Fungal Volatile Compounds}} as {{Solution}} for {{Sustainable Agriculture}}},
  author = {Kaddes, Amine and Fauconnier, Marie-Laure and Sassi, Khaled and Nasraoui, Bouzid and Jijakli, Mohamed-Haïssam},
  date = {2019-03-18},
  journaltitle = {Molecules},
  shortjournal = {Molecules},
  volume = {24},
  number = {6},
  pages = {1065},
  issn = {1420-3049},
  doi = {10.3390/molecules24061065},
  url = {https://www.mdpi.com/1420-3049/24/6/1065},
  urldate = {2024-04-08},
  abstract = {Endophytic fungi produce various mixtures of carbon-based compounds, which are known as volatile organic compounds (VOCs). Research regarding the use of VOCs as pesticide substitutes has garnered much attention. This review summarizes the recent knowledge about VOCs regarding their origin and chemical properties and emphasizes their antimicrobial potential against a wide variety of agricultural pathogens. Several studies have highlighted the importance of VOCs as antimicrobial agents. Nevertheless, the application of VOCs in biofumigation methods still requires the advanced evaluation of their phytotoxicity.},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Kaddes et al. - 2019 - Endophytic Fungal Volatile Compounds as Solution f.pdf}
}

@software{kassambara2023,
  title = {Rstatix: {{Pipe-Friendly Framework}} for {{Basic Statistical Tests}}},
  author = {Kassambara, Alboukadel},
  date = {2023},
  url = {https://rpkgs.datanovia.com/rstatix/},
  version = {R package version 0.7.2}
}

@software{kassambara2023a,
  title = {Ggpubr: 'ggplot2' {{Based Publication Ready Plots}}},
  author = {Kassambara, Alboukadel},
  date = {2023},
  url = {https://rpkgs.datanovia.com/ggpubr/},
  version = {R package version 0.6.0}
}

@article{kazenel2019,
  title = {Altitudinal Gradients Fail to Predict Fungal Symbiont Responses to Warming.},
  author = {Kazenel, Melanie R. and Kivlin, Stephanie N. and Taylor, D. Lee and Lynn, Joshua S. and Rudgers, Jennifer A.},
  date = {2019-08-01},
  journaltitle = {Ecology},
  volume = {100},
  number = {8},
  eprint = {31006112},
  eprinttype = {pmid},
  doi = {10.1002/ecy.2740},
  abstract = {Climate change is shifting altitudinal species ranges, with potential to disrupt species interactions. Altitudinal gradient studies and warming experiments can both increase understanding of climate effects on species interactions, but few studies have used both together to improve predictions. We examined whether plant–fungal symbioses responded similarly to altitude and 23yr of experimental warming. Root‐ and leaf‐associated fungi, which can mediate plants’ climate sensitivity, responded divergently to elevation vs. warming. Fungal colonization, diversity, and composition varied with altitude, but climate variables were generally weak predictors; other factors such as host plant identity, plant community composition, or edaphic variables likely drive fungal altitudinal distributions. Manipulated warming altered fungal colonization, but not composition or diversity. Leaf symbionts were more sensitive to climate and experimental warming than root symbionts. Altitudinal patterns and responses to warming differed among host plant species and fungal groups, indicating that predicting climate effects on symbioses will require tracking both host and symbiont identities. Combining experimental and observational methods can yield valuable insight into how climate change may alter plant–symbiont interactions, but our results indicate that altitude does not always serve as an adequate proxy for warming effects on fungal symbionts of plants.},
  annotation = {MAG ID: 2935927366\\
S2ID: 759ccd5f5d315d666831afdaf8153348f7d89431},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Melanie R. Kazenel et al. - 2019 - Altitudinal gradients fail to predict fungal symbi.pdf}
}

@article{kelly1998,
  title = {Polymorphic Microsatellite Loci in {{{\emph{Mimulus}}}}{\emph{ Guttatus}} and Related Species},
  author = {Kelly, Alan J. and Willis, John H.},
  date = {1998},
  journaltitle = {Molecular Ecology},
  volume = {7},
  number = {6},
  pages = {769--774},
  doi = {10.1046/j.1365-294x.1998.00328.x},
  abstract = {The evolution of self-fertilization from outcrossing is one of the most common evolutionary transitions in flowering plants. One goal of our research is to develop a linkage map based upon microsatellite loci in Mimulus guttatus and the selfing derivative M. nasutus in order to examine the genetics of one such transition. Here we present 19 primer pairs that detect polymorphisms between these two species. Within-population allelic surveys demonstrate the value of these markers for detailed analysis of population structure. We have found also that many of the microsatellites are conserved in more distantly related Mimulus species, and may thus serve as useful genetic markers for population genetic and comparative mapping studies within this diverse genus.},
  keywords = {Microsatellites,Mimulus,Outcrossing,Population structure,Self-fertilization}
}

@article{kitajima2013,
  title = {Leaf Life Span Spectrum of Tropical Woody Seedlings: {{Effects}} of Light and Ontogeny and Consequences for Survival},
  author = {Kitajima, Kaoru and Cordero, Roberto A. and Wright, S. Joseph},
  date = {2013},
  journaltitle = {Annals of Botany},
  volume = {112},
  number = {4},
  pages = {685--699},
  doi = {10.1093/aob/mct036},
  abstract = {Background and AimsLeaf life span is widely recognized as a key life history trait associated with herbivory resistance, but rigorous comparative data are rare for seedlings. The goal of this study was to examine how light environment affects leaf life span, and how ontogenetic development during the first year may influence leaf fracture toughness, lamina density and stem density that are relevant for herbivory resistance, leaf life span and seedling survival.MethodsData from three experiments encompassing 104 neotropical woody species were combined. Leaf life span, lamina and vein fracture toughness, leaf and stem tissue density and seedling survival were quantified for the first-year seedlings at standardized ontogenetic stages in shade houses and common gardens established in gaps and shaded understorey in a moist tropical forest in Panama. Mortality of naturally recruited seedlings till 1 year later was quantified in 800 1-m2 plots from 1994 to 2011.Key ResultsMedian leaf life span ranged widely among species, always greater in shade (ranging from 151 to {$>$}1790 d in the understorey and shade houses) than in gaps (115-867 d), but with strong correlation between gaps and shade. Leaf and stem tissue density increased with seedling age, whereas leaf fracture toughness showed only a weak increase. All these traits were positively correlated with leaf life span. Leaf life span and stem density were negatively correlated with seedling mortality in shade, while gap mortality showed no correlation with these traits.ConclusionsThe wide spectrum of leaf life span and associated functional traits reflects variation in shade tolerance of first-year seedlings among coexisting trees, shrubs and lianas in this neotropical forest. High leaf tissue density is important in enhancing leaf toughness, a known physical defence, and leaf life span. Both seedling leaf life span and stem density should be considered as key functional traits that contribute to seedling survival in tropical forest understoreys. © The Author 2013.},
  keywords = {Fracture toughness,Herbivory,Leaf density,Leaf life span,Leaf toughness,Lightenvironment,Ontogenetic changes,Phenotypic plasticity,Seedling survival,Stem density,Tropical lianas,Tropical trees},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Kitajima et al. - 2013 - Leaf life span spectrum of tropical woody seedling.pdf}
}

@article{kivlin2013,
  title = {Fungal Symbionts Alter Plant Responses to Global Change},
  author = {Kivlin, Stephanie N. and Emery, Sarah M. and Rudgers, Jennifer A.},
  date = {2013-07},
  journaltitle = {American Journal of Botany},
  shortjournal = {American J of Botany},
  volume = {100},
  number = {7},
  pages = {1445--1457},
  issn = {0002-9122, 1537-2197},
  doi = {10.3732/ajb.1200558},
  url = {https://bsapubs.onlinelibrary.wiley.com/doi/10.3732/ajb.1200558},
  urldate = {2024-03-08},
  abstract = {While direct plant responses to global change have been well characterized, indirect plant responses to global change, via altered species interactions, have received less attention. Here, we examined how plants associated with four classes of fungal symbionts (class I leaf endophytes [EF], arbuscular mycorrhizal fungi [AMF], ectomycorrhizal fungi [ECM], and dark septate endophytes [DSE]) responded to four global change factors (enriched CO               2               , drought, N deposition, and warming). We performed a meta‐analysis of 434 studies spanning 174 publications to search for generalizable trends in responses of plant–fungal symbioses to future environments. Specifically, we addressed the following questions: (1) Can fungal symbionts ameliorate responses of plants to global change? (2) Do fungal symbiont groups differ in the degree to which they modify plant response to global change? (3) Do particular global change factors affect plant–fungal symbioses more than others? In all global change scenarios, except elevated CO               2               , fungal symbionts significantly altered plant responses to global change. In most cases, fungal symbionts increased plant biomass in response to global change. However, increased N deposition reduced the benefits of symbiosis. Of the global change factors we considered, drought and N deposition resulted in the strongest fungal mediation of plant responses. Our analysis highlighted gaps in current knowledge for responses of particular fungal groups and revealed the importance of considering not only the nonadditive effects of multiple global change factors, but also the interactive effects of multiple fungal symbioses. Our results show that considering plant–fungal symbioses is critical to predicting ecosystem response to global change.},
  langid = {english}
}

@article{kivlin2019,
  title = {Direct and Indirect Influences of Warming on Leaf Endophytic Fungi: {{A}} Physiological and Compositional Approach},
  author = {Kivlin, Stephanie N. and Rudgers, Jennifer A.},
  date = {2019-01-01},
  journaltitle = {Ecosystem Consequences of Soil Warming},
  pages = {125--140},
  doi = {10.1016/b978-0-12-813493-1.00006-5},
  abstract = {Abstract   Endophytic fungi inhabit the leaf tissues of all living plants where they can buffer or exacerbate plant responses to climate change. Because many of these fungi have only recently been discovered and sequenced, the independent and interactive responses of plants and their fungal symbionts to a warming climate is an area of active research. Here we describe a conceptual framework linking the range of phenotypic plasticity and rates of shifts in community composition of each symbiont (plants and fungal leaf endophytes) to overall changes in abundance of each organism in a 26-year-long warming experiment in the Colorado Rocky Mountains. In this system, leaf endophytic fungi exhibit large plasticity in growth rates in response to experimental warming in the laboratory, but no shifts in composition after 26years of warming in the field. Instead, fungal composition in the field changed in response to plant species composition. In contrast, the C3 grasses examined in this study shifted in composition in response to field warming within 4years. In addition, the abundance of individual fungi was much more variable among field temperatures than that of plants. Overall, we find support that fungi are potentially more phenotypically plastic in response to warming whereas plants are more likely to shift composition.},
  annotation = {MAG ID: 2939617615\\
S2ID: e8a7987b70b928f14b84265cb36e693fc9f9547e},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Kivlin and Rudgers - 2019 - Direct and indirect influences of warming on leaf .pdf}
}

@article{kivlin2022,
  title = {Grass Species Identity Shapes Communities of Root and Leaf Fungi More than Elevation},
  author = {Kivlin, Stephanie N. and Mann, Michael A. and Lynn, Joshua S. and Kazenel, Melanie R. and Taylor, D. Lee and Rudgers, Jennifer A.},
  date = {2022-03-17},
  journaltitle = {ISME Communications},
  shortjournal = {ISME Communications},
  volume = {2},
  number = {1},
  pages = {25},
  issn = {2730-6151},
  doi = {10.1038/s43705-022-00107-6},
  url = {https://doi.org/10.1038/s43705-022-00107-6},
  abstract = {Fungal symbionts can buffer plants from environmental extremes and may affect host capacities to acclimate, adapt, or redistribute under environmental change; however, the distributions of fungal symbionts along abiotic gradients are poorly described. Fungal mutualists should be the most beneficial in abiotically stressful environments, and the structure of networks of plant-fungal interactions likely shift along gradients, even when fungal community composition does not track environmental stress. We sampled 634 unique combinations of fungal endophytes and mycorrhizal fungi, grass species identities, and sampling locations from 66 sites across six replicate altitudinal gradients in the western Colorado Rocky Mountains. The diversity and composition of leaf endophytic, root endophytic, and arbuscular mycorrhizal (AM) fungal guilds and the overall abundance of fungal functional groups (pathogens, saprotrophs, mutualists) tracked grass host identity more closely than elevation. Network structures of root endophytes become more nested and less specialized at higher elevations, but network structures of other fungal guilds did not vary with elevation. Overall, grass species identity had overriding influence on the diversity and composition of above- and belowground fungal endophytes and AM fungi, despite large environmental variation. Therefore, in our system climate change may rarely directly affect fungal symbionts. Instead, fungal symbiont distributions will most likely track the range dynamics of host grasses.},
  file = {/home/baponte/Zotero/storage/XPG6KLCT/Kivlin et al. - 2022 - Grass species identity shapes communities of root .pdf}
}

@article{koornneef2010,
  title = {The Development of {{{\emph{Arabidopsis}}}} as a Model Plant},
  author = {Koornneef, Maarten and Meinke, David},
  date = {2010-03},
  journaltitle = {The Plant Journal},
  shortjournal = {The Plant Journal},
  volume = {61},
  number = {6},
  pages = {909--921},
  issn = {0960-7412, 1365-313X},
  doi = {10.1111/j.1365-313X.2009.04086.x},
  url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2009.04086.x},
  urldate = {2024-05-13},
  abstract = {Summary                            Twenty‐five years ago,               Arabidopsis thaliana               emerged as the model organism of choice for research in plant biology. A consensus was reached about the need to focus on a single organism to integrate the classical disciplines of plant science with the expanding fields of genetics and molecular biology. Ten years after publication of its genome sequence, Arabidopsis remains the standard reference plant for all of biology. We reflect here on the major advances and shared resources that led to the extraordinary growth of the Arabidopsis research community. We also underscore the importance of continuing to expand and refine our detailed knowledge of Arabidopsis while seeking to appreciate the remarkable diversity that characterizes the plant kingdom.},
  langid = {english},
  file = {/home/baponte/Zotero/storage/M62JP25A/Koornneef and Meinke - 2010 - The development of Arabidopsis as a model plant.pdf}
}

@article{kraft2011,
  title = {Disentangling the {{Drivers}} of β {{Diversity Along Latitudinal}} and {{Elevational Gradients}}},
  author = {Kraft, Nathan J. B. and Comita, Liza S. and Chase, Jonathan M. and Sanders, Nathan J. and Swenson, Nathan G. and Crist, Thomas O. and Stegen, James C. and Vellend, Mark and Boyle, Brad and Anderson, Marti J. and Cornell, Howard V. and Davies, Kendi F. and Freestone, Amy L. and Inouye, Brian D. and Harrison, Susan P. and Myers, Jonathan A.},
  date = {2011-09-23},
  journaltitle = {Science},
  shortjournal = {Science},
  volume = {333},
  number = {6050},
  pages = {1755--1758},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.1208584},
  url = {https://www.science.org/doi/10.1126/science.1208584},
  urldate = {2024-03-20},
  abstract = {Increases in species turnover of woody plants at low latitudes and elevations are explained by the size of species pools alone.           ,              Understanding spatial variation in biodiversity along environmental gradients is a central theme in ecology. Differences in species compositional turnover among sites (β diversity) occurring along gradients are often used to infer variation in the processes structuring communities. Here, we show that sampling alone predicts changes in β diversity caused simply by changes in the sizes of species pools. For example, forest inventories sampled along latitudinal and elevational gradients show the well-documented pattern that β diversity is higher in the tropics and at low elevations. However, after correcting for variation in pooled species richness (γ diversity), these differences in β diversity disappear. Therefore, there is no need to invoke differences in the mechanisms of community assembly in temperate versus tropical systems to explain these global-scale patterns of β diversity.},
  langid = {english}
}

@article{kramer2015,
  title = {Planting Molecular Functions in an Ecological Context with {{{\emph{Arabidopsis}}}}{\emph{ Thaliana}}},
  author = {Krämer, Ute},
  date = {2015-03-25},
  journaltitle = {eLife},
  volume = {4},
  pages = {e06100},
  issn = {2050-084X},
  doi = {10.7554/eLife.06100},
  url = {https://elifesciences.org/articles/06100},
  urldate = {2024-05-13},
  abstract = {The vascular plant Arabidopsis thaliana is a central genetic model and universal reference organism in plant and crop science. The successful integration of different fields of research in the study of A. thaliana has made a large contribution to our molecular understanding of key concepts in biology. The availability and active development of experimental tools and resources, in combination with the accessibility of a wealth of cumulatively acquired knowledge about this plant, support the most advanced systems biology approaches among all land plants. Research in molecular ecology and evolution has also brought the natural history of A. thaliana into the limelight. This article showcases our current knowledge of the natural history of A. thaliana from the perspective of the most closely related plant species, providing an evolutionary framework for interpreting novel findings and for developing new hypotheses based on our knowledge of this plant.},
  langid = {english},
  file = {/home/baponte/Zotero/storage/2SZKDK49/Krämer - 2015 - Planting molecular functions in an ecological cont.pdf}
}

@misc{lahti2012,
  title = {Microbiome {{R}} Package},
  author = {Lahti, Leo and Shetty, Sudarshan},
  date = {2012/2019}
}

@article{legendre1999,
  title = {Distance-Based Redundancy Analysis: {{Testing}} Multispecies Responses in Multifactorial Ecological Experiments},
  author = {Legendre, Pierre and Anderson, Marti J.},
  date = {1999},
  journaltitle = {Ecological Monographs},
  volume = {69},
  number = {1},
  eprint = {https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1890/0012-9615%281999%29069%5B0001%3ADBRATM%5D2.0.CO%3B2},
  pages = {1--24},
  doi = {10.1890/0012-9615(1999)069[0001:DBRATM]2.0.CO;2},
  url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/0012-9615%281999%29069%5B0001%3ADBRATM%5D2.0.CO%3B2},
  abstract = {We present a new multivariate technique for testing the significance of individual terms in a multifactorial analysis-of-variance model for multispecies response variables. The technique will allow researchers to base analyses on measures of association (distance measures) that are ecologically relevant. In addition, unlike other distance-based hypothesis-testing techniques, this method allows tests of significance of interaction terms in a linear model. The technique uses the existing method of redundancy analysis (RDA) but allows the analysis to be based on Bray-Curtis or other ecologically meaningful measures through the use of principal coordinate analysis (PCoA). Steps in the procedure include: (1) calculating a matrix of distances among replicates using a distance measure of choice (e.g., Bray-Curtis); (2) determining the principal coordinates (including a correction for negative eigenvalues, if necessary), which preserve these distances; (3) creating a matrix of dummy variables corresponding to the design of the experiment (i.e., individual terms in a linear model); (4) analyzing the relationship between the principal coordinates (species data) and the dummy variables (model) using RDA; and (5) implementing a test by permutation for particular statistics corresponding to the particular terms in the model. This method has certain advantages not shared by other multivariate testing procedures. We demonstrate the use of this technique with experimental ecological data from intertidal assemblages and show how the presence of significant multivariate interactions can be interpreted. It is our view that distance-based RDA will be extremely useful to ecologists measuring multispecies responses to structured multifactorial experimental designs.},
  keywords = {experimental ecology,interaction terms in multifactorial ANOVA,intertidal estuarine assemblage,multifactorial experimental design,multivariate permutational tests of interactions,permutations,principal coordinate analysis,redundancy analysis,testing multispecies responses}
}

@article{legendre2011,
  title = {Testing the Significance of Canonical Axes in Redundancy Analysis},
  author = {Legendre, Pierre and Oksanen, Jari and Ter Braak, Cajo J. F.},
  date = {2011-06},
  journaltitle = {Methods in Ecology and Evolution},
  shortjournal = {Methods Ecol Evol},
  volume = {2},
  number = {3},
  pages = {269--277},
  issn = {2041-210X, 2041-210X},
  doi = {10.1111/j.2041-210X.2010.00078.x},
  url = {https://besjournals.onlinelibrary.wiley.com/doi/10.1111/j.2041-210X.2010.00078.x},
  urldate = {2024-01-17},
  abstract = {Summary 1. Tests of significance of the individual canonical axes in redundancy analysis allow researchers to determine which of the axes represent variation that can be distinguished from random. Variation along the significant axes can be mapped, used to draw biplots or interpreted through subsequent analyses, whilst the nonsignificant axes may be dropped from further consideration. 2. Three methods have been implemented in computer programs to test the significance of the canonical axes; they are compared in this paper. The simultaneous test of all individual canonical axes, which is appealing because of its simplicity, produced incorrect (highly inflated) levels of type I error for the axes following those corresponding to true relationships in the data, so it is invalid. The ‘marginal’ testing method implemented in the ‘vegan’ R package and the ‘forward’ testing method implemented in the program CANOCO were found to have correct levels of type I error and comparable power. Permutation of the residuals achieved greater power than permutation of the raw data. 3. R functions found in a Supplement to this paper provide the first formal description of the ‘marginal’ and ‘forward’ testing methods.},
  langid = {english}
}

@book{legendre2012,
  title = {Numerical Ecology},
  author = {Legendre, Pierre and Legendre, Louis},
  date = {2012},
  series = {Developments in Environmental Modelling},
  edition = {3d English edition},
  number = {24},
  publisher = {Elsevier},
  location = {Amsterdam},
  abstract = {The book describes and discusses the numerical methods which are successfully being used for analysing ecological data, using a clear and comprehensive approach. These methods are derived from the fields of mathematical physics, parametric and nonparametric statistics, information theory, numerical taxonomy, archaeology, psychometry, sociometry, econometry and others. Relates ecological questions to methods of statistical analysis, with a clear description of complex numerical methods. All methods are illustrated by examples from the ecological literature so that ecologists clearly see how to use the methods and approaches in their own research. All calculations are available in R language functions},
  isbn = {978-0-444-53868-0},
  langid = {english}
}

@article{liu2023,
  title = {An {{SPRI}} Beads-Based {{DNA}} Purification Strategy for Flexibility and Cost-Effectiveness},
  author = {Liu, Danli and Li, Qiujia and Luo, Jing and Huang, Qitong and Zhang, Yubo},
  date = {2023-03-16},
  journaltitle = {BMC Genomics},
  shortjournal = {BMC Genomics},
  volume = {24},
  number = {1},
  pages = {125},
  issn = {1471-2164},
  doi = {10.1186/s12864-023-09211-w},
  url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-023-09211-w},
  urldate = {2024-02-10},
  abstract = {Abstract Background Current solid-phase reversible immobilization (SPRI) beads technology is widely used in molecular biology due to its convenience for DNA manipulation. However, the high performance commercial SPRI beads have no price advantage over our method. Furthermore, the use of commercially available SPRI beads standards does not provide the flexibility required for a number of specific nucleic acid handling scenarios. Results We report an efficient DNA purification strategy by combining home-made beads-suspension buffer with SPRI beads. The method tests the critical concentrations of polyethylene glycol (PEG) 8000 and beads to maximise recovery. And the composition of the SPRI beads DNA purification system (SDPS) was determined at 20\% PEG 8000, 2\,M NaCl and 16.3\,mM MgCl 2 , and 1.25\,mg/ml beads (1/8th original concentration). Then, we tested the DNA recovery of the SDPS, and the result showed that it was comparable to the control (AMPure XP beads). In the study, we have also developed an adjustment SPRI beads DNA purification system (ASDPS), the volume of ASDPS per reaction is 0.6× reaction volume (beads/samples). The performance of ASDPS is similar to SDPS and the control. But the cost of our methods is only about 1/24th of the control. To further assess its performance, we prepare the DNA-seq libraries to evaluate the yield, library quality, capture efficiency and consistency. We have compared all these results with the performance of the control and confirmed its efficiency. Conclusion We have proposed an alternative DNA purification approach with great flexibility, allowing researchers to manipulate DNA in different conditions. And ultimately, its application will benefit molecular biology research in the future.},
  langid = {english},
  file = {/home/baponte/Zotero/storage/HFYACG5B/Liu et al. - 2023 - An SPRI beads-based DNA purification strategy for .pdf}
}

@article{lovell2021,
  title = {Genomic Mechanisms of Climate Adaptation in Polyploid Bioenergy Switchgrass},
  author = {Lovell, John T. and MacQueen, Alice H. and Mamidi, Sujan and Bonnette, Jason and Jenkins, Jerry and Napier, Joseph D. and Sreedasyam, Avinash and Healey, Adam and Session, Adam and Shu, Shengqiang and Barry, Kerrie and Bonos, Stacy and Boston, LoriBeth and Daum, Christopher and Deshpande, Shweta and Ewing, Aren and Grabowski, Paul P. and Haque, Taslima and Harrison, Melanie and Jiang, Jiming and Kudrna, Dave and Lipzen, Anna and Pendergast, Thomas H. and Plott, Chris and Qi, Peng and Saski, Christopher A. and Shakirov, Eugene V. and Sims, David and Sharma, Manoj and Sharma, Rita and Stewart, Ada and Singan, Vasanth R. and Tang, Yuhong and Thibivillier, Sandra and Webber, Jenell and Weng, Xiaoyu and Williams, Melissa and Wu, Guohong Albert and Yoshinaga, Yuko and Zane, Matthew and Zhang, Li and Zhang, Jiyi and Behrman, Kathrine D. and Boe, Arvid R. and Fay, Philip A. and Fritschi, Felix B. and Jastrow, Julie D. and Lloyd-Reilley, John and Martínez-Reyna, Juan Manuel and Matamala, Roser and Mitchell, Robert B. and Rouquette, Francis M. and Ronald, Pamela and Saha, Malay and Tobias, Christian M. and Udvardi, Michael and Wing, Rod A. and Wu, Yanqi and Bartley, Laura E. and Casler, Michael and Devos, Katrien M. and Lowry, David B. and Rokhsar, Daniel S. and Grimwood, Jane and Juenger, Thomas E. and Schmutz, Jeremy},
  date = {2021-02-18},
  journaltitle = {Nature},
  shortjournal = {Nature},
  volume = {590},
  number = {7846},
  pages = {438--444},
  issn = {0028-0836, 1476-4687},
  doi = {10.1038/s41586-020-03127-1},
  url = {https://www.nature.com/articles/s41586-020-03127-1},
  urldate = {2024-04-10},
  abstract = {Abstract                            Long-term climate change and periodic environmental extremes threaten food and fuel security               1               and global crop productivity               2–4               . Although molecular and adaptive breeding strategies can buffer the effects of climatic stress and improve crop resilience               5               , these approaches require sufficient knowledge of the genes that underlie productivity and adaptation               6               —knowledge that has been limited to a small number of well-studied model systems. Here we present the assembly and annotation of the large and complex genome of the polyploid bioenergy crop switchgrass (               Panicum virgatum               ). Analysis of biomass and survival among 732~resequenced genotypes, which were grown across 10~common gardens that span 1,800~km of latitude, jointly revealed extensive genomic evidence of climate adaptation. Climate–gene–biomass associations were abundant but varied considerably among deeply diverged gene pools. Furthermore, we found that gene flow accelerated climate adaptation during the postglacial colonization of northern habitats through introgression of alleles from a pre-adapted northern gene pool. The polyploid nature of switchgrass also enhanced adaptive potential through the fractionation of gene function, as there was an increased level of heritable genetic diversity on the nondominant subgenome. In addition to investigating patterns of climate adaptation, the genome resources and gene–trait associations developed here provide breeders with the necessary tools to increase switchgrass yield for the sustainable production of bioenergy.},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Lovell et al. - 2021 - Genomic mechanisms of climate adaptation in polypl.pdf}
}

@article{lowry2019,
  title = {Mechanisms of a Locally Adaptive Shift in Allocation among Growth , Reproduction , and Herbivore Resistance in {{{\emph{Mimulus}}}}{\emph{ Guttatus}}},
  author = {Lowry, David B and Popovic, Damian and Brennan, Darlene J and Holeski, Liza M},
  date = {2019},
  pages = {1--14},
  doi = {10.1111/evo.13699},
  keywords = {adaptation of organisms to,chromosomal inversion,ecotype,gibberellin,is that,mimulus guttatus,one of the fundamental,specific environmental conditions in-,supergene,tenets of evolutionary biology,trade-offs},
  file = {/home/baponte/Zotero/storage/HFGC2F74/Lowry et al. - 2019 - Mechanisms of a locally adaptive shift in allocati.pdf}
}

@article{lowry2019a,
  title = {The Case for the Continued Use of the Genus Name {{{\emph{Mimulus}}}} for All Monkeyflowers},
  author = {Lowry, David B. and Sobel, James M. and Angert, Amy L. and Ashman, Tia‐Lynn and Baker, Robert L. and Blackman, Benjamin K. and Brandvain, Yaniv and Byers, Kelsey J.R.P. and Cooley, Arielle M. and Coughlan, Jennifer M. and Dudash, Michele R. and Fenster, Charles B. and Ferris, Kathleen G. and Fishman, Lila and Friedman, Jannice and Grossenbacher, Dena L. and Holeski, Liza M. and Ivey, Christopher T. and Kay, Kathleen M. and Koelling, Vanessa A. and Kooyers, Nicholas J. and Murren, Courtney J. and Muir, Christopher D. and Nelson, Thomas C. and Peterson, Megan L. and Puzey, Joshua R. and Rotter, Michael C. and Seemann, Jeffrey R. and Sexton, Jason P. and Sheth, Seema N. and Streisfeld, Matthew A. and Sweigart, Andrea L. and Twyford, Alex D. and Vallejo‐Marín, Mario and Willis, John H. and Wright, Kevin M. and Wu, Carrie A. and Yuan, Yao‐Wu},
  date = {2019-08},
  journaltitle = {TAXON},
  shortjournal = {TAXON},
  volume = {68},
  number = {4},
  pages = {617--623},
  issn = {0040-0262, 1996-8175},
  doi = {10.1002/tax.12122},
  url = {https://onlinelibrary.wiley.com/doi/10.1002/tax.12122},
  urldate = {2023-09-26},
  langid = {english}
}

@article{lumibao2018,
  title = {Persisting Responses of Salt Marsh Fungal Communities to the {{Deepwater Horizon}} Oil Spill},
  author = {Lumibao, Candice Y. and Formel, Stephen and Elango, Vijaikrishnah and Pardue, John H. and Blum, Michael and Van Bael, Sunshine A.},
  date = {2018-11},
  journaltitle = {Science of The Total Environment},
  shortjournal = {Science of The Total Environment},
  volume = {642},
  pages = {904--913},
  issn = {00489697},
  doi = {10.1016/j.scitotenv.2018.06.077},
  url = {https://linkinghub.elsevier.com/retrieve/pii/S004896971832148X},
  urldate = {2024-02-10},
  langid = {english}
}

@article{lutz2020,
  title = {Semi-Commercial Testing of Regional Yeasts Selected from {{North Patagonia Argentina}} for the Biocontrol of Pear Postharvest Decays},
  author = {Lutz, María Cecilia and Lopes, Christian Ariel and Sosa, María Cristina and Sangorrín, Marcela Paula},
  date = {2020-11},
  journaltitle = {Biological Control},
  shortjournal = {Biological Control},
  volume = {150},
  pages = {104246},
  issn = {10499644},
  doi = {10.1016/j.biocontrol.2020.104246},
  url = {https://linkinghub.elsevier.com/retrieve/pii/S1049964419307625},
  urldate = {2024-03-20},
  langid = {english}
}

@article{m.aminehassani2018,
  title = {Microbial Interactions within the Plant Holobiont.},
  author = {{M. Amine Hassani} and Ma, Hassani and {Paloma Durán} and Durán, Paloma and {Stéphane Hacquard} and Hacquard, Stéphane},
  date = {2018-03-27},
  journaltitle = {Microbiome},
  volume = {6},
  number = {1},
  eprint = {29587885},
  eprinttype = {pmid},
  pages = {58--58},
  doi = {10.1186/s40168-018-0445-0},
  abstract = {Since the colonization of land by ancestral plant lineages 450 million years ago, plants and their associated microbes have been interacting with each other, forming an assemblage of species that is often referred to as a “holobiont.” Selective pressure acting on holobiont components has likely shaped plant-associated microbial communities and selected for host-adapted microorganisms that impact plant fitness. However, the high microbial densities detected on plant tissues, together with the fast generation time of microbes and their more ancient origin compared to their host, suggest that microbe-microbe interactions are also important selective forces sculpting complex microbial assemblages in the phyllosphere, rhizosphere, and plant endosphere compartments. Reductionist approaches conducted under laboratory conditions have been critical to decipher the strategies used by specific microbes to cooperate and compete within or outside plant tissues. Nonetheless, our understanding of these microbial interactions in shaping more complex plant-associated microbial communities, along with their relevance for host health in a more natural context, remains sparse. Using examples obtained from reductionist and community-level approaches, we discuss the fundamental role of microbe-microbe interactions (prokaryotes and micro-eukaryotes) for microbial community structure and plant health. We provide a conceptual framework illustrating that interactions among microbiota members are critical for the establishment and the maintenance of host-microbial homeostasis.},
  pmcid = {5870681},
  annotation = {MAG ID: 2795321853\\
S2ID: 79b7ffbd0a23745682f26671ea7bc629fa8ef92f}
}

@article{marian2022,
  title = {Ecology and Potential Functions of Plant-Associated Microbial Communities in Cold Environments},
  author = {Marian, Malek and Licciardello, Giorgio and Vicelli, Bianca and Pertot, Ilaria and Perazzolli, Michele},
  date = {2022-01-19},
  journaltitle = {FEMS Microbiology Ecology},
  volume = {98},
  number = {1},
  pages = {fiab161},
  issn = {1574-6941},
  doi = {10.1093/femsec/fiab161},
  url = {https://academic.oup.com/femsec/article/doi/10.1093/femsec/fiab161/6462900},
  urldate = {2024-03-21},
  abstract = {ABSTRACT             Complex microbial communities are associated with plants and can improve their resilience under harsh environmental conditions. In particular, plants and their associated communities have developed complex adaptation strategies against cold stress. Although changes in plant-associated microbial community structure have been analysed in different cold regions, scarce information is available on possible common taxonomic and functional features of microbial communities across cold environments. In this review, we discuss recent advances in taxonomic and functional characterization of plant-associated microbial communities in three main cold regions, such as alpine, Arctic and Antarctica environments. Culture-independent and culture-dependent approaches are analysed, in order to highlight the main factors affecting the taxonomic structure of plant-associated communities in cold environments. Moreover, biotechnological applications of plant-associated microorganisms from cold environments are proposed for agriculture, industry and medicine, according to biological functions and cold adaptation strategies of bacteria and fungi. Although further functional studies may improve our knowledge, the existing literature suggest that plants growing in cold environments harbor complex, host-specific and cold-adapted microbial communities, which may play key functional roles in plant growth and survival under cold conditions.},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Marian et al. - 2022 - Ecology and potential functions of plant-associate.pdf}
}

@article{martin2011,
  title = {Cutadapt Removes Adapter Sequences from High-Throughput Sequencing Reads},
  author = {Martin, Marcel},
  date = {2011-05-02},
  journaltitle = {EMBnet.journal},
  shortjournal = {EMBnet j.},
  volume = {17},
  number = {1},
  pages = {10},
  issn = {2226-6089},
  doi = {10.14806/ej.17.1.200},
  url = {http://journal.embnet.org/index.php/embnetjournal/article/view/200},
  urldate = {2024-02-10},
  file = {/home/baponte/Zotero/storage/F99LG3JP/Martin - 2011 - Cutadapt removes adapter sequences from high-throu.pdf}
}

@article{mason2015,
  title = {Does Investment in Leaf Defenses Drive Changes in Leaf Economic Strategy? {{A}} Focus on Whole-Plant Ontogeny},
  author = {Mason, Chase M. and Donovan, Lisa A.},
  date = {2015},
  journaltitle = {Oecologia},
  volume = {177},
  number = {4},
  pages = {1053--1066},
  doi = {10.1007/s00442-014-3177-2},
  abstract = {Leaf defenses have long been studied in the context of plant growth rate, resource availability, and optimal investment theory. Likewise, one of the central modern paradigms of plant ecophysiology, the leaf economics spectrum (LES), has been extensively studied in the context of these factors across ecological scales ranging from global species data sets to temporal shifts within individuals. Despite strong physiological links between LES strategy and leaf defenses in structure, function, and resource investment, the relationship between these trait classes has not been well explored. This study investigates the relationship between leaf defenses and LES strategy across whole-plant ontogeny in three diverse Helianthus species known to exhibit dramatic ontogenetic shifts in LES strategy, focusing primarily on physical and quantitative chemical defenses. Plants were grown under controlled environmental conditions and sampled for LES and defense traits at four ontogenetic stages. Defenses were found to shift strongly with ontogeny, and to correlate strongly with LES strategy. More advanced ontogenetic stages with more conservative LES strategy leaves had higher tannin activity and toughness in all species, and higher leaf dry matter content in two of three species. Modeling results in two species support the conclusion that changes in defenses drive changes in LES strategy through ontogeny, and in one species that changes in defenses and LES strategy are likely independently driven by ontogeny. Results of this study support the hypothesis that leaf-level allocation to defenses might be an important determinant of leaf economic traits, where high investment in defenses drives a conservative LES strategy.},
  keywords = {Helianthus,Leaf dry matter content,Sunflower,Tannin,Toughness},
  file = {/home/baponte/Zotero/storage/5ZRCABT7/Mason and Donovan - 2015 - Does investment in leaf defenses drive changes in .pdf}
}

@article{mathew2023,
  title = {Epichloë {{Endophytes Shape}} the {{Foliar Endophytic Fungal Microbiome}} and {{Alter}} the {{Auxin}} and {{Salicylic Acid Phytohormone Levels}} in {{Two Meadow Fescue Cultivars}}},
  author = {Mathew, Suni Anie and Helander, Marjo and Saikkonen, Kari and Vankova, Radomira and Dobrev, Petre I. and Dirihan, Serdar and Fuchs, Benjamin},
  date = {2023-01-06},
  journaltitle = {Journal of Fungi},
  shortjournal = {JoF},
  volume = {9},
  number = {1},
  pages = {90},
  issn = {2309-608X},
  doi = {10.3390/jof9010090},
  url = {https://www.mdpi.com/2309-608X/9/1/90},
  urldate = {2024-03-20},
  abstract = {Plants harbor a large diversity of endophytic microbes. Meadow fescue (Festuca pratensis) is a cool-season grass known for its symbiotic relationship with the systemic and vertically—via seeds—transmitted fungal endophyte Epichloë uncinata, yet its effects on plant hormones and the microbial community is largely unexplored. Here, we sequenced the endophytic bacterial and fungal communities in the leaves and roots, analyzing phytohormone concentrations and plant performance parameters in Epichloë-symbiotic (E+) and Epichloë-free (E-) individuals of two meadow fescue cultivars. The endophytic microbial community differed between leaf and root tissues independent of Epichloë symbiosis, while the fungal community was different in the leaves of Epichloë-symbiotic and Epichloë-free plants in both cultivars. At the same time, Epichloë symbiosis decreased salicylic acid and increased auxin concentrations in leaves. Epichloë-symbiotic plants showed higher biomass and higher seed mass at the end of the season. Our results demonstrate that Epichloë symbiosis alters the leaf fungal microbiota, which coincides with changes in phytohormone concentrations, indicating that Epichloë endophytes affect both plant immune responses and other fungal endophytes. Whether the effect of Epichloë endophytes on other fungal endophytes is connected to changes in phytohormone concentrations remains to be elucidated.},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Mathew et al. - 2023 - Epichloë Endophytes Shape the Foliar Endophytic Fu.pdf}
}

@article{mcardle2001,
  title = {Fitting {{Multivariate Models}} to {{Community Data}}: A {{Comment}} on {{Distance-Based Redundancy Analysis}}},
  author = {McArdle, Brian H. and Anderson, Marti J.},
  date = {2001},
  journaltitle = {Ecology},
  volume = {82},
  number = {1},
  eprint = {https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1890/0012-9658%282001%29082%5B0290%3AFMMTCD%5D2.0.CO%3B2},
  pages = {290--297},
  doi = {10.1890/0012-9658(2001)082[0290:FMMTCD]2.0.CO;2},
  url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/0012-9658%282001%29082%5B0290%3AFMMTCD%5D2.0.CO%3B2},
  abstract = {Nonparametric multivariate analysis of ecological data using permutation tests has two main challenges: (1) to partition the variability in the data according to a complex design or model, as is often required in ecological experiments, and (2) to base the analysis on a multivariate distance measure (such as the semimetric Bray-Curtis measure) that is reasonable for ecological data sets. Previous nonparametric methods have succeeded in one or other of these areas, but not in both. A recent contribution to Ecological Monographs by Legendre and Anderson, called distance-based redundancy analysis (db-RDA), does achieve both. It does this by calculating principal coordinates and subsequently correcting for negative eigenvalues, if they are present, by adding a constant to squared distances. We show here that such a correction is not necessary. Partitioning can be achieved directly from the distance matrix itself, with no corrections and no eigenanalysis, even if the distance measure used is semimetric. An ecological example is given to show the differences in these statistical methods. Empirical simulations, based on parameters estimated from real ecological species abundance data, showed that db-RDA done on multifactorial designs (using the correction) does not have type 1 error consistent with the significance level chosen for the analysis (i.e., does not provide an exact test), whereas the direct method described and advocated here does.},
  keywords = {distance measures,distance-based redundancy analysis (db-RDA),hypothesis testing,linear models,MANOVA,multivariate analysis,nonparametric,partitioning,principal coordinate analysis,redundancy analysis,semimetric measures,statistical method}
}

@article{mcintosh2024,
  title = {Divergence in Responsiveness to Soil Biota and Mycorrhizal Partner-Specificity between Montane Annual and Coastal Perennial Ecotypes of Yellow Monkeyflower ({{{\emph{Mimulus}}}}{\emph{ Guttatus}})},
  author = {McIntosh, Mariah and Bullington, Lorinda S. and Lekberg, Ylva and Fishman, Lila},
  date = {2024-03-21},
  journaltitle = {International Journal of Plant Sciences},
  shortjournal = {International Journal of Plant Sciences},
  pages = {730540},
  issn = {1058-5893, 1537-5315},
  doi = {10.1086/730540},
  url = {https://www.journals.uchicago.edu/doi/10.1086/730540},
  urldate = {2024-04-08},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/McIntosh et al. - 2024 - Divergence in responsiveness to soil biota and myc.pdf}
}

@article{mcmurdie2013,
  title = {Phyloseq: {{An R Package}} for {{Reproducible Interactive Analysis}} and {{Graphics}} of {{Microbiome Census Data}}},
  shorttitle = {Phyloseq},
  author = {McMurdie, Paul J. and Holmes, Susan},
  editor = {Watson, Michael},
  date = {2013-04-22},
  journaltitle = {PLoS ONE},
  shortjournal = {PLoS ONE},
  volume = {8},
  number = {4},
  pages = {e61217},
  issn = {1932-6203},
  doi = {10.1371/journal.pone.0061217},
  url = {https://dx.plos.org/10.1371/journal.pone.0061217},
  urldate = {2023-11-26},
  langid = {english}
}

@article{mcmurdie2014,
  title = {Waste {{Not}}, {{Want Not}}: {{Why Rarefying Microbiome Data Is Inadmissible}}},
  shorttitle = {Waste {{Not}}, {{Want Not}}},
  author = {McMurdie, Paul J. and Holmes, Susan},
  editor = {McHardy, Alice Carolyn},
  date = {2014-04-03},
  journaltitle = {PLoS Computational Biology},
  shortjournal = {PLoS Comput Biol},
  volume = {10},
  number = {4},
  pages = {e1003531},
  issn = {1553-7358},
  doi = {10.1371/journal.pcbi.1003531},
  url = {https://dx.plos.org/10.1371/journal.pcbi.1003531},
  urldate = {2024-03-09},
  langid = {english},
  file = {/home/baponte/Zotero/storage/8NHQU5M6/McMurdie and Holmes - 2014 - Waste Not, Want Not Why Rarefying Microbiome Data.pdf}
}

@article{mejia2008,
  title = {Endophytic Fungi as Biocontrol Agents of {{{\emph{Theobroma}}}}{\emph{ Cacao}} Pathogens},
  author = {Mejía, Luis C. and Rojas, Enith I. and Maynard, Zuleyka and Bael, Sunshine Van and Arnold, A. Elizabeth and Hebbar, Prakash and Samuels, Gary J. and Robbins, Nancy and Herre, Edward Allen},
  date = {2008},
  journaltitle = {Biological Control},
  volume = {46},
  number = {1},
  pages = {4--14},
  doi = {10.1016/j.biocontrol.2008.01.012},
  abstract = {Fungal endophytes isolated from healthy Theobroma cacao tissues were screened in vitro for antagonism against major pathogens of cacao. Of tested endophytic morphospecies, 40\% (21/52), 65\% (28/43) and 27\% percent (4/15) showed in vitro antagonism against Moniliophthora roreri (frosty pod rot), Phytophthora palmivora (black pod rot) and Moniliophthora perniciosa (witches broom), respectively. The most common antagonistic mechanism was simple competition for substrate. Nonetheless, 13\%, 21\%, and 0\% of tested morphospecies showed clear antibiosis against M. roreri, P. palmivora, and M. perniciosa, respectively. One isolate of Trichoderma was observed to be parasitic on M. roreri. Endophyte species that were common in the host plants under natural conditions often are good colonizers and grow fast in vitro whereas antibiosis producers usually appear to be relatively rare in nature, tend to grow slowly in vitro, and often are not good colonizers. We suggest that there is an inherent general trade-off between fast growth (high colonization) and production of chemicals that produce antibiosis reactions. Finally, field trials assessing the effects of three endophytic fungi (Colletotrichum gloeosporioides, Clonostachys rosea and Botryosphaeria ribis) on pod loss due to M. roreri and Phytophthora spp. were conducted at four farms in Panama. Although the overall incidence of black pod rot was very low during the tests, treatment with C. gloeosporioides significantly decreased pod loss due to that disease. We observed no decrease in pod loss due to frosty pod rot, but treatment with C. rosea reduced the incidence of cacao pods with sporulating lesions of M. roreri by 10\%. The observed reduction in pod loss due to Phytophthora spp., and sporulation by M. roreri, supports the potential of fungal endophytes as biological control agents. Further, these studies suggest that combined information from field censuses of endophytic fungi, in vitro studies, and greenhouse experiments can provide useful a priori criteria for identifying desirable attributes for potential biocontrol agents. © 2008 Elsevier Inc. All rights reserved.},
  keywords = {Biological control,Botryosphaeria,Clonostachys,Colletotrichum,Crinipellis,Endophytic fungi,Moniliophthora,Phytophthora,Theobroma cacao}
}

@article{mejia2014,
  title = {Pervasive Effects of a Dominant Foliar Endophytic Fungus on Host Genetic and Phenotypic Expression in a Tropical Tree},
  author = {Mejía, Luis C. and Herre, Edward A. and Sparks, Jed P. and Winter, Klaus and García, Milton N. and Van Bael, Sunshine A. and Stitt, Joseph and Shi, Zi and Zhang, Yufan and Guiltinan, Mark J. and Maximova, Siela N.},
  date = {2014},
  journaltitle = {Frontiers in Microbiology},
  volume = {5},
  pages = {1--16},
  doi = {10.3389/fmicb.2014.00479},
  abstract = {It is increasingly recognized that macro-organisms (corals, insects, plants, vertebrates) consist of both host tissues and multiple microbial symbionts that play essential roles in their host's ecological and evolutionary success. Consequently, identifying benefits and costs of symbioses, as well as mechanisms underlying them are research priorities. All plants surveyed under natural conditions harbor foliar endophytic fungi (FEF) in their leaf tissues, often at high densities. Despite producing no visible effects on their hosts, experiments have nonetheless shown that FEF reduce pathogen and herbivore damage. Here, combining results from three genomic, and two physiological experiments, we demonstrate pervasive genetic and phenotypic effects of the apparently asymptomatic endophytes on their hosts. Specifically, inoculation of endophyte-free (E-) Theobroma cacao leaves with Colletotrichum tropicale (E+), the dominant FEF species in healthy T. cacao, induces consistent changes in the expression of hundreds of host genes, including many with known defensive functions. Further, E+ plants exhibited increased lignin and cellulose content, reduced maximum rates of photosynthesis (Amax), and enrichment of nitrogen-15 and carbon-13 isotopes. These phenotypic changes observed in E+ plants correspond to changes in expression of specific functional genes in related pathways. Moreover, a cacao gene (Tc00g04254) highly up-regulated by C. tropicale also confers resistance to pathogen damage in the absence of endophytes or their products in host tissues. Thus, the benefits of increased pathogen resistance in E+ plants are derived in part from up-regulation of intrinsic host defense responses, and appear to be offset by potential costs including reduced photosynthesis, altered host nitrogen metabolism, and endophyte heterotrophy of host tissues. Similar effects are likely in most plant-endophyte interactions, and should be recognized in the design and interpretation of genetic and phenotypic studies of plants.},
  issue = {SEP},
  keywords = {Arabidopsis,Colletotrichum,Fungal endophytes,Gene expression,Plant defense,Populus,Symbiosis,Theobroma}
}

@article{michellee.afkhami2014,
  title = {Mutualist-Mediated Effects on Species' Range Limits across Large Geographic Scales},
  author = {{Michelle E. Afkhami} and Afkhami, Michelle E. and {Patrick J. McIntyre} and McIntyre, Patrick J. and {Sharon Y. Strauss} and Strauss, Sharon Y. and {Sharon Y. Strauss} and {Sharon Y. Strauss}},
  date = {2014-10-01},
  journaltitle = {Ecology Letters},
  volume = {17},
  number = {10},
  eprint = {25052023},
  eprinttype = {pmid},
  pages = {1265--1273},
  doi = {10.1111/ele.12332},
  abstract = {Understanding the processes determining species range limits is central to predicting species distributions under climate change. Projected future ranges are extrapolated from distribution models based on climate layers, and few models incorporate the effects of biotic interactions on species' distributions. Here, we show that a positive species interaction ameliorates abiotic stress, and has a profound effect on a species' range limits. Combining field surveys of 92 populations, 10 common garden experiments throughout the range, species distribution models and greenhouse experiments, we show that mutualistic fungal endophytes ameliorate drought stress and broaden the geographic range of their native grass host Bromus laevipes by thousands of square kilometres (\textasciitilde{} 20\% larger) into drier habitats. Range differentiation between fungal-associated and fungal-free grasses was comparable to species-level range divergence of congeners, indicating large impacts on range limits. Positive biotic interactions may be underappreciated in determining species' ranges and species' responses to future climates across large geographic scales.},
  annotation = {MAG ID: 2025767761\\
S2ID: 6f4479198485247355de40f4059b6424e8efaf24}
}

@article{miglia2007,
  title = {Genotype, Soil Type, and Locale Effects on Reciprocal Transplant Vigor, Endophyte Growth, and Microbial Functional Diversity of a Narrow Sagebrush Hybrid Zone in {{Salt Creek Canyon}}, {{Utah}}},
  author = {Miglia, Kathleen J. and McArthur, E. Durant and Redman, Regina S. and Rodriguez, Russell J. and Zak, John C. and Freeman, D. Carl},
  date = {2007-03},
  journaltitle = {American Journal of Botany},
  shortjournal = {American J of Botany},
  volume = {94},
  number = {3},
  pages = {425--436},
  issn = {0002-9122, 1537-2197},
  doi = {10.3732/ajb.94.3.425},
  url = {https://bsapubs.onlinelibrary.wiley.com/doi/10.3732/ajb.94.3.425},
  urldate = {2024-04-10},
  abstract = {When addressing the nature of ecological adaptation and environmental factors limiting population ranges and contributing to speciation, it is important to consider not only the plant's genotype and its response to the environment, but also any close interactions that it has with other organisms, specifically, symbiotic microorganisms. To investigate this, soils and seedlings were reciprocally transplanted into common gardens of the big sagebrush hybrid zone in Salt Creek Canyon, Utah, to determine location and edaphic effects on the fitness of parental and hybrid plants. Endophytic symbionts and functional microbial diversity of indigenous and transplanted soils and sagebrush plants were also examined. Strong selection occurred against the parental genotypes in the middle hybrid zone garden in middle hybrid zone soil; F               1               hybrids had the highest fitness under these conditions. Neither of the parental genotypes had superior fitness in their indigenous soils and habitats; rather F               1               hybrids with the nonindigenous maternal parent were superiorly fit. Significant garden‐by‐soil type interactions indicate adaptation of both plant and soil microorganisms to their indigenous soils and habitats, most notably in the middle hybrid zone garden in middle hybrid zone soil. Contrasting performances of F               1               hybrids suggest asymmetrical gene flow with mountain, rather than basin, big sagebrush acting as the maternal parent. We showed that the microbial community impacted the performance of parental and hybrid plants in different soils, likely limiting the ranges of the different genotypes.},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Miglia et al. - 2007 - Genotype, soil type, and locale effects on recipro.pdf}
}

@article{moeller2020,
  title = {The {{Lizard Gut Microbiome Changes}} with {{Temperature}} and {{Is Associated}} with {{Heat Tolerance}}},
  author = {Moeller, Andrew H. and Ivey, Kathleen and Cornwall, Margaret B. and Herr, Kathryn and Rede, Jordan and Taylor, Emily N. and Gunderson, Alex R.},
  editor = {Dozois, Charles M.},
  date = {2020-08-18},
  journaltitle = {Applied and Environmental Microbiology},
  shortjournal = {Appl Environ Microbiol},
  volume = {86},
  number = {17},
  pages = {e01181-20},
  issn = {0099-2240, 1098-5336},
  doi = {10.1128/AEM.01181-20},
  url = {https://journals.asm.org/doi/10.1128/AEM.01181-20},
  urldate = {2024-06-13},
  abstract = {Gut microbial communities affect their animal hosts in numerous ways, motivating investigations of the factors that shape the gut microbiota and the consequences of gut microbiota variation for host traits. In this study, we tested the effects of increases in environmental temperatures on the gut microbiota of fence lizards, a vertebrate ectotherm threatened by warming climates. By monitoring lizards and their gut microbes during an experimental temperature treatment, we showed that the warming altered and destabilized the lizard gut microbiota. Moreover, measuring thermal performance of lizard hosts at the end of the experiment indicated that the composition of the gut microbiota was associated with host thermal tolerance. These results indicate that warming temperatures can alter the gut microbiota of vertebrate ectotherms and suggest relationships between variation in the gut microbiota and the thermal physiology of natural host populations.           ,              ABSTRACT                            Vertebrates harbor trillions of microorganisms in the gut, collectively termed the gut microbiota, which affect a wide range of host functions. Recent experiments in lab-reared vertebrates have shown that changes in environmental temperature can induce shifts in the gut microbiota, and in some cases these shifts have been shown to affect host thermal physiology. However, there is a lack of information about the effects of temperature on the gut microbiota of wild-caught vertebrates. Moreover, in ectotherms, which are particularly vulnerable to changing temperature regimens, the extent to which microbiota composition is shaped by temperature and associated with host thermal tolerance has not been investigated. To address these issues, we monitored the gut microbiota composition of wild-caught western fence lizards (               Sceloporus occidentalis               ) experimentally exposed to a cool-to-warm temperature transition. Comparing experimentally exposed and control lizards indicated that warm temperatures altered and destabilized the composition of the               S. occidentalis               gut microbiota. Warming drove a significant reduction in the relative abundances of a clade of               Firmicutes               , a significant increase in the rate of compositional turnover in the gut microbiota within individual lizards, and increases in the abundances of bacteria from predicted pathogenic clades. In addition, the composition of the microbiota was significantly associated with the thermal tolerance of lizards measured at the end of the experiment. These results suggest that temperature can alter the lizard gut microbiota, with potential implications for the physiological performance and fitness of natural populations.                                         IMPORTANCE               Gut microbial communities affect their animal hosts in numerous ways, motivating investigations of the factors that shape the gut microbiota and the consequences of gut microbiota variation for host traits. In this study, we tested the effects of increases in environmental temperatures on the gut microbiota of fence lizards, a vertebrate ectotherm threatened by warming climates. By monitoring lizards and their gut microbes during an experimental temperature treatment, we showed that the warming altered and destabilized the lizard gut microbiota. Moreover, measuring thermal performance of lizard hosts at the end of the experiment indicated that the composition of the gut microbiota was associated with host thermal tolerance. These results indicate that warming temperatures can alter the gut microbiota of vertebrate ectotherms and suggest relationships between variation in the gut microbiota and the thermal physiology of natural host populations.},
  langid = {english},
  file = {/home/baponte/Box/Dissertation/master_papers/Moeller et al. - 2020 - The Lizard Gut Microbiome Changes with Temperature.pdf}
}

@article{mojica2012,
  title = {Spatially and Temporally Varying Selection on Intrapopulation Quantitative Trait Loci for a Life History Trade‐off in {{{\emph{Mimulus}}}}{\emph{ Guttatus}}},
  author = {Mojica, Julius P. and Lee, Young Wha and Willis, John H. and Kelly, John K.},
  date = {2012-08},
  journaltitle = {Molecular Ecology},
  shortjournal = {Molecular Ecology},
  volume = {21},
  number = {15},
  pages = {3718--3728},
  issn = {0962-1083, 1365-294X},
  doi = {10.1111/j.1365-294X.2012.05662.x},
  url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1365-294X.2012.05662.x},
  urldate = {2024-04-08},
  abstract = {Abstract                            Why do populations remain genetically variable despite strong continuous natural selection? Mutation reconstitutes variation eliminated by selection and genetic drift, but theoretical and experimental studies each suggest that mutation‐selection balance insufficient to explain extant genetic variation in most complex traits. The alternative hypothesis of balancing selection, wherein selection maintains genetic variation, is an aggregate of multiple mechanisms (spatial and temporal heterogeneity in selection, frequency‐dependent selection, antagonistic pleiotropy, etc.). Most of these mechanisms have been demonstrated for Mendelian traits, but there is little comparable data for loci affecting quantitative characters. Here, we report a 3‐year field study of selection on intrapopulation quantitative trait loci (QTL) of flower size, a highly polygenic trait in               Mimulus guttatus               . The QTL exhibit antagonistic pleiotropy: alleles that increase flower size, reduce viability, but increase fecundity. The magnitude and direction of selection fluctuates yearly and on a spatial scale of metres. This study provides direct evidence of balancing selection mechanisms on QTL of an ecologically relevant trait.},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Mojica et al. - 2012 - Spatially and temporally varying selection on intr.pdf}
}

@article{monnahan2021,
  title = {Predicting Evolutionary Change at the {{DNA}} Level in a Natural {{{\emph{Mimulus}}}} Population},
  author = {Monnahan, Patrick J. and Colicchio, Jack and Fishman, Lila and Macdonald, Stuart J. and Kelly, John K.},
  editor = {Buerkle, Alex},
  date = {2021-01-13},
  journaltitle = {PLOS Genetics},
  shortjournal = {PLoS Genet},
  volume = {17},
  number = {1},
  pages = {e1008945},
  issn = {1553-7404},
  doi = {10.1371/journal.pgen.1008945},
  url = {https://dx.plos.org/10.1371/journal.pgen.1008945},
  urldate = {2024-03-03},
  abstract = {Evolution by natural selection occurs when the frequencies of genetic variants change because individuals differ in Darwinian fitness components such as survival or reproductive success. Differential fitness has been demonstrated in field studies of many organisms, but it remains unclear how well we can quantitatively predict allele frequency changes from fitness measurements. Here, we characterize natural selection on millions of Single Nucleotide Polymorphisms (SNPs) across the genome of the annual plant               Mimulus guttatus               . We use fitness estimates to calibrate population genetic models that effectively predict allele frequency changes into the next generation. Hundreds of SNPs experienced “male selection” in 2013 with one allele at each SNP elevated in frequency among successful male gametes relative to the entire population of adults. In the following generation, allele frequencies at these SNPs consistently shifted in the predicted direction. A second year of study revealed that SNPs had effects on both viability and reproductive success with pervasive trade-offs between fitness components. SNPs favored by male selection were, on average, detrimental to survival. These trade-offs (antagonistic pleiotropy and temporal fluctuations in fitness) may be essential to the long-term maintenance of alleles. Despite the challenges of measuring selection in the wild, the strong correlation between predicted and observed allele frequency changes suggests that population genetic models have a much greater role to play in forward-time prediction of evolutionary change.},
  langid = {english},
  file = {/home/baponte/Zotero/storage/YRYN8Y2H/Monnahan et al. - 2021 - Predicting evolutionary change at the DNA level in.pdf}
}

@article{montes1999,
  title = {Polyphasic {{Taxonomy}} of a {{Novel Yeast Isolated}} from {{Antarctic Environment}}; {{Description}} of {{{\emph{Cryptococcus}}}}{\emph{ Victoriae}} {{Sp}}. {{Nov}}.},
  author = {Montes, Ma Jesús and Belloch, Carmela and Galiana, Monica and Garcia, Ma Dolores and Andrés, Carmen and Ferrer, Santiago and Torres-Rodriguez, Jose Ma and Guinea, Jesús},
  date = {1999-02},
  journaltitle = {Systematic and Applied Microbiology},
  shortjournal = {Systematic and Applied Microbiology},
  volume = {22},
  number = {1},
  pages = {97--105},
  issn = {07232020},
  doi = {10.1016/S0723-2020(99)80032-0},
  url = {https://linkinghub.elsevier.com/retrieve/pii/S0723202099800320},
  urldate = {2024-03-20},
  langid = {english}
}

@online{nationalparkservice2023,
  title = {Fire {{History}}},
  author = {National Park Service},
  date = {2023},
  url = {https://www.nps.gov/yose/learn/nature/firehistory.htm},
  organization = {Fire History - Yosemite National Park (U.S. National Park Service)}
}

@online{nelson2019,
  title = {{{BestRAD}} Protocol V1},
  author = {Nelson, Thom},
  date = {2019-08-08},
  doi = {10.17504/protocols.io.6awhafe},
  url = {https://www.protocols.io/view/bestrad-protocol-6awhafe},
  urldate = {2024-04-07},
  abstract = {Modified from protocol of Sean O’Rourke and Mike Miller published in:},
  pubstate = {prepublished}
}

@online{nelson2020,
  title = {Processing {{ddRAD}} Data from Raw Fastqs to Vcf V1},
  author = {Nelson, Thom and Finseth, Findley and Fishman, Lila and Sevier Berg, Colette},
  date = {2020-08-12},
  doi = {10.17504/protocols.io.bjnbkman},
  url = {https://www.protocols.io/view/processing-ddrad-data-from-raw-fastqs-to-vcf-bjnbkman},
  urldate = {2024-04-07},
  abstract = {This is a pipeline that the Fishman lab uses for processing paired-end ddRAD data, from fastq to vcf. These scripts were written and pipeline developed by Findley Finseth and Thom Nelson.},
  pubstate = {prepublished},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Nelson et al. - 2020 - Processing ddRAD data from raw fastqs to vcf v1.pdf}
}

@article{nesomResponseCaseContinued2019,
  title = {Response to “{{The}} Case for the Continued Use of the Genus Name {{{\emph{Mimulus}}}} for All Monkeyflowers”},
  author = {Nesom, Guy L. and Fraga, Naomi S. and Barker, William R. and Beardsley, Paul M. and Tank, David C. and Baldwin, Bruce G. and Olmstead, Richard G.},
  date = {2019-08},
  journaltitle = {TAXON},
  shortjournal = {TAXON},
  volume = {68},
  number = {4},
  pages = {624--627},
  issn = {0040-0262, 1996-8175},
  doi = {10.1002/tax.12124},
  url = {https://onlinelibrary.wiley.com/doi/10.1002/tax.12124},
  urldate = {2023-09-26},
  langid = {english}
}

@article{nicotra2010,
  title = {Plant Phenotypic Plasticity in a Changing Climate},
  author = {Nicotra, A.B. and Atkin, O.K. and Bonser, S.P. and Davidson, A.M. and Finnegan, E.J. and Mathesius, U. and Poot, P. and Purugganan, M.D. and Richards, C.L. and Valladares, F. and Van Kleunen, M.},
  date = {2010-12},
  journaltitle = {Trends in Plant Science},
  shortjournal = {Trends in Plant Science},
  volume = {15},
  number = {12},
  pages = {684--692},
  issn = {13601385},
  doi = {10.1016/j.tplants.2010.09.008},
  url = {https://linkinghub.elsevier.com/retrieve/pii/S1360138510001986},
  urldate = {2024-05-10},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Nicotra et al. - 2010 - Plant phenotypic plasticity in a changing climate2.pdf}
}

@article{nicotra2011,
  title = {The Evolution and Functional Significance of Leaf Shape in the Angiosperms},
  author = {Nicotra, Adrienne B. and Leigh, Andrea and Boyce, C. Kevin and Jones, Cynthia S. and Niklas, Karl J. and Royer, Dana L. and Tsukaya, Hirokazu},
  date = {2011},
  journaltitle = {Functional Plant Biology},
  shortjournal = {Functional Plant Biol.},
  volume = {38},
  number = {7},
  pages = {535},
  issn = {1445-4408},
  doi = {10.1071/FP11057},
  url = {http://www.publish.csiro.au/?paper=FP11057},
  urldate = {2024-04-13},
  abstract = {Angiosperm leaves manifest a remarkable diversity of shapes that range from developmental sequences within a shoot and within crown response to microenvironment to variation among species within and between communities and among orders or families. It is generally assumed that because photosynthetic leaves are critical to plant growth and survival, variation in their shape reflects natural selection operating on function. Several non-mutually exclusive theories have been proposed to explain leaf shape diversity. These include: thermoregulation of leaves especially in arid and hot environments, hydraulic constraints, patterns of leaf expansion in deciduous species, biomechanical constraints, adaptations to avoid herbivory, adaptations to optimise light interception and even that leaf shape variation is a response to selection on flower form. However, the relative importance, or likelihood, of each of these factors is unclear. Here we review the evolutionary context of leaf shape diversification, discuss the proximal mechanisms that generate the diversity in extant systems, and consider the evidence for each the above hypotheses in the context of the functional significance of leaf shape. The synthesis of these broad ranging areas helps to identify points of conceptual convergence for ongoing discussion and integrated directions for future research.},
  langid = {english},
  keywords = {Leaf area,leaf boundary layer,leaf economic spectrum},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Nicotra et al. - 2011 - The evolution and functional significance of leaf .pdf}
}

@book{nobel2009,
  title = {Physicochemical and Environmental Plant Physiology},
  author = {Nobel, Park S.},
  date = {2009},
  edition = {Fourth edition},
  publisher = {Academic Press},
  location = {Amsterdam},
  abstract = {"Physicochemical and Environmental Plant Physiology, Fourth Edition, is the updated version of an established and successful reference for plant scientists. The author has taken into consideration extensive reviews performed by colleagues and students who have touted this book as the ultimate reference for research and learning. The original structure and philosophy of the book continue in this new edition, providing a genuine synthesis of modern physicochemical and physiological thinking, while entirely updating the detailed content. This version contains more than 40\% new coverage; five brand new equations and four new tables, with updates to 24 equations and six tables; and 30 new figures have been added with more than three-quarters of figures and legends improved. Key concepts in plant physiology are developed with the use of chemistry, physics, and mathematics fundamentals. The book is organized so that a student has easy access to locate any biophysical phenomenon in which he or she is interested. * More than 40\% new coverage * Incorporates student-recommended changes from the previous edition * Five brand new equations and four new tables, with updates to 24 equations and six tables * 30 new figures added with more than three-quarters of figures and legends improved * Organized so that a student has easy access to locate any biophysical phenomenon in which he or she is interested * Per-chapter key equation tables * Problems with solutions presented in the back of the book * Appendices with conversion factors, constants/coefficients, abbreviations and symbols."},
  isbn = {978-0-12-374143-1},
  langid = {english},
  annotation = {OCLC: 370436048}
}

@article{ogaki2020,
  title = {Diversity and Bioprospecting of Cultivable Fungal Assemblages in Sediments of Lakes in the {{Antarctic Peninsula}}},
  author = {Ogaki, Mayara B. and Teixeira, Daniela R. and Vieira, Rosemary and Lírio, Juan M. and Felizardo, João P.S. and Abuchacra, Rodrigo C. and Cardoso, Renan P. and Zani, Carlos L. and Alves, Tânia M.A. and Junior, Policarpo A.S. and Murta, Silvane M.F. and Barbosa, Emerson C. and Oliveira, Jaquelline G. and Ceravolo, Isabela P. and Pereira, Patrícia O. and Rosa, Carlos A. and Rosa, Luiz H.},
  date = {2020-06},
  journaltitle = {Fungal Biology},
  shortjournal = {Fungal Biology},
  volume = {124},
  number = {6},
  pages = {601--611},
  issn = {18786146},
  doi = {10.1016/j.funbio.2020.02.015},
  url = {https://linkinghub.elsevier.com/retrieve/pii/S1878614620300350},
  urldate = {2024-03-20},
  langid = {english}
}

@incollection{oguchi2018,
  title = {Leaf {{Anatomy}} and {{Function}}},
  booktitle = {The {{Leaf}}: {{A Platform}} for {{Performing Photosynthesis}}},
  author = {Oguchi, Riichi and Onoda, Yusuke and Terashima, Ichiro and Tholen, Danny},
  editor = {Adams Iii, William W. and Terashima, Ichiro},
  date = {2018},
  volume = {44},
  pages = {97--139},
  publisher = {Springer International Publishing},
  location = {Cham},
  doi = {10.1007/978-3-319-93594-2_5},
  url = {http://link.springer.com/10.1007/978-3-319-93594-2_5},
  urldate = {2024-05-09},
  isbn = {978-3-319-93592-8 978-3-319-93594-2},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Oguchi et al. - 2018 - Leaf Anatomy and Function.pdf}
}

@article{oita2021,
  title = {Climate and Seasonality Drive the Richness and Composition of Tropical Fungal Endophytes at a Landscape Scale},
  author = {Oita, Shuzo and Ibáñez, Alicia and Lutzoni, François and Miadlikowska, Jolanta and Geml, József and Lewis, Louise A. and Hom, Erik F. Y. and Carbone, Ignazio and U’Ren, Jana M. and Arnold, A. Elizabeth},
  date = {2021-03-09},
  journaltitle = {Communications Biology},
  shortjournal = {Commun Biol},
  volume = {4},
  number = {1},
  pages = {313},
  issn = {2399-3642},
  doi = {10.1038/s42003-021-01826-7},
  url = {https://www.nature.com/articles/s42003-021-01826-7},
  urldate = {2023-11-06},
  abstract = {Abstract Understanding how species-rich communities persist is a foundational question in ecology. In tropical forests, tree diversity is structured by edaphic factors, climate, and biotic interactions, with seasonality playing an essential role at landscape scales: wetter and less seasonal forests typically harbor higher tree diversity than more seasonal forests. We posited that the abiotic factors shaping tree diversity extend to hyperdiverse symbionts in leaves—fungal endophytes—that influence plant health, function, and resilience to stress. Through surveys in forests across Panama that considered climate, seasonality, and covarying biotic factors, we demonstrate that endophyte richness varies negatively with temperature seasonality. Endophyte community structure and taxonomic composition reflect both temperature seasonality and climate (mean annual temperature and precipitation). Overall our findings highlight the vital role of climate-related factors in shaping the hyperdiversity of these important and little-known symbionts of the trees that, in turn, form the foundations of tropical forest biodiversity.},
  langid = {english}
}

@misc{oksanen2022,
  title = {Vegan: {{Community Ecology Package}}},
  author = {Oksanen, Jari and Simpson, Gavin L and Blanchet, F Guillaume and Kindt, Roeland and Legendre, Pierre and Minchin, Peter R and O'Hara, R B and Solymos, Peter and Stevens, M Henry H and Szoecs, Eduard and Wagner, Helene and Barbour, Matt and Bedward, Michael and Bolker, Ben and Borcard, Daniel and Carvalho, Gustavo and Chirico, Michael and De Caceres, Miquel and Durand, Sebastien and Evangelista, Heloisa Beatriz Antoniazi and FitzJohn, Rich and Friendly, Michael and Furneaux, Brendan and Hannigan, Geoffrey and Hill, Mark O and Lahti, Leo and McGlinn, Dan and Ouellette, Marie-Helene and Ribeiro Cunha, Eduardo and Smith, Tyler and Stier, Adrian and Ter Braak, Cajo J F and Weedon, James},
  date = {2022},
  url = {https://github.com/vegandevs/vegan}
}

@online{opti-sciencesinc,
  title = {{{ACM-200plus}}},
  shorttitle = {Anthocyanin {{Content Meter}}},
  author = {, Opti-Sciences Inc.},
  url = {https://www.optisci.com/acm-200.html},
  urldate = {2023-11-29},
  organization = {ACM-200plus},
  annotation = {Opti-Sciences Inc., Hudson, New Hampshire, U.S.A.}
}

@article{peay2016,
  title = {Dimensions of Biodiversity in the {{Earth}} Mycobiome},
  author = {Peay, Kabir G. and Kennedy, Peter G. and Talbot, Jennifer M.},
  date = {2016-07},
  journaltitle = {Nature Reviews Microbiology},
  shortjournal = {Nat Rev Microbiol},
  volume = {14},
  number = {7},
  pages = {434--447},
  issn = {1740-1526, 1740-1534},
  doi = {10.1038/nrmicro.2016.59},
  url = {https://www.nature.com/articles/nrmicro.2016.59},
  urldate = {2024-04-08},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Peay et al. - 2016 - Dimensions of biodiversity in the Earth mycobiome.pdf}
}

@article{pecl2017,
  title = {Biodiversity Redistribution under Climate Change: {{Impacts}} on Ecosystems and Human Well-Being},
  shorttitle = {Biodiversity Redistribution under Climate Change},
  author = {Pecl, Gretta T. and Araújo, Miguel B. and Bell, Johann D. and Blanchard, Julia and Bonebrake, Timothy C. and Chen, I-Ching and Clark, Timothy D. and Colwell, Robert K. and Danielsen, Finn and Evengård, Birgitta and Falconi, Lorena and Ferrier, Simon and Frusher, Stewart and Garcia, Raquel A. and Griffis, Roger B. and Hobday, Alistair J. and Janion-Scheepers, Charlene and Jarzyna, Marta A. and Jennings, Sarah and Lenoir, Jonathan and Linnetved, Hlif I. and Martin, Victoria Y. and McCormack, Phillipa C. and McDonald, Jan and Mitchell, Nicola J. and Mustonen, Tero and Pandolfi, John M. and Pettorelli, Nathalie and Popova, Ekaterina and Robinson, Sharon A. and Scheffers, Brett R. and Shaw, Justine D. and Sorte, Cascade J. B. and Strugnell, Jan M. and Sunday, Jennifer M. and Tuanmu, Mao-Ning and Vergés, Adriana and Villanueva, Cecilia and Wernberg, Thomas and Wapstra, Erik and Williams, Stephen E.},
  date = {2017-03-31},
  journaltitle = {Science},
  shortjournal = {Science},
  volume = {355},
  number = {6332},
  pages = {eaai9214},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.aai9214},
  url = {https://www.science.org/doi/10.1126/science.aai9214},
  urldate = {2024-04-08},
  abstract = {Consequences of shifting species distributions                            Climate change is causing geographical redistribution of plant and animal species globally. These distributional shifts are leading to new ecosystems and ecological communities, changes that will affect human society. Pecl               et al.               review these current and future impacts and assess their implications for sustainable development goals.                                         Science               , this issue p.               eaai9214                        ,                             BACKGROUND               The success of human societies depends intimately on the living components of natural and managed systems. Although the geographical range limits of species are dynamic and fluctuate over time, climate change is impelling a universal redistribution of life on Earth. For marine, freshwater, and terrestrial species alike, the first response to changing climate is often a shift in location, to stay within preferred environmental conditions. At the cooler extremes of their distributions, species are moving poleward, whereas range limits are contracting at the warmer range edge, where temperatures are no longer tolerable. On land, species are also moving to cooler, higher elevations; in the ocean, they are moving to colder water at greater depths. Because different species respond at different rates and to varying degrees, key interactions among species are often disrupted, and new interactions develop. These idiosyncrasies can result in novel biotic communities and rapid changes in ecosystem functioning, with pervasive and sometimes unexpected consequences that propagate through and affect both biological and human communities.                                         ADVANCES               At a time when the world is anticipating unprecedented increases in human population growth and demands, the ability of natural ecosystems to deliver ecosystem services is being challenged by the largest climate-driven global redistribution of species since the Last Glacial Maximum. We demonstrate the serious consequences of this species redistribution for economic development, livelihoods, food security, human health, and culture, and we document feedbacks on climate itself. As with other impacts of climate change, species range shifts will leave “winners” and “losers” in their wake, radically reshaping the pattern of human well-being between regions and different sectors and potentially leading to substantial conflict. The pervasive impacts of changes in species distribution transcend single systems or dimensions, with feedbacks and linkages between multiple interacting scales and through whole ecosystems, inclusive of humans. We argue that the negative effects of climate change cannot be adequately anticipated or prepared for unless species responses are explicitly included in decision-making and global strategic frameworks.                                         OUTLOOK               Despite mounting evidence for the pervasive and substantial impacts of a climate-driven redistribution of Earth’s species, current global goals, policies, and international agreements fail to account for these effects. With the predicted intensification of species movements and their diverse societal and environmental impacts, awareness of species “on the move” should be incorporated into local, regional, and global assessments as standard practice. This will raise hope that future targets—whether they be global sustainability goals, plans for regional biodiversity maintenance, or local fishing or forestry harvest strategies—can be achievable and that society is prepared for a world of universal ecological change. Human society has yet to appreciate the implications of unprecedented species redistribution for life on Earth, including for human lives. Even if greenhouse gas emissions stopped today, the responses required in human systems to adapt to the most serious effects of climate-driven species redistribution would be massive. Meeting these challenges requires governance that can anticipate and adapt to changing conditions, as well as minimize negative consequences.                                                   As the global climate changes, human well-being, ecosystem function, and even climate itself are increasingly affected by the shifting geography of life.                   Climate-driven changes in species distributions, or range shifts, affect human well-being both directly (for example, through emerging diseases and changes in food supply) and indirectly (by degrading ecosystem health). Some range shifts even create feedbacks (positive or negative) on the climate system, altering the pace of climate change.                                                                         ,              Distributions of Earth’s species are changing at accelerating rates, increasingly driven by human-mediated climate change. Such changes are already altering the composition of ecological communities, but beyond conservation of natural systems, how and why does this matter? We review evidence that climate-driven species redistribution at regional to global scales affects ecosystem functioning, human well-being, and the dynamics of climate change itself. Production of natural resources required for food security, patterns of disease transmission, and processes of carbon sequestration are all altered by changes in species distribution. Consideration of these effects of biodiversity redistribution is critical yet lacking in most mitigation and adaptation strategies, including the United Nation’s Sustainable Development Goals.},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Pecl et al. - 2017 - Biodiversity redistribution under climate change 2.pdf}
}

@article{peterson2012,
  title = {Double {{Digest RADseq}}: {{An Inexpensive Method}} for {{De Novo SNP Discovery}} and {{Genotyping}} in {{Model}} and {{Non-Model Species}}},
  shorttitle = {Double {{Digest RADseq}}},
  author = {Peterson, Brant K. and Weber, Jesse N. and Kay, Emily H. and Fisher, Heidi S. and Hoekstra, Hopi E.},
  editor = {Orlando, Ludovic},
  date = {2012-05-31},
  journaltitle = {PLoS ONE},
  shortjournal = {PLoS ONE},
  volume = {7},
  number = {5},
  pages = {e37135},
  issn = {1932-6203},
  doi = {10.1371/journal.pone.0037135},
  url = {https://dx.plos.org/10.1371/journal.pone.0037135},
  urldate = {2024-04-07},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Peterson et al. - 2012 - Double Digest RADseq An Inexpensive Method for De.pdf}
}

@article{petipas2021,
  title = {Microbe‐mediated Adaptation in Plants},
  author = {Petipas, Renee H. and Geber, Monica A. and Lau, Jennifer A.},
  editor = {Thrall, Peter},
  date = {2021-07},
  journaltitle = {Ecology Letters},
  shortjournal = {Ecology Letters},
  volume = {24},
  number = {7},
  pages = {1302--1317},
  issn = {1461-023X, 1461-0248},
  doi = {10.1111/ele.13755},
  url = {https://onlinelibrary.wiley.com/doi/10.1111/ele.13755},
  urldate = {2024-04-10},
  abstract = {Abstract             Interactions with microbial symbionts have yielded great macroevolutionary innovations across the tree of life, like the origins of chloroplasts and the mitochondrial powerhouses of eukaryotic cells. There is also increasing evidence that host‐associated microbiomes influence patterns of microevolutionary adaptation in plants and animals. Here we describe how microbes can facilitate adaptation in plants and how to test for and differentiate between the two main mechanisms by which microbes can produce adaptive responses in higher organisms: microbe‐mediated local adaptation and microbe‐mediated adaptive plasticity. Microbe‐mediated local adaptation is when local plant genotypes have higher fitness than foreign genotypes because of a genotype‐specific affiliation with locally beneficial microbes. Microbe‐mediated adaptive plasticity occurs when local plant phenotypes, elicited by either the microbial community or the non‐microbial environment, have higher fitness than foreign phenotypes as a result of interactions with locally beneficial microbes. These microbial effects on adaptation can be difficult to differentiate from traditional modes of adaptation but may be prevalent. Ignoring microbial effects may lead to erroneous conclusions about the traits and mechanisms underlying adaptation, hindering management decisions in conservation, restoration, and agriculture.},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Petipas et al. - 2021 - Microbe‐mediated adaptation in plants.pdf}
}

@article{piersondelmer1974,
  title = {Studies on the Nature of the Adaptations of the Monkey Flower , {{{\emph{Mimulus}}}}{\emph{ Guttatus}}, to a Thermophilic Environment},
  author = {Pierson Delmer, Deborah},
  date = {1974},
  journaltitle = {Canadian Journal of Botany},
  volume = {52},
  number = {7},
  pages = {1509--1514},
  doi = {10.1139/b74-198}
}

@book{pinheiro2000,
  title = {Mixed-{{Effects Models}} in {{S}} and {{S-PLUS}}},
  author = {Pinheiro, José C and Bates, Douglas M},
  date = {2000},
  publisher = {Springer},
  location = {New York},
  doi = {10.1007/b98882}
}

@software{pinheiro2024,
  title = {\_nlme: {{Linear}} and {{Nonlinear Mixed Effects Models}}\_. {{R}}   Package Version 3.1-165},
  author = {Pinheiro, José and Bates, Douglas and R Core Team},
  date = {2024},
  url = {https://svn.r-project.org/R-packages/trunk/nlme/},
  version = {3.1-165}
}

@article{poorter2006,
  title = {{{LEAF TRAITS ARE GOOD PREDICTORS OF PLANT PERFORMANCE ACROSS}} 53 {{RAIN FOREST SPECIES}}},
  author = {Poorter, Lourens and Bongers, Frans},
  date = {2006},
  journaltitle = {Ecology},
  volume = {87},
  number = {7},
  eprint = {https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1890/0012-9658%282006%2987%5B1733%3ALTAGPO%5D2.0.CO%3B2},
  pages = {1733--1743},
  doi = {10.1890/0012-9658(2006)87[1733:LTAGPO]2.0.CO;2},
  url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/0012-9658%282006%2987%5B1733%3ALTAGPO%5D2.0.CO%3B2},
  abstract = {We compared the leaf traits and plant performance of 53 co-occurring tree species in a semi-evergreen tropical moist forest community. The species differed in all leaf traits analyzed: leaf life span varied 11-fold among species, specific leaf area 5-fold, mass-based nitrogen 3-fold, mass-based assimilation rate 13-fold, mass-based respiration rate 15-fold, stomatal conductance 8-fold, and photosynthetic water use efficiency 4-fold. Photosynthetic traits were strongly coordinated, and specific leaf area predicted mass-based rates of assimilation and respiration; leaf life span predicted many other leaf characteristics. Leaf traits were closely associated with growth, survival, and light requirement of the species. Leaf investment strategies varied on a continuum trading off short-term carbon gain against long-term leaf persistence that, in turn, is linked to variation in whole-plant growth and survival. Leaf traits were good predictors of plant performance, both in gaps and in the forest understory. High growth in gaps is promoted by cheap, short-lived, and physiologically active leaves. High survival in the forest understory is enhanced by the formation of long-lived well protected leaves that reduce biomass loss by herbivory, mechanical disturbance, or leaf turnover. Leaf traits underlay this growth–survival trade-off; species with short-lived, physiologically active leaves have high growth but low survival. This continuum in leaf traits, through its effect on plant performance, in turn gives rise to a continuum in species' light requirements.},
  keywords = {bolivia,Bolivia,differentiation,growth,leaf life span,light,light requirements,niche,niche differentiation,photosynthesis,shade tolerance,survival,tropical rain forest}
}

@article{prive2018,
  title = {Efficient Analysis of Large-Scale Genome-Wide Data with Two {{R}} Packages: Bigstatsr and Bigsnpr},
  shorttitle = {Efficient Analysis of Large-Scale Genome-Wide Data with Two {{R}} Packages},
  author = {Privé, Florian and Aschard, Hugues and Ziyatdinov, Andrey and Blum, Michael G B},
  editor = {Stegle, Oliver},
  date = {2018-08-15},
  journaltitle = {Bioinformatics},
  volume = {34},
  number = {16},
  pages = {2781--2787},
  issn = {1367-4803, 1367-4811},
  doi = {10.1093/bioinformatics/bty185},
  url = {https://academic.oup.com/bioinformatics/article/34/16/2781/4956666},
  urldate = {2024-04-10},
  abstract = {Abstract                            Motivation               Genome-wide datasets produced for association studies have dramatically increased in size over the past few years, with modern datasets commonly including millions of variants measured in dozens of thousands of individuals. This increase in data size is a major challenge severely slowing down genomic analyses, leading to some software becoming obsolete and researchers having limited access to diverse analysis tools.                                         Results               Here we present two R packages, bigstatsr and bigsnpr, allowing for the analysis of large scale genomic data to be performed within R. To address large data size, the packages use memory-mapping for accessing data matrices stored on disk instead of in RAM. To perform data pre-processing and data analysis, the packages integrate most of the tools that are commonly used, either through transparent system calls to existing software, or through updated or improved implementation of existing methods. In particular, the packages implement fast and accurate computations of principal component analysis and association studies, functions to remove single nucleotide polymorphisms in linkage disequilibrium and algorithms to learn polygenic risk scores on millions of single nucleotide polymorphisms. We illustrate applications of the two R packages by analyzing a case–control genomic dataset for celiac disease, performing an association study and computing polygenic risk scores. Finally, we demonstrate the scalability of the R packages by analyzing a simulated genome-wide dataset including 500\,000 individuals and 1 million markers on a single desktop computer.                                         Availability and implementation               https://privefl.github.io/bigstatsr/ and https://privefl.github.io/bigsnpr/.                                         Supplementary information               Supplementary data are available at Bioinformatics online.},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Privé et al. - 2018 - Efficient analysis of large-scale genome-wide data.pdf}
}

@article{ranelli2015,
  title = {Biotic and Abiotic Predictors of Fungal Colonization in Grasses of the {{Colorado Rockies}}.},
  author = {Ranelli, Luciana B. and Hendricks, Will Q. and Lynn, Joshua S. and Kivlin, Stephanie N. and Rudgers, Jennifer A.},
  date = {2015-08-01},
  journaltitle = {Diversity and Distributions},
  volume = {21},
  number = {8},
  pages = {962--976},
  doi = {10.1111/ddi.12310},
  abstract = {Aim Fungal symbionts are ubiquitous in plants and can mitigate abiotic stressors associated with climate change. Predicting fungal symbiont distributions under future climates first requires knowledge of current distributions and their potential drivers. Location We documented colonization by fungal symbionts in perennial, cool-season grasses along altitudinal gradients in the Rocky Mountains of Colorado, USA. Methods Across seven replicate altitudinal gradients, spanning c.1400 vertical meters, we scored fungal colonization for 46 grass species. We documented altitudinal clines in colonization by both above-ground and below-ground fungal symbionts for the first time, including localized foliar endophytes (LFE) and systemic endophytes (epichloae) in leaves and arbuscular mycorrhizal fungi (AMF) and dark septate endophytes (DSE) in roots. For a subset of 16 well-sampled grass species, we used model selection procedures to evaluate the relative importance of geography, edaphic factors and host plant identity. We also assessed the influence of host phylogenetic relatedness and colonization by co-infecting fungi. Results Levels of fungal colonization varied strongly with host plant identity, but the effects of particular host species were not consistent across fungal groups. In addition to the influence of host identity, epichloae colonization declined with elevation and varied with geography (latitude/longitude) and edaphic factors. Geography and collection date were important predictors of LFE colonization, with higher colonization later in the growing season. Colonization estimates for the obligately plant-associated fungi (epichloae, AMF) were phylogenetically conserved across the grass supertree. Positive correlations between AMF and DSE, which remained even after accounting for host plant relatedness, suggested possible synergisms between these fungal groups. Main conclusions Our survey showed greater host specificity in patterns of fungal colonization than prior reports and revealed that different fungal symbiont groups do not share similar drivers. Conserving plant–fungal symbioses under future climates may require unique strategies for different plant species and fungal symbiont types.},
  annotation = {MAG ID: 2151977558\\
S2ID: e9978588366c9f6d58aeefb9d6098901e93daba3}
}

@article{rasmussen2008,
  title = {Plant-Endophyte-Herbivore Interactions: {{More}} than Just Alkaloids?},
  shorttitle = {Plant-Endophyte-Herbivore Interactions},
  author = {Rasmussen, Susanne and Parsons, Anthony J. and Popay, Alison and Xue, Hong and Newman, Jonathan A.},
  date = {2008-11},
  journaltitle = {Plant Signaling \& Behavior},
  shortjournal = {Plant Signaling \& Behavior},
  volume = {3},
  number = {11},
  pages = {974--977},
  issn = {1559-2324},
  doi = {10.4161/psb.6171},
  url = {http://www.tandfonline.com/doi/abs/10.4161/psb.6171},
  urldate = {2024-04-08},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Rasmussen et al. - 2008 - Plant-endophyte-herbivore interactions More than .pdf}
}

@software{rcoreteam2023,
  title = {R: {{A Language}} and {{Environment}} for {{Statistical Computing}}},
  author = {{R Core Team}},
  date = {2023-10-31},
  location = {Vienna, Austria},
  url = {https://www.R-project.org/},
  organization = {R Foundation for Statistical Computing}
}

@manual{rcoreteam2024,
  type = {manual},
  title = {R: {{A}} Language and Environment for Statistical Computing},
  author = {{R Core Team}},
  date = {2024},
  publisher = {R Foundation for Statistical Computing},
  location = {Vienna, Austria},
  url = {https://www.R-project.org/}
}

@article{rebolledagomez2019,
  title = {Floral Organs Act as Environmental Filters and Interact with Pollinators to Structure the Yellow Monkeyflower ( {{{\emph{Mimulus}}}}{\emph{ Guttatus}} ) Floral Microbiome},
  author = {Rebolleda Gómez, María and Ashman, Tia‐Lynn},
  date = {2019-12},
  journaltitle = {Molecular Ecology},
  shortjournal = {Molecular Ecology},
  volume = {28},
  number = {23},
  pages = {5155--5171},
  issn = {0962-1083, 1365-294X},
  doi = {10.1111/mec.15280},
  url = {https://onlinelibrary.wiley.com/doi/10.1111/mec.15280},
  urldate = {2024-05-21},
  abstract = {Abstract                            Assembly of microbial communities is the result of neutral and selective processes. However, the relative importance of these processes is still debated. Microbial communities of flowers, in particular, have gained recent attention because of their potential impact to plant fitness and plant‐pollinator interactions. However, the role of selection and dispersal in the assembly of these communities remains poorly understood. Here, we evaluated the role of pollinator‐mediated dispersal on the contribution of neutral and selective processes in the assembly of floral microbiomes of the yellow monkeyflower (               Mimulus guttatus               ). We sampled floral organs from flowers in the presence and absence of pollinators within five different serpentine seeps in CA and obtained 16S amplicon data on the epiphytic bacterial communities. Consistent with strong microenvironment selection within flowers we observed significant differences in community composition across floral organs and only a small effect of geographic distance. Pollinator exposure affected the contribution of environmental selection and depended on the rate and intimacy of interactions with flower visitors. This study provides evidence of the importance of dispersal and within‐flower heterogeneity in shaping epiphytic bacterial communities of flowers, and highlights the complex interplay between pollinator behaviour, environmental selection and additional abiotic factors in shaping the epiphytic bacterial communities of flowers.},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Rebolleda Gómez and Ashman - 2019 - Floral organs act as environmental filters and int.pdf}
}

@article{remy1994,
  title = {Four Hundred-Million-Year-Old Vesicular Arbuscular Mycorrhizae.},
  author = {Remy, W and Taylor, T N and Hass, H and Kerp, H},
  date = {1994-12-06},
  journaltitle = {Proceedings of the National Academy of Sciences},
  shortjournal = {Proc. Natl. Acad. Sci. U.S.A.},
  volume = {91},
  number = {25},
  pages = {11841--11843},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.91.25.11841},
  url = {https://pnas.org/doi/full/10.1073/pnas.91.25.11841},
  urldate = {2024-04-08},
  abstract = {The discovery of arbuscules in Aglaophyton major, an Early Devonian land plant, provides unequivocal evidence that mycorrhizae were established {$>$}400 million years ago. Nonseptate hyphac and arbuscules occur in a specialized meristematic region of the cortex that continually provided new cells for fungal infection. Arbuscules are morphologically identical to those of living arbuscular mycorrhizae in consisting of a basal trunk and repeatedly branched bush-like tuft within the plant cell. Although interpretations of the evolution of mycorrhizal mutualisms continue to be speculative, the existence of arbuscules in the Early Devonian indicates that nutrient transfer mutualism may have been in existence when plants invaded the land.},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Remy et al. - 1994 - Four hundred-million-year-old vesicular arbuscular.pdf}
}

@article{rocha2017,
  title = {Recognition of Endophytic {{{\emph{Trichoderma}}}} Species by Leaf-Cutting Ants and Their Potential in a {{Trojan-horse}} Management Strategy},
  author = {Rocha, Silma L. and Evans, Harry C. and Jorge, Vanessa L. and Cardoso, Lucimar A. O. and Pereira, Fernanda S. T. and Rocha, Fabiano B. and Barreto, Robert W. and Hart, Adam G. and Elliot, Simon L.},
  date = {2017-04},
  journaltitle = {Royal Society Open Science},
  shortjournal = {R. Soc. open sci.},
  volume = {4},
  number = {4},
  pages = {160628},
  issn = {2054-5703},
  doi = {10.1098/rsos.160628},
  url = {https://royalsocietypublishing.org/doi/10.1098/rsos.160628},
  urldate = {2024-01-30},
  abstract = {Interactions between leaf-cutting ants, their fungal symbiont (               Leucoagaricus               ) and the endophytic fungi within the vegetation they carry into their colonies are still poorly understood. If endophytes antagonistic to               Leucoagaricus               were found in plant material being carried by these ants, then this might indicate a potential mechanism for plants to defend themselves from leaf-cutter attack. In addition, it could offer possibilities for the management of these important Neotropical pests. Here, we show that, for               Atta sexdens rubropilosa               , there was a significantly greater incidence of               Trichoderma               species in the vegetation removed from the nests—and deposited around the entrances—than in that being transported into the nests. In a no-choice test,               Trichoderma-               infested rice was taken into the nest, with deleterious effects on both the fungal gardens and ant survival. The endophytic ability of selected strains of               Trichoderma               was also confirmed, following their inoculation and subsequent reisolation from seedlings of eucalyptus. These results indicate that endophytic fungi which pose a threat to ant fungal gardens through their antagonistic traits, such as               Trichoderma               , have the potential to act as bodyguards of their plant hosts and thus might be employed in a Trojan-horse strategy to mitigate the negative impact of leaf-cutting ants in both agriculture and silviculture in the Neotropics. We posit that the ants would detect and evict such ‘malign’ endophytes—artificially inoculated into vulnerable crops—during the quality-control process within the nest, and, moreover, that the foraging ants may then be deterred from further harvesting of ‘               Trichoderma               -enriched’ plants.},
  langid = {english},
  keywords = {Fungal bodyguards,Leucoagaricus,Pest management,Silviculture,Trichoderma endophytes},
  file = {/home/baponte/Zotero/storage/GDLDYR29/Rocha et al. - 2017 - Recognition of endophytic Trichoderma speci.pdf}
}

@article{rohland2012,
  title = {Cost-Effective, High-Throughput {{DNA}} Sequencing Libraries for Multiplexed Target Capture},
  author = {Rohland, Nadin and Reich, David},
  date = {2012-05},
  journaltitle = {Genome Research},
  shortjournal = {Genome Res.},
  volume = {22},
  number = {5},
  pages = {939--946},
  issn = {1088-9051},
  doi = {10.1101/gr.128124.111},
  url = {http://genome.cshlp.org/lookup/doi/10.1101/gr.128124.111},
  urldate = {2024-02-10},
  abstract = {Improvements in technology have reduced the cost of DNA sequencing to the point that the limiting factor for many experiments is the time and reagent cost of sample preparation. We present an approach in which 192 sequencing libraries can be produced in a single day of technician time at a cost of about \$15 per sample. These libraries are effective not only for low-pass whole-genome sequencing, but also for simultaneously enriching them in pools of approximately 100 individually barcoded samples for a subset of the genome without substantial loss in efficiency of target capture. We illustrate the power and effectiveness of this approach on about 2000 samples from a prostate cancer study.},
  langid = {english},
  file = {/home/baponte/Zotero/storage/S9SBYWH5/Rohland and Reich - 2012 - Cost-effective, high-throughput DNA sequencing lib.pdf}
}

@article{rondot2019,
  title = {Endophytic {{{\emph{Beauveria}}}}{\emph{ Bassiana}} Activates Expression of Defence Genes in Grapevine and Prevents Infections by Grapevine Downy Mildew {{{\emph{Plasmopara}}}}{\emph{ Viticola}}},
  author = {Rondot, Y. and Reineke, A.},
  date = {2019-12},
  journaltitle = {Plant Pathology},
  shortjournal = {Plant Pathology},
  volume = {68},
  number = {9},
  pages = {1719--1731},
  issn = {0032-0862, 1365-3059},
  doi = {10.1111/ppa.13089},
  url = {https://bsppjournals.onlinelibrary.wiley.com/doi/10.1111/ppa.13089},
  urldate = {2024-04-14},
  abstract = {Fungal entomopathogens like               Beauveria bassiana               (Ascomycota: Hypocreales) are known as antagonists of insects with multiple functional and ecological roles, and have attracted increased attention as biocontrol agents in integrated pest management programmes. For some crop plants, it has been proven that endophytic               B.~bassiana               , besides its entomopathogenic habit, can provide protection against plant pathogens or limit their damaging effects. However, for grapevine, limited knowledge is available on the influence of endophytic               B.~bassiana               on fungal pathogens and about the mechanisms underlying putative protection effects. This study assessed the protective potential of endophytic               B.~bassiana               against grapevine downy mildew               Plasmopara viticola               in greenhouse experiments. Three and seven days after a               B.~bassiana               treatment, potted grapevine plants were inoculated with               P.~viticola               and the evolving disease severity was assessed. Disease severity was significantly reduced in               B.~bassiana               ‐treated plants compared to control plants, depending on the age of leaves. Furthermore, a microarray and an RT‐qPCR analysis were performed to work out fundamental aspects of genes involved in the interaction between grapevine and               B.~bassiana               . The results indicate an up‐regulation of diverse defence‐related genes in grapevine as a response to endophytic establishment of               B.~bassiana               . Thus, endophytic establishment of an entomopathogenic fungus such as               B.~bassiana               in grapevine plants would represent an alternative and sustainable plant protection strategy, with the potential for reducing pesticide applications in viticulture.},
  langid = {english},
  file = {/home/baponte/Zotero/storage/8VXEXJNH/Rondot and Reineke - 2019 - Endophytic Beauveria bassiana activates exp.pdf}
}

@article{rosen2012,
  title = {Denoising {{PCR-amplified}} Metagenome Data},
  author = {Rosen, Michael J and Callahan, Benjamin J and Fisher, Daniel S and Holmes, Susan P},
  date = {2012-12},
  journaltitle = {BMC Bioinformatics},
  shortjournal = {BMC Bioinformatics},
  volume = {13},
  number = {1},
  pages = {283},
  issn = {1471-2105},
  doi = {10.1186/1471-2105-13-283},
  url = {https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-283},
  urldate = {2024-02-10},
  langid = {english},
  file = {/home/baponte/Zotero/storage/7R9DMRGK/Rosen et al. - 2012 - Denoising PCR-amplified metagenome data.pdf}
}

@article{rush2023,
  title = {Persisting {{{\emph{Cryptococcus}}}} Yeast Species {{{\emph{Vishniacozyma}}}}{\emph{ Victoriae}} and {{{\emph{Cryptococcus}}}}{\emph{ Neoformans}} Elicit Unique Airway Inflammation in Mice Following Repeated Exposure},
  author = {Rush, Rachael E. and Blackwood, Catherine B. and Lemons, Angela R. and Dannemiller, Karen C. and Green, Brett J. and Croston, Tara L.},
  date = {2023-02-14},
  journaltitle = {Frontiers in Cellular and Infection Microbiology},
  shortjournal = {Front. Cell. Infect. Microbiol.},
  volume = {13},
  pages = {1067475},
  issn = {2235-2988},
  doi = {10.3389/fcimb.2023.1067475},
  url = {https://www.frontiersin.org/articles/10.3389/fcimb.2023.1067475/full},
  urldate = {2024-03-20},
  abstract = {Background                                Allergic airway disease (AAD) is a growing concern in industrialized nations and can be influenced by fungal exposures. Basidiomycota yeast species such as                 Cryptococcus neoformans                 are known to exacerbate allergic airway disease; however, recent indoor assessments have identified other Basidiomycota yeasts, including                 Vishniacozyma victoriae                 (syn.                 Cryptococcus victoriae                 ), to be prevalent and potentially associated with asthma. Until now, the murine pulmonary immune response to repeated                 V. victoriae                 exposure was previously unexplored.                                                        Objective                                This study aimed to compare the immunological impact of repeated pulmonary exposure to                 Cryptococcus                 yeasts.                                                        Methods                                Mice were repeatedly exposed to an immunogenic dose of                 C. neoformans                 or                 V. victoriae via                 oropharyngeal aspiration. Bronchoalveolar lavage fluid (BALF) and lungs were collected to examine airway remodeling, inflammation, mucous production, cellular influx, and cytokine responses at 1 day and 21 days post final exposure. The responses to                 C. neoformans                 and                 V. victoriae                 were analyzed and compared.                                                        Results                                Following repeated exposure, both                 C. neoformans                 and                 V. victoriae                 cells were still detectable in the lungs 21 days post final exposure. Repeated                 C. neoformans                 exposure initiated myeloid and lymphoid cellular infiltration into the lung that worsened over time, as well as an IL-4 and IL-5 response compared to PBS-exposed controls. In contrast, repeated                 V. victoriae                 exposure induced a strong CD4                 +                 T cell-driven lymphoid response that started to resolve by 21 days post final exposure.                                                        Discussion                                C. neoformans                 remained in the lungs and exacerbated the pulmonary immune responses as expected following repeated exposure. The persistence of                 V. victoriae                 in the lung and strong lymphoid response following repeated exposure were unexpected given its lack of reported involvement in AAD. Given the abundance in indoor environments and industrial utilization of                 V. victoriae                 , these results highlight the importance to investigate the impact of frequently detected fungal organisms on the pulmonary response following inhalational exposure. Moreover, it is important to continue to address the knowledge gap involving Basidiomycota yeasts and their impact on AAD.},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Rush et al. - 2023 - Persisting Cryptococcus yeast species Vishniacozym.pdf}
}

@article{russo2022,
  title = {Low-{{Input High-Molecular-Weight DNA Extraction}} for {{Long-Read Sequencing From Plants}} of {{Diverse Families}}},
  author = {Russo, Alessia and Mayjonade, Baptiste and Frei, Daniel and Potente, Giacomo and Kellenberger, Roman T. and Frachon, Léa and Copetti, Dario and Studer, Bruno and Frey, Jürg E. and Grossniklaus, Ueli and Schlüter, Philipp M.},
  date = {2022-05-19},
  journaltitle = {Frontiers in Plant Science},
  shortjournal = {Front. Plant Sci.},
  volume = {13},
  pages = {883897},
  issn = {1664-462X},
  doi = {10.3389/fpls.2022.883897},
  url = {https://www.frontiersin.org/articles/10.3389/fpls.2022.883897/full},
  urldate = {2024-02-05},
  abstract = {Long-read DNA sequencing technologies require high molecular weight (HMW) DNA of adequate purity and integrity, which can be difficult to isolate from plant material. Plant leaves usually contain high levels of carbohydrates and secondary metabolites that can impact DNA purity, affecting downstream applications. Several protocols and kits are available for HMW DNA extraction, but they usually require a high amount of input material and often lead to substantial DNA fragmentation, making sequencing suboptimal in terms of read length and data yield. We here describe a protocol for plant HMW DNA extraction from low input material (0.1 g) which is easy to follow and quick (2.5 h). This method successfully enabled us to extract HMW from four species from different families (Orchidaceae, Poaceae, Brassicaceae, Asteraceae). In the case of recalcitrant species, we show that an additional purification step is sufficient to deliver a clean DNA sample. We demonstrate the suitability of our protocol for long-read sequencing on the Oxford Nanopore Technologies PromethION ® platform, with and without the use of a short fragment depletion kit.},
  file = {/home/baponte/Zotero/storage/KQCP6D89/Russo et al. - 2022 - Low-Input High-Molecular-Weight DNA Extraction for.pdf}
}

@article{sabatini2018,
  title = {Beta‐diversity of Central {{European}} Forests Decreases along an Elevational Gradient Due to the Variation in Local Community Assembly Processes},
  author = {Sabatini, Francesco Maria and Jiménez‐Alfaro, Borja and Burrascano, Sabina and Lora, Andrea and Chytrý, Milan},
  date = {2018-06},
  journaltitle = {Ecography},
  shortjournal = {Ecography},
  volume = {41},
  number = {6},
  pages = {1038--1048},
  issn = {0906-7590, 1600-0587},
  doi = {10.1111/ecog.02809},
  url = {https://onlinelibrary.wiley.com/doi/10.1111/ecog.02809},
  urldate = {2024-03-20},
  abstract = {Beta‐diversity has been repeatedly shown to decline with increasing elevation, but the causes of this pattern remain unclear, partly because they are confounded by coincident variation in alpha‐ and gamma‐diversity. We used 8795 forest vegetation‐plot records from the Czech National Phytosociological Database to compare the observed patterns of beta diversity to null‐model expectations (beta‐deviation) controlling for the effects of alpha‐ and gamma‐diversity. We tested whether β‐diversity patterns along a 1200 m elevation gradient exclusively depend on the effect of varying species pool size, or also on the variation of the magnitude of community assembly mechanisms determining the distribution of species across communities (e.g. environmental filtering, dispersal limitation). The null model we used is a novel extension of an existing null‐model designed for presence/absence data and was specifically designed to disrupt the effect of community assembly mechanisms, while retaining some key features of observed communities such as average species richness and species abundance distribution. Analyses were replicated in ten subregions with comparable elevation ranges. Beta‐diversity declined along the elevation gradient due to a decrease in gamma‐diversity, which was steeper than the decrease in alpha‐diversity. This pattern persisted after controlling for alpha‐ and gamma‐diversity variation, and the results were robust when different resampling schemes and diversity metrics were used. We conclude that in temperate forests the pattern of decreasing beta‐diversity with elevation does not exclusively depend on variation in species pool size, as has been hypothesized, but also on variation in community assembly mechanisms. The results were consistent across resampling schemes and diversity measures, thus supporting the use of vegetation‐plot databases for understanding patterns of beta‐diversity at the regional scale.},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Sabatini et al. - 2018 - Beta‐diversity of central European forests decreas.pdf}
}

@article{sack2013,
  title = {Leaf Venation: Structure, Function, Development, Evolution, Ecology and Applications in the Past, Present and Future},
  shorttitle = {Leaf Venation},
  author = {Sack, Lawren and Scoffoni, Christine},
  date = {2013-06},
  journaltitle = {New Phytologist},
  shortjournal = {New Phytologist},
  volume = {198},
  number = {4},
  pages = {983--1000},
  issn = {0028-646X, 1469-8137},
  doi = {10.1111/nph.12253},
  url = {https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.12253},
  urldate = {2024-05-07},
  abstract = {Summary             The design and function of leaf venation are important to plant performance, with key implications for the distribution and productivity of ecosystems, and applications in paleobiology, agriculture and technology. We synthesize classical concepts and the recent literature on a wide range of aspects of leaf venation. We describe 10 major structural features that contribute to multiple key functions, and scale up to leaf and plant performance. We describe the development and plasticity of leaf venation and its adaptation across environments globally, and a new global data compilation indicating trends relating vein length per unit area to climate, growth form and habitat worldwide. We synthesize the evolution of vein traits in the major plant lineages throughout paleohistory, highlighting the multiple origins of individual traits. We summarize the strikingly diverse current applications of leaf vein research in multiple fields of science and industry. A unified core understanding will enable an increasing range of plant biologists to incorporate leaf venation into their research.                                                                                                                                                                                            Contents                                                                                                                                                     Summary                       983                                                                 I.                                                Introduction                                              983                                                                 II.                                                Overall structure of the leaf venation                                              983                                                                 III.                                                Function of leaf venation traits: a ‘Rosetta Stone’                                              984                                                                 IV.                                                Development of the leaf vein system                                              990                                                                 V.                                                Function of the coordinated vein system and scaling up                                              992                                                                 VI.                                                Plasticity, evolution and assembly of leaf vein traits across growth forms, environments and biomes                                              992                                                                 VII.                                                Evolution of the leaf vascular system across plant lineages, paleohistory and biogeography                                              993                                                                 VIII.                                                Applications of leaf venation architecture                                              995                                                                 IX.                                                Conclusions                                              996                                                                                                                 Acknowledgements                                              996                                                                                                                 References                                              996},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Sack and Scoffoni - 2013 - Leaf venation structure, function, development, e.pdf}
}

@book{samson2004,
  title = {Introduction to Food- and Airborne Fungi},
  author = {Samson, R.A. and Hoekstra, E.S. and Frisvad, Jens Christian},
  date = {2004},
  edition = {7},
  publisher = {Centraalbureau voor Schimmelcultures},
  langid = {english},
  pagetotal = {389}
}

@article{sarmiento2017,
  title = {Soilborne Fungi Have Host Affinity and Host-Specific Effects on Seed Germination and Survival in a Lowland Tropical Forest},
  author = {Sarmiento, Carolina and Zalamea, Paul Camilo and Dalling, James W. and Davis, Adam S. and Simon, Stump M. and U'Ren, Jana M. and Arnold, A. Elizabeth},
  date = {2017},
  journaltitle = {Proceedings of the National Academy of Sciences of the United States of America},
  volume = {114},
  number = {43},
  pages = {11458--11463},
  doi = {10.1073/pnas.1706324114},
  abstract = {The Janzen-Connell (JC) hypothesis provides a conceptual framework for explaining the maintenance of tree diversity in tropical forests. Its central tenet - that recruits experience high mortality near conspecifics and at high densities - assumes a degree of host specialization in interactions between plants and natural enemies. Studies confirming JC effects have focused primarily on spatial distributions of seedlings and saplings, leaving major knowledge gaps regarding the fate of seeds in soil and the specificity of the soilborne fungi that are their most important antagonists. Here we use a common garden experiment in a lowland tropical forest in Panama to show that communities of seed-infecting fungi are structured predominantly by plant species, with only minor influences of factors such as local soil type, forest characteristics, or time in soil (1- 12 months). Inoculation experiments confirmed that fungi affected seed viability and germination in a host-specific manner and that effects on seed viability preceded seedling emergence. Seeds are critical components of reproduction for tropical trees, and the factors influencing their persistence, survival, and germination shape the populations of seedlings and saplings on which current perspectives regarding forest dynamics are based. Together these findings bring seed dynamics to light in the context of the JC hypothesis, implicating them directly in the processes that have emerged as critical for diversity maintenance in species-rich tropical forests.},
  keywords = {Diversity,Janzen-Connell,Pathogen,Pioneer species,Soil seed bank}
}

@article{saunders2010,
  title = {Exploring the Evolutionary Ecology of Fungal Endophytes in Agricultural Systems: Using Functional Traits to Reveal Mechanisms in Community Processes},
  shorttitle = {Exploring the Evolutionary Ecology of Fungal Endophytes in Agricultural Systems},
  author = {Saunders, Megan and Glenn, Anthony E. and Kohn, Linda M.},
  date = {2010-09},
  journaltitle = {Evolutionary Applications},
  shortjournal = {Evolutionary Applications},
  volume = {3},
  number = {5-6},
  pages = {525--537},
  issn = {1752-4571, 1752-4571},
  doi = {10.1111/j.1752-4571.2010.00141.x},
  url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1752-4571.2010.00141.x},
  urldate = {2024-01-31},
  abstract = {Abstract             All plants, including crop species, harbor a community of fungal endophyte species, yet we know little about the biotic factors that are important in endophyte community assembly. We suggest that the most direct route to understanding the mechanisms underlying community assembly is through the study of functional trait variation in the host and its fungal consortium. We review studies on crop endophytes that investigate plant and fungal traits likely to be important in endophyte community processes. We focus on approaches that could speed detection of general trends in endophyte community assembly: (i) use of the ‘assembly rules’ concept to identify specific mechanisms that influence endophyte community dynamics, (ii) measurement of functional trait variation in plants and fungi to better understand endophyte community processes and plant–fungal interactions, and (iii) investigation of microbe–microbe interactions, and fungal traits that mediate them. This approach is well suited for research in agricultural systems, where pair‐wise host–fungus interactions and mechanisms of fungal–fungal competition have frequently been described. Areas for consideration include the possibility that human manipulation of crop phenotype and deployment of fungal biocontrol species can significantly influence endophyte community assembly. Evaluation of endophyte assembly rules may help to fine‐tune crop management strategies.},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Saunders et al. - 2010 - Exploring the evolutionary ecology of fungal endop.pdf}
}

@article{schloss2024,
  title = {Rarefaction Is Currently the Best Approach to Control for Uneven Sequencing Effort in Amplicon Sequence Analyses},
  author = {Schloss, Patrick D.},
  editor = {McMahon, Katherine},
  date = {2024-02-28},
  journaltitle = {mSphere},
  shortjournal = {mSphere},
  volume = {9},
  number = {2},
  pages = {e00354-23},
  issn = {2379-5042},
  doi = {10.1128/msphere.00354-23},
  url = {https://journals.asm.org/doi/10.1128/msphere.00354-23},
  urldate = {2024-03-09},
  abstract = {ABSTRACT                                           Considering it is common to find as much as 100-fold variation in the number of 16S rRNA gene sequences across samples in a study, researchers need to control for the effect of uneven sequencing effort. How to do this has become a contentious question. Some have argued that rarefying or rarefaction is “inadmissible” because it omits valid data. A number of alternative approaches have been developed to normalize and rescale the data that purport to be invariant to the number of observations. I generated community distributions based on 12 published data sets where I was able to assess the ability of multiple methods to control for uneven sequencing effort. Rarefaction was the only method that could control for variation in uneven sequencing effort when measuring commonly used alpha and beta diversity metrics. Next, I compared the false detection rate and power to detect true differences between simulated communities with a known effect size using various alpha and beta diversity metrics. Although all methods of controlling for uneven sequencing effort had an acceptable false detection rate when samples were randomly assigned to two treatment groups, rarefaction was consistently able to control for differences in sequencing effort when sequencing depth was confounded with treatment group. Finally, the statistical power to detect differences in alpha and beta diversity metrics was consistently the highest when using rarefaction. These simulations underscore the importance of using rarefaction to normalize the number of sequences across samples in amplicon sequencing analyses.                                         IMPORTANCE               Sequencing 16S rRNA gene fragments has become a fundamental tool for understanding the diversity of microbial communities and the factors that affect their diversity. Due to technical challenges, it is common to observe wide variation in the number of sequences that are collected from different samples within the same study. However, the diversity metrics used by microbial ecologists are sensitive to differences in sequencing effort. Therefore, tools are needed to control for the uneven levels of sequencing. This simulation-based analysis shows that despite a longstanding controversy, rarefaction is the most robust approach to control for uneven sequencing effort. The controversy started because of confusion over the definition of rarefaction and violation of assumptions that are made by methods that have been borrowed from other fields. Microbial ecologists should use rarefaction.                        ,              Sequencing 16S rRNA gene fragments has become a fundamental tool for understanding the diversity of microbial communities and the factors that affect their diversity. Due to technical challenges, it is common to observe wide variation in the number of sequences that are collected from different samples within the same study. However, the diversity metrics used by microbial ecologists are sensitive to differences in sequencing effort. Therefore, tools are needed to control for the uneven levels of sequencing. This simulation-based analysis shows that despite a longstanding controversy, rarefaction is the most robust approach to control for uneven sequencing effort. The controversy started because of confusion over the definition of rarefaction and violation of assumptions that are made by methods that have been borrowed from other fields. Microbial ecologists should use rarefaction.},
  langid = {english},
  keywords = {Microbial ecology,Microbiome,rarefaction},
  file = {/home/baponte/Boxx/Dissertation/master_papers/msphere.00354-23-s0001.pdf;/home/baponte/Boxx/Dissertation/master_papers/Schloss - 2024 - Rarefaction is currently the best approach to cont.pdf}
}

@article{schneider2012,
  title = {{{NIH Image}} to {{ImageJ}}: 25 Years of Image Analysis},
  shorttitle = {{{NIH Image}} to {{ImageJ}}},
  author = {Schneider, Caroline A and Rasband, Wayne S and Eliceiri, Kevin W},
  date = {2012-07},
  journaltitle = {Nature Methods},
  shortjournal = {Nat Methods},
  volume = {9},
  number = {7},
  pages = {671--675},
  issn = {1548-7091, 1548-7105},
  doi = {10.1038/nmeth.2089},
  url = {https://www.nature.com/articles/nmeth.2089},
  urldate = {2023-11-29},
  langid = {english}
}

@article{schubert2007,
  title = {Biodiversity in the {{{\emph{Cladosporium}}}}{\emph{ Herbarum}} Complex ({{Davidiellaceae}}, {{Capnodiales}}), with Standardisation of Methods for {{{\emph{Cladosporium}}}} Taxonomy and Diagnostics},
  author = {Schubert, K. and Groenewald, J.Z. and Braun, U. and Dijksterhuis, J. and Starink, M. and Hill, C.F. and Zalar, P. and De Hoog, G.S. and Crous, P.W.},
  date = {2007},
  journaltitle = {Studies in Mycology},
  shortjournal = {Studies in Mycology},
  volume = {58},
  pages = {105--156},
  issn = {01660616},
  doi = {10.3114/sim.2007.58.05},
  url = {https://www.ingentaconnect.com/content/10.3114/sim.2007.58.05},
  urldate = {2024-03-20},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Schubert et al. - 2007 - Biodiversity in the Cladosporium herbarum complex .pdf}
}

@article{schuepp1993,
  title = {Tansley {{Review No}}. 59 {{Leaf}} Boundary Layers},
  author = {Schuepp, P. H.},
  date = {1993-11},
  journaltitle = {New Phytologist},
  shortjournal = {New Phytologist},
  volume = {125},
  number = {3},
  pages = {477--507},
  issn = {0028-646X, 1469-8137},
  doi = {10.1111/j.1469-8137.1993.tb03898.x},
  url = {https://nph.onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.1993.tb03898.x},
  urldate = {2024-05-13},
  abstract = {Studies of heat and mass exchange between leaves and their local environment are central to our understanding of plant‐atmosphere interactions. The transfer across aerodynamic leaf boundary layers is generally described by non‐dimensional expressions which reflect largely empirical adaptations of engineering models derived for flat plates. This paper reviews studies on leaves, and leaf models with varying degrees of abstraction, in free and forced convection. It discusses implecations of finding for leaf morphology as it affects – and is affected by – the local microclimate. Predictions of transfer from many leaves in plant communities are complicated by physical and physiological feedback mechanisms between leaves and their environment. Some common approaches, and the current challenge of integrating leaf‐atmosphere interactions into models of global relevance, are also briefly addressed.                                                                                                                                                                                            Contents                                                                                                                                                     Summary                       477                                                                 I.                       Introduction                       478                                                                 II.                       Early studies                       479                                                                 III.                       The formal description of leaf transfer                       480                                                                 IV.                       Effects of turbulence on idealized shapes                       484                                                                 V.                       Effects of aspect ratio and inclination                       486                                                                 VI.                       Leaves and leaf models in forced convection                       491                                                                 VII.                       Leaves and leaf models in mixed and free convection                       493                                                                 VIII.                       Interpretation of leaf shape                       494                                                                 IX.                       Leaves in plant canopies                       499                                                                 X.                       Synopsis and conclusions                       502                                                                                        References                       502},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Schuepp - 1993 - Tansley Review No. 59 Leaf boundary layers.pdf}
}

@article{sexton2013a,
  title = {The {{Fern-Leaved Monkeyflower}} ({{Phrymaceae}}), a {{New Species}} from the {{Northern Sierra Nevada}} of {{California}}},
  author = {Sexton, Jason P. and Ferris, Kathleen G. and Schoenig, Steve E.},
  date = {2013-07},
  journaltitle = {Madroño},
  shortjournal = {Madroño},
  volume = {60},
  number = {3},
  pages = {236--242},
  issn = {0024-9637, 1943-6297},
  doi = {10.3120/0024-9637-60.3.236},
  url = {http://www.bioone.org/doi/abs/10.3120/0024-9637-60.3.236},
  urldate = {2024-07-13},
  langid = {english},
  file = {/home/baponte/Box/Dissertation/master_papers/Sexton et al. - 2013 - The Fern-Leaved Monkeyflower (Phrymaceae), a New S.pdf}
}

@article{shade2012,
  title = {Beyond the {{Venn}} Diagram: The Hunt for a Core Microbiome},
  shorttitle = {Beyond the {{Venn}} Diagram},
  author = {Shade, Ashley and Handelsman, Jo},
  date = {2012-01},
  journaltitle = {Environmental Microbiology},
  shortjournal = {Environmental Microbiology},
  volume = {14},
  number = {1},
  pages = {4--12},
  issn = {1462-2912, 1462-2920},
  doi = {10.1111/j.1462-2920.2011.02585.x},
  url = {https://sfamjournals.onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02585.x},
  urldate = {2024-04-10},
  abstract = {Summary             Discovering a core microbiome is important for understanding the stable, consistent components across complex microbial assemblages. A core is typically defined as the suite of members shared among microbial consortia from similar habitats, and is represented by the overlapping areas of circles in Venn diagrams, in which each circle contains the membership of the sample or habitats being compared. Ecological insight into core microbiomes can be enriched by 'omics approaches that assess gene expression, thereby extending the concept of the core beyond taxonomically defined membership to community function and behaviour. Parameters defined by traditional ecology theory, such as composition, phylogeny, persistence and connectivity, will also create a more complex portrait of the core microbiome and advance understanding of the role of key microorganisms and functions within and across ecosystems.},
  langid = {english},
  file = {/home/baponte/Zotero/storage/PHNNPWZN/Shade and Handelsman - 2012 - Beyond the Venn diagram the hunt for a core micro.pdf}
}

@article{shankarnaik2019,
  title = {Functional Roles of Fungal Endophytes in Host Fitness during Stress Conditions},
  author = {Shankar Naik, B.},
  date = {2019-10},
  journaltitle = {Symbiosis},
  shortjournal = {Symbiosis},
  volume = {79},
  number = {2},
  pages = {99--115},
  issn = {0334-5114, 1878-7665},
  doi = {10.1007/s13199-019-00635-1},
  url = {http://link.springer.com/10.1007/s13199-019-00635-1},
  urldate = {2024-07-11},
  langid = {english},
  file = {/home/baponte/Zotero/storage/5YGA8IQA/Shankar Naik - 2019 - Functional roles of fungal endophytes in host fitn.pdf}
}

@article{siddiqueabubakar2016,
  title = {A Cost-Effective and Efficient Strategy for {{Illumina}} Sequencing of Fungal Communities: {{A}} Case Study of Beech Endophytes Identified Elevation as Main Explanatory Factor for Diversity and Community Composition},
  author = {{Siddique, Abu Bakar} and Unterseher, Martin},
  date = {2016-04-01},
  journaltitle = {Fungal Ecology},
  volume = {20},
  pages = {175--185},
  doi = {10.1016/j.funeco.2015.12.009},
  abstract = {Abstract   We describe an accurate and efficient workflow for highly multiplexed paired-end Illumina sequencing of fungal full-length ITS amplicons. The impact of habitat and substratum conditions on leaf-inhabiting fungal communities was analysed. Fully vital and clearly senescent leaves of European beech (Fagus sylvatica) were sampled along an elevation gradient of about 1000m in the Bavarian Alps, Germany, in autumn 2013. Surface-sterilised leaves were used for genomic DNA extraction, tagging-by-amplification and high-throughput sequencing. Significant correlation of community composition with elevation was observed. The mycobiome was little affected by the physiological state of the leaves, because only a partial shift of taxonomic composition was observed from vital towards clearly senescent leaves.},
  annotation = {MAG ID: 2255124090\\
S2ID: eec5cbf2484e9694f55bdd752ee74e56805657e3},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Siddique, Abu Bakar and Unterseher - 2016 - A cost-effective and efficient strategy for Illumi.pdf}
}

@article{sobel2014,
  title = {Ecogeographic {{Isolation}} and {{Speciation}} in the {{Genus}} {{{\emph{Mimulus}}}}},
  author = {Sobel, James M.},
  date = {2014-11},
  journaltitle = {The American Naturalist},
  shortjournal = {The American Naturalist},
  volume = {184},
  number = {5},
  pages = {565--579},
  issn = {0003-0147, 1537-5323},
  doi = {10.1086/678235},
  url = {https://www.journals.uchicago.edu/doi/10.1086/678235},
  urldate = {2024-05-02},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Sobel - 2014 - Ecogeographic Isolation and Speciation in the Genu.pdf}
}

@article{society2019,
  title = {Seep {{Monkey Flower}}},
  author = {Society, California Native Plant},
  date = {2019},
  url = {https://calscape.org/Mimulus-guttatus-(Seep-Monkey-Flower)}
}

@article{soltis1995,
  title = {Chloroplast Gene Sequence Data Suggest a Single Origin of the Predisposition for Symbiotic Nitrogen Fixation in Angiosperms.},
  author = {Soltis, D E and Soltis, P S and Morgan, D R and Swensen, S M and Mullin, B C and Dowd, J M and Martin, P G},
  date = {1995-03-28},
  journaltitle = {Proceedings of the National Academy of Sciences},
  shortjournal = {Proc. Natl. Acad. Sci. U.S.A.},
  volume = {92},
  number = {7},
  pages = {2647--2651},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.92.7.2647},
  url = {https://pnas.org/doi/full/10.1073/pnas.92.7.2647},
  urldate = {2024-05-02},
  abstract = {Of the approximately 380 families of angiosperms, representatives of only 10 are known to form symbiotic associations with nitrogen-fixing bacteria in root nodules. The morphologically based classification schemes proposed by taxonomists suggest that many of these 10 families of plants are only distantly related, engendering the hypothesis that the capacity to fix nitrogen evolved independently several, if not many, times. This has in turn influenced attitudes toward the likelihood of transferring genes responsible for symbiotic nitrogen fixation to crop species lacking this ability. Phylogenetic analysis of DNA sequences for the chloroplast gene rbcL indicates, however, that representatives of all 10 families with nitrogen-fixing symbioses occur together, with several families lacking this association, in a single clade. This study therefore indicates that only one lineage of closely related taxa achieved the underlying genetic architecture necessary for symbiotic nitrogen fixation in root nodules.},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Soltis et al. - 1995 - Chloroplast gene sequence data suggest a single or.pdf}
}

@article{song2016,
  title = {Advances in {{Research}} on {{{\emph{Epichloë}}}} Endophytes in {{Chinese Native Grasses}}},
  author = {Song, Hui and Nan, Zhibiao and Song, Qiuyan and Xia, Chao and Li, Xiuzhang and Yao, Xiang and Xu, Wenbo and Kuang, Yu and Tian, Pei and Zhang, Qingping},
  date = {2016},
  journaltitle = {Frontiers in Microbiology},
  volume = {7},
  pages = {1399--1399},
  doi = {10.3389/fmicb.2016.01399},
  url = {https://www.frontiersin.org/article/10.3389/fmicb.2016.01399},
  abstract = {Epichloë fungal endophytes are broadly found in cool-season grasses. The symbiosis between these grasses and Epichloë may improve the abiotic and biotic resistance of the grass plant, but some Epichloë species produce alkaloids that are toxic for livestock. Therefore, it is important to understand the characteristics of the grass-Epichloë s symbiosis so that the beneficial aspects can be preserved and the toxic effects to livestock can be avoided. Since the 1990s, Chinese researchers have conducted a series of studies on grass-Epichloë symbiosis. In this review, we describe the current state of Epichloë endophyte research in Chinese native grasses. We found that more than 77 species of native grasses in China are associated with Epichloë endophytes. In addition, we review the effects of various Epichloë species on native grass responses to abiotic and biotic stress, phylogeny, and alkaloid production. We provide an overview of the study of Epichloë species on native grasses in China and directions for future research.},
  issue = {SEP},
  keywords = {Alkaloid,Chinese native grass,Epichlo� endophyte,Epichlo� phylogeny,Grass stress response,Grass-Epichlo� symbiosis}
}

@article{stevene.lindow2003,
  title = {Microbiology of the {{Phyllosphere}}},
  author = {{Steven E. Lindow} and Lindow, Steven E. and {Maria T. Brandl} and Brandl, Maria T.},
  date = {2003-04-01},
  journaltitle = {Applied and Environmental Microbiology},
  volume = {69},
  number = {4},
  eprint = {12676659},
  eprinttype = {pmid},
  pages = {1875--1883},
  doi = {10.1128/aem.69.4.1875-1883.2003},
  abstract = {The above-ground parts of plants are normally colonized by a variety of bacteria, yeasts, and fungi. While a few microbial species can be isolated from within plant tissues, many more are recovered from the surfaces of healthy plants. The aerial habitat colonized by these microbes is termed the},
  pmcid = {154815},
  annotation = {MAG ID: 2147739650}
}

@article{sullivan2008,
  title = {Local {{Adaptation}} in {{Festuca}} Arizonica {{Infected}} by {{Hybrid}} and {{Nonhybrid Neotyphodium Endophytes}}},
  author = {Sullivan, T. J. and Faeth, Stanley H.},
  date = {2008-05},
  journaltitle = {Microbial Ecology},
  shortjournal = {Microb Ecol},
  volume = {55},
  number = {4},
  pages = {697--704},
  issn = {0095-3628, 1432-184X},
  doi = {10.1007/s00248-007-9312-4},
  url = {http://link.springer.com/10.1007/s00248-007-9312-4},
  urldate = {2024-04-10},
  langid = {english}
}

@online{syrotchen2023,
  title = {Local Adaptation to an Altitudinal Gradient: The Interplay between Mean Phenotypic Trait Variation and Phenotypic Plasticity in {{{\emph{Mimulus}}}}{\emph{ Laciniatus}}},
  shorttitle = {Local Adaptation to an Altitudinal Gradient},
  author = {Syrotchen, Jill M. and Ferris, Kathleen G.},
  date = {2023-08-02},
  doi = {10.1101/2023.08.02.551729},
  url = {http://biorxiv.org/lookup/doi/10.1101/2023.08.02.551729},
  urldate = {2024-04-15},
  abstract = {ABSTRACT                        Organisms can adapt to environmental heterogeneity through two mechanisms: (1) expression of population genetic variation or (2) phenotypic plasticity. In this study we investigated whether patterns of variation in both trait means and phenotypic plasticity along elevational and latitudinal clines in a North American endemic plant,             Mimulus laciniatus             , were consistent with local adaptation. We grew inbred lines of             M. laciniatus             from across the species’ range in two common gardens varying in day length to measure mean and plastic trait expression in several traits previously shown to be involved in adaptation to             M. laciniatus’s             rocky outcrop microhabitat: flowering time, size-related traits, and leaf shape. We examined correlations between the mean phenotype and phenotypic plasticity, and tested for a relationship between trait variation and population elevation and latitude. We did not find a strong correlation between mean and plastic trait expression at the individual genotype level suggesting that they operate under independent genetic controls. We identified multiple traits that show patterns consistent with local adaptation to elevation: critical photoperiod, flowering time, flower size, mean leaf lobing, and leaf lobing plasticity. These trends occur along multiple geographically independent altitudinal clines indicating that selection is a more likely cause of this pattern than gene flow among nearby populations with similar trait values. We also found that population variation in mean leaf lobing is associated with latitude. Our results indicate that both having more highly lobed leaves and greater leaf shape plasticity may be adaptive at high elevation within             M. laciniatus.             Our data strongly suggest that traits known to be under divergent selection between             M. laciniatus             and close relative             Mimulus guttatus             are also under locally varying selection within             M. laciniatus             .},
  langid = {english},
  pubstate = {prepublished},
  file = {/home/baponte/Zotero/storage/G2W5C3Y4/Syrotchen and Ferris - 2023 - Local adaptation to an altitudinal gradient the i.pdf}
}

@article{tataru2023,
  title = {Spatially and Temporally Varying Selection Influence Species Boundaries in Two Sympatric {{{\emph{Mimulus}}}}},
  author = {Tataru, Diana and Wheeler, Emma C. and Ferris, Kathleen G.},
  date = {2023-02-08},
  journaltitle = {Proceedings of the Royal Society B: Biological Sciences},
  shortjournal = {Proc. R. Soc. B.},
  volume = {290},
  number = {1992},
  pages = {20222279},
  issn = {0962-8452, 1471-2954},
  doi = {10.1098/rspb.2022.2279},
  url = {https://royalsocietypublishing.org/doi/10.1098/rspb.2022.2279},
  urldate = {2024-04-08},
  abstract = {Spatially and temporally varying selection can maintain genetic variation within and between populations, but it is less well known how these forces influence divergence between closely related species. We identify the interaction of temporal and spatial variation in selection and their role in either reinforcing or eroding divergence between two closely related               Mimulus               species. Using repeated reciprocal transplant experiments with advanced generation hybrids, we compare the strength of selection on quantitative traits involved in adaptation and reproductive isolation in               Mimulus guttatus               and               Mimulus laciniatus               between two years with dramatically different water availability               .               We found strong divergent habitat-mediated selection on traits in the direction of species differences during a drought in 2013, suggesting that spatially varying selection maintains species divergence. However, a relaxation in divergent selection on most traits in an unusually wet year (2019), including flowering time, which is involved in pre-zygotic isolation, suggests that temporal variation in selection may weaken species differences. Therefore, we find evidence that temporally and spatially varying selection may have opposing roles in mediating species boundaries. Given our changing climate, future growing seasons are expected to be more similar to the dry year, suggesting that in this system climate change may actually increase species divergence.},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Tataru et al. - 2023 - Spatially and temporally varying selection influen.pdf}
}

@article{tellezTraits2022,
  title = {Traits along the Leaf Economics Spectrum Are Associated with Communities of Foliar Endophytic Symbionts},
  author = {Tellez, Peter H. and Arnold, A. Elizabeth and Leo, Ashton B. and Kitajima, Kaoru and Van Bael, Sunshine A.},
  date = {2022-07-28},
  journaltitle = {Frontiers in Microbiology},
  shortjournal = {Front. Microbiol.},
  volume = {13},
  pages = {927780},
  issn = {1664-302X},
  doi = {lutzoni},
  url = {https://www.frontiersin.org/articles/10.3389/fmicb.2022.927780/full},
  urldate = {2023-05-29},
  abstract = {Leaf traits of plants worldwide are classified according to the Leaf Economics Spectrum (LES), which links leaf functional traits to evolutionary life history strategies. As a continuum ranging from thicker, tough leaves that are low in nitrogen (N) to thinner, softer, leaves that are high in N, the LES brings together physical, chemical, and ecological traits. Fungal endophytes are common foliar symbionts that occur in healthy, living leaves, especially in tropical forests. Their community composition often differs among co-occurring host species in ways that cannot be explained by environmental conditions or host phylogenetic relationships. Here, we tested the over-arching hypothesis that LES traits act as habitat filters that shape communities of endophytes both in terms of composition, and in terms of selecting for endophytes with particular suites of functional traits. We used culture-based and culture-free surveys to characterize foliar endophytes in mature leaves of 30 phylogenetically diverse plant species with divergent LES traits in lowland Panama, and then measured functional traits of dominant endophyte taxa in vitro . Endophytes were less abundant and less diverse in thick, tough, leaves compared to thin, softer, leaves in the same forest, even in closely related plants. Endophyte communities differed according to leaf traits, including leaf punch strength and carbon and nitrogen content. The most common endophyte taxa in leaves at different ends of the LES differ in their cellulase, protease, chitinase, and antipathogen activity. Our results extend the LES framework for the first time to diverse and ecologically important endophytes, opening new hypotheses regarding the degree to which foliar symbionts respond to, and extend, the functional traits of leaves they inhabit.},
  file = {/home/baponte/Zotero/storage/DIMZ3WWD/Tellez et al. - 2022 - Traits along the leaf economics spectrum are assoc.pdf}
}

@article{tristancordier2012,
  title = {Spatial Variability of Phyllosphere Fungal Assemblages: Genetic Distance Predominates over Geographic Distance in a {{European}} Beech Stand ({{Fagus}} Sylvatica)},
  author = {{Tristan Cordier} and Cordier, Tristan and {Cécile Robin} and Robin, Cécile and {Cécile Robin} and {Xavier Capdevielle} and Capdevielle, Xavier and {Marie‐Laure Desprez‐Loustau} and Desprez-Loustau, Marie-Laure and {Corinne Vacher} and Vacher, Corinne},
  date = {2012-10-01},
  journaltitle = {Fungal Ecology},
  volume = {5},
  number = {5},
  pages = {509--520},
  doi = {10.1016/j.funeco.2011.12.004},
  abstract = {Abstract   Despite being major drivers of the dynamics and diversity of plant populations and communities, the spatial variability of phyllosphere fungal assemblages has been seldom explored. We used CE-SSCP and 454 pyrosequencing to quantify the spatial variability of European beech phyllosphere fungal assemblages with a hierarchical sampling de#cluding four different spatial scales (tree, branch, group of leaves and individual leaf). Fungal assemblages were highly diverse, with high proportions of generalist and cosmopolitan fungi. The major part of the variability was at the smallest spatial scale, between individual leaves. Within a single tree canopy, dissimilarity between fungal assemblages generally increased with distance between leaves. This pattern may be driven by within-canopy gradients of leaf traits and microclimate. At the stand scale, dissimilarity between fungal assemblages was correlated with the genetic distance rather than the geographic distance between trees, consistent with the findings of community genetics studies. Our results were constant over a small simulated sequencing depth, providing opportunities for the design of large-scale studies addressing the relationship between the genetic variation of trees and the variation of associated phyllosphere fungal assemblages.},
  annotation = {MAG ID: 2096502675}
}

@article{tsukaya2005,
  title = {Leaf Shape: Genetic Controls and Environmental Factors},
  shorttitle = {Leaf Shape},
  author = {Tsukaya, Hirokazu},
  date = {2005},
  journaltitle = {The International Journal of Developmental Biology},
  shortjournal = {Int. J. Dev. Biol.},
  volume = {49},
  number = {5-6},
  pages = {547--555},
  issn = {0214-6282},
  doi = {10.1387/ijdb.041921ht},
  url = {http://www.intjdevbiol.com/paper.php?doi=041921ht},
  urldate = {2024-05-10},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Tsukaya - 2005 - Leaf shape genetic controls and environmental fac.pdf}
}

@article{tsukaya2013,
  title = {Leaf {{Development}}},
  author = {Tsukaya, Hirokazu},
  date = {2013-01},
  journaltitle = {The Arabidopsis Book},
  shortjournal = {The Arabidopsis Book},
  volume = {11},
  pages = {e0163},
  issn = {1543-8120},
  doi = {10.1199/tab.0163},
  url = {http://www.bioone.org/doi/abs/10.1199/tab.0163},
  urldate = {2024-05-07},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Tsukaya - 2013 - Leaf Development.pdf}
}

@incollection{tsukaya2018,
  title = {A {{Consideration}} of {{Leaf Shape Evolution}} in the {{Context}} of the {{Primary Function}} of the {{Leaf}} as a {{Photosynthetic Organ}}},
  booktitle = {The {{Leaf}}: {{A Platform}} for {{Performing Photosynthesis}}},
  author = {Tsukaya, Hirokazu},
  editor = {Adams Iii, William W. and Terashima, Ichiro},
  date = {2018},
  volume = {44},
  pages = {1--26},
  publisher = {Springer International Publishing},
  location = {Cham},
  doi = {10.1007/978-3-319-93594-2_1},
  url = {http://link.springer.com/10.1007/978-3-319-93594-2_1},
  urldate = {2024-05-07},
  isbn = {978-3-319-93592-8 978-3-319-93594-2},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Tsukaya - 2018 - A Consideration of Leaf Shape Evolution in the Con.pdf}
}

@article{twyford2015,
  title = {Adaptive Divergence in the Monkey Flower {{{\emph{Mimulus}}}}{\emph{ Guttatus}} Is Maintained by a Chromosomal Inversion},
  shorttitle = {Adaptive Divergence in the Monkey Flower {{{\emph{Mimulus}}}}{\emph{ Guttatus}} Is Maintained by a Chromosomal Inversion},
  author = {Twyford, Alex D. and Friedman, Jannice},
  date = {2015-06},
  journaltitle = {Evolution},
  shortjournal = {Evolution},
  volume = {69},
  number = {6},
  pages = {1476--1486},
  issn = {00143820},
  doi = {10.1111/evo.12663},
  url = {https://academic.oup.com/evolut/article/69/6/1476/6851903},
  urldate = {2024-04-08},
  langid = {english},
  file = {/home/baponte/Zotero/storage/NQZXY2QA/Twyford and Friedman - 2015 - Adaptive divergence in the monkey flower Mimulu.pdf}
}

@article{twyford2020,
  title = {Multi-Level Patterns of Genetic Structure and Isolation by Distance in the Widespread Plant {{{\emph{Mimulus}}}}{\emph{ Guttatus}}},
  author = {Twyford, Alex D and Wong, Edgar L Y},
  date = {2020},
  journaltitle = {Heredity},
  pages = {227--239},
  publisher = {Springer US},
  doi = {10.1038/s41437-020-0335-7},
  url = {http://dx.doi.org/10.1038/s41437-020-0335-7}
}

@article{urban2014,
  title = {Plasticity and Genetic Adaptation Mediate Amphibian and Reptile Responses to Climate Change.},
  author = {Urban, Mark C. and Richardson, Jonathan L. and Freidenfelds, Nicole A.},
  date = {2014-01-01},
  journaltitle = {Evolutionary Applications},
  volume = {7},
  number = {1},
  eprint = {24454550},
  eprinttype = {pmid},
  pages = {88--103},
  doi = {10.1111/eva.12114},
  abstract = {Phenotypic plasticity and genetic adaptation are predicted to mitigate some of the negative biotic consequences of climate change. Here, we evaluate evidence for plastic and evolutionary responses to climate variation in amphibians and reptiles via a literature review and meta-analysis. We included studies that either document phenotypic changes through time or space. Plasticity had a clear and ubiquitous role in promoting phenotypic changes in response to climate variation. For adaptive evolution, we found no direct evidence for evolution of amphibians or reptiles in response to climate change over time. However, we found many studies that documented adaptive responses to climate along spatial gradients. Plasticity provided a mixture of adaptive and maladaptive responses to climate change, highlighting that plasticity frequently, but not always, could ameliorate climate change. Based on our review, we advocate for more experiments that survey genetic changes through time in response to climate change. Overall, plastic and genetic variation in amphibians and reptiles could buffer some of the formidable threats from climate change, but large uncertainties remain owing to limited data.},
  pmcid = {3894900},
  annotation = {MAG ID: 2017384636}
}

@article{uren2017,
  title = {96 Well {{DNA Extraction Protocol}} for {{Plant}} and {{Lichen Tissue Stored}} in {{CTAB}}},
  author = {U'Ren, Jana M and Arnold, A Elizabeth},
  date = {2017},
  journaltitle = {protocols.io},
  pages = {1--5},
  doi = {dx.doi.org/10.17504/protocols.io.fscbnaw}
}

@book{vansteenis1981,
  title = {Rheophytes of the World : An Account of the Flood-Resistant Flowering Plants and Ferns and the Theory of Autonomous Evolution | {{WorldCat}}.Org},
  author = {family=Steenis, given=C. G. G. J., prefix=van, useprefix=true},
  date = {1981},
  publisher = {search.worldcat.org}
}

@article{vanwallendael2022,
  title = {Host Genotype Controls Ecological Change in the Leaf Fungal Microbiome},
  author = {VanWallendael, Acer and Benucci, Gian Maria Niccolo and Da Costa, Pedro Beschoren and Fraser, Linnea and Sreedasyam, Avinash and Fritschi, Felix and Juenger, Thomas E. and Lovell, John T. and Bonito, Gregory and Lowry, David B.},
  editor = {Dong, Xinnian},
  date = {2022-08-11},
  journaltitle = {PLOS Biology},
  shortjournal = {PLoS Biol},
  volume = {20},
  number = {8},
  pages = {e3001681},
  issn = {1545-7885},
  doi = {10.1371/journal.pbio.3001681},
  url = {https://dx.plos.org/10.1371/journal.pbio.3001681},
  urldate = {2023-09-26},
  abstract = {ALeUaf: fPulnegasaelcmonicfirrombtiohamtaelslhceandibngelefuvneldsarmereenptraelsdernivteedrcsoorrfehcotlsyt: plant success, as they contain pathogens that devastate crop plants and taxa that enhance nutrient uptake, discourage herbivory, and antagonize pathogens. We measured leaf fungal diversity with amplicon sequencing across an entire growing season in a diversity panel of switchgrass (Panicum virgatum). We also sampled a replicated subset of genotypes across 3 additional sites to compare the importance of time, space, ecology, and genetics. We found a strong successional pattern in the microbiome shaped both by host genetics and environmental factors. Further, we used genome-wide association (GWA) mapping and RNA sequencing to show that 3 cysteine-rich receptor-like kinases (crRLKs) were linked to a genetic locus associated with microbiome structure. We confirmed GWAS results in an independent set of genotypes for both the internal transcribed spacer (ITS) and large subunit (LSU) ribosomal DNA markers. Fungal pathogens were central to microbial covariance networks, and genotypes susceptible to pathogens differed in their expression of the 3 crRLKs, suggesting that host immune genes are a principal means of controlling the entire leaf microbiome.},
  langid = {english},
  file = {/home/baponte/Zotero/storage/ESHU8TSC/VanWallendael et al. - 2022 - Host genotype controls ecological change in the le.pdf}
}

@article{vickery1964,
  title = {{{BARRIERS TO GENE EXCHANGE BETWEEN MEMBERS OF THE}} {{{\emph{MIMULUS GUTTATUS}}}} {{COMPLEX}} ({{SCROPHULARIACEAE}})},
  author = {Vickery, Robert K.},
  date = {1964-03},
  journaltitle = {Evolution},
  shortjournal = {Evolution},
  volume = {18},
  number = {1},
  pages = {52--69},
  issn = {0014-3820, 1558-5646},
  doi = {10.1111/j.1558-5646.1964.tb01567.x},
  url = {https://academic.oup.com/evolut/article/18/1/52/6868492},
  urldate = {2024-05-02},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Vickery - 1964 - BARRIERS TO GENE EXCHANGE BETWEEN MEMBERS OF THE .pdf}
}

@incollection{vickery1978,
  title = {Case {{Studies}} in the {{Evolution}} of {{Species Complexes}} in {{{\emph{Mimulus}}}}},
  booktitle = {Evolutionary {{Biology}}},
  author = {Vickery, Robert K.},
  editor = {Hecht, Max K. and Steere, William C. and Wallace, Bruce},
  date = {1978},
  volume = {11},
  pages = {405--507},
  publisher = {Springer US},
  location = {Boston, MA},
  doi = {10.1007/978-1-4615-6956-5_7},
  url = {http://link.springer.com/10.1007/978-1-4615-6956-5_7},
  urldate = {2024-05-02},
  isbn = {978-1-4615-6958-9 978-1-4615-6956-5},
  langid = {english}
}

@article{villacampa2019,
  title = {Altitudinal Differences in Alpha, Beta and Functional Diversity of an Amphibian Community in a Biodiversity Hotspot},
  author = {Villacampa, Jaime and Whitworth, Andrew and Allen, Laura and Malo, Juan E.},
  date = {2019-01-01},
  journaltitle = {Neotropical Biodiversity},
  shortjournal = {Neotropical Biodiversity},
  volume = {5},
  number = {1},
  pages = {60--68},
  issn = {2376-6808},
  doi = {10.1080/23766808.2019.1659022},
  url = {https://www.tandfonline.com/doi/full/10.1080/23766808.2019.1659022},
  urldate = {2024-03-20},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Villacampa et al. - 2019 - Altitudinal differences in alpha, beta and functio.pdf}
}

@article{vorholt2012,
  title = {Microbial Life in the Phyllosphere},
  author = {Vorholt, Julia A.},
  date = {2012-12},
  journaltitle = {Nature Reviews Microbiology},
  shortjournal = {Nat Rev Microbiol},
  volume = {10},
  number = {12},
  pages = {828--840},
  issn = {1740-1526, 1740-1534},
  doi = {10.1038/nrmicro2910},
  url = {https://www.nature.com/articles/nrmicro2910},
  urldate = {2024-04-14},
  langid = {english},
  file = {/home/baponte/Zotero/storage/VMZ45TJF/Vorholt - 2012 - Microbial life in the phyllosphere.pdf}
}

@article{vujanovic2021,
  title = {Tremellomycetes {{Yeasts}} in {{Kernel Ecological Niche}}: {{Early Indicators}} of {{Enhanced Competitiveness}} of {{Endophytic}} and {{Mycoparasitic Symbionts}} against {{Wheat Pathobiota}}},
  shorttitle = {Tremellomycetes {{Yeasts}} in {{Kernel Ecological Niche}}},
  author = {Vujanovic, Vladimir},
  date = {2021-04-30},
  journaltitle = {Plants},
  shortjournal = {Plants},
  volume = {10},
  number = {5},
  pages = {905},
  issn = {2223-7747},
  doi = {10.3390/plants10050905},
  url = {https://www.mdpi.com/2223-7747/10/5/905},
  urldate = {2024-03-20},
  abstract = {Tremellomycetes rDNA sequences previously detected in wheat kernels by MiSeq were not reliably assigned to a genus or clade. From comparisons of ribosomal internal transcribed spacer region (ITS) and subsequent phylogenetic analyses, the following three basidiomycetous yeasts were resolved and identified: Vishniacozymavictoriae, V. tephrensis, and an undescribed Vishniacozyma rDNA variant. The Vishniacozyma variant’s clade is evolutionarily close to, but phylogenetically distinct from, the V. carnescens clade. These three yeasts were discovered in wheat kernel samples from the Canadian prairies. Variations in relative Vishniacozyma species abundances coincided with altered wheat kernel weight, as well as host resistance to chemibiotrophic Tilletia (Common bunt—CB) and necrotrophic Fusarium (Fusarium head blight—FHB) pathogens. Wheat kernel weight was influenced by the coexistence of Vishniacozyma with endophytic plant growth-promoting and mycoparasitic biocontrol fungi that were acquired by plants. Kernels were coated with beneficial Penicillium endophyte and Sphaerodes mycoparasite, each of which had different influences on the wild yeast population. Its integral role in the kernel microbiome renders Vishniacozyma a measurable indicator of the microbiome–plant interaction. The ability of NGS technology to detect specific endophytic DNA variants and early changes in dynamics among symbionts within the kernel ecological niche enables the prediction of crop disease emergence, suggesting that advanced microbiological testing may be a potentially useful tool for both phytoprotection and more efficient wheat breeding programs.},
  langid = {english},
  file = {/home/baponte/Zotero/storage/IGDFG8C4/Vujanovic - 2021 - Tremellomycetes Yeasts in Kernel Ecological Niche.pdf}
}

@article{wang2006,
  title = {Phylogenetic Distribution and Evolution of Mycorrhizas in Land Plants},
  author = {Wang, B. and Qiu, Y.-L.},
  date = {2006-07},
  journaltitle = {Mycorrhiza},
  shortjournal = {Mycorrhiza},
  volume = {16},
  number = {5},
  pages = {299--363},
  issn = {0940-6360, 1432-1890},
  doi = {10.1007/s00572-005-0033-6},
  url = {http://link.springer.com/10.1007/s00572-005-0033-6},
  urldate = {2024-05-02},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Wang and Qiu - 2006 - Phylogenetic distribution and evolution of mycorrh.pdf}
}

@article{wang2022,
  title = {The Cellular Basis for Synergy between {{RCO}} and {{KNOX1}} Homeobox Genes in Leaf Shape Diversity},
  author = {Wang, Yi and Strauss, Sören and Liu, Shanda and Pieper, Bjorn and Lymbouridou, Rena and Runions, Adam and Tsiantis, Miltos},
  date = {2022-09},
  journaltitle = {Current Biology},
  shortjournal = {Current Biology},
  volume = {32},
  number = {17},
  pages = {3773-3784.e5},
  issn = {09609822},
  doi = {10.1016/j.cub.2022.08.020},
  url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982222012970},
  urldate = {2024-05-13},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Wang et al. - 2022 - The cellular basis for synergy between RCO and KNO.pdf}
}

@article{wemheuer2019,
  title = {Deciphering Bacterial and Fungal Endophyte Communities in Leaves of Two Maple Trees with Green Islands},
  author = {Wemheuer, Franziska and Wemheuer, Bernd and Daniel, Rolf and Vidal, Stefan},
  date = {2019-10-02},
  journaltitle = {Scientific Reports},
  shortjournal = {Sci Rep},
  volume = {9},
  number = {1},
  pages = {14183},
  issn = {2045-2322},
  doi = {10.1038/s41598-019-50540-2},
  url = {https://www.nature.com/articles/s41598-019-50540-2},
  urldate = {2024-03-19},
  abstract = {Abstract                            Green islands (the re-greening of senescent leaf tissues) are particularly evident on leaves infected with fungal pathogens. To date, there is only a limited number of studies investigating foliar endophytic microorganisms in phytopathogen-infected leaves. Here, we analysed bacterial and fungal endophyte communities in leaves without green islands (control leaves; CL), within green island areas (GLA) and the surrounding yellow leaf areas (YLA) of leaves with green islands of               Acer campestre               and               A. platanoides               . GLA samples of               A. campestre               and               A. platanoides               were dominated by               Sawadaea polyfida               and               S. bicornis               , respectively, suggesting that these fungi might be responsible for the green islands. We detected a higher fungal richness and diversity in CL compared to GLA samples of               A. campestre               . Leaf status (CL, GLA, YLA) significantly altered the composition of fungal communities of               A. campestre               . This was related to differences in fungal community composition between YLA and GLA samples. Site was the main driver of bacterial communities, suggesting that bacterial and fungal endophytes are shaped by different factors. Overall, we observed               Acer               species-specific responses of endophyte communities towards the presence of green islands and/or leaf type, which might be attributed to several fungi and bacteria specifically associated with one               Acer               species.},
  langid = {english},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Wemheuer et al. - 2019 - Deciphering bacterial and fungal endophyte communi.pdf}
}

@article{willis1993,
  title = {Fitness Components in {{{\emph{Mimulus}}}}{\emph{ Guttatus}}},
  author = {Willis, John H},
  date = {1993},
  volume = {47},
  number = {3},
  pages = {864--876},
  keywords = {- dominance,epistasis,fitness components,inbreeding depression,mimulus,syner-}
}

@article{wright2004,
  title = {The Worldwide Leaf Economics Spectrum},
  author = {Wright, Ian J and Reich, Peter B and Westoby, Mark and Ackerly, David D and Baruch, Zdravko and Bongers, Frans and Cavender-Bares, Jeannine and Chapin, Terry and Cornelissen, Johannes H C and Diemer, Matthias and Flexas, Jaume and Garnier, Eric and Groom, Philip K and Gulias, Javier and Hikosaka, Kouki and Lamont, Byron B and Lee, Tali and Lee, William and Lusk, Christopher and Midgley, Jeremy J and Navas, Marie-Laure and Niinemets, Ülo and Oleksyn, Jacek and Osada, Noriyuki and Poorter, Hendrik and Poot, Pieter and Prior, Lynda and Pyankov, Vladimir I and Roumet, Catherine and Thomas, Sean C and Tjoelker, Mark G and Veneklaas, Erik J and Villar, Rafael},
  date = {2004},
  journaltitle = {Nature},
  volume = {428},
  number = {6985},
  pages = {821--827},
  doi = {10.1038/nature02403},
  url = {https://doi.org/10.1038/nature02403},
  abstract = {Bringing together leaf trait data spanning 2,548 species and 175 sites we describe, for the first time at global scale, a universal spectrum of leaf economics consisting of key chemical, structural and physiological properties. The spectrum runs from quick to slow return on investments of nutrients and dry mass in leaves, and operates largely independently of growth form, plant functional type or biome. Categories along the spectrum would, in general, describe leaf economic variation at the global scale better than plant functional types, because functional types overlap substantially in their leaf traits. Overall, modulation of leaf traits and trait relationships by climate is surprisingly modest, although some striking and significant patterns can be seen. Reliable quantification of the leaf economics spectrum and its interaction with climate will prove valuable for modelling nutrient fluxes and vegetation boundaries under changing land-use and climate.},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Wright et al. - 2004 - The worldwide leaf economics spectrum.pdf}
}

@article{wu2008,
  title = {\emph{Mimulus} Is an Emerging Model System for the Integration of Ecological and Genomic Studies},
  author = {Wu, C. A. and Lowry, D. B. and Cooley, A. M. and Wright, K. M. and Lee, Y. W. and Willis, J. H.},
  date = {2008},
  journaltitle = {Heredity},
  volume = {100},
  number = {2},
  pages = {220--230},
  doi = {10.1038/sj.hdy.6801018},
  abstract = {The plant genus Mimulus is rapidly emerging as a model system for studies of evolutionary and ecological functional genomics. Mimulus contains a wide array of phenotypic, ecological and genomic diversity. Numerous studies have proven the experimental tractability of Mimulus in laboratory and field studies. Genomic resources currently under development are making Mimulus an excellent system for determining the genetic and genomic basis of adaptation and speciation. Here, we introduce some of the phenotypic and genetic diversity in the genus Mimulus and highlight how direct genetic studies with Mimulus can address a wide spectrum of ecological and evolutionary questions. In addition, we present the genomic resources currently available for Mimulus and discuss future directions for research. The integration of ecology and genetics with bioinformatics and genome technology offers great promise for exploring the mechanistic basis of adaptive evolution and the genetics of speciation.},
  keywords = {adaptation,Adaptation,ecological and evolutionary functional,ecological genetics,Ecological genetics,eefg,floral evolution,Floral evolution,genomics,is to understand both,maintain genomic and pheno-,mimulus guttatus,Mimulus guttatus,mimulus lewisii,Mimulus lewisii,processes that create and,speciation,Speciation,the broad goal of,the evolutionary},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Wu et al. - 2008 - Mimulus is an emerging model system for the integr.pdf}
}

@article{wu2010,
  title = {Natural Variation for Drought-Response Traits in the {{{\emph{Mimulus}}}}{\emph{ Guttatus}} Species Complex},
  author = {Wu, Carrie A and Lowry, David B and Nutter, Laura I and Willis, John H},
  date = {2010},
  journaltitle = {Oecologia},
  number = {162},
  pages = {23--33},
  doi = {10.1007/s00442-009-1448-0},
  keywords = {dehydration avoidance,drought escape,flowering time,monkey x owers,water de w cit},
  file = {/home/baponte/Boxx/Dissertation/master_papers/Wu et al. - 2010 - Natural variation for drought-response traits in t.pdf}
}

@article{xiong2019,
  title = {The {{Diverse Roles}} of {{Auxin}} in {{Regulating Leaf Development}}},
  author = {Xiong, Yuanyuan and Jiao, Yuling},
  date = {2019-07-23},
  journaltitle = {Plants},
  shortjournal = {Plants},
  volume = {8},
  number = {7},
  pages = {243},
  issn = {2223-7747},
  doi = {10.3390/plants8070243},
  url = {https://www.mdpi.com/2223-7747/8/7/243},
  urldate = {2024-05-13},
  abstract = {Leaves, the primary plant organs that function in photosynthesis and respiration, have highly organized, flat structures that vary within and among species. In recent years, it has become evident that auxin plays central roles in leaf development, including leaf initiation, blade formation, and compound leaf patterning. In this review, we discuss how auxin maxima form to define leaf primordium formation. We summarize recent progress in understanding of how spatial auxin signaling promotes leaf blade formation. Finally, we discuss how spatial auxin transport and signaling regulate the patterning of compound leaves and leaf serration.},
  langid = {english},
  file = {/home/baponte/Zotero/storage/VEK5F6WM/Xiong and Jiao - 2019 - The Diverse Roles of Auxin in Regulating Leaf Deve.pdf}
}

@article{yates2023,
  title = {Cross Validation for Model Selection: {{A}} Review with Examples from Ecology},
  shorttitle = {Cross Validation for Model Selection},
  author = {Yates, Luke A. and Aandahl, Zach and Richards, Shane A. and Brook, Barry W.},
  date = {2023-02},
  journaltitle = {Ecological Monographs},
  shortjournal = {Ecological Monographs},
  volume = {93},
  number = {1},
  pages = {e1557},
  issn = {0012-9615, 1557-7015},
  doi = {10.1002/ecm.1557},
  url = {https://esajournals.onlinelibrary.wiley.com/doi/10.1002/ecm.1557},
  urldate = {2024-06-25},
  abstract = {Abstract                            Specifying, assessing, and selecting among candidate statistical models is fundamental to ecological research. Commonly used approaches to model selection are based on predictive scores and include information criteria such as Akaike's information criterion, and cross validation. Based on data splitting, cross validation is particularly versatile because it can be used even when it is not possible to derive a likelihood (e.g., many forms of machine learning) or count parameters precisely (e.g., mixed‐effects models). However, much of the literature on cross validation is technical and spread across statistical journals, making it difficult for ecological analysts to assess and choose among the wide range of options. Here we provide a comprehensive, accessible review that explains important—but often overlooked—technical aspects of cross validation for model selection, such as: bias correction, estimation uncertainty, choice of scores, and selection rules to mitigate overfitting. We synthesize the relevant statistical advances to make recommendations for the choice of cross‐validation technique and we present two ecological case studies to illustrate their application. In most instances, we recommend using exact or approximate leave‐one‐out cross validation to minimize bias, or otherwise               k               ‐fold with bias correction if               k               \,{$<$}\,10. To mitigate overfitting when using cross validation, we recommend calibrated selection via our recently introduced modified one‐standard‐error rule. We advocate for the use of predictive scores in model selection across a range of typical modeling goals, such as exploration, hypothesis testing, and prediction, provided that models are specified in accordance with the stated goal. We also emphasize, as others have done, that inference on parameter estimates is biased if preceded by model selection and instead requires a carefully specified single model or further technical adjustments.},
  langid = {english},
  file = {/home/baponte/Box/Dissertation/master_papers/Yates et al. - 2023 - Cross validation for model selection A review wit.pdf}
}

@article{yuan2019,
  title = {Monkeyflowers ({{{\emph{Mimulus}}}}): {{New}} Model for Plant Developmental Genetics and Evo-Devo},
  author = {Yuan, Yao Wu},
  date = {2019},
  journaltitle = {New Phytologist},
  volume = {222},
  number = {2},
  pages = {694--700},
  doi = {10.1111/nph.15560},
  abstract = {(Table presented.). Summary: Monkeyflowers (Mimulus) have long been recognized as a classic ecological and evolutionary model system. However, only recently has it been realized that this system also holds great promise for studying the developmental genetics and evo-devo of important plant traits that are not found in well-established model systems such as Arabidopsis. Here, I review recent progress in four different areas of plant research enabled by this new model, including transcriptional regulation of carotenoid biosynthesis, formation of periodic pigmentation patterns, developmental genetics of corolla tube formation and elaboration, and the molecular basis of floral trait divergence underlying pollinator shift. These examples suggest that Mimulus offers ample opportunities to make exciting discoveries in plant development and evolution.},
  keywords = {carotenoids,corolla tube,floral trait,in planta transformation,monkeyflowers (Mimulus),mutagenesis,periodic pigmentation pattern}
}