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pages = {1410.0846v1},
doi = {},
url = {http://arxiv.org/abs/1410.0846v1 http://arxiv.org/pdf/1410.0846v1},
keywords = {}
}
@manual{renv,
title = {renv: Project Environments},
author = {Kevin Ushey},
year = 2021,
url = {https://rstudio.github.io/renv/},
note = {R package version 0.14.0}
}
@article{sf,
title = {{Simple Features for R: Standardized Support for Spatial Vector Data}},
author = {Edzer Pebesma},
year = 2018,
journal = {{The R Journal}},
volume = 10,
number = 1,
pages = {439--446},
doi = {10.32614/RJ-2018-009},
url = {https://doi.org/10.32614/RJ-2018-009}
}
@article{ggmap,
title = {ggmap: Spatial Visualization with ggplot2},
author = {David Kahle and Hadley Wickham},
year = 2013,
journal = {The R Journal},
volume = 5,
number = 1,
pages = {144--161},
url = {https://journal.r-project.org/archive/2013-1/kahle-wickham.pdf}
}
@article{Rodriguez2009,
title = {Fungal endophytes: diversity and functional roles},
author = {Rodriguez, R. J. and White Jr, J. F. and Arnold, A. E. and Redman, R. S.},
year = 2009,
journal = {New Phytologist},
volume = 182,
number = 2,
pages = {314--330},
doi = {https://doi.org/10.1111/j.1469-8137.2009.02773.x},
url = {https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/j.1469-8137.2009.02773.x},
keywords = {fungal taxonomy, habitat adapted symbiosis, mutualism, plant-fungal interactions, symbiosis, symbiotic continuum},
eprint = {https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1469-8137.2009.02773.x}
}
@article{Oono2020,
title = {Species diversity of fungal endophytes across a stress gradient for plants},
author = {Oono, Ryoko and Black, Danielle and Slessarev, Eric and Sickler, Burton and Strom, Amanda and Apigo, Austen},
year = 2020,
journal = {New Phytologist},
volume = 228,
number = 1,
pages = {210--225},
doi = {https://doi.org/10.1111/nph.16709},
url = {https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.16709},
keywords = {endophytes, nitrogen, phenolics, Pinus muricata, resource availability, sodium, species richness, Vaccinium ovatum},
eprint = {https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.16709},
abstract = {Summary Foliar fungal endophytes are one of the most diverse guilds of symbiotic fungi found in the photosynthetic tissues of every plant lineage, but it is unclear how plant environments and leaf resource availability shape their diversity. We explored correlations between leaf nutrient availability and endophyte diversity among Pinus muricata and Vaccinium ovatum plants growing across a soil nutrient gradient spanning a series of coastal terraces in Mendocino, California. Endophyte richness decreased in plants with higher leaf nitrogen-to-phosphorus ratios for both host species, but increased with sodium, which may be toxic to fungi at high concentrations. Isolation frequency, a proxy of fungal biomass, was not significantly predicted by any of the same leaf constituents in the two plant species. We propose that stressed plants can exhibit both low foliar nutrients or high levels of toxic compounds, and that both of these stress responses predict endophyte species richness. Stressful conditions that limit growth of fungi may increase their diversity due to the suppression of otherwise dominating species. Differences between the host species in their endophyte communities may be explained by host specificity, leaf phenology, or microclimates.}
}
@article{darcy2020,
title = {Fungal communities living within leaves of native Hawaiian dicots are structured by landscape-scale variables as well as by host plants.},
author = {Darcy, JL and Swift, SOI and Cobian, GM and Zahn, GL and Perry, BA and Amend, AS},
year = 2020,
journal = {Mol Ecol},
location = {Department of Botany, University of Hawaii, Honolulu, HI, USA. Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA. Department of Botany, University of Hawaii, Honolulu, HI, USA. Department of Botany, University of Hawaii, Honolulu, HI, USA. Department of Biological Sciences, California State University Chico, Chico, CA, USA. Department of Biology, Utah Valley University, Orem, UT, USA. Department of Biological Sciences, California State University East Bay, Hayward, CA, USA. Department of Botany, University of Hawaii, Honolulu, HI, USA.},
volume = 29,
number = 16,
pages = {3103–3116},
doi = {10.1111/mec.15544},
url = {https://pubmed.ncbi.nlm.nih.gov/32640084},
abstract = {A phylogenetically diverse array of fungi live within healthy leaf tissue of dicotyledonous plants. Many studies have examined these endophytes within a single plant species and/or at small spatial scales, but landscape-scale variables that determine their community composition are not well understood, either across geographic space, across climatic conditions, or in the context of host plant phylogeny. Here, we evaluate the contributions of these variables to endophyte beta diversity using a survey of foliar endophytic fungi in native Hawaiian dicots sampled across the Hawaiian archipelago. We used Illumina technology to sequence fungal ITS1 amplicons to characterize foliar endophyte communities across five islands and 80 host plant genera. We found that communities of foliar endophytic fungi showed strong geographic structuring between distances of 7 and 36 km. Endophyte community structure was most strongly associated with host plant phylogeny and evapotranspiration, and was also significantly associated with NDVI, elevation and solar radiation. Additionally, our bipartite network analysis revealed that the five islands we sampled each harboured significantly specialized endophyte communities. These results demonstrate how the interaction of factors at large and small spatial and phylogenetic scales shapes fungal symbiont communities.}
}
@article{uren2019,
title = {Host availability drives distributions of fungal endophytes in the imperilled boreal realm.},
author = {U'Ren, JM and Lutzoni, F and Miadlikowska, J and Zimmerman, NB and Carbone, I and May, G and Arnold, AE},
year = 2019,
journal = {Nat Ecol Evol},
location = {Department of Biosystems Engineering and BIO5 Institute, University of Arizona, Tucson, AZ, USA. Department of Biology, Duke University, Durham, NC, USA. Department of Biology, Duke University, Durham, NC, USA. Department of Biology, University of San Francisco, San Francisco, CA, USA. Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA. Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, USA. School of Plant Sciences, University of Arizona, Tucson, AZ, USA. [email protected]. Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA. [email protected].},
volume = 3,
number = 10,
pages = {1430–1437},
doi = {10.1038/s41559-019-0975-2},
url = {https://www.ncbi.nlm.nih.gov/pubmed/31548643},
abstract = {Boreal forests represent the world’s largest terrestrial biome and provide ecosystem services of global importance. Highly imperilled by climate change, these forests host Earth’s greatest phylogenetic diversity of endophytes, a hyperdiverse group of symbionts that are defined by their occurrence within living, symptomless plant and lichen tissues. Endophytes shape the ecological and evolutionary trajectories of plants and are therefore key to the function and resilience of terrestrial ecosystems. A critical step in linking the ecological functions of endophytes with those of their hosts is to understand the distributions of these symbionts at the global scale; however, turnover in host taxa with geography and climate can confound insights into endophyte biogeography. As a result, global drivers of endophyte diversity and distributions are not known. Here, we leverage sampling from phylogenetically diverse boreal plants and lichens across North America and Eurasia to show that host filtering in distinctive environments, rather than turnover with geographical or environmental distance, is the main determinant of the community composition and diversity of endophytes. We reveal the distinctiveness of boreal endophytes relative to soil fungi worldwide and endophytes from diverse temperate biomes, highlighting a high degree of global endemism. Overall, the distributions of endophytes are directly linked to the availability of compatible hosts, highlighting the role of biotic interactions in shaping fungal communities across large spatial scales, and the threat that climate change poses to biological diversity and function in the imperilled boreal realm.}
}
@Article{chao1987a,
author = {Chao, Anne},
title = {Estimating the Population-Size for Capture Recapture Data with Unequal Catchability},
journal = {Biometrics},
volume = {43},
number = {4},
pages = {783–791},
year = {1987},
doi = {10.2307/2531532},
}
@Article{chiu2014a,
author = {Chiu, CH and Wang, YT and Walther, BA and Chao, A},
title = {An improved nonparametric lower bound of species richness via a modified good-turing frequency formula.},
journal = {Biometrics},
volume = {70},
number = {3},
pages = {671–682},
year = {2014},
abstract = {It is difficult to accurately estimate species richness if there are many almost undetectable species in a hyper-diverse community. Practically, an accurate lower bound for species richness is preferable to an inaccurate point estimator. The traditional nonparametric lower bound developed by Chao (1984, Scandinavian Journal of Statistics 11, 265-270) for individual-based abundance data uses only the information on the rarest species (the numbers of singletons and doubletons) to estimate the number of undetected species in samples. Applying a modified Good-Turing frequency formula, we derive an approximate formula for the first-order bias of this traditional lower bound. The approximate bias is estimated by using additional information (namely, the numbers of tripletons and quadrupletons). This approximate bias can be corrected, and an improved lower bound is thus obtained. The proposed lower bound is nonparametric in the sense that it is universally valid for any species abundance distribution. A similar type of improved lower bound can be derived for incidence data. We test our proposed lower bounds on simulated data sets generated from various species abundance models. Simulation results show that the proposed lower bounds always reduce bias over the traditional lower bounds and improve accuracy (as measured by mean squared error) when the heterogeneity of species abundances is relatively high. We also apply the proposed new lower bounds to real data for illustration and for comparisons with previously developed estimators.},
location = {Institute of Statistics, National Tsing Hua University, Hsin-Chu 30043, Taiwan. Master Program in Global Health and Development, College of Public Health and Nutrition, Taipei Medical University, 250 Wu-Hsing St., Taipei 110, Taiwan. Institute of Statistics, National Tsing Hua University, Hsin-Chu 30043, Taiwan.},
doi = {10.1111/biom.12200},
url = {https://pubmed.ncbi.nlm.nih.gov/24945937},
}