Journal ArticleDOI
Picante: R tools for integrating phylogenies and ecology
Steven W. Kembel,Peter Cowan,Matthew R. Helmus,William K. Cornwell,Hélène Morlon,David D. Ackerly,Simon P. Blomberg,Campbell O. Webb +7 more
TLDR
Picante is a software package that provides a comprehensive set of tools for analyzing the phylogenetic and trait diversity of ecological communities and performs tests for phylogenetic signal in trait distributions, community structure and species interactions.Abstract:
Summary: Picante is a software package that provides a comprehensive set of tools for analyzing the phylogenetic and trait diversity of ecological communities. The package calculates phylogenetic diversity metrics, performs trait comparative analyses, manipulates phenotypic and phylogenetic data, and performs tests for phylogenetic signal in trait distributions, community structure and species interactions. Availability: Picante is a package for the R statistical language and environment written in R and C, released under a GPL v2 open-source license, and freely available on the web (http://picante .r-forge.r-project.org) and from CRAN (http://cran.r-project.org).read more
Citations
More filters
Journal ArticleDOI
phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data.
Paul J. McMurdie,Susan Holmes +1 more
TL;DR: The phyloseq project for R is a new open-source software package dedicated to the object-oriented representation and analysis of microbiome census data in R, which supports importing data from a variety of common formats, as well as many analysis techniques.
Journal ArticleDOI
Discriminant analysis of principal components: a new method for the analysis of genetically structured populations
TL;DR: The Discriminant Analysis of Principal Components (DAPC) is introduced, a multivariate method designed to identify and describe clusters of genetically related individuals that performs generally better than STRUCTURE at characterizing population subdivision.
Journal ArticleDOI
Stochastic Community Assembly: Does It Matter in Microbial Ecology?
TL;DR: Both stochastic and deterministic components embedded in various ecological processes, including selection, dispersal, diversification, and drift are described.
Journal ArticleDOI
An Update of Wallace’s Zoogeographic Regions of the World
Ben G. Holt,Jean-Philippe Lessard,Michael K. Borregaard,Susanne A. Fritz,Miguel B. Araújo,Miguel B. Araújo,Miguel B. Araújo,Dimitar Dimitrov,Pierre-Henri Fabre,Catherine H. Graham,Gary R. Graves,Gary R. Graves,Knud A. Jønsson,David Nogués-Bravo,Zhiheng Wang,Robert J. Whittaker,Robert J. Whittaker,Jon Fjeldså,Carsten Rahbek +18 more
TL;DR: A global map of zoogeographic regions is generated by combining data on the distributions and phylogenetic relationships of 21,037 species of amphibians, birds, and mammals, and it is shown that spatial turnover in the phylogenetic composition of vertebrate assemblages is higher in the Southern than in the Northern Hemisphere.
Journal ArticleDOI
How to measure and test phylogenetic signal
Tamara Münkemüller,Sébastien Lavergne,Bruno Bzeznik,Stéphane Dray,Thibaut Jombart,Katja Schiffers,Wilfried Thuiller +6 more
TL;DR: Phylogenetic signal is the tendency of related species to resemble each other more than species drawn at random from the same tree and various indices have been proposed for quantifying it.
References
More filters
Journal ArticleDOI
APE: Analyses of Phylogenetics and Evolution in R language
TL;DR: UNLABELLED Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evolution and phylogenetics that provides both utility functions for reading and writing data and manipulating phylogenetic trees.
Journal ArticleDOI
UniFrac: a New Phylogenetic Method for Comparing Microbial Communities
Catherine A. Lozupone,Rob Knight +1 more
TL;DR: The results illustrate that UniFrac provides a new way of characterizing microbial communities, using the wealth of environmental rRNA sequences, and allows quantitative insight into the factors that underlie the distribution of lineages among environments.
Journal ArticleDOI
Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness
TL;DR: A series of common pitfalls in quantifying and comparing taxon richness are surveyed, including category‐subcategory ratios (species-to-genus and species-toindividual ratios) and rarefaction methods, which allow for meaningful standardization and comparison of datasets.
Journal ArticleDOI
Conservation evaluation and phylogenetic diversity
TL;DR: Calculation of PD for different population subsets shows that protection of populations at either of two extremes of the geographic range of the group can significantly increase the phylogenetic diversity that is protected.
Related Papers (5)
APE: Analyses of Phylogenetics and Evolution in R language
QIIME allows analysis of high-throughput community sequencing data.
J. Gregory Caporaso,Justin Kuczynski,Jesse Stombaugh,Kyle Bittinger,Frederic D. Bushman,Elizabeth K. Costello,Noah Fierer,Antonio Gonzalez Peña,Julia K. Goodrich,Jeffrey I. Gordon,Gavin A. Huttley,Scott T. Kelley,Dan Knights,Jeremy E. Koenig,Ruth E. Ley,Catherine A. Lozupone,Daniel McDonald,Brian D. Muegge,Meg Pirrung,Jens Reeder,Joel Sevinsky,Peter J. Turnbaugh,William A. Walters,Jeremy Widmann,Tanya Yatsunenko,Jesse R. Zaneveld,Rob Knight,Rob Knight +27 more