Phylocom: software for the analysis of phylogenetic community structure and trait evolution.
Reads0
Chats0
TLDR
Phylocom calculates numerous metrics of phylogenetic community structure and trait similarity within communities and measures phylogenetic signal and correlated evolution for species traits.Abstract:
Motivation: The increasing availability of phylogenetic and trait data for communities of co-occurring species has created a need for software that integrates ecological and evolutionary analyses. Capabilities: Phylocom calculates numerous metrics of phylogenetic community structure and trait similarity within communities. Hypothesis testing is implemented using several null models. Within the same framework, it measures phylogenetic signal and correlated evolution for species traits. A range of utility functions allow community and phylogenetic data manipulation, tree and trait generation, and integration into scientific workflows. Availability: Open source at: http://phylodiversity.net/phylocom/read more
Citations
More filters
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
TL;DR: 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.
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
A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses
Ryan T. Jones,Michael S. Robeson,Christian L. Lauber,Micah Hamady,Rob Knight,Noah Fierer,Noah Fierer +6 more
TL;DR: Acidobacteria communities were more phylogenetically clustered as soil pH departed from neutrality, suggesting that pH is an effective habitat filter, restricting community membership to progressively more narrowly defined lineages as pH deviates from neutrality.
Journal ArticleDOI
Plant-Pollinator Interactions over 120 Years: Loss of Species, Co-Occurrence and Function
TL;DR: Using historic data sets, the degree to which global change over 120 years disrupted plant-pollinator interactions in a temperate forest understory community in Illinois, USA is quantified and it is suggested that networks will be less resilient to future changes.
Journal ArticleDOI
Functional traits and the growth–mortality trade-off in tropical trees
S. Joseph Wright,Kaoru Kitajima,Kaoru Kitajima,Nathan J. B. Kraft,Peter B. Reich,Ian J. Wright,Daniel E. Bunker,Richard Condit,James W. Dalling,James W. Dalling,Stuart J. Davies,Sandra Díaz,Bettina M. J. Engelbrecht,Bettina M. J. Engelbrecht,Kyle E. Harms,Kyle E. Harms,Stephen P. Hubbell,Stephen P. Hubbell,Christian O. Marks,Maria C. Ruiz-Jaen,Cristina M. Salvador,Amy E. Zanne +21 more
TL;DR: A trade-off between growth and mortality rates characterizes tree species in closed canopy forests and a growing consensus that seed mass, leaf mass per area, wood density, and maximum height are key traits among forest trees is agreed.
References
More filters
Journal ArticleDOI
Phylogenies and the Comparative Method
TL;DR: A method of correcting for the phylogeny has been proposed, which specifies a set of contrasts among species, contrasts that are statistically independent and can be used in regression or correlation studies.
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.
Journal ArticleDOI
Testing for phylogenetic signal in comparative data: behavioral traits are more labile.
TL;DR: Analysis of variance of log K for all 121 traits indicated that behavioral traits exhibit lower signal than body size, morphological, life-history, or physiological traits, and this work presents new methods for continuous-valued characters that can be implemented with either phylogenetically independent contrasts or generalized least-squares models.
Journal ArticleDOI
Phylogenies and Community Ecology
TL;DR: A common pattern of phylogenetic conservatism in ecological character is recognized and the challenges of using phylogenies of partial lineages are highlighted and phylogenetic approaches to three emergent properties of communities: species diversity, relative abundance distributions, and range sizes are reviewed.
Journal ArticleDOI
Procedures for the Analysis of Comparative Data Using Phylogenetically Independent Contrasts
TL;DR: In this article, the authors discuss the application of Felsenstein's (1985, Am. Nat. 125: 1n15) procedures to test for correlated evolution of continuous traits.