Virtual Issue: Advances in Phylogenetic Methods

Edited by Jana Vamosi
June 2015

Original Image ©PLOS One PhylogenyMethods in Ecology and Evolution has recently celebrated its 5th Anniversary. We continue to bring together research in ecology and evolution, and provide a unique platform for authors developing new methods. For Evolution 2015, this Virtual Issue highlights some of the papers in the exciting field of phylogenetics published in the past year or so.

Our Applications and Research articles include papers that describe methods for incorporating phylogenetic analyses in ecological and evolutionary studies. Applications papers introduce new tools for research, which provide practitioners with an important source of information and background on the tools they use. In this Virtual Issue we have highlighted the newest Applications papers that describe how phylogenetic methods are contributing to the fields of ecology and evolution. These include tools with aims as diverse as phylogenetic tree reconstruction and analysing phylogenetic diversity in communities. All Applications papers are free to access.

The Research papers we have highlighted include excellent examples of new ways that phylogenies can be applied to central questions in ecology, evolution and biodiversity, such as measuring niche conservatism, trait evolution and diversification rates. We also include barcoding methods, which increasingly are used to understand phylogenetic and functional diversity.

An understanding of the tree of life contributes to many facets of biology. This Virtual Issue has assembled studies that showcase the breadth of the utility of phylogenetic trees, including phylogenetic beta diversity, trait evolution, diversification, biodiversity studies, phylogenetic signal, biogeography, ecosystem functioning, and host-pathogen dynamics.

Jana Vamosi, Senior Editor

Research Articles

A simple measure of the strength of convergent evolution
Kevin Arbuckle, Cheryl M. Bennett and Michael P. Speed

Node-based analysis of species distributions
Michael K. Borregaard, Carsten Rahbek, Jon Fjeldså, Juan L. Parra, Robert J. Whittaker and Catherine H. Graham

A new frontier in biodiversity inventory: a proposal for estimators of phylogenetic and functional diversity
Pedro Cardoso, François Rigal, Paulo A. V. Borges and José C. Carvalho

Decomposing changes in phylogenetic and functional diversity over space and time
Loïc Chalmandrier, Tamara Münkemüller, Vincent Devictor, Sébastien Lavergne and Wilfried Thuiller

A DNA Barcoding system integrating multigene sequence data
Douglas Chesters, Wei-Min Zheng and Chao-Dong Zhu

Computation of diversification rates from molecular phylogenies: introducing a new efficient summary statistic, the nLTT
Thijs Janzen, Sebastian Höhna and Rampal S. Etienne

Trees, branches and (square) roots: why evolutionary relatedness is not linearly related to functional distance
Andrew D. Letten, and William K. Cornwell

Decomposing phylodiversity
Eric Marcon and Bruno Hérault

New biodiversity measure that includes consistent interspecific and intraspecific components
Sandrine Pavoine and Janos Izsák

Functional and phylogenetic similarity among communities
Sandrine Pavoine and Carlo Ricotta

Effects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data
Cuong Q. Tang, Aelys M. Humphreys, Diego Fontaneto and Timothy G. Barraclough

Simultaneously estimating evolutionary history and repeated traits phylogenetic signal: applications to viral and host phenotypic evolution
Bram Vrancken, Philippe Lemey, Andrew Rambaut, Trevor Bedford, Ben Longdon, Huldrych F. Günthard and Marc A. Suchard


BAT – Biodiversity Assessment Tools, an R package for the measurement and estimation of alpha and beta taxon, phylogenetic and functional diversity
Pedro Cardoso, François Rigal and José C. Carvalho

treeNODF: nestedness to phylogenetic, functional and other tree-based diversity metrics
Adriano S. Melo, Marcus V. Cianciaruso and Mário Almeida-Neto

VirtualCom: a simulation model for eco-evolutionary community assembly and invasion
Tamara Münkemüller and Laure Gallien

BAMMtools: an R package for the analysis of evolutionary dynamics on phylogenetic trees
Daniel L. Rabosky, Michael Grundler, Carlos Anderson, Pascal Title, Jeff J. Shi, Joseph W. Brown, Huateng Huang and Joanna G. Larson

Rphylip: an R interface for PHYLIP
Liam J. Revell and Scott A. Chamberlain

Original Image used above ©PLOS One Phylogeny

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