Advances in Phylogenetic Methods – The Applications Papers

Original Image ©PLOS One Phylogeny

Original Image ©PLOS One Phylogeny

Timed to coincide with Evolution 2015, we have released a new Virtual Issue on Phylogenetic Methods. All of the articles in this Virtual Issue will be freely available for a limited period.

On Friday, we gave some more information about the research articles in this Virtual Issue. In this post, we will be focusing on the Applications papers.

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, not just those in the Virtual Issue, are free to access.

You can see a little more information on each of the Applications Papers below.


The R package BAT – Biodiversity Assessment Tools – performs a number of analyses based on either species identities or trees depicting species relationships. Its functions include building randomized accumulation curves for alpha and beta diversity, alpha diversity estimation from incomplete samples and the partitioning of beta diversity in its replacement and richness difference components. In this paper Cardoso et al. demonstrate the usefulness of BAT using the data included in the package.

Issue 6.6 Cover_RockfishFunctional Diversity and Invasion Dynamics

What is the relative importance of environmental filtering and competition in community assembly and invasion? At large spatial scales and for species-rich systems, this question can be answered by studying functional and phylogenetic diversity patterns. In this Applications paper, Münkemüller and Gallien introduce VirtualCom, a tool which simulates the evolution of the pool of regionally occurring species, the process-based assembly of native communities and the invasion of novel species into native communities.

mee-5-7-coverlargeEvolutionary Dynamics

In this paper from the July 2014 issue of MethodsRabosky et al. introduce BAMMtools, an R package for the analysis and visualization of macroevolutionary dynamics on phylogenetic trees. BAMMtools enables users to extract credible sets of diversification shifts and to identify diversification histories with the maximum a posteriori probability. Users can compare the fit of alternative diversification models using Bayes factors and by directly comparing model posterior probabilities.

MEE cover Sept 2014Phylogenetic Comparative Biology

The phylogeny methods software package PHYLIP has long been among the most widely used packages for phylogeny inference and phylogenetic comparative biology. Here, Revell and Chamberlain introduce Rphylip, an R interface for the PHYLIP package. Functions of Rphylip interface seamlessly with all of the major analysis functions of the PHYLIP package. This new interface will enable the much easier use of PHYLIP programs in an integrated R workflow.



Looking for information on the Research Articles in the Virtual Issue? You can see the post on them HERE.



One thought on “Advances in Phylogenetic Methods – The Applications Papers

  1. Pingback: Virtual Issue: Advances in Phylogenetic Methods |

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