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RPANDA : an R package for macroevolutionary analyses on phylogenetic trees.

Morlon, Hélène and Lewitus, Eric and Condamine, Fabien L. and Manceau, Marc and Clavel, Julien and Drury, Jonathan (2016) 'RPANDA : an R package for macroevolutionary analyses on phylogenetic trees.', Methods in ecology and evolution., 7 (5). pp. 589-597.

Abstract

A number of approaches for studying macroevolution using phylogenetic trees have been developed in the last few years. Here, we present RPANDA, an R package that implements model‐free and model‐based phylogenetic comparative methods for macroevolutionary analyses. The model‐free approaches implemented in RPANDA are recently developed approaches stemming from graph theory that allow summarizing the information contained in phylogenetic trees, computing distances between trees, and clustering them accordingly. They also allow identifying distinct branching patterns within single trees. RPANDA also implements likelihood‐based models for fitting various diversification models to phylogenetic trees. It includes birth–death models with i) constant, ii) time‐dependent and iii) environmental‐dependent speciation and extinction rates. It also includes models with equilibrium diversity derived from the coalescent process, as well as a likelihood‐based inference framework to fit the individual‐based model of Speciation by Genetic Differentiation, which is an extension of Hubbell's neutral theory of biodiversity. RPANDA can be used to (i) characterize trees by plotting their spectral density profiles (ii) compare trees and cluster them according to their similarities, (iii) identify and plot distinct branching patterns within trees, (iv) compare the fit of alternative diversification models to phylogenetic trees, (v) estimate rates of speciation and extinction, (vi) estimate and plot how these rates have varied with time and environmental variables and (vii) deduce and plot estimates of species richness through geological time. RPANDA provides investigators with a set of tools for exploring patterns in phylogenetic trees and fitting various models to these trees, thereby contributing to the ongoing development of phylogenetics in the life sciences.

Item Type:Article
Full text:(AM) Accepted Manuscript
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Status:Peer-reviewed
Publisher Web site:https://doi.org/10.1111/2041-210X.12526
Publisher statement:This is the accepted version of the following article: Morlon, Hélène, Lewitus, Eric, Condamine, Fabien L., Manceau, Marc, Clavel, Julien & Drury, Jonathan (2016). RPANDA: an R package for macroevolutionary analyses on phylogenetic trees. Methods in Ecology and Evolution 7(5): 589-597, which has been published in final form at https://doi.org/10.1111/2041-210X.12526. This article may be used for non-commercial purposes in accordance With Wiley Terms and Conditions for self-archiving.
Date accepted:03 December 2015
Date deposited:13 September 2018
Date of first online publication:03 February 2016
Date first made open access:13 September 2018

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