Journal ArticleDOI
SURFACE: detecting convergent evolution from comparative data by fitting Ornstein-Uhlenbeck models with stepwise Akaike Information Criterion
Travis Ingram,D. Luke Mahler +1 more
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This work presents a method, ‘SURFACE’, that uses the Ornstein‐Uhlenbeck stabilizing selection model to identify cases of convergent evolution using only continuous phenotypic characters and a phylogenetic tree, and demonstrates the method with an application to Hawaiian Tetragnatha spiders.Abstract:
Summary 1. We present a method, ‘SURFACE’, that uses the Ornstein-Uhlenbeck stabilizing selection model to identify cases of convergent evolution using only continuous phenotypic characters and a phylogenetic tree. 2. SURFACE uses stepwise Akaike Information Criterion first to locate regime shifts on a tree, then to identify whether shifts are towards convergent regimes. Simulations can be used to test the hypothesis that a clade contains more convergence than expected by chance. 3. We demonstrate the method with an application to HawaiianTetragnatha spiders, and present numerical simulations showing that the method has desirable statistical properties given data for multiple traits. 4. The R packagesurface is available as open source software from the Comprehensive RA rchive Network.read more
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BAMMtools: an R package for the analysis of evolutionary dynamics on phylogenetic trees
Daniel L. Rabosky,Michael C. Grundler,Carlos J. R. Anderson,Pascal O. Title,Jeff J. Shi,Joseph W. Brown,Huateng Huang,Joanna G. Larson +7 more
TL;DR: BAMMtools enables users to extract credible sets of diversification shifts and to identify diversification histories with the maximum a posteriori probability, and will facilitate inference on the complex mixture of processes that have shaped the distribution of species and phenotypes across the tree of life.
Journal ArticleDOI
Exceptional Convergence on the Macroevolutionary Landscape in Island Lizard Radiations
TL;DR: For example, this paper showed that diversification on similar Simpsonian landscapes leads to striking convergence of entire faunas on four islands in the Caribbean Anolis lizards, indicating that the adaptive landscape may give rise to predictable evolutionary patterns in nature, that adaptive peaks may be stable over macroevolutionary time and that available geographic area influences the ability of lineages to discover new adaptive peaks.
Journal ArticleDOI
Cryptic species as a window into the paradigm shift of the species concept
TL;DR: It is time for incorporating multicriteria species approaches aiming to understand speciation across space and taxa, thus allowing integration into biodiversity conservation while accommodating for species uncertainty.
Journal ArticleDOI
mvmorph: an r package for fitting multivariate evolutionary models to morphometric data
TL;DR: New features provided by the mvmorph package include the possibility of fitting models with changes in the mode of evolution along the phylogeny, which will be particularly meaningful in comparative analyses that include extinct taxa, for example when testing changes in evolutionary mode associated with global biotic/abiotic events.
Supplementary Materials for Exceptional Convergence on the Macroevolutionary Landscape in Island Lizard Radiations
TL;DR: For Caribbean Anolis lizards, diversification on similar Simpsonian landscapes leads to striking convergence of entire faunas on four islands, indicating that the adaptive landscape may give rise to predictable evolutionary patterns in nature, that adaptive peaks may be stable over macroevolutionary time, and that available geographic area influences the ability of lineages to discover new adaptive peaks.
References
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R: A language and environment for statistical computing.
TL;DR: Copyright (©) 1999–2012 R Foundation for Statistical Computing; permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and permission notice are preserved on all copies.
Book
Model Selection and Multimodel Inference: A Practical Information-Theoretic Approach
TL;DR: The second edition of this book is unique in that it focuses on methods for making formal statistical inference from all the models in an a priori set (Multi-Model Inference).
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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.
The igraph software package for complex network research
Gábor Csárdi,Tamás Nepusz +1 more
TL;DR: Platform-independent and open source igraph aims to satisfy all the requirements of a graph package while possibly remaining easy to use in interactive mode as well.
Book
The comparative method in evolutionary biology
Paul H. Harvey,Mark Pagel +1 more
TL;DR: The comparative method for studying adaptation why worry about phylogeny?