Simultaneous detection of macroevolutionary patterns in phenotypic means and rate of change with and within phylogenetic trees including extinct species

• Published in: PloS one Vol. 14; no. 1; p. e0210101
• Main Authors: Castiglione, S, Serio, C, Mondanaro, A, Di Febbraro, M, Profico, A, Girardi, G, Raia, P
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 25.01.2019; Public Library of Science (PLoS)
• Subjects: Algorithms; Analysis; Bioinformatics; Biological Evolution; Biology and Life Sciences; Computational Biology - methods; Computer and Information Sciences; Computer simulation; Data processing; Earth science; Earth Sciences; Endangered & extinct species; Evolution; Evolution & development; Evolutionary algorithms; Extinct species; Extinction; Extinction, Biological; Fossils; Methods; Phenotype; Phenotypes; Phylogenetics; Phylogeny; Physical Sciences; Research and Analysis Methods; Software; Trees; Trends; Italy
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0210101

Recognizing evolutionary trends in phenotypic means and rates requires the application of phylogenetic comparative methods (PCMs). Most PCMs are unsuited to make full use of fossil information, which is a drawback, given the inclusion of such data improves, and in some cases even corrects, the proper understanding of trait evolution. Here we present a new computer application, written in R, that allows the simultaneous computation of temporal trends in phenotypic mean and evolutionary rate along a phylogeny, and to contrast such patterns among different clades within the tree. By using simulation experiments, we show the new implementation, names search.trend is as powerful as existing PCM tools in discerning macroevolutionary patterns in phenotypic means and rates, but differently from any other PCM allows comparing individual clades to each other, and provides rich information about trait evolution for all lineages in the tree.