title: Concatenation and Species Tree Methods Exhibit Statistically Indistinguishable Accuracy under a Range of Simulated Conditions.
abstract: Phylogeneticists have long understood that several biological processes can cause a gene tree to disagree with its species tree. In recent years, molecular phylogeneticists have increasingly foregone traditional supermatrix approaches in favor of species tree methods that account for one such source of error, incomplete lineage sorting (ILS). While gene tree-species tree discordance no doubt poses a significant challenge to phylogenetic inference with molecular data, researchers have only recently begun to systematically evaluate the relative accuracy of traditional and ILS-sensitive methods. Here, we report on simulations demonstrating that concatenation can perform as well or better than methods that attempt to account for sources of error introduced by ILS. Based on these and similar results from other researchers, we argue that concatenation remains a useful component of the phylogeneticist's toolbox and highlight that phylogeneticists should continue to make explicit comparisons of results produced by contemporaneous and classical methods.
authors.affiliation: Department of Biological Sciences, The George Washington Univerisity, Washington, District of Columbia, USA.
authors.forename: João
authors.initials: J
authors.lastname: Tonini
authors.affiliation: Department of Biological Sciences, The George Washington University, Washington, District of Columbia, USA.
authors.forename: Andrew
authors.initials: A
authors.lastname: Moore
authors.affiliation: Computational Biology Institute, Department of Biological Sciences, The George Washington University, Washington, District of Columbia, USA.
authors.forename: David
authors.initials: D
authors.lastname: Stern
authors.affiliation: Department of Geography & Environmental Systems, University of Maryland Baltimore County, Baltimore, MD, USA.
authors.forename: Maryia
authors.initials: M
authors.lastname: Shcheglovitova
authors.affiliation: Department of Biological Sciences, The George Washington Univerisity, Washington, District of Columbia, USA.
authors.forename: Guillermo
authors.initials: G
authors.lastname: Ortí