Estimation of Species Trees

Abstract

Abstract During the last decades, gene trees have been often interpreted as species phylogenies. However, the extensive gene tree discordance found in multi‐locus datasets has put into question this interpretation, and a variety of new methods that explicitly consider species trees have been proposed in recent years. Some of these explicitly consider evolutionary processes that can lead to true gene tree discordance, namely incomplete lineage sorting, gene duplication and loss and horizontal gene transfer. Choosing the most appropriate species tree method for the data at hand is not straightforward due to different data prerequisites, model assumptions, analytical strategies and computational implementations. Key Concepts: We could think of at least three different phylogenetic layers corresponding to species trees, locus trees and gene trees. These depict, respectively, the history of the sampled species, loci and genes copies. Traditional phylogenetic inference has focused on the reconstruction of gene trees, assumed to be accurate proxies for species history. True species, locus and gene trees can be incongruent due to the effect of evolutionary processes like incomplete lineage sorting, gene duplication and loss and horizontal gene transfer. This incongruence might appear larger due to estimation error. Extensive gene tree incongruence unveiled in multi‐locus datasets has encouraged the development of methods that explicitly reconstruct species trees. The supermatrix approach combines loci into a super‐alignment and estimates the corresponding supergene tree. Supertree methods combine gene trees to obtain an estimate of the species tree. Other methods co‐estimate gene and species trees in a single step using full probabilistic models. Different species tree methods require distinct data specifications, mainly related with the consideration of paralogs, number of sampled species, missing taxa and number of loci. Rooting and reconstruction uncertainty must be carefully considered before choosing a species tree method.