title: PoMo: An Allele Frequency-Based Approach for Species Tree Estimation.
abstract: Incomplete lineage sorting can cause incongruencies of the overall species-level phylogenetic tree with the phylogenetic trees for individual genes or genomic segments. If these incongruencies are not accounted for, it is possible to incur several biases in species tree estimation. Here, we present a simple maximum likelihood approach that accounts for ancestral variation and incomplete lineage sorting. We use a POlymorphisms-aware phylogenetic MOdel (PoMo) that we have recently shown to efficiently estimate mutation rates and fixation biases from within and between-species variation data. We extend this model to perform efficient estimation of species trees. We test the performance of PoMo in several different scenarios of incomplete lineage sorting using simulations and compare it with existing methods both in accuracy and computational speed. In contrast to other approaches, our model does not use coalescent theory but is allele frequency based. We show that PoMo is well suited for genome-wide species tree estimation and that on such data it is more accurate than previous approaches.
authors.affiliation: Institut für Populationsgenetik, Vetmeduni Vienna, Wien 1210, Austria; Vienna Graduate School of Population Genetics, Wien, Austria; and Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7BN, UK.
authors.forename: Nicola
authors.initials: N
authors.lastname: De Maio
authors.affiliation: Institut für Populationsgenetik, Vetmeduni Vienna, Wien 1210, Austria; Vienna Graduate School of Population Genetics, Wien, Austria; and.
authors.forename: Dominik
authors.initials: D
authors.lastname: Schrempf
authors.affiliation: Institut für Populationsgenetik, Vetmeduni Vienna, Wien 1210, Austria; carolin.kosiol@vetmeduni.ac.at.
authors.forename: Carolin
authors.initials: C
authors.lastname: Kosiol
mesh_terms: D000818:Animals; D002965:Classification / Q000379:methods*; D003198:Computer Simulation; D005787:Gene Frequency; D015186:Hominidae / Q000145:classification / Q000235:genetics; D009154:Mutation; D010802:Phylogeny; D011110:Polymorphism, Genetic
keywords: Incomplete lineage sorting; Phylogenetics; PoMo; Species tree