Discordance of Species Trees with Their Most Likely Gene Trees

• Published in: PLoS genetics Vol. 2; no. 5; p. e68
• Main Authors: Degnan, James H, Rosenberg, Noah A
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.05.2006; Public Library of Science (PLoS)
• Subjects: Algorithms; Animals; Computational Biology - methods; Evolution; Evolution, Molecular; Genes; Genetic Speciation; Genetics; Genetics, Population; Genetics/Population Genetics; Genomics; Genomics - methods; Humans; Models, Genetic; Models, Statistical; None; Origin of species; Phylogenetics; Phylogeny; Plant genetics; Species Specificity; Statistics; Stochastic Processes; Trees; United States
• ISSN: 1553-7404; 1553-7390; 1553-7404
• DOI: 10.1371/journal.pgen.0020068

Because of the stochastic way in which lineages sort during speciation, gene trees may differ in topology from each other and from species trees. Surprisingly, assuming that genetic lineages follow a coalescent model of within-species evolution, we find that for any species tree topology with five or more species, there exist branch lengths for which gene tree discordance is so common that the most likely gene tree topology to evolve along the branches of a species tree differs from the species phylogeny. This counterintuitive result implies that in combining data on multiple loci, the straightforward procedure of using the most frequently observed gene tree topology as an estimate of the species tree topology can be asymptotically guaranteed to produce an incorrect estimate. We conclude with suggestions that can aid in overcoming this new obstacle to accurate genomic inference of species phylogenies.