title: Gene Tree Discordance Does Not Explain Away the Temporal Decline of Convergence in Mammalian Protein Sequence Evolution.
abstract: Several authors reported lower frequencies of protein sequence convergence between more distantly related evolutionary lineages and attributed this trend to epistasis, which renders the acceptable amino acids at a site more different and convergence less likely in more divergent lineages. A recent primate study, however, suggested that this trend is at least partially and potentially entirely an artifact of gene tree discordance (GTD). Here, we demonstrate in a genome-wide data set from 17 mammals that the temporal trend remains (1) upon the control of the GTD level, (2) in genes whose genealogies are concordant with the species tree, and (3) for convergent changes, which are extremely unlikely to be caused by GTD. Similar results are observed in a comparable data set of 12 fruit flies in some but not all of these tests. We conclude that, at least in some cases, the temporal decline of convergence is genuine, reflecting an impact of epistasis on protein evolution.
authors.affiliation: Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI.
authors.forename: Zhengting
authors.initials: Z
authors.lastname: Zou
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI.
authors.forename: Jianzhi
authors.initials: J
authors.lastname: Zhang
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D005075:Biological Evolution; D004843:Epistasis, Genetic; D019143:Evolution, Molecular; D016678:Genome; D008322:Mammals / Q000235:genetics*; D008957:Models, Genetic; D010802:Phylogeny; D011323:Primates / Q000235:genetics; D011506:Proteins / Q000235:genetics*; D012641:Selection, Genetic; D017421:Sequence Analysis
chemical_list: D011506:Proteins
keywords: convergent evolution; epistasis; incomplete lineage sorting; parallel evolution