title: The Effects of Increasing the Number of Taxa on Inferences of Molecular Convergence.
abstract: Convergent evolution provides insight into the link between phenotype and genotype. Recently, large-scale comparative studies of convergent evolution have become possible, but researchers are still trying to determine the best way to design these types of analyses. One aspect of molecular convergence studies that has not yet been investigated is how taxonomic sample size affects inferences of molecular convergence. Here we show that increased sample size decreases the amount of inferred molecular convergence associated with the three convergent transitions to a marine environment in mammals. The sampling of more taxa-both with and without the convergent phenotype-reveals that alleles associated only with marine mammals in small datasets are actually more widespread, or are not shared by all marine species. The sampling of more taxa also allows finer resolution of ancestral substitutions, revealing that they are not in fact on lineages leading to solely marine species. We revisit a previous study on marine mammals and find that only 7 of the reported 43 genes with convergent substitutions still show signs of convergence with a larger number of background species. However, four of those seven genes also showed signs of positive selection in the original analysis and may still be good candidates for adaptive convergence. Though our study is framed around the convergence of marine mammals, we expect our conclusions on taxonomic sampling are generalizable to any study of molecular convergence.
authors.affiliation: Department of Biology and School of Informatics and Computing, Indiana University, Bloomington, Indiana.
authors.forename: Gregg W C
authors.initials: GW
authors.lastname: Thomas
authors.affiliation: Department of Biology and School of Informatics and Computing, Indiana University, Bloomington, Indiana.
authors.forename: Matthew W
authors.initials: MW
authors.lastname: Hahn
authors.affiliation: Department of Life Science, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul, Republic of Korea.
authors.forename: Yoonsoo
authors.initials: Y
authors.lastname: Hahn
mesh_terms: D000222:Adaptation, Physiological; D019943:Amino Acid Substitution; D000818:Animals; D005075:Biological Evolution; D006801:Humans; D008322:Mammals / Q000145:classification* / Q000235:genetics* / Q000502:physiology; D010802:Phylogeny; D018401:Sample Size; D012641:Selection, Genetic
keywords: convergent evolution; molecular convergence; taxonomic sampling