title: Maximum likelihood methods for detecting adaptive evolution after gene duplication.
abstract: The rapid accumulation of genomic sequences in public databases will finally allow large scale studies of gene family evolution, including evaluation of the role of positive Darwinian selection following a duplication event. This will be possible because recent statistical methods of comparing synonymous and nonsynonymous substitution rates permit reliable detection of positive selection at individual amino acid sites and along evolutionary lineages. Here, we summarize maximum-likelihood based methods, and present a framework for their application to analysis of gene families. Using these methods, we investigated the role of positive Darwinian selection in the ECP-EDN gene family of primates and the Troponin C gene family of vertebrates. We also comment on the limitations of these methods and discuss directions for further improvements.
authors.affiliation: Department of Biology, University College London, Darwin Building, Gower Street, London WCIE 6BT, United Kingdom. j.bielawski@ucl.ac.uk
authors.forename: Joseph P
authors.initials: JP
authors.lastname: Bielawski
authors.forename: Ziheng
authors.initials: Z
authors.lastname: Yang
mesh_terms: D019943:Amino Acid Substitution; D000818:Animals; D003627:Data Interpretation, Statistical; D019143:Evolution, Molecular; D020440:Gene Duplication; D006801:Humans; D016013:Likelihood Functions; D008390:Markov Chains; D005810:Multigene Family; D010802:Phylogeny; D012641:Selection, Genetic; D019209:Troponin C / Q000235:genetics
chemical_list: D019209:Troponin C