FAB*Lab at Simon Fraser University, Canada http://www.citeulike.org/groupfunc/894 CiteULike.org en-gb Copyright © 2004-2007 Oversity Limited http://www.citeulike.org/group/894/article/1402531 Observations of numerous dramatic and presumably adaptive phenotypic modifications during human evolution prompt the common belief that more genes have undergone positive Darwinian selection in the human lineage than in the chimpanzee lineage since their evolutionary divergence 6-7 million years ago. Here, we test this hypothesis by analyzing nearly 14,000 genes of humans and chimps. To ensure an accurate and unbiased comparison, we select a proper outgroup, avoid sequencing errors, and verify statistical methods. Our results show that the number of positively selected genes is substantially smaller in humans than in chimps, despite a generally higher nonsynonymous substitution rate in humans. These observations are explainable by the reduced efficacy of natural selection in humans because of their smaller long-term effective population size but refute the anthropocentric view that a grand enhancement in Darwinian selection underlies human origins. Although human and chimp positively selected genes have different molecular functions and participate in different biological processes, the differences do not ostensibly correspond to the widely assumed adaptations of these species, suggesting how little is currently known about which traits have been under positive selection. Our analysis of the identified positively selected genes lends support to the association between human Mendelian diseases and past adaptations but provides no evidence for either the chromosomal speciation hypothesis or the widespread brain-gene acceleration hypothesis of human origins. 2008-08-29T23:24:04+00:00 http://www.citeulike.org/group/894/article/309796 <i>no abstract</i> 2008-08-29T23:20:10+00:00 http://www.citeulike.org/group/894/article/3130673 <i>no abstract</i> 2008-08-18T01:27:00+00:00 http://www.citeulike.org/group/894/article/3130661 The rate at which a given site in a gene-sequence alignment evolves over time may vary. This phenomenon -- known as heterotachy -- can bias or distort phylogenetic trees inferred from models of sequence evolution that assume rates of evolution are constant. Here we describe a phylogenetic mixture-model designed to accommodate heterotachy. The method sums the likelihood of the data at each site over more than one set of branch lengths on the same tree topology. A branch-length set that is best for one site may differ from the branch-length set that is best for some other site, thereby allowing different sites to have different rates of change throughout the tree. Because rate variation may not be present in all branches, we use a reversible-jump Markov chain Monte Carlo algorithm to identify those branches in which reliable amounts of heterotachy occur. We implement the method in combination with our ‘pattern-heterogeneity’ mixture model, apply it to simulated data and to five published datasets. We find that complex evolutionary signals of heterotachy are routinely present over and above variation in the rate or pattern of evolution across sites, that the reversible-jump method requires far fewer parameters than conventional mixture models to describe it, and serves to identify the regions of the tree in which heterotachy is most pronounced. The reversible-jump procedure also removes the need for a posteriori tests of ‘significance’ such as the Akaike or Bayesian information criterion tests, or Bayes Factors. Heterotachy has important consequences for the correct reconstruction of phylogenies as well as for tests of hypotheses that rely on accurate branch length information. These include, molecular clocks, analyses of tempo and mode of evolution, comparative studies and ancestral state reconstruction. The model is available from the authors’ web site, and can be used for the analysis of both nucleotide and morphological data. 2008-08-18T00:50:23+00:00