![]() Some sites, such as CpG islands in mammalian taxa, have a higher propensity to mutate. In reality, however, rates of mutation can vary among sites because of selective pressures associated with structural and functional constraints –. In their basic form, nucleotide substitution models assume that the evolutionary process is homogeneous across sites. ![]() This gives rise to special cases of the GTR model, such as the Jukes–Cantor, Kimura, and Hasegawa–Kishino–Yano models. By constraining one or more of these parameters, a family of time-reversible models can be generated. The general time-reversible (GTR) model, formally described by Tavaré, includes parameters that allow unequal frequencies for the four nucleotides and a distinct rate for each of the six pairwise nucleotide substitutions. In practice, almost all models of nucleotide substitution are time-reversible. These models commonly assume that substitutions occurring at each site are described by a Markov chain and that different sites evolve in a mutually independent manner. In phylogenetic analyses of DNA sequence data, the evolutionary process is usually described using models of nucleotide substitution. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Ĭompeting interests: The authors have declared that no competing interests exist. NL and SYWH were supported by the Australian Research Council (DP1097265 and DP110100383). This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.įunding: FJ was supported by an Australian Postgraduate Award. Received: DecemAccepted: MaPublished: May 5, 2014Ĭopyright: © 2014 Jia et al. ![]() Moreau, Field Museum of Natural History, United States of America The concurrent use of gamma and invariable-site models for intraspecific data is not biologically meaningful and has been challenged on statistical grounds here we have found that the assumption of a proportion of invariable sites has no obvious impact on Bayesian estimates of rates and timescales from intraspecific data.Ĭitation: Jia F, Lo N, Ho SYW (2014) The Impact of Modelling Rate Heterogeneity among Sites on Phylogenetic Estimates of Intraspecific Evolutionary Rates and Timescales. However, the estimated proportion of invariable sites was highly susceptible to changes in the number of gamma rate categories. The assumption of a proportion of invariable sites provided a better approximation of the asymptotic marginal likelihood when the number of gamma categories was small, but had minimal impact on estimates of rates and coalescence times. Increasing the number of gamma rate categories did not have a substantial effect on estimates of the substitution rate or coalescence time, unless rates varied strongly among sites in a non-gamma-distributed manner. We show that using 6–10 rate categories for the discrete gamma distribution of rates among sites is sufficient to provide a good approximation of the marginal likelihood. We examined the use of these models in analyses of five intraspecific data sets. ![]() For data sampled at the intraspecific level, however, biological assumptions involved in the invariable-sites model are commonly violated. A widely used derivative of this is the gamma-invariable mixture model, which assumes that a proportion of sites in the sequence are completely resistant to change, while substitution rates at the remaining sites are gamma-distributed. A key feature of molecular evolution is the heterogeneity of substitution rates among sites, which is often modelled using a discrete gamma distribution. Nearly all phylogenetic methods rely on accurate models of nucleotide substitution. Phylogenetic analyses of DNA sequence data can provide estimates of evolutionary rates and timescales. ![]()
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