Genetic distance for a general non-stationary markov substitution process.
Bottom Line: Our measure of genetic distance reduces to the standard formulation if the data in question are consistent with the stationarity assumption.The magnitude of the distance bias is proportional to departure from stationarity, which we demonstrate to be associated with longer edge lengths.The marked improvement in consistency between the general nonstationary Markov model and sequence alignments leads us to conclude that analyses of evolutionary rates and phylogenies will be substantively improved by application of this model.
Affiliation: John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2600, Australia; and.Show MeSH
Mentions: It is common to describe the hierarchy of substitution models that nest in GTR via the way in which they parametrize (e.g., Felsenstein 2004, pp. 196–206). We include a possible parametrization of for the General model here for the purpose of comparison with such characterizations:Q=(−α−β−γαβγδ−δ−ϵ−ζϵζηθ−η−θ−ιικλμ−κ−λ−μ).We also show the variation of by edge for the General model in the example topology in Figure 2.
Affiliation: John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2600, Australia; and.