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
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Mentions: In the Methods section, we hypothesized that the nonstationarity between sequences should increase with genetic distance. Figure 6 plots JSD against genetic distance under the General model for the mouse to human path in the nuclear data for alignments plausibly modeled by the General model. We do not postulate the nature of the relationship between and JSD, other than that it is increasing, so we provide a LOESS plot of , as it is expected and observed to be significantly more noisy than JSD. The relationship is observed to be increasing, supporting the hypothesis that sequences that are further apart in a phylogenetic sense tend to display greater compositional heterogeneity. Note that there is a gray area here—tests of compositional heterogeneity will lack power for closely related sequences, so the question really pertains to long edges only.
Affiliation: John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2600, Australia; and.