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
Related in: MedlinePlus
Mentions: Figure 9 illustrates a more direct comparison, where we plot the ratio of between mouse and human edges to the ratio of and between mouse and human edges. There is a tendency for the length of the mouse edge to exceed that of the human edge by a greater amount under both the GTR and GTR models. In other words, the speedup of substitution rates on the mouse lineage is overstated by the stationary models.
Affiliation: John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2600, Australia; and.