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Genetic distance for a general non-stationary markov substitution process.

Kaehler BD, Yap VB, Zhang R, Huttley GA - Syst. Biol. (2014)

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.

View Article: PubMed Central - PubMed

Affiliation: John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2600, Australia; and.

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The General model allows  and  to vary between edges and independently of the starting marginal probability vector .
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Figure 2: The General model allows and to vary between edges and independently of the starting marginal probability vector .

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.


Genetic distance for a general non-stationary markov substitution process.

Kaehler BD, Yap VB, Zhang R, Huttley GA - Syst. Biol. (2014)

The General model allows  and  to vary between edges and independently of the starting marginal probability vector .
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4380038&req=5

Figure 2: The General model allows and to vary between edges and independently of the starting marginal probability vector .
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.

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.

View Article: PubMed Central - PubMed

Affiliation: John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2600, Australia; and.

Show MeSH
Related in: MedlinePlus