Using equilibrium frequencies in models of sequence evolution.
BACKGROUND
The f factor is a new parameter for accommodating the influence of both the starting and ending states in the rate matrices of "generalized weighted frequencies" (+gwF) models for sequence evolution. In this study, we derive an expected value for f, starting from a nearly neutral model of weak selection, and then assess the biological interpretation of this factor with evolutionary simulations.


RESULTS
An expected value of f = 0.5 (i.e., equal dependency on the starting and ending states) is derived for sequences that are evolving under the nearly neutral model of this study. However, this expectation is sensitive to violations of its underlying assumptions as illustrated with the evolutionary simulations.


CONCLUSIONS
This study illustrates how selection, drift, and mutation at the population level can be linked to the rate matrices of models for sequence evolution to derive an expected value of f. However, as f is affected by a number of factors that limit its biological interpretation, this factor should normally be estimated as a free parameter rather than fixed a priori in a +gwF analysis.
Knudsen
Bjarne
B
Department of Zoology, Box 118525, University of Florida, Gainesville, FL 32611-8525, USA. bk@birc.dk
Miyamoto
Michael M
MM
D005075:Biological Evolution; D003627:Data Interpretation, Statistical; D019143:Evolution, Molecular; D005787:Gene Frequency; D040961:Genetic Drift; D008954:Models, Biological; D008957:Models, Genetic; D015233:Models, Statistical; D008962:Models, Theoretical; D009154:Mutation; D012641:Selection, Genetic
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