title: Using equilibrium frequencies in models of sequence evolution.
abstract: 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.
authors.affiliation: Department of Zoology, Box 118525, University of Florida, Gainesville, FL 32611-8525, USA. bk@birc.dk
authors.forename: Bjarne
authors.initials: B
authors.lastname: Knudsen
authors.forename: Michael M
authors.initials: MM
authors.lastname: Miyamoto
mesh_terms: 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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