Estimating the time since the fixation of a beneficial allele.
The fixation of a beneficial allele in a population leaves a well-characterized signature in patterns of nucleotide variation at linked sites. This signature can be used to estimate the time since fixation from patterns of polymorphism in extant individuals. I introduce a method to assess the support in polymorphism data for a recent episode of directional positive selection and to estimate the time since fixation. I summarize the polymorphism data by three statistics that carry information about levels of diversity, the allele frequency spectrum, and the extent of allelic associations. Simulations are then used to obtain a sample from the posterior distribution of the time since fixation, conditional on the observed summaries. I test the performance of the approach on simulated data and apply it to the gene tb1 in maize. The data support the recent fixation of a favored allele, consistent with what is known about the importance of tb1 in the domestication process of maize.
Przeworski
Molly
M
Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany. przewors@eva.mpg.de
D000465:Algorithms; D000483:Alleles; D001483:Base Sequence; D003198:Computer Simulation; D003434:Crossing Over, Genetic; D004171:Diploidy; D005787:Gene Frequency; D017343:Genes, Plant; D008040:Genetic Linkage; D014644:Genetic Variation; D005828:Genetics, Population; D007700:Kinetics; D008957:Models, Genetic; D009154:Mutation; D011110:Polymorphism, Genetic; D011995:Recombination, Genetic; D012641:Selection, Genetic; D013997:Time Factors; D003313:Zea mays / Q000235:genetics