On the divergence of alleles in nested subsamples from finite populations.

Genetics
R R Hudson, N L Kaplan

Abstract

Within-population variation at the DNA level will rarely be studied by sequencing of loci of randomly chosen individuals. Instead, individuals will usually be chosen for sequencing based on some knowledge of their genotype. Data collected in this way require new sampling theory. Motivated by these observations, we have examined the sampling properties of a finite population model with two mutation processes and with no selection or recombination. One mutation process generates new alleles according to an infinite-alleles model, and the other generates polymorphisms at sites according to an infinite-sites model. A sample of n genes is considered. The stationary distribution of the number of segregating sites in a subsample from one of the allelic classes in the sample conditional on the allelic configuration of the sample is studied. A recursive scheme is developed to compute the moments of this distribution, and it is shown that the distribution is functionally independent of the number of additional alleles in the sample and their respective frequencies in the sample. For the case in which the sample contains only two alleles, the distribution of the number of segregating sites in a subsample containing both alleles conditiona...Continue Reading

Citations

Jul 14, 2004·Proceedings of the National Academy of Sciences of the United States of America·Hideki Innan, Yuseob Kim
Sep 3, 2004·Genetics·Naoki TakebayashiMarcy K Uyenoyama
May 15, 2013·G3 : Genes - Genomes - Genetics·Andre G WallaceStephen W Schaeffer
Nov 9, 2005·PLoS Biology·Matthew V RockmanGregory A Wray
Feb 22, 2005·The New Phytologist·Marcy K Uyenoyama
Mar 10, 2016·Genetics·Nicholas H Barton
Dec 26, 2008·Briefings in Bioinformatics·Yuseob Kim, Thomas Wiehe

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