DEMEtics (version 0.8.0)

DEMEtics: Calculation of Gst and D values characterizing the genetic differentiation between populations.

Description

Out of a table comprising allelic data of at least one locus for several individuals and from at least two populations, measurements of genetic differentiation (i.e. D, Dest, Dest.Chao, Gst and Gst.est (Jost, 2008)) can be calculated. P-values and 95 percent confidence intervals are calculated according to Manly (1997) using a bootstrap method. Thereby, for each locus, alleles are reallocated over populations if they are all in Hardy Weinberg Equilibrium (HWE). If not, the genotypes are reallocated, since alleles can not be assumed to be inherited independently from each other (Goudet, 1996). The p-values state how much the empirical found allocation of alleles over populations differs from an allocation that could arise by chance alone. In the case that more than two populations are compared pairwise, the p-values are adjusted besides using bonferroni correction in several other ways due to the multiple comparison from one data set.

Details

ll{ Package: DEMEtics Type: Package Version: 0.8.0 Date: 2010-02-11 Depends: R (>= 2.8.0) License: GPL (>= 2) Literature: Goudet, J., Raymond, M., deMeeues, T. and Rousset, F. 1996 Testing differentiation in diploid populations. Genetics 144, 4, p. 1933--1940. Jost, L. 2008 Gst and its relatives do not measure differentiation. Molecular Ecology 17, 18, p. 4015--4026. Manly, B.F.J. 1997 Randomization, bootstrap and Monte Carlo methods in biology Chapman & Hall. Nei M., Chesser R. 1983 Estimation of fixation indices and gene diversities. Annals of Human Genetics 47, 253--259. Wright, S.P 1992 Adjusted p-values for simultaneous inference. Biometrics 48, 1005--1013. LazyLoad: yes Built: R 2.8.1; ; 2010-02-10 08:45:20; unix }

Index: Bootstrapping Resampling of Alleles or Genotypes Using a Bootstrap Method D and Dest D and Dest - Differentiation Indices Dest.Chao A Measure of Genetic Differentiation Dest.Chao.calc A Measure of Genetic Differentiation Calculated From Allelefrequencies. calc Genetic Differentiation - For Each lLcus Separately and Averaged Over all Loci. Example.transformed Allelic Data of Three Populations for Three Loci Example.untransformed Allelic Data of Three Populations for Three Loci Gst and Gst.est Gst and Gst.est - Fixation Indices Hardy.Weinberg Test for Hardy Weinberg Equilibrium (HWE) Hj Heterozygosity Level Within a Single Population H.out Heterozygosities Hs Mean Heterozygosity Within Populations Ht Total Heterozygosity all.pops Genetic Differentiation Averaged Over all Populations allelefreq Calculation of Allelefrequencies and Sample Sizes per Locus inputformat Transformation of a Data Table Containing Allelic Data for Several Loci p.val Bootstrap Test of Significance pair.pops Pairwise Genetic Differentiation

The following functions carry out the appropriate calculations in the right order automatically to obtain data tables listing measures of genetic differentiation between populations with 95% confidence intervals and p-values from a data table containing allelic data: all.pops.D, all.pops.Dest, all.pops.Dest.Chao, all.pops.Gst, all.pops.Gst.est, pair.pops.D, pair.pops.Dest, pair.pops.Dest.Chao, pair.pops.Gst, pair.pops.Gst.est.