inst/doc/opt31-32.md

In genepop: Population Genetic Data Analysis Using Genepop

Sub-options 1 or 2 (genic differentiation)

\index{Differentiation!genic} They are concerned with the distribution of alleles is the various samples. The null hypothesis tested is “alleles are drawn from the same distribution in all populations”. For each locus, the test is performed on a contingency table like this one:

          Sub-Pop.  Alleles
                    1    2   Total
                    _______
           1        14   46   60
           2        6    76   82
           3        10   74   84
           4        4    58   62
                    _______
          Total     34   254  288

For each locus, an unbiased estimate of the P-value is computed. The test statistic is either the probability of the sample conditional on marginal values, the $G$ log likelihood ratio, or the level of gene diversity. In the first case, the test is Fisher’s exact probability test, and the algorithm is described in @RaymondR95evol. A simple modification of this algorithm is used for the exact $G$ test.[^16] Genepop’s default is the $G$ test. You can revert to Fisher’s test by using the DifferentiationTest=Proba\index{DifferentiationTest setting} setting. Finally, the level of gene diversity can be used as a test statistic when coupled with the GeneDivRanks setting (this was new to version 4.1; see Section \@ref(gene-diversity-as-a-test-statistic)).

For sub-option 2, the tests are the same, but they are performed for all pairs of samples for all loci.

genepop documentation built on Jan. 22, 2023, 1:07 a.m.