inst/doc/opt33-34.md

In genepop: Population Genetic Data Analysis Using Genepop

Sub-options 3 or 4 (genotypic differentiation)

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

                  Genotypes:
                  -------------------------
                  1    1   2   1   2   3
         Pop:     1    2   2   3   3   3   All
         ----
         Pop1     142  27  0   13  1   0   183
         Pop2     149  20  0   11  0   4   184
         Pop3     131  12  0   9   0   1   153
         Pop4     119  22  1   10  0   0   152
         Pop5     120  17  1   10  1   0   149
         Pop6     134  18  2   15  0   0   169
         Pop7     116  15  1   10  1   1   144
         Pop8     214  41  3   14  2   1   275
         Pop9     84   17  0   7   2   0   110
         Pop10    107  18  0   15  3   0   143
         Pop11    134  32  1   21  4   0   192
         Pop12    105  26  1   11  1   4   148
         Pop13    97   19  2   23  4   0   145
         Pop14    95   28  3   19  3   1   149

         All:     1747 312 15  188 22  12  2296

An unbiased estimate of the P-value of a log-likelihood ratio ($G$) based exact test is performed. For this test, the statistics defining the rejection zone is the $G$ value computed on the genic table derived from the genotypic one [see @GoudetRMR96 for the choice of this statistic],\index{Differentiation!genic-genotypic test} so that the rejection zone is defined as the sum of the probabilities of all tables (with the same marginal genotypic values as the observed one) having a $G$ value computed on the derived genic table higher than or equal to the observed $G$ value.

For sub-option 4, the test is the same but is performed for all pairs of samples for all loci.

Output

For the four sub-options, results are stored in a file named as follows:[^17]

| sub-option | test |output file name | |------------ |------------------ |-----------------| |1 |Probability test |yourdata.PR | |1 |$G$ |yourdata.GE | |2 |Probability test |yourdata.PR2 | |2 |$G$ |yourdata.GE2 | |3 |$G$ |yourdata.G | |4 |$G$ |yourdata.2G2 |

All contingency tables are saved in the output file. Two intractable situations are indicated: empty tables or tables with one row or one column only (“No table”), and tables for which all rows or all columns marginal sums are 1 (“No information”). Estimates of P-values are given, as well as (for sub-options 1 and 3) a combination of all test results (Fisher’s method), which assumes a statistical independence across loci. For sub-options 2 and 4, this combination of all tests across loci (Fisher’s method) is performed for each sample pair. The result Highly sign.[ificant] is reported when at least one of the individual tests being combined yielded a zero $P$-value estimate.

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