(adapted from the original Genepop 4.0 documentation written by Francois Rousset)

All tests are based on Markov chain algorithms. The Markov chain parameters are controlled exactly as in option 1.

These are concerned with the distribution of alleles in the various samples. The null hypothesis tested is Ho: '*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, or the G log likelihood ratio. In the first case, the test is Fisher's exact probability test, and the algorithm is described in Raymond & Rousset (1995a). A simple modification of this algorithm is used for the exact G test. Genepop's default is now the G test.

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

These are concerned with the
distribution of diploid genotypes in the various populations. The null hypothesis tested is
Ho: "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 (G) based exact test is
performed (Goudet *et al*. 1996). For this test, the statistic defining the rejection zone is the G value
computed on the genic table derived from the genotypic one (see Goudet et al.,
1996 for the choice of this statistic), 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 automatically for all pairs of populations for all loci.

Results are returned via your web browser if you select the HTML option for Output Delivery. You can also have the results emailed to you if you choose this option (which is advisable for datafiles with 1) numerous loci or 2) numerous unique alleles for each locus or 3) increased Markov chain parameters). 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.

**Please report any problems or bugs that you encounter with the web version
of this option to
Eleanor Morgan**

*Last Modified on
September 29, 2009
by Eleanor Morgan*

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