OPTION 2 - Genotypic linkage disequilibrium

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

Suboption 1 - Tests

For this option the null hypothesis Ho is: "Genotypes at one locus are independent from genotypes at the other locus". For a pair of diploid loci, no assumption is made about the gametic phase in double heterozygotes. In particular, it is not inferred assuming one-locus HW equilibrium, as such equilibrium is not assumed anywhere in the formulation of the test. The test is thus one of association between diploid genotypes at both loci, sometimes described as a test of the composite linkage disequilibrium (Weir, 1996, p. 126{128). For a haploid locus and a diploid one, a test of association between the haploid and diploid genotypes is computed (there is no concern about gametic phase in this case). This makes it easy to test for cytonuclear disequilibria. For a pair of loci with haploid information, a straightforward test of association of alleles at the two loci is computed.

The default test statistic is now the log likelihood ratio statistic (G-test). However one can still perform probability tests (as implemented in earlier versions of Genepop) by using the Gametic Disequilibrium Test = Probability setting on the input form.

For a given pair of loci within one sample, the relevant information is represented by a contingency table looking e.g. like

       1.1   1.3   3.3   1.7   3.7 
EST    ______________________________
 1.1   1     1     0     0     1        3 
 1.2   16    6     1     3     2        28 
       17    7     1     3     3        31 

for two diploid loci (1.1, etc., are the diploid genotypes at each locus). Contingency tables are created for all pairs of loci in each sample, then a G test or a probability test for each table is computed for each table using the Markov chain algorithm of Raymond & Rousset (1995a). The number of switches of the algorithm is given for each table analyzed.

OUTPUT. Results are returned via the web browser (and/or you can also have the results emailed to you - this may be advisable for users with large data files as the computations may take some time). Three intractable situations are indicated: empty tables ('No data'), table with one row or one column only ('No contingency table'), and tables for which all rows or all columns marginal sums are 1 ('No information'). For each locus pair within each sample, the unbiased estimate of the P-value is indicated, as well as the standard error. Next, a global test (Fisher's method) for each pair of loci is performed across samples.

Suboption 2 - create tables

All contingency tables (for n loci and p populations, there are p.n.(n-1)/2 tables) are available through sub-option 2. Tables will be returned to you via the web browser (and/or email).

Last Modified on December 1, 2020 by Eleanor Morgan

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