Advanced: Handling sex-linked markers

This can be accommodated by using an extra allele to denote the missing allele on the Y chromosome in males – or on the W chromosome in female birds. It is good to not list the missing allele as the first allele – as this would be reported in the top histogram (frequency of first allele) for that marker, and would contain the certain information of a frequency of 0.5 in progeny, being the expected proportion of the heterogametic sex.

With reference to the table above, and for two “real” alleles segregating, you can take this approach:

Use field name, for example, g_3_6_MS1-_1_2_Y . Here we name the locus MS1 and we take the two alleles to be named 1 and 2, and the missing allele is denoted Y. The genotypes are laid out as follows:

3_6     11    12    1Y
              22    2Y
                    YY

So that the genotypes in the datafile should be entered as follows:

3_6     1     2     3
              4     5
                    6

Genotype 6 (YY) cannot exist. Genotypes 3 and 5 (1Y and 2Y) are for the heterogametic sex, and 1, 2 and 4 (11, 12, and 22) are for the homogametic sex.

As this is set up as a 3-allele scenario, you will see 10 histograms on expected progeny outcomes for this marker – one for the frequency of allele 1, and 3x3 for the 9 ordered genotypes.