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The question are there alleles on the y chromosomes is unclear. Here are two possible things you might mean Is there genetic variation among individuals on the y chromosomes Is there anything functional on the Y chromosome Is there genetic variation among individuals on the y chromosomes Yes, of course, there is genetic variation of the Y chromosome ...


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This can occur if the Ab genotype is lethal, i.e. you won't observe individuals with a Ab genotype. Allele lethality is a common mechanisms that can explain non-mendelian inheritance of a trait. For the question of which LD metric to use, this is tricky. Under the assumption that allele lethality is indeed at play, you observed perfect haplotypes, so D'=1 ...


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