Uniparentally-transmitted chromosome in hermaphrodite populations

[vsudbrack]

I'm opening this Gtihub Issue following a quick chat to Ben.

Currently, SLiM supports haploid-female ('HF') and haploid-male ('HM') chromosome inheritance only in dioecious populations (i.e., those with separate males and females, specified via InitializeSex()). However, in some biological systems, certain chromosomes or organelles are inherited uniparentally — for example, mitochondrial DNA in plants, which is transmitted only through the egg or ovule — even when individuals are hermaphroditic. In such cases, SLiM would need to define inheritance asymmetry by convention: treating 'parent1' as the hermaphroditic egg donor (functionally the "mother") and 'parent2' as the hermaphroditic sperm donor (functionally the "father" for a given child). With this convention in place, it's possible to model HF or HM lineages in hermaphroditic populations. That is, an HF chromosome would always be inherited from parent1, and an HM chromosome from parent2.

Interestingly, this breaks the symmetry across children: a child with parent1=A and parent2=B is not equivalent to one with parent1=B and parent2=A if HF/HM chromosomes are present.

This is of course an enhancement, this is totally possible to do with modifyChild callback - it just seems restrictive not to be able to do, since it is biologically 'acceptable' and present in many (mostly non-animal) species.

[bhaller]

Yes, upon reflection I think this is probably a good idea. And I don't think the objection I raised (that the names "HF" and "HM" explicitly tie these chromosome types to a sexual model) is dispositive; the documentation can simply explain that in the hermaphroditic case the first parent is considered the female parent, and the second is considered the male, for the purposes of these dynamics. I think I'll add this extension at some point, thanks for suggesting it.

[petrelharp]

Whoops! This was a major oversight (sorry, plants)!