multiple alleles: within-species alleles not monophyletic

[crsl4]

Based on a google user post, there could be cases when the multiple alleles of a species are not monophyletic. Currently, when we randomly choose two alleles per species, we assume that these alleles are sisters and force them to stay as sisters while searching network space. I do not recall at this point if we check that the two sampled alleles are in fact sisters, or if we need to add this check.

[cecileane]

The 2 alleles don't need to be sister in every single gene trees, because of ILS. If the user wants to test the assumption that their species delimitation is correct, they can run analyses in which each individual is its own species. So I don't see a problem there (other than the computational problem when each species is its own species: many more species...).

[crsl4]

The problem I think is in the implementation of how new networks are proposed (unless I am missing something). If we choose two alleles on the same species that are not sisters in the network, do we want to allow moves on this tip? Currently, we do not. In the multiple alleles setup, we do not allow free moves on the tips and we force the two alleles from the same species to stay together as sisters

[crsl4]

I guess my overall question is: if all gene trees have the two alleles from one species not as sisters, do we want the network to also put the allele tips as not sisters (treat each allele tip as its own species) or do we want to force them as sisters because we know they are from the same species? Currently, we force them as sisters