[adegenet-forum] DAPC in mixed ploidy species

[Jokela, Jukka]

thanks for developing DAPC, it is a really nice analysis tool.
I am working on triploid(asexual)-diploid(sexual) mixed populations with SNP markers which have two alleles per locus. I can score heterozygotes AB in both diploid and triploid but cannot separate AAB and ABB heterozygotes. Now I am analysing the data with DAPC as if all individuals were diploid, but I do know the ploidy of each individual and can use that as a prior substructure within populations if I want.

you write in your BMCGenetics paper (2010) about the versatility of DAPC with respect to ploidy. I understand this so that one can use data sets of different ploidy (I have done that, looks good and makes sense) but is a bit unclear what would happen if one has a mixed sample of alterative ploidy in the same dataset coded as diploid as I describe above. In my study species (Potamopyrgus antipodarum) triploids are supposedly derived from local sexual diploids, and this is one reason why we would like to ask if DAPC supports that prediction. I have now looked at the results but I am worried that using mixed samples as above is not justified and that I am introducing a bias that I cannot control. What would be your opinion?
Thanks a lot if you have time to comment on this.

cheers, jukka
jukka jokela / ETH-Zürich

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