Hello Biostars community,
I'm looking into population structure of honey bees using the programs ANGSD and NGSadmix. However, my samples represent a mix of both males, which are haploid, and females, which are diploid. My first pass at running these samples through the programs revealed strong structuring of males belonging to the same colony which leads me to believe that there is a skew for haploid individuals. This strong structuring is observed even after thinning for linkage disequilibrium. The challenge that I am facing is that the reference individuals, which help me identify known lineages, contains all diploid individuals. Thus, I'm wondering:
1) If someone could explain why haploid individuals may lead to potential biases in ancestral inference when also including diploid individuals in the analysis?
2) Are there flags that I can include in my ANGSD and NGSadmix analysis to handle multi-ploidy? Or, are there are programs which may be better suited to handle my specific data?