Can BONE handle admixture?

[kwojtusik]

Hello Dr. @markkukuismin,

This is not an issue but a question about BONE.

As indicated by the title, I was curious if/how BONE might handle admixture. I am working on trying to conduct mixed stock analyses on an anadromous fish, however, some of our baseline populations show evidence of gene flow/admixture. However, our population genetic analyses showed that our baseline populations were in fact genetically distinct, despite this admixture.

We were going to use Rubias to conduct our mixture analyses, however the bayesian model it is built upon cannot handle any admixture among baseline populations, which led me to finding BONE.

So my question is, can BONE accurately assign mixture individuals in the face of admixture in the baseline populations?

Thank you.

-Kris

[markkukuismin]

Hello Kris,

the admixture in the baseline is not taken into account in the model part of the BONE procedure and very strong admixture in the baseline populations has an effect on the assignment accuracy. If you want to use BONE, I recommend that you use the WTA method which can somewhat mitigate the assignment error caused by the admixture in the baseline populations.

Best,
Markku