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millanek / Dsuite

Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species
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Mixed sample size #62

Closed Jolvii85 closed 1 year ago

Jolvii85 commented 1 year ago

Hi,

I am analyzing a dataset with a mixed sample size, i.e. most species/groups have only 1 individual, and only 4 groups have multi-samples (6-8), is it ok to use such a dataset to perform Dsuite analysis?

And second question: if I have many species but all samples are haploid, is it ok to use such a dataset to run Dsuite?

Thank you!

feilchenfeldt commented 1 year ago

Hello @Jolvii85 ,

Having mixed sample size in different populations is not a problem.

In principle the method should also work for haploid individuals, only the f4ratio cannot be estimated for populations with a single haploid sample. I am not sure whether Dsuite would handle that nicely or not, but Dsuite has a --ploidy option to set the ploidy. That said, if they are truly haploid, do you expect to see introgression?

Best wishes, Hannes

millanek commented 1 year ago

I agree with Hannes' reply.

Best wishes Milan