outflank Fst vs uncorrected Fst odd results

[Gabriella Scatà]

Hi everyone,

this is more of a theoretical question about Outflank.

I hope you can provide your feedback or experience.

I know that the Uncorrected Fst (used by Outflank) should be similar to the corrected Fst, so they should lie on the middle line when plotting them against each other.

This would mean that the the sample is not so different across loci (I think).

However, in my case I have 2 lines of loci one shifted slightly higher than the other...I am assuming it means that a group of loci has different (I think higher ?) sample size than the other group of loci...now how much of a problem is this in Outflank?

In the Whitlock paper (2015), I read that "For datasets that have unequal sample sizes among populations but no missing data (i.e., all loci are equally unbalanced), the inference of outliers from our procedure will not be affected. However, for datasets that have large differences in per-population sample size among loci(perhaps due to sequencing errors or differences in coverage), inference on loci with different sampling properties than the rest of the dataset should be interpreted with caution and confirmed with re-sequencing".

In my case, I don't seem to  have different coverage/call rate of loci per population (as assessed through gl.report.callrate by locus), so does it mean I should not worry about this?

Plot attached.

I would appreciate any feedback!

Thank you!

Best,

Gabriella

[Gabriella Scatà]

Hi everyone,

just checking again if anyone has encountered this problem with outflank at all?

I have obtained a similar plot again where the corrected vs uncorrected Fst appear not to be highly correlated. I just feel that outflank would not be highly reliable in this case.

Would love some feedback from whoever among you is using this method often

Thanks!

Gabriella