Can we interpret significant gross result as "natural selection favored derived allele"?

[WeiCSong]

HI,
I notice that the GROSS result is derived from chi statistics and is non-negative, thus I'm a bit puzzle about the direction of detected positive selection. For an SNP with a significant GROSS result, can we state that the derived allele of this SNP is favored by natural selection, and its frequency was elevating during the tested branch? Thanks for your help.

[FerRacimo]

Hi Song, The score only provides evidence for positive selection along a specific branch of the graph. It will be the same regardless of whether the ancestral or derived allele is selected. What I recommend to do is, after finding sites and branches with strong evidence for selection (highly significant statistics), to then query the population allele frequencies in each of the population panels. If those populations subtended by the selected branch have the derived allele at high frequency (relative to those that are not subtended) then positive selection must have occurred on the derived allele. Hope that helps!

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On Fri, Apr 30, 2021 at 4:05 AM Song Weichen ***@***.***> wrote: HI, I notice that the GROSS result is derived from chi statistics and is non-negative, thus I'm a bit puzzle about the direction of detected positive selection. For an SNP with a significant GROSS result, can we state that the derived allele of this SNP is favored by natural selection, and its frequency was elevating during the tested branch? Thanks for your help. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#7>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABLXSAVEYQWAJNRQQZFZO63TLIF63ANCNFSM433DRJYQ> .

-- Fernando Racimo, PhD Associate Professor of Population Genetics Globe Institute University of Copenhagen Øster Voldgade 5-7, DK-1350 Copenhagen, Denmark

[WeiCSong]

Got it, thanks a lot!