how to understand the picture of frequency spectrum of two populations

[gump vito]

hi Ryan

the EPAS1 strong deviated from dominated continuous spectrum in the picture

 in <Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude>
i just wonder may i say "continuous allele frequency spectrum suggest that most of the allele frequency are dominated by the population drift rather than incomplete lineage sorting ,gene flow or selection"
are there more examples?

[Gutenkunst, Ryan N - (rgutenk)]

Hello Gump Vito,

A continuous spectrum is perfectly compatible with incomplete lineage sorting, gene flow, and broad scale selection. The EPAS1 story is that they have two strong outliers, suggesting some strong local selection.

I’m not aware of other examples with such strong outliers with a nice story behind them, but I can’t follow all the literature that has applied AFS analysis.

Best,

Ryan

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Ryan Gutenkunst
Assistant Professor of Molecular and Cellular Biology, University of Arizona
phone: (520) 626-0569, office: LSS 325, web: http://gutengroup.mcb.arizona.edu

Latest papers: 
“Selection on network dynamics drives differential rates of protein domain evolution”
PLoS Genetics; http://dx.doi.org/10.1371/journal.pgen.1006132
"Triallelic population genomics for inferring correlated fitness effects of same site nonsynonymous mutations"
Genetics; http://dx.doi.org/10.1534/genetics.115.184812

[gump vito]

so it looks like my understanding with some mistakes . for instance , does these pictures look like with incomplete lineage sorting, gene flow? and may i ask why? thank you so much.

[Gutenkunst, Ryan N - (rgutenk)]

It’s not obvious from these pictures. That’s why we fit models. See the dadi paper for discussion of how the frequency spectrum differentiates migration from reduced divergence.

(Although I note your second spectrum is strange given the large number of fixed fixed differences and low number of nearly-fixed.)

Best,

Ryan