December 12, 2013

No evidence for selection since admixture in sample of 29,141 African Americans

arXiv:1312.2675 [q-bio.PE]

Genome-wide scan of 29,141 African Americans finds no evidence of selection since admixture

Gaurav Bhatia et al.

We scanned through the genomes of 29,141 African Americans, searching for loci where the average proportion of African ancestry deviates significantly from the genome-wide average. We failed to find any genome-wide significant deviations, and conclude that any selection in African Americans since admixture is sufficiently weak that it falls below the threshold of our power to detect it using a large sample size. These results stand in contrast to the findings of a recent study of selection in African Americans. That study, which had 15 times fewer samples, reported six loci with significant deviations. We show that the discrepancy is likely due to insufficient correction for multiple hypothesis testing in the previous study. The same study reported 14 loci that showed greater population differentiation between African Americans and Nigerian Yoruba than would be expected in the absence of natural selection. Four such loci were previously shown to be genome-wide significant and likely to be affected by selection, but we show that most of the 10 additional loci are likely to be false positives. Additionally, the most parsimonious explanation for the loci that have significant evidence of unusual differentiation in frequency between Nigerians and Africans Americans is selection in Africa prior to their forced migration to the Americas.

Link

6 comments:

eurologist said...

Additionally, the most parsimonious explanation for the loci that have significant evidence of unusual differentiation in frequency between Nigerians and Africans Americans is selection in Africa prior to their forced migration to the Americas.

Or, during transport - like the retention of salt in hot environments with insufficient hydration and salt intake (the "cargo hold" of the transporting boat).

astenb said...

Or perhaps all African Americans do not come from Nigeria.

Grognard said...

Doesn't seem like a very reasonable conclusion, sounds like one or the other papers has a bad methodology. Since this one is claiming that the difference means nothing, I am guessing it's this one.

Even if there was selection on before slaves show up in america it will show linkage disequilibrium. But if it's not selection they are saying it's just a big coincidence that the results are different.

I am pretty sure the other paper did detect linkage disequillibrium so I have to conclude this is probably invalid.

Annie Mouse said...

Not sure I trust the conclusions of this paper. I cant get to the link, but if they only looked at Nigerians as a Yoruba proxy, then the study is flawed from the start. African Americans have more diverse origins, including the Mandinka. Plus a lot of folk travelled first to the Caribbean before moving on to the mainland. That has been shown to populated by multiple waves of Africans from different regions.

Basically they differ from Nigerians because in general they weren't just Nigerians.

Interesting exercise though, the idea of tracking selection in historical times.

I wondering if they would have seen a pattern if they looked at the folk who bred into the white population and live on as small fragments in the colonial white population. These folk avoided discrimination, and had the resources to obtain more prestigious pale partners in the first place. In that sense can be regarded as more "successful".

raymond finney said...

Is this some sort of revelation. Quit using fantasy for history. The people who wanted and used slavery did not care what the slaves looked like or where they came from.

That is why black Americans look the way they do. That is why Puerto Ricans and Dominicans look the way they do.

Enslaved people came from all over the globe and its a fact. Research it yourselves.

The entertainment industry and educational institutions need for slaves to be a specific "type" of African so that their "paying audiences" and "students" will feel less guilty. Which is a testimony to how sick the audiences and students are. It should not make any difference to those clowns what the enslaved person looked like, but to them it does for some reason.

Unknown said...

It may depend on the sample size and location. There is no doubt that many African American came from West Africa but a recent (N=1) sample pertaining to Morgan Freeman showed a Mali-Mauritania connection based on where an ancestor was captured and shipped to the "land of freedom for all" by US capitalist interests. Other studies show that although U6 has been seen in Cameroon and surrounding areas, that specific identification is not seen in African American populations studied. Where is this leading? Perhaps nowhere but it is a telling example of what researchers are looking for and the ideas they carry about their research.