Post by djoser-xyyman on Jul 6, 2017 12:20:32 GMT -5
Notice that the time estimate is African “pastoralist” SLC24A5 is 5ky older than European. In other word…..no wonder Europeans were black about 6000BC. La Brana
---------------
Mechanisms of phenotype evolution
OTH-MP10
Rapid Evolution of Lighter Skin Pigmentation in Southern Africa
Meng Lin , Carlos Bustamante 3, 3, Brenna Henn 2
Abstract: Skin pigmentation is under strong directional selection, with lighter skin in northern European and East Asian populations, and darker skin in equatorial populations. However, selection on skin color and its mechanisms have only rarely been elucidated in studies of other populations worldwide. KhoeSan populations in far southern Africa, who are among the earliest diverged human populations, possess lightened skin pigmentation. We sequenced pigmentation genes to high coverage in over 400 KhoeSan individuals and demonstrate that a canonical skin pigmentation gene, SLC24A5, experienced recent adaptive evolution in the KhoeSan. The functionally causative skin lightening allele is present at a high frequency of 24% in the KhoeSan, ***after controlling ****for the recent European gene flow. The effect size of the allele is slightly larger than the mean pigmentation difference between Europeans and East Asians, explaining 11.9% of the variance in pigmentation in the KhoeSan. Haplotype analysis indicates that the derived haplotypes in these populations are identical to those fixed in Europeans. Using a hidden Markov model, we estimate the age of the ancestral haplotype carrying the derived allele in KhoeSan to be 18 kya [12 kya – 42 kya], somewhat older than the age of the allele in Europeans at 13 kya [6 kya – 41 kya]. We hypothesize!!!!!!! that the allele was only introduced into the KhoeSan within the past 3,000 years, likely by pastoralists moving from eastern Africa to southern Africa while retaining non-African admixture. We test this hypothesis using an approximate Bayesian computation (ABC) approach, incorporating demographic models and selection. The SLC24A5 locus is a rare example of strong, ongoing, parallel adaptation adopted through gene flow in recent human history. We demonstrate a novel strategy of tracing the selection on both the genotype and corresponding phenotype, by modeling the signal from the genetic association and its selection through demographic history.
Expanded summary*: Human skin pigmentation is among the most notably diverse phenotypes across populations. It’s also one of the most strongly selected phenotypes in the recent human adaptation history, mirroring the migration paths to different latitudes where ultraviolet radiation (UVR) varies. To present, the genetic basis and evolution of skin pigmentation have been primarily studied in light skinned northern Europeans and East Asians, mostly discovered through strong signals in selection scans. The evolution mechanism of skin color in other parts of the world remains a huge mystery.
In this study, we explore a rapid adaptation scenario of a skin lightening allele with large effect in KhoeSan population from the far southern Africa. Among the earliest diverged human populations, KhoeSan possess relatively light skin as compared to their Bantu-speaking neighbors. Through our association study in two KhoeSan communities, we found a large effect variant in the canonical pigmentation gene SLC24A5 that lightens skin pigmentation by 4 melanin units, and explains 12% of the phenotypic variance. This nonsynonymous variant is present at a high allele frequency of 38% in our cohort, which cannot be explained by the proportion of recent gene flow from Europeans. After targeted sequencing this region at high coverage in 430 individuals from this cohort, we demonstrate that the derived haplotypes in KhoeSan are identical to those fixed in Europeans, forming a strong starburst pattern in the network. Time of origin of the derived allele in the two populations are estimated to overlap with each other (18 kya[12 kya – 42 kya] in KhoeSan vs. 13kya[6 kya – 41 kya] in Europeans). The possible introduction of this allele to KhoeSan is about 2~3 kya via gene flow from eastern African pastoralists, who carried non-African admixture HA! Ha! hA! hA!. We test this hypothesis using an approximate Bayesian computation (ABC) approach, incorporating demographic models and selection.
The broader implications and significance include that 1) our finding shows a rare case of strong selection on an allele introduced through introgression in human history; 2) method wise, we demonstrate a novel strategy of tracing the selection on both the genotype and corresponding phenotype, by modeling the signal from the genetic association and its selection through demographic history; 3) as an example of exploring selection in an understudied population, our finding enriches the understanding of the story on convergent evolution of light skin pigmentation
