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East African Hunter-Gatherer Populations Share Common Genetic Ancestry

NEW YORK (GenomeWeb) – East African populations that are or were until recently hunter-gatherers share a common ancestry, according to a new analysis.

Anatomically modern humans arose in Africa about 300,000 years ago, but because the archaeological record within Africa is incomplete during the late Pleistocene, what is known about historical demographics is largely influenced by linguistic studies. But linguists have been divided on how to group some populations that speak click languages.

To address this and other questions, a University of Pennsylvania-led team of researchers analyzed the genomes of 840 Africans who belonged to 50 different ethnicities, spoke languages belonging to four different language groups, and followed various subsistence lifestyles. They reported in the Proceedings of the National Academy of Sciences yesterday that genetic structure in Africa is associated with geography, but also with language and lifestyle. In particular, they found common ancestry among click-speaking hunter-gatherer populations, even though they live in distinct regions of East Africa.

"Typically, what we see is that populations cluster by geography, but here we're seeing an exception to that," senior author Sarah Tishkoff from UPenn said in a statement. "Here you have three groups that either speak a click language, have remnant clicks, or have an unclassified language, and they're showing a common ancestry even though they're spread across different countries."

Tishkoff and her colleagues genotyped 724 individuals from 46 different populations in central and eastern Africa, and combined that data with publicly available data from Mbuti, San, Mandenka, and Mozabite individuals. In all, their datasets included 840 individuals from 50 populations who were genotyped at about 621,000 markers.

Through principal component analysis, they found that the samples clustered first by geography and then by language. In particular, individuals speaking Niger-Congo languages clustered together at the end of one axis and the San, who speak a click language, at the other end.

Additional population structure analyses likewise found that individuals from populations that speak languages belonging to the same language families share similar proportions of ancestral allele clusters.

When the researchers built a population tree based on genetic distances, they found that the Hadza, Sabue, Sandawe, and Dahalo — four geographically dispersed East African hunter-gather populations, three of which speak a language with click sounds — formed a clade, with the Hadza as a subclade with the Sabue. This suggests a common genetic ancestry of the populations, which the researchers traced back to more than 20,000 years ago, about the time of the beginning of the last glacial maximum.

"The idea is that this may have changed environmental conditions and introduced a barrier between populations," co-first author Laura Scheinfeldt, now with the Coriell Institute for Medical Research, said in a statement.

Meanwhile, other hunter-gather populations like the Wata, El Molo, and Yaaku exhibited shared ancestry with their agriculturalist and pastoralist neighbors.

The researchers also examined genome-wide patterns of adaptation and shared adaptive signals within these African populations. The MCM6 locus, which is located upstream of the lactase gene, stood out among several pastoralist populations, including the Eastern-Cushitic, Beja, Dato, Southern-Nilotic, and Fulani.

Many other loci with shared signals of selection are linked to the innate and adaptive immune systems. The researchers noted that these signals also correlated with whether or not malaria was endemic in the population's region and the population's subsistence strategy.

Other candidate loci were involved in digestion and metabolism. The researchers particularly noticed an enrichment of the cholesterol biosynthesis pathway among the predominantly pastoral southern-Nilotic population.

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