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Study Uncovers Genetic Patterns in Click-Speaking Populations in Sub-Saharan Africa

NEW YORK (GenomeWeb News) – Modern humans may have originated from multiple sites within Africa, according to a genetic study that provides new details about the history of click-speaking populations in sub-Saharan Africa.

Researchers from Sweden, South Africa, France, and the US used arrays to look at genome-wide SNP patterns in hundreds of individuals from southern Africa. These included representatives from seven Khoe and San click-speaking populations in sub-Saharan Africa. Previous analyses have shown that these Khoisan populations, which appear to have descended from a deeply diverged modern human lineage, have very high genetic diversity.

As they reported in the early, online edition of Science today, the researchers estimated that the ancestors of these populations split from other modern humans in Africa more than 100,000 years ago. The populations appear to have remained relatively genetically isolated, though individuals from at least one pastoral Khoe population, the Nama, carry sequences in their genomes that are reminiscent of those found in East Africa's Maasai population, hinting at historical mixing between these groups.

"The most striking result is the deep population structure that we find," Uppsala University evolutionary biologist Mattias Jakobsson, the study's senior author, said during a telephone briefing with reporters this week. "The deepest split that we find, if we try to put on a population divergence model, is between Khoisan individuals and all other humans including other sub-Saharan Africans and non-Africans."

For their analyses, Jakobsson and his colleagues genotyped 220 individuals at roughly 2.3 million SNPs genome-wide. These included individuals from seven Khoe or San populations as well as representatives from other populations in southern Africa.

Their analyses suggest that the lineage leading to the Khoe-San populations split from other modern human groups is at least 100,000 years ago — roughly twice as far back as the split estimated for Central African Pygmy populations, which were next to diverge.

Within the click-speaking Khoe and San populations themselves, researchers saw inter-population divergence times stretching back some 35,000 years, most notably between northern and southern Khoisan groups.

They also uncovered subtle genetic differences between a pastoral Khoe population known as the Nama and the San populations, which have traditionally had a hunter-gatherer lifestyle.

While the Nama population clusters genetically with present-day southern San populations, it also contains a small amount of East African ancestry that is most similar to the genetic profiles described for the Maasai, a pastoral population from Kenya and Tanzania.

Because this East African ancestry was absent or found at very low frequencies in the San populations, study authors suspected that mixing between ancestors of the Nama and the Maasai may have coincided with the introduction of pastoral practices to southern Africa.

"We put the hypothesis forward that the Nama originated from a southern San population that adopted pastoralist practices from an East African group," first author Carina Schlebusch, an evolutionary biology researcher based at Uppsala University, said during this week's press briefing. "And together with the adoption of this cultural practice, this subsistence practice, there was also a limited amount of gene flow."

Consistent with that notion, researchers found that around 50 percent of individuals from the Nama population carry a genetic haplotype implicated in lactase persistence in the Maasai. That same haplotype is far less common in the San populations or in Bantu-speaking pastoralist populations.

Another analysis — a search for population-specific signals of selection — led the investigators to immune genes, which showed signs of selection in the southern San populations. In at least one of the northern San populations, on the other hand, they saw selective signals associated with a muscle function gene. Meanwhile, signs of selection in the Nama population pointed to a gene involved in UV-light protection.

In addition, by bringing together the Khoe-San genetic data with information on other human populations, researchers got a glimpse at genetic changes that may have spurred the evolution of some of the anatomical features that are distinct to modern humans.

Specifically, the team used a method known as the ancestral population branch statistic, or APBS, to search for derived variants or sets of variants that are shared across existing human populations, Jakobsson explained. "Those regions, they should pinpoint genes that have been modified or changed prior to the first split or the deepest splits among modern humans — prior to 100,000 years ago."

That analysis highlighted genes involved in skeletal morphology and cartilage-related pathways. And, encouragingly for the study's authors, prior research indicated that alterations to at least one of the genes identified, RUNX2, can cause brow ridges and rib cage structures reminiscent of those described in Neandertals.

Even so, researchers say, they weren't able to trace modern human origins back to any one region in Africa. Rather, Jakobsson said, "different parts of Africa show up as potentially being the origin of anatomically modern humans."

"So, that leads us to kind of a postulate that potentially modern humans arose from a structured population or a non-homogenous group," he added.

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