STANFORD (US) — Bushmen from southern Africa are most likely the source population from which all other African populations evolved, according to a large study of genetic variation.
The new research, which focuses attention in particular on those hunter-gatherers who speak one of the Khoisan languages, characterized by the presence of “click” sounds, contradicts previously held theories that modern humans originated in eastern Africa.
Details are published online in the journal Proceedings of the National Academy of Sciences.
About 60,000 years ago, modern humans left Africa and began the spread to other regions of the world. But the great genetic diversity of African populations made it hard to accurately predict where in Africa humans might have originated.
The continent has been inferred to be the origin for all modern human populations, with the earliest skulls of modern humans having been discovered in the east.
In addition, populations outside Africa contain a subset of the genetic diversity found there. As modern humans moved eastward, the level of variation decreased, reaching its minimum in the Americas.
But the details of genetic evolution within Africa have always been hazy.
This is mainly because African populations are some of the most genetically diverse in the world. A lack of sufficient genetic samples, especially from the hunter-gatherer populations, made it hard to infer much about early human evolutionary history.
“Our belief used to be that the center of humans leaving Africa was in East Africa,” says Marcus Feldman, professor of biology at Stanford University.
“We’ve just never had enough people represented in our studies before. Without the participation of these people, patterns of evolution within Africa can’t be determined.”
The current study provides “a much more satisfying answer,” Feldman says. “We just didn’t have as much DNA data earlier.”
Before this study, only a handful of Namibian Khoisan-speakers had been compared with other Africans. To get an accurate picture, researchers needed to compare genetics of different hunter-gatherer populations, as well as individuals within each population, at hundreds of thousands of sites in the DNA.
Feldman and postdoctoral fellow Brenna Henn, the paper’s first author, analyzed variations in the individual nucleotide bases that make up DNA and genotyped 650,000 such individual changes or “single-nucleotide polymorphisms” in people from 25 African populations.
Apart from the click-speaking hunter-gatherer populations from South Africa and Tanzania, they also studied Pygmies and 21 agriculturalist populations.
Statistical analysis showed the Bushmen have the greatest genetic variation and are most likely to be the source population from which all other African populations diverged.
Different genetic variants contain different combinations of genes, which can be thought of as appearing on a single string. Genetic recombination breaks these strings into smaller segments. The older the population, the shorter the segments and the greater the genetic variation.
It was already known that the most variation and hence the shortest segments occurred in Africa. The new study found that within Africa, the Bushmen have the shortest segments, and segment length increases as one moves from south to north.
More than 5,000 years ago, sub-Saharan Africa was populated mainly by linguistically and culturally diverse hunter-gatherer populations. Since then, most of these populations have either gone extinct or turned to agriculture and pastoral living, leaving only the Pygmies in central Africa, a click-speaking tribe of Tanzania, the Hadza, and southern African Bushmen, as the last hunter-gatherers.
“The paper is also fascinating in that some hunter-gatherer groups have never mixed with their neighbors,” says Feldman. “The mystery is whether there ever was a connection between the different click-speaking peoples in the past. Brenna and the team have shown that if such a connection ever existed, it was a long time before the invention of agriculture.”
Researchers found that certain immune system proteins that show up almost nowhere else on the planet occur at a relatively high frequency in one hunter-gatherer group. The scientists also found signs of natural selection related to genes involved in immune response and protection against pathogens.
Despite large ongoing projects, researchers still don’t know enough about human variation, Feldman says.
“There’s a tremendous amount of genomic variation, but not enough populations around the world have been studied. We don’t know very much about Australian Aboriginals, indigenous Americans or even South Asian people, who comprise nearly a sixth of the world’s population.”
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