Stanford researchers find that modern humans originated in southern Africa

Modern humans likely originated in southern Africa, rather than eastern Africa as is generally assumed, according to the results of a large study of genetic variation.

Photos courtesy of Brenna Henn Khomani Bushman woman and her grandchild

The research focused on the Khomani, such as this Bushman woman and her grandchild, who live in the Kalahari desert of South Africa.

The largest analysis of the genomic diversity of African hunter-gatherer populations reveals that modern humans likely originated in southern Africa, rather than eastern Africa as is generally assumed. This study provides the clearest idea of where modern humans actually originated.

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.

Now, a Stanford team led by postdoctoral fellow Brenna Henn of the Department of Genetics and biology Professor Marcus Feldman has found that modern humans likely originated in southern Africa. To come to this conclusion, the researchers analyzed the largest dataset to date for hunter-gatherer populations. The study appears online March 7 in the Proceedings of the National Academy of Sciences.

"Our belief used to be that the center of humans leaving Africa was in East Africa. This paper focuses attention on southern Africa, and in particular to a group of hunter-gatherers, the Bushmen, who speak one of the Khoisan languages," said Feldman. These languages are characterized by the presence of "click" sounds.

Africa has been inferred to be the continent of origin for all modern human populations, with the earliest skulls of modern humans having been discovered in east Africa. 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. "We've just never had enough people represented in our studies before," Feldman said. "Without the participation of these people, patterns of evolution within Africa can't be determined," he said.

Researchers Brenna Henn and Christopher Gignoux conducting field interviews

Researchers Brenna Henn, center, and Christopher Gignoux collecting genetic samples for the study in a Khomani Bushmen community.

The current study provides "a much more satisfying answer," said Feldman. "We just didn’t have as much DNA data earlier," he said. Before this study, only a handful of Namibian Khoisan-speakers had been compared with other Africans. To get an accurate picture, the group needed to compare the genetics of different hunter-gatherer populations, as well as individuals within each population, at hundreds of thousands of sites in the DNA. According to Feldman, the researchers needed the participation of more Bushmen, and Brenna Henn, the paper’s first author, accomplished this.

The scientists analyzed variations in the individual nucleotide bases that make up DNA. They 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 that the Bushmen had 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," said 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."

As evidence of the uniqueness of some of these populations, the researchers found that certain immune system proteins that show up almost nowhere else on the planet occurred 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.

Henn and Julie Granka, a graduate student in biology, recently revisited the South African Bushmen who participated in the study and took height and skin color measurements from the people whose DNA they had analyzed. "We will be collaborating with several South African scholars to look at such phenotypes in more detail," Feldman said.

According to Feldman, despite some large ongoing projects researchers still don't know enough about human variation. "There's a tremendous amount of genomic variation," he said, "but not enough populations around the world have been studied." For example, "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," Feldman said.

Feldman said that he and other researchers working with the Human Genome Diversity Project, based at CEPH (Centre d'Étude du Polymorphisme Humain) in Paris, hope to engage other populations around the world in the search for their evolutionary ancestry. "There are lots of evolutionary problems that are still to be solved," he said, "and analysis of DNA is our best chance to solve them."

Sandeep Ravindran is a science-writing intern at the Stanford News Service.

Dan Stober, Stanford News Service: (650) 721-6965,