Whole-genome sequencing of African hunter-gatherers reveals human genetic diversity

Africa is the ancestral homeland of all modern humans and contains the highest level of genetic diversity among all of the continents. "Even though African populations have played an important role in human evolutionary history, relatively little is known about variation in African genomes," says senior study author Sarah Tishkoff of the University of Pennsylvania. Until now, scientists have analyzed only six African genomes that had been sequenced at high coverage, which involves sequencing regions numerous times to achieve high accuracy.

To gain a deeper understanding of human genetic diversity and the genetic basis of adaptation to diverse environments, Tishkoff and her team sequenced the whole genomes of 15 African hunter-gatherers from three different populations: forest-dwelling, short-statured Pygmies from Cameroon, and click-speaking Hadza and Sandawe individuals from Tanzania. The researchers identified more than 13 million variations in DNA sequences in these genomes, and more than 3 million of these were absent from existing databases. "This is the first population genomics analysis using high-coverage whole-genome sequencing," Tishkoff says. "Many of the variants we found would not have been identified without this kind of analysis."

The study also revealed genetic signs of natural selection. Compared with agricultural and pastoral populations, the hunter-gatherer populations showed distinct DNA patterns in genes involved in immunity, metabolism, smell, and taste, suggesting that the populations adapted to specific pathogens, food sources, and other local environmental factors. Moreover, the researchers identified several candidate genes that could be responsible for short stature in Pygmies. In addition, they found evidence of ancient interbreeding between the ancestors of modern Africans and another hominin lineage. "Our study has not only vastly increased knowledge about human genomic variation, but also shed light on human evolutionary history and the origins of traits that make each of us unique," Tishkoff says.