African pygmies may be older than thought

Despite their diminutive size, African pygmies have taken a giant step back in time. A new genetic investigation indicates that common ancestors of these hunter-gatherers and their taller, farming neighbors diverged approximately 60,000 years ago.

Cold temperatures and a decline in rainfall at that time, already linked to ancient human migrations out of Africa, sparked the evolution of different human populations within Africa, conclude geneticist Lluís Quintana-Murci of the Pasteur Institute in Paris and his colleagues.

If the new genetic scenario holds up, it undermines an earlier proposal that ancestors of today’s pygmies and farmers parted ways as agriculture took root in sub-Saharan Africa around 5,000 years ago, the researchers say in a paper published online April 9 in PLoS Genetics.

Little is known about the prehistoric roots of these people because fossils and cultural remains disintegrate rapidly in the acidic soils of equatorial rainforests.

A 2008 study directed by Quintana-Murci, based on an analysis of one mitochondrial DNA region, suggested that maternal ancestors of African pygmies and farmers diverged no more than 70,000 years ago. The new study focused on 23 nuclear DNA regions and one stretch of mitochondrial DNA.

“We can now provide a more general view of the genetic history of these African populations,” Quintana-Murci says.

Quintana-Murci’s team further concludes that two groups of modern-day pygmies, one located in west-central Africa and the other in east-central Africa, separated from an ancestral population roughly 20,000 years ago. That makes sense in light of earlier evidence that global cooling around that time led to a shrinking of central African forests into separate eastern and western zones, where different groups of pygmies would have settled, according to the researchers.

Still, pygmies’ retreat into different forested regions did not totally prevent gene flow between western and eastern groups, the new study suggests. In addition, the study finds that Bakola pygmies in western Africa and Twa pygmies in eastern Africa share a substantial amount of DNA with neighboring farmers, suggesting breeding with the taller populations.

Pygmies’ DNA also contains signatures of steep population declines that occurred as recently as 250 years ago in eastern Africa and 2,500 years ago in western Africa. Agricultural expansion into forests or major epidemics could have drastically cut pygmies’ numbers, Quintana-Murci speculates.

“Despite some limitations, this paper helps clarify the demographic history of African pygmies,” remarks geneticist Céline Becquet of the University of California, Berkeley.

But, Becquet cautions, the data allow a wide range of possible age estimates for the initial split of pygmy and farmer ancestors, as well as the later split of eastern and western pygmy groups. Thus, the team’s calculations for the timing of population divisions may be off by a few thousand or even tens of thousands of years, in her view.

If pygmies indeed split into eastern and western groups around 20,000 years ago, it’s also unclear when they began to interbreed with nearby farmers, Becquet adds.

Quintana-Murci and his colleagues’ study investigated present-day genetic variation in 236 Africans recruited from five agricultural and seven pygmy populations. Participants came either from eastern or western Africa.

Analyses focused on patterns of variation in genetic regions uninvolved in protein production. By sticking to those areas, which have a presumed constant mutation rate, the scientists could reconstruct evolutionary relationships among African groups and estimate times of ancient population splits.

Computer simulations of different evolutionary scenarios yielded a model that most closely fit the genetic data.