Ancient DNA is revealing the origins of livestock herding in Africa

Visitors to East Africa are often amazed by massive herds of cattle with a gorgeous array of horn, hump and coat patterns. Pastoralism – a way of life centered around herding – is a central part of many Africans’ identity. It’s also a key economic strategy that is now threatened by climate change, rising demands for meat, urban sprawl and land conflicts.

Pastoralism’s roots could hold clues to help solve these modern challenges. Studies suggest that traditional ways of managing livestock – moving around and exchanging with other herders – enabled herders to cope with environmental instability and economic change over the past several thousand years. Research is also helping scientists understand how millennia of herding – and livestock dung – have shaped East Africa’s savannas and wildlife diversity.

So how did pastoralism get started in Africa? Currently most archaeologists think wild ancestors of today’s domestic cattle, sheep and goats were first domesticated in the “Fertile Crescent” of the Middle East. Archaeological research shows herding began to appear in and spread from what is now Egypt around 8,000 years ago. By 5,000 years ago, herders were burying their dead in elaborate monumental cemeteries near a lakeshore in Kenya. Two millennia later, pastoralist settlements were present across a wide part of East Africa and by at least 2,000 years ago, livestock appear in South Africa.

Large herds of cattle graze near Lake Manyara in Tanzania, where they’ve been a key part of the economy for 3,000 years. Mary Prendergast, CC BY-ND
Much remains unanswered: Did animals spread mostly through exchange, just like cash circulates widely while people mostly stay put? Were people moving long distances with their herds, traversing the continent generation by generation? Were there many separate migrations or few, and what happened when immigrant herders met indigenous foragers? We decided to ask these questions using ancient DNA from archaeological skeletons from across East Africa.

Piecing together the genetic history of herders

Archaeologists study ancient people’s trash – broken clay pots, abandoned jewelry, leftover meals, even feces – but we also study the people themselves. Bioarchaeologists examine human bones and teeth as indicators of health, lifestyle and identity.

Now it’s also possible to sequence ancient DNA to look at genetic ancestry. Until recently, though, Africa has been on the sidelines of the “ancient DNA revolution” for a variety of reasons. Advances in DNA sequencing have created new opportunities to study African population history.

In our new research, our team sequenced the genomes of 41 people buried at archaeological sites in Kenya and Tanzania, more than doubling the number of ancient individuals with genome-wide data from sub-Saharan Africa. We obtained radiocarbon dates from the bones of 35 of these people – important because direct dates on human remains are virtually nonexistent in East Africa. Working as a team meant forging partnerships among curators, archaeologists and geneticists, despite our different work cultures and specialized vocabularies.

The people we studied were buried with a wide variety of archaeological evidence linking them to foraging, pastoralism and, in one case, farming. These associations are not airtight – people may have shifted between foraging and herding – but we rely on cultural traditions, artifact types and food remains to try to understand how people were getting their meals.

Red dots are archaeological sites in the authors’ study. Gray dots mark selected Rift Valley sites. Prettejohn’s Gully geological survey, marked by a black star, produced the oldest ancient DNA in Kenya. Elizabeth Sawchuk, CC BY-ND
After we grouped individuals based on the lifestyles we inferred from associated archaeological evidence, we compared their ancient genomes to those of hundreds of living people, and a few dozen ancient people from across Africa and the adjacent Middle East. We were looking for patterns of genetic relatedness.

Some of our ancient samples did not resemble other known groups. Despite major efforts to document the vast genetic variation in Africa, there’s a long way to go. There are still gaps in modern data, and no ancient data at all for much of the continent. Although we can identify groups that share genetic similarities with the ancient herders, this picture no doubt will become clearer as more data become available.

Herding expanded in stages

So far we can tell that herding spread via a complex, multi-step process. The first step involved a “ghost population” – one for which we don’t have direct genetic evidence yet. These people drew about half of their ancestry from groups who lived in either the Middle East or presumably northeastern Africa (a region for which we have no relevant aDNA) or both, and about half from Sudanese groups. As this group spread southward – likely with livestock – they interacted and genetically integrated with foragers already living in East Africa. This period of interaction lasted from perhaps around 4,500-3,500 years ago.