As it was domesticated, the African yam got bigger, starchier, and more regular in shape.

SIA KAMBOU/AFP/GETTY IMAGES

Plant studies show where Africa’s early farmers tamed some of the continent’s key crops

Wheat and other plants that feed much of the world today were likely first domesticated in the Fertile Crescent of the Middle East. But another early cradle of agriculture lay thousands of kilometers away, around West Africa's Niger River Basin, a flurry of plant genomic studies is showing. Several of the continent's traditional food crops got their start there: a cereal called pearl millet and Africa's own version of rice. Now, a report out this week in Science Advances adds yams to the list of African crops domesticated thousands of years ago in that same area. A drying climate may have spurred the move to farming, says Yves Vigouroux, a population geneticist at the French Research Institute for Development (IRD) in Montpellier who led some of the new work.

The recent findings pinpoint the wild ancestors of some of Africa's most important crops, highlighting reservoirs of genes that could be exploited to boost the productivity and disease resistance of the domesticated varieties, he adds. Such improvements could be life savers on a continent where population is expanding, and climate change threatens crop yields. "When we study evolution of crops across time, it helps us to see varieties [that] are more resilient," says Alemseged Beldados, an archaeobotanist at Addis Ababa University. "It will help us single out better breeds."

Generations of archaeologists have studied plant domestication in the Middle East as well as in Asia and the Americas. "But Africa has very much lagged behind," says Dorian Fuller, an archaeobotanist at University College London. Plant fossils and farming artifacts are less likely to be preserved in Africa's warm, moist environments, funding is scarce, and field research often faces political and logistical challenges.

Genetic studies, however, bypass some of these difficulties. In 2002, Nora Scarcelli, a population geneticist colleague of Vigouroux's at IRD, took an interest in yams, the most important root crop in Africa before the introduction of cassava in the 1500s and still more important than maize in parts of Africa.

The vines of the African yam (Dioscorea rotundata) produce large tubers that look a bit like American sweet potatoes (sometimes mistakenly called yams), but the plant is a different species that is also distinct from Asian yams. But whether the modern African crop was derived from D. abyssinica, a wild yam that grows in the savanna, or D. praehensilis, which thrives in the wetter rainforests, was not known. Hoping to resolve the issue, Scarcelli and colleagues recently sequenced and compared 167 genomes of wild and domesticated yams gathered from Ghana, Benin, Nigeria, and Cameroon. The DNA of savanna wild yams was fairly similar, but the forest wild yams split into two groups, one centered in Cameroon and another much farther west.

Wild yams such as these were cultivated into an African crop.

NORA SCARCELLI/IRD

Scarcelli, Vigouroux, and their colleagues further identified forest yams in the Niger River Basin, between eastern Ghana and western Nigeria, as the source of the modern domesticate. Their analysis could not pinpoint the date of domestication, but it did identify genes that changed along the way. Variations in genes for water regulation probably helped convert a forest dweller into a plant that thrives in open sun. Alterations in root development and starch production genes also likely made tubers regularly shaped and richer in starch.

A similar study of pearl millet (Cenchrus americanus), the most important cereal for arid areas of Africa and Asia with poor soils, also pointed to a West African origin. When Vigouroux and his colleagues sequenced and compared the genomes of 221 wild (Pennisetum glaucum monodii) and domesticated millets, they concluded that all domesticated pearl millet varieties came from a single ancestor growing north of the Niger River in part of the western Sahara Desert that today includes northern Mali and Mauritania. The genetic work, reported last year in Nature Ecology & Evolution, dovetails nicely with a 2011 discovery of 4500-year-old pearl millet remains in an archaeological site in southeastern Mali, Fuller adds.

Previous studies had shown that about 6000 years ago, probably before millet was domesticated, a moist climate created a network of lakes in the region, yielding abundant wild food. As the climate dried and those lakes vanished, Vigouroux hypothesizes, the local people began to cultivate plants.

And over more time, people and plants shifted southward, with cultivated plants intermittently interbreeding with wild plants. The mingling slowed full domestication but added genetic variation to the millet. "Our findings stressed the importance of wild-to-crop gene flow during and after crop domestication," Vigouroux and his colleagues wrote.

African rice (Oryza glaberrima) is less important today than the other traditional crops, having been mostly replaced with Asian rice. But it, too, got a West African start. Last year in Current Biology, Vigouroux and his colleagues analyzed 163 varieties of the domesticated African rice and 83 samples of wild rice collected from west and east Africa. Their analysis showed the cultivated species has about half as much genetic diversity as the wild species, and that it arose from wild relatives in northern Mali. They also found that some of the same genetic changes central to the taming of Asian rice, such as a gene deletion that made the plant grow more erect, also played a part in the domestication of African rice.

Other researchers have tracked down additional genes that aided African rice domestication. In the March issue of PLOS Genetics, they described the evolution of genes that make rice seeds less likely to fall off the stalks. Such a detailed history is easier to piece together for African rice than Asian rice because so many wild populations are still intact, says evolutionary geneticist Michael Purugganan of New York University in New York City, who led the work. Studies in Africa "may tell us more about crop domestication than what people have learned about other crops elsewhere," he adds.

While Vigouroux focuses on climate to explain why agriculture arose in this part of Africa, archaeologist Sylvain Ozainne from the University of Geneva in Switzerland suggests movements of Saharan pastoralists helped initiate and spread a culture of crop growing, particularly of pearl millet. "Rather than a direct response to abrupt climatic change, the expansion of African agriculture may be better explained through a more complex process, which involved socioeconomic transformations," he says.

In Africa, as elsewhere, crop domestication was a long, drawn-out process. It happened outside the Niger River Basin as well. Sorghum was likely tamed in East Africa. Last month, Nature Plants published a genetic analysis of wild and domesticated sorghum samples excavated from an archaeological site in Egypt that spans several thousands years. It showed that early farmers either deliberately crossed this crop—now the sixth most widely grown in the world—with wild relatives and with domesticates from other places, or cultivated varieties that naturally interbred.

All this genetic exchange ultimately helped improve the final crop, says Emuobosa Akpo Orijemie, an archaeobotanist at the University of Ibadan in Nigeria. The new findings, he adds, "speak about how intelligent our ancestors were in terms of selecting and managing crops for a variety of uses."

*Correction, 3 May, 9:50 a.m.: An earlier version of this story misstated that the Nok were Saharan pastoralists.