While there has been progress in our understanding of the origin and history of agriculture in sub-Saharan Africa, a unified perspective is still lacking on where and how major crops were domesticated in the region. Here, we investigated the domestication of African yam (Dioscorea rotundata), a key crop in early African agriculture. Using whole-genome resequencing and statistical models, we show that cultivated yam was domesticated from a forest species. We infer that the expansion of African yam agriculture started in the Niger River basin. This result, alongside with the origins of African rice and pearl millet, supports the hypothesis that the vicinity of the Niger River was a major cradle of African agriculture.

Background and Aims Inferring the diffusion history of many human-dispersed species is still not straightforward due to unsolved past human migrations. The centre of diversification and routes of migration of the autopolyploid and clonally propagated greater yam, Dioscorea alata, one of the oldest edible tubers is still unsolved. Here, we address yam demographic and dispersal history using a worldwide sample. Methods We characterized genome-wide patterns of genetic variation by genotyping by sequencing 643 greater yam accessions spanning four continents. First, we disentangled the polyploid and clonal components of yam diversity using alleles frequency distribution and identity by descent approaches. Then, we addressed yam geographical origin and diffusion history with a model-based coalescent inferential approach. Key Results Diploid genotypes were more frequent than triploids and tetraploids in all the continents. Genetic diversity was generally low and clonality appeared to be a main factor of diversification. The most likely evolutionary scenario supported an early divergence of mainland Southeast Asian and Pacific gene pools with continuous migration between them. Triploids and tetraploids genetic make-up suggests that they have originated from these two regions before westward yam migration. The Indian Peninsula gene pool gave origin to the African gene pool, which was later introduced in the Caribbean region. Conclusions Our results are congruent with the hypothesis of independent domestication origins of the two main Asian and Pacific gene pools. The low genetic diversity and high clonality observed suggest a strong domestication bottleneck followed by thousands of years of widespread vegetative propagation and polyploidisation. Both processes reduced the extent of diversity available for breeding, which most likely threaten future adaptation.