Abstract
Background and AimsInferring the diffusion history of many human-dispersed species is still not straightforward due to unresolved 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, remain unclear. Here, we address yam demographic and dispersal history using a worldwide sample.MethodsWe characterized genome-wide patterns of genetic variation using genotyping by sequencing 643 greater yam accessions spanning four continents. First, we disentangled the polyploid and clonal components of yam diversity using allele frequency distribution and identity by descent approaches. We then addressed yam geographical origin and diffusion history with a model-based coalescent inferential approach.Key ResultsDiploid genotypes were more frequent than triploids and tetraploids worldwide. 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. The genetic make-up of triploids and tetraploids 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 to the Caribbean region.ConclusionsOur 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 polyploidization. Both processes reduced the extent of diversity available for breeding, and this is likely to threaten future adaptation.
Highlights
The present geographical distribution of flora and fauna is often the result of a long process of human-mediated dispersal, which had profound effects on the genetic diversity and demographic histories of plant and animal populations (Boivin et al, 2012; Almathena et al, 2016)
genotyping by sequencing (GBS) of all samples produced more than 5 billion raw reads that were mapped to the D. rotundata V1 reference genome (Tamiru et al, 2017), resulting in the identification of 15 048 820 Single nucleotide polymorphism (SNP)
We showed that worldwide diversity of greater yam is characterized by a high extent of clonality, corroborating findings from our previous studies (Arnau et al, 2017)
Summary
The present geographical distribution of flora and fauna is often the result of a long process of human-mediated dispersal, which had profound effects on the genetic diversity and demographic histories of plant and animal populations (Boivin et al, 2012; Almathena et al, 2016). From a practical point of view, addressing the diffusion and diversification of domesticated species gives insight into diversity that is relevant for breeding programmes and metrics for biodiversity conservation. After domestication in their centres of origin, most crop species have gone through different waves of translocation through human migrations and have colonized different continents. Significant progress in our understanding of crop domestication and evolution has been made in recent years thanks to the development of whole genomic approaches and the availability of genome sequences for many species, such as cassava (Bredeson et al, 2016), potato (Hardigan et al, 2017), maize (Kistler et al, 2018) and rice (Choi and Purugganan, 2018)
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