Abstract Background and Aims Inferring 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. Methods We 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 Results Diploid 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. 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 polyploidization. Both processes reduced the extent of diversity available for breeding, and this is likely to threaten future adaptation.

中文翻译：

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全基因组基因分型阐明了多倍体和无性繁殖山药（Dioscorea alata）的地理多样化和分散

摘要 背景和目的 由于过去的人类迁徙问题尚未解决，因此推断许多人类分散物种的扩散历史仍然不是一件容易的事。同源多倍体和克隆繁殖的大山药（最古老的可食用块茎之一）的多样化中心和迁移路线仍不清楚。在这里，我们使用全球样本来解决山药人口统计和传播历史。方法我们通过对跨越四大洲的 643 个较大的山药种质进行测序，使用基因分型来表征全基因组的遗传变异模式。首先，我们通过下降方法使用等位基因频率分布和同一性来解开山药多样性的多倍体和克隆成分。然后，我们使用基于模型的聚结推理方法解决了山药的地理起源和传播历史。主要结果 二倍体基因型在全球范围内比三倍体和四倍体更常见。遗传多样性普遍较低，克隆性似乎是多样化的主要因素。最可能的进化情景支持东南亚和太平洋大陆基因库的早期分化，它们之间不断迁移。三倍体和四倍体的基因组成表明，它们在向西山药迁移之前起源于这两个地区。印度半岛基因库起源于非洲基因库，后来被引入加勒比地区。结论我们的结果与亚洲和太平洋两个主要基因库的独立驯化起源的假设一致。观察到的低遗传多样性和高克隆性表明存在强烈的驯化瓶颈，随后是数千年的广泛营养繁殖和多倍化。这两个过程都降低了可用于育种的多样性程度，这可能会威胁到未来的适应。