South Eastern Bantu-speaking (SEB) groups constitute more than 80% of the population in South Africa. Despite clear linguistic and geographic diversity, the genetic differences between these groups have not been systematically investigated. Based on genome-wide data of over 5000 individuals, representing eight major SEB groups, we provide strong evidence for fine-scale population structure that broadly aligns with geographic distribution and is also congruent with linguistic phylogeny (separation of Nguni, Sotho-Tswana and Tsonga speakers). Although differential Khoe-San admixture plays a key role, the structure persists after Khoe-San ancestry-masking. The timing of admixture, levels of sex-biased gene flow and population size dynamics also highlight differences in the demographic histories of individual groups. The comparisons with five Iron Age farmer genomes further support genetic continuity over ~400 years in certain regions of the country. Simulated trait genome-wide association studies further show that the observed population structure could have major implications for biomedical genomics research in South Africa.

中文翻译：

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南非班图人的遗传子结构和复杂的人口历史

讲东南语（SEB）的人群占南非人口的80％以上。尽管语言和地理上存在明显差异，但尚未系统研究这些群体之间的遗传差异。基于代表8个主要SEB组的5000多个个体的全基因组数据，我们为具有与地理分布大致一致的精细规模的人口结构提供了有力的证据，并且还与语言系统发育一致（Nguni，Sotho-Tswana和Tsonga的分离）扬声器）。尽管差异化的Khoe-San外加剂起关键作用，但在Khoe-San祖先掩盖后该结构仍然存在。混合的时间，性别偏向的基因流水平和种群大小动态也突出了各个群体的人口历史差异。与五个铁器时代农民基因组的比较进一步支持了该国某些地区约400年的遗传连续性。模拟性状全基因组关联研究进一步表明，观察到的种群结构可能会对南非的生物医学基因组学研究产生重大影响。