Southern Africa has one of the longest records of fossil hominins and harbours the largest human genetic diversity in the world. Yet, despite its relevance for human origins and spread around the globe, the formation and processes of its gene pool in the past are still largely unknown. Here, we present a time transect of genome-wide sequences from nine individuals recovered from a single site in South Africa, Oakhurst Rockshelter. Spanning the whole Holocene, the ancient DNA of these individuals allows us to reconstruct the demographic trajectories of the indigenous San population and their ancestors during the last 10,000 years. We show that, in contrast to most regions around the world, the population history of southernmost Africa was not characterized by several waves of migration, replacement and admixture but by long-lasting genetic continuity from the early Holocene to the end of the Later Stone Age. Although the advent of pastoralism and farming substantially transformed the gene pool in most parts of southern Africa after 1,300 bp, we demonstrate using allele-frequency and identity-by-descent segment-based methods that the ‡Khomani San and Karretjiemense from South Africa still show direct signs of relatedness to the Oakhurst hunter-gatherers, a pattern obscured by recent, extensive non-Southern African admixture. Yet, some southern San in South Africa still preserve this ancient, Pleistocene-derived genetic signature, extending the period of genetic continuity until today.

南部非洲是人类化石记录最长的国家之一，拥有世界上最大的人类遗传多样性。然而，尽管它与人类起源相关并传播到全球，但过去其基因库的形成和过程在很大程度上仍然未知。在这里，我们展示了从南非的一个地点 Oakhurst Rockshelter 发现的 9 个个体的全基因组序列的时间横断面。跨越整个全新世，这些个体的古老 DNA 使我们能够重建过去 10,000 年土著 San 人口及其祖先的人口轨迹。我们表明，与世界上大多数地区相比，非洲最南端的人口历史并非以几波迁移、替代和混合为特征，而是从全新世早期到石器时代晚期结束的长期遗传连续性。尽管畜牧业和农业的出现在 1,300 bp 后极大地改变了南部非洲大部分地区的基因库，但我们使用等位基因频率和基于血统鉴定片段的方法证明，来自南非的 ‡Khomani San 和 Karretjiemense 仍然显示出与 Oakhurst 狩猎采集者的直接相关性迹象，这种模式被最近广泛的非南部非洲混合所掩盖。然而，南非南部的一些桑人仍然保留了这种古老的、源自更新世的遗传特征，将遗传连续性延长到今天。