Male-biased migration from East Africa introduced pastoralism into southern Africa

Abstract

Background Hunter-gatherer lifestyles dominated the southern African landscape up to ~ 2000 years ago, when herding and farming groups started to arrive in the area. First, herding and livestock, likely of East African origin, appeared in southern Africa, preceding the arrival of the large-scale Bantu-speaking agro-pastoralist expansion that introduced West African-related genetic ancestry into the area. Present-day Khoekhoe-speaking Namaqua (or Nama in short) pastoralists show high proportions of East African admixture, linking the East African ancestry with Khoekhoe herders. Most other historical Khoekhoe populations have, however, disappeared over the last few centuries and their contribution to the genetic structure of present-day populations is not well understood. In our study, we analyzed genome-wide autosomal and full mitochondrial data from a population who trace their ancestry to the Khoekhoe-speaking Hessequa herders from the southern Cape region of what is now South Africa. Results We generated genome-wide data from 162 individuals and mitochondrial DNA data of a subset of 87 individuals, sampled in the Western Cape Province, South Africa, where the Hessequa population once lived. Using available comparative data from Khoe-speaking and related groups, we aligned genetic date estimates and admixture proportions to the archaeological proposed dates and routes for the arrival of the East African pastoralists in southern Africa. We identified several Afro-Asiatic-speaking pastoralist groups from Ethiopia and Tanzania who share high affinities with the East African ancestry present in southern Africa. We also found that the East African pastoralist expansion was heavily male-biased, akin to a pastoralist migration previously observed on the genetic level in ancient Europe, by which Pontic-Caspian Steppe pastoralist groups represented by the Yamnaya culture spread across the Eurasian continent during the late Neolithic/Bronze Age. Conclusion We propose that pastoralism in southern Africa arrived through male-biased migration of an East African Afro-Asiatic-related group(s) who introduced new subsistence and livestock practices to local southern African hunter-gatherers. Our results add to the understanding of historical human migration and mobility in Africa, connected to the spread of food-producing and livestock practices.

Wide-scale Geographical Analysis of Genetic Ancestry in the South African Coloured Population

“…However, we do not observe the same generation time-frame for the admixture event between Asian and West-African/Bantuspeaker ancestries in the SAC individuals, possibly indicating that most of these ancestries came from Asian, West-Africans, and Bantu-speakers directly, and not from Malagasy populations. This observation fits with the small Malagasy contributions observed at K = 11 (Supplementary Figure 5) and is in line with what has been observed in other SAC populations [11].…”

“…DNA was extracted using the prepIT L2P extraction protocol. The extraction of the biological samples and genotyping followed the procedure described in [11]. The data were generated in four genotyping runs on the Illumina Infinium TM H3Africa Consortium Array by the SNP&SEQ Technology Platform in Uppsala, Sweden.…”

Genome-wide variation in the Angolan Namib Desert reveals unique pre-Bantu ancestry

“…A defining characteristic of all these areas is an admixture history, which starts with the fusion between an eastern African ancestry and different resident southern African forager components, later followed by various degrees of admixture with Bantu speakers from the western and eastern streams of the Bantu migrations ( 19 ). Considering the available genetic, linguistic, and archaeological data ( 19 , 40 , 56 ), we hypothesize that proto–Khoe-Kwadi speakers split in the northwestern Kalahari, contrary to previous proposals that assume a southwestward movement from an intermediate homeland in northeastern Botswana ( 43 , 57 ). Following their split, the Khoe-Kwadi diverged into different groups migrating into specific contact areas (figs.…”

Evolutionary Genetics and Admixture in African Populations

“…Concordantly, another study estimated that all modern Khoe-San populations received 9–30% gene flow from an admixed East African/Eurasian pastoralist group 1.5–1.3 kya ( Schlebusch et al 2017 ). Furthermore, east African pastoralist contributions to Khoe-San groups are lower on X chromosomes than autosomes ( Vicente et al 2021 ), indicating that male-biased admixture occurred. Overall, these results suggest that eastern African pastoralists reached southern Africa prior to and independently of Bantu-speaking groups.…”