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.
ADDITIONAL FILE 1: PDF file with supplementary figures: FIGURE S1. Distribution of Cape Khoekhoe groups along the Cape west, south and southeast coasts. FIGURE S2. ADMIXTURE clustering analysis. The analyses are based on 1811 samples with 233,254 overlapping autosomal SNPs. FIGURE S3. ADMIXTURE clustering analysis zoom-in for Hessequadescendants and Coloured groups across K2-10. FIGURE S4. ADMIXTURE cross-validation error. FIGURE S5. Demographic model testing for the Hessequa-descendants using qpGraph. FIGURE S 6. 1–FST estimates between local ancestral groups of the Hessequa-descendants and each donor panel. FIGURES S7–S12. 1–FST estimates between local ancestral groups of the each Khoe-San comparative group and their donor panels. FIGURE S13. Inferred pairwise coancestry curves in the Hessequadescendants under a 5-way admixture model without pre-defining reference panel. FIGURE S14. Pairwise coancestry curves in the Hessequadescendants under a 3-way admixture model using a reference panel. FIGURES S15–S20. Inferred pairwise coancestry curves for each comparative group under their best admixture model. FIGURES S21–S29. 1–FST estimates between local ancestral groups of each Hessequa-descendants sampling site and each donor panel. FIGURE S30. Supervised ADMIXTURE clustering analysis for the X-chromosome at K = 5. FIGURE S31. Xchromosome to autosomal ratio for each Hessequa-descendants sampling site.
ADDITIONAL FILE 2: Excel file with supplementary tables: TABLE S1. Internal classification of Southern African Khoisan linguistic groups. TABLE S2. East African ADMIXTURE proportions in relation to East Africa and autochthonous San ancestries (i.e. excluding recent admixture from West Africans and Eurasians). TABLE S3. Allele frequencies of LP associated variants present in the H3Africa SNP array. TABLE S4. Relevant admixture time estimates based on pairwise coancestry curves. TABLE S5. Xchromosome to autosomal ratio based on the average ancestry proportion. TABLE S6. Summary results for the mitochondrial haplogroup assignment for the 87 sub-sampled Hessequa-descendants. TABLE S7. Summary results for the Ychr haplogroup assignment for the 58 male Hessequa-descendants. TABLE S8. List of populations included in the dataset.