Heritage Cases

San and Khoe communities currently represent remnant groups of a much larger and widely distributed population of hunter-gatherers and pastoralists who had exclusive occupation of southern Africa before the arrival of Bantu-speaking groups since about 2000 years ago and seaborne immigrants of the last 350 years. Mitochondrial DNA and Y-chromosome studies conducted on contemporary Khoe-San groups revealed that they harbor some of the most divergent lineages found in living peoples throughout the world (Behar et al. 2008; Karafet et al. 2008; Schlebusch 2010; Schlebusch et al. 2013). Recently, we conducted a high coverage autosomal genetic study in contemporary Khoe and San populations and showed that these populations form a common lineage, basal to all other modern human populations (Schlebusch et al. 2012). This basal Khoe-San lineage split from other human populations around 100,000 – 150,000 years BP (Gronau et al. 2011; Veeramah et al. 2011; Schlebusch et al. 2012). Thus genetics confirms a deep split between the ancestors of modern Khoe-San populations and all other humans, which imply isolation of Khoe-San populations from other populations prior to contact with Bantu-speaking people and colonists. It is not known to what extent admixture with Bantu-speaking people and non-Africans influenced the genetic makeup of current San and Khoe groups, in particular, events that occurred during early contact between Bantu-speakers and Khoe-San groups. This is largely due to the lack of completely non-admixed comparative/reference Khoe-San groups and Pickrell et al. (Pickrell et al. 2012) suggested that all current-day Khoe and San people represent groups with some admixture with Bantu speakers. Thus obtaining genetic material from individuals in time periods that precede these admixture events is critical to estimate exact admixture proportions and understanding the history of southern African peoples.Furthermore, in the high coverage autosomal genetic study (Schlebusch et al. 2012), we found that Khoe-San populations are genetically distinct from each other and a clear geographic structuring among contemporary Khoe-San groups was observed. The northern (Angola and northern Namibia; Ju speakers) and southern (South Africa, Tuu speakers) Khoe-San groups were most distinct from each other with the central Khoe-San groups (Botswana, Khoe speakers) being intermediate. Population divergence within the Khoe-San group was approximately 1/3 as ancient as the divergence of the Khoe-San as a whole to other human populations (thus ~ 25,000- 43,000 years BP – on the same order as the time of divergence between West Africans and Eurasians). Our study included one pastoralist Khoe group (KhoeKhoe linguistic division), namely the Nama from Namibia, and we identified a Nilo-Saharan (East African) ancestral component in the group (around 16% of the genomes of Nama individuals were assigned to the East African component), possibly related to the introduction of pastoralism to southern Africa (Schlebusch et al. 2012). However, the rest of the Nama genetic component was similar to other San groups and mostly similar to descendants of the southern San (Tuu speakers), the ≠Khomani and the Karretjie People. It is known that many other Khoe as well as San groups existed historically throughout the Cape region of southern Africa. In the last 400 years, however, it seems that they started to lose their socio-cultural identities as Khoe and San groups, and many of their descendants were integrated in mixed ancestry populations such as the Coloured and Griqua populations of South Africa. By studying ancient DNA of different sites in southern Africa (before the disruptive influences of colonialism) we could investigate if the contemporary structure among Khoe-San and Coloured groups can be linked to specific geographic areas and/or cultural complexes in the past. Thus, testing the high coverage autosomal data that point to genetic distinction and geographic structuring and contributing more accurate knowledge about the region’s population history that cannot be obtained in any other way. We will identify similarities/differences between the historic individuals and different current-day Khoe, San and Bantu-speaking groups. The different contemporary Khoe and San groups also showed diverse histories of gene flow with surrounding populations, and through ancient DNA studies on dated material, hypotheses can be formulated about when this gene flow started. This can be especially useful in studying the two independent waves of pastoralist and farming practices to southern Africa; namely the Khoe lifeway, generally associated with the introduction of pastoralism, and the arrival of Bantuspeaking farmers in southern Africa. For the KwaZulu-Natal region specifically, changes in the archeological record, morphological changes in skeletons and isotope changes relating to dietary subsistence indicates that this region was colonized by Bantu-speaking, Iron Age farmers around 400 AD (Ribot et al. 2010). Skeletal remains predating this date would thus be representative of indigenous hunter-gatherer San groups from the region. Since today San groups have completely disappeared from this region, and form most of the eastern parts of southern Africa, it would be invaluable to have genetic information of these eastern San groups to compare to genetic information from contemporary western San groups