The Disappearing San of Southeastern Africa and Their Genetic Affinities
Total Page：16
File Type：pdf, Size：1020Kb
Hum Genet (2016) 135:1365–1373 DOI 10.1007/s00439-016-1729-8 ORIGINAL INVESTIGATION The disappearing San of southeastern Africa and their genetic affinities Carina M. Schlebusch1 · Frans Prins2 · Marlize Lombard3 · Mattias Jakobsson1,4 · Himla Soodyall5 Received: 30 June 2016 / Accepted: 11 September 2016 / Published online: 20 September 2016 © The Author(s) 2016. This article is published with open access at Springerlink.com Abstract Southern Africa was likely exclusively inhabited open up new ways to understand the population history by San hunter-gatherers before ~2000 years ago. Around of southeastern Africa. We investigate the genomic varia- that time, East African groups assimilated with local San tion of the remaining individuals from two South African groups and gave rise to the Khoekhoe herders. Subse- groups with oral histories connecting them to eastern San quently, Bantu-speaking farmers, arriving from the north groups, i.e., the San from Lake Chrissie and the Duma (~1800 years ago), assimilated and displaced San and San of the uKhahlamba-Drakensberg. Using ~2.2 million Khoekhoe groups, a process that intensified with the arrival genetic markers, combined with comparative published of European colonists ~350 years ago. In contrast to the data sets, we show that the Lake Chrissie San have genetic western parts of southern Africa, where several Khoe-San ancestry from both Khoe-San (likely the ||Xegwi San) groups still live today, the eastern parts are largely popu- and Bantu speakers. Specifically, we found that the Lake lated by Bantu speakers and individuals of non-African Chrissie San are closely related to the current southern San descent. Only a few scattered groups with oral traditions of groups (i.e., the Karretjie people). Duma San individuals, Khoe-San ancestry remain. Advances in genetic research on the other hand, were genetically similar to southeastern Bantu speakers from South Africa. This study illustrates Electronic supplementary material The online version of this how genetic tools can be used to assess hypotheses about article (doi:10.1007/s00439-016-1729-8) contains supplementary the ancestry of people who seemingly lost their historic material, which is available to authorized users. roots, only recalling a vague oral tradition of their origin. * Carina M. Schlebusch [email protected] Introduction * Himla Soodyall [email protected] The history of the San and Khoekhoe groups (some- 1 Department of Organismal Biology, Evolutionary Biology times also referred to as Khoisan, Bushmen, or Batwa— Centre, Uppsala University, Norbyvägen 18C, SE‑752 see Online Resource 1, Supplementary Note 1 on the termi- 36 Uppsala, Sweden nology used in the article) in the eastern parts of southern 2 School of Anthropology, Gender and Historical Studies, Africa remains poorly understood. There is a continuous University of KwaZulu-Natal, Durban, South Africa loss of oral traditions, and only fragmentary documen- 3 Department of Anthropology and Development Studies, tation by European settlers arrives a few hundred years University of Johannesburg, Auckland Park, 2006, ago (Adhikari 2010; Vinnicombe 1976; Wright 1971). Johannesburg, South Africa Unlike the Kalahari San of the western parts of southern 4 Science for Life Laboratory, Uppsala University, Norbyvägen Africa, most of the southeastern groups disappeared before 18C, SE‑752 36 Uppsala, Sweden detailed anthropological studies could be undertaken. 5 Division of Human Genetics, School of Pathology, Faculty Thus, the origins and affinities of the groups and individu- of Health Sciences, University of the Witwatersrand, and National Health Laboratory Service, Johannesburg, als with oral traditions of San ancestry, such as the Lake South Africa Chrissie San and the Duma San groups of South Africa, are 1 3 1366 Hum Genet (2016) 135:1365–1373 Fig. 1 Distribution and population structure of the southern African flipped to correspond to geography. For full PCA (PC1 to PC8) and data set. a Geographical locations of new samples (black) and com- unmodified PC1 2 of the southern African data set, see Fig. S2. c parative data populations from Schlebusch et al. (2012). b Principal Admixture analysis+ of the southern African data set showing K2, K3, component (PC) analysis, showing PC1 and PC2. PC1 and PC2 were K5, K7, and K8. For full admixture analysis (K2-10), see Fig. S3 uncertain. In the 1950s, there were only about 50 San indi- (Korsman and Plug 1992), scattered refugee groups from viduals left near Lake Chrissie (Fig. 1; Fig. S1) (Barnard the Free State Province (Potgieter 1955; Prins 1999, 2001), 1992; Potgieter 1955; Ziervogel 1955). Most of the older and/or groups from the uKhahlamba-Drakensberg of Leso- generation still knew their own San language, ||Xegwi, at tho (Mitchell 1990; Prins 1999, 2001). These groups fled the time. Today, only a few individuals still recognize their from the in-coming European settlers and the turmoil that San ancestry, and no one speaks the language or knows the resulted from clashes between settlers and Bantu-speaking ||Xegwi cultural practices (see Online Resource 1, Sup- farmers. Historical documents record a large group of San plementary Note 2 for a more comprehensive review of individuals migrating from the central uKhahlamba-Drak- ||Xegwi history). It has been suggested that the ||Xegwi ensberg to the Highveld north of the Vaal River (southern were remnant individuals from the original ‘Transvaal’ San Transvaal Highveld) (Filter 1925; Prins 1999, 2001), and (Sanders 2013; Schoonraad and Schoonraad 1972), such as they could represent a large part of the more recent San those who inhabited the Honingklip Shelter in Mpumalanga groups from Lake Chrissie. This inference is corroborated 1 3 Hum Genet (2016) 135:1365–1373 1367 by the fact that the second language spoken by the San of to have disappeared (Wright 1971). The Duma San are Lake Chrissie was Southern Sotho, which is spoken by thought to be remnants of the amaThola and other admixed people from Lesotho and surrounding areas (Lanham and San groups now residing in KwaZulu-Natal, South Africa Hallowes 1956; Potgieter 1955; Prins 1999, 2001). (see Online Resource 1, Supplementary Note 3 for a more The ‘Mountain Bushmen’ (Walsham How 1962) or comprehensive review of Duma San history). ‘People of the Eland’ (Vinnicombe 1976) were groups of Today, skeletal material from archaeological contexts San individuals who inhabited the mountainous regions interpreted as a mixture between San and African farmers of the current Lesotho, KwaZulu-Natal, Griqualand East, (Beaumont 1967; Galloway 1936; Murray 1933; Wells and and the former Transkei (Barnard 1992). Walsham How Dart 1934), and residual Khoe-San physical and linguis- (1962) reports that when the first Sotho-speaking farmers tic features amongst many southeastern Bantu-speaking arrived in Lesotho at about 1600 AD, they found the region groups (Bourquin 1951; De Villiers 1968; Greenberg 1966) (mostly the lowlands) occupied by nomadic San hunter- are considered as bearing testimony to admixture between gatherers. Initially, hunter-gatherers and farmers lived with- the hunter-gathers and farmers (Vinnicombe 1976). Indeed, out much conflict, and occasionally, Sotho men would take the previous genetic work attests to such admixture (Pick- San women as wives, or employ young San men for herd- rell et al. 2012; Schlebusch et al. 2012). In addition, the ing cattle (Walsham How 1962). As a result of encroach- recent work has shown that San hunter-gatherers of south- ing Bantu-speaking farmers from the north and European ern Africa also admixed with East African pastoralists, settlers from the south-west, the San of southeastern Africa before they came into contact with Bantu-speaking farm- was mostly confined to the high mountains in and around ers (Breton et al. 2014; Macholdt et al. 2014a; Schlebusch current-day Lesotho (Wright 1971), where the Later Stone et al. 2012), probably resulting in what is today known as Age archaeological record attest to the long-term hunter- the Khoekhoe population of southern Africa, who are tra- gatherer occupation. For example, at Melikane Rock Shel- ditionally associated with a herding lifeway, but who still ter, there is evidence of hunter-gatherers from at least about hunted and gathered wild plant foods. Admixture, socio- 80,000 years ago (Stewart et al. 2012). Here, in the moun- economic diffusion of hunting and herding lifeways, lin- tains, the San hunted relatively undisturbed until game guistic affinities, and shared worldviews between the vari- became scarce, and they began stealing livestock from ous San and Khoekhoe groups of southern Africa resulted the Bantu-speaking and European farmers. Both the lat- in the currently used collective term ‘Khoe-San’. Distin- ter groups retaliated by ‘hunting’ and executing San men, guishing between populations, for example, to determine while San women and children were often taken as pris- specific group relations or closest affinities, is becom- oners and servants, causing those who remained to flee or ing increasingly difficult as a result of lost traditions and seek protection (Walsham How 1962; Wright 1971). A San merged cultural and genetic histories. language was still much spoken in Lesotho by the 1870s, Linguistic classification is the traditional method used to and before 1879, there were still numerous San individuals help decipher Khoe-San population histories and relation- in southern Lesotho. Subsequently, their numbers dwindled