Admixture history of the South African "Coloured" populations

Thesis

Admixed people formed from colonial era migrations are a major feature of present-day diversity. In Southern Africa, establishment of the Dutch Cape Colony instigated the so-called "Coloured" communities, associated, essentialistically, with 'mixed descent'. This multi-way admixture involved diverse regional groups producing a fascinating genetic story. In this thesis I develop further the history of the Cape Colony admixture using genome-wide SNP chip data.

In chapter 4 I characterise the ancestry of 733 Cape Town "Coloured" individuals, identifying specific contributions using haplotype coalescence. I find no substructure despite identifying 11 ancestral contributions. Results concur with historic accounts of South Asian, European, African KhoeSan and Bantu-speakers, and South-East Asian contributions from slaves, indigenous people and settlers. Signals from known slaving regions are detected as is a previously unknown Central European and Iberian contribution. In chapter 5 I explore evidence of admixture events and sources using linkage-disequilibrium decay curve fitting for the above dataset. Results indicate recent, continuous admixture pre-dating the Cape Colony. Europeans, South-East Asians and the KhoeSan are likely sources for the pre-Colonial signals possibly reflecting shipwrecks along the coast. I find no clear evidence for Southern Bantu and Malagasy contributions to the South African Coloured (SAC).

In chapter 6, I evaluate geographic expansion and admixture in the "Coloured" sub-identity: Cape Malay, Griekwa and Baster. I genotype 116 new individuals. Geography and ethnicity correlate with genetics but inconsistently. Griekwa and Cape Malay show evidence of gene flow with geographic neighbouring communities while the Namibian Baster are the clearest example of endogamy, associated with isolation and inbreeding.

Novel and challenging aspects are added to our understanding of the "Coloured" communities. This work highlights that admixture pre-dates the arrival of settlers and how social identities are formed along more dynamic processes than simple admixture proportions.

Authors: Daniels, RJ

• DOI: 10.5287/ora-bxrvg0mwe
• Type of award: DPhil
• Level of award: Doctoral
• Awarding institution: University of Oxford
• Language: English
• Keywords: single nucleotide polymorphism; African; KhoeSan; Colonialism; Admixture; Linkage disequilibrium; Vereenigde Oostindische Compagnie; Slave Trade; Creole
• Subjects: History; Genomics; Anthropology