Bird, Nancy; (2023) Investigating the impact of environmental, cultural and historical factors on African genomes. Doctoral thesis (Ph.D), UCL (University College London).

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Abstract

The patterns of genetic diversity observed among present-day individuals are influenced by a variety of factors, from geography to culture. Indeed, past events, such as migrations and empires, can leave signals in the genome. However, many of these factors are relatively uncharacterised in certain groups. For example, in Africa most studies so far have been limited by sparse sampling. In this thesis I aim to elucidate factors affecting genetic variation in different worldwide groups, with a particular focus on African genomes. I primarily use haplotype-based methods, which have increased power to detect fine-scale genetic structure. I begin by analysing a densely sampled dataset of West and Central Africans and Sudanese. I demonstrate a previously underappreciated level of fine-scale genetic structure correlating with ethnolinguistic group and/or geography, and extensive signals of historical admixture. This mixing correlates with recorded events in African history, including the expansion of Bantu language-speaking peoples, the Kanem Empire and the Kingdom of Makuria. I then test hypotheses about the history of a particular African ethnic group sampled from South Africa, the Lemba, who have an oral history of non-African origins. Since some people theorise that the Lemba have Jewish origins, I first describe and analyse a novel dataset of Jewish individuals, in particular comparing published and unpublished Jewish groups to geographically-matched non-Jewish groups. I demonstrate that the majority of Jewish groups are relatively isolated and have varying amounts of ancestry related to Middle Eastern groups, while some Jewish groups have additional southern European-like ancestry, potentially as a result of conversion during the Roman Empire. I also show that Jewish groups were on the whole less genetically influenced by the Arabic expansion than non-Jewish groups. However, I demonstrate a lack of strong evidence for ancient Jewish origins in the Lemba. Instead, using simulations, I show that they likely descend from admixture with non-African merchants during the medieval Indian Ocean trade. Overall, I demonstrate how using genetic data together with historical, linguistic and archaeological sources can provide increased resolution to our understanding of human history. I advocate for more dense sampling of groups within African countries to reveal the full extent of genetic diversity present.

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