Cornish, Dean James; (2023) Inferences of Local Genetic Adaptation from Palaeolithic Hunter Gatherers. Masters thesis (M.Phil), UCL (University College London).

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Abstract

Ancient human genomes are an extremely powerful tool for exploring human demography and local genetic adaptation. Despite the thousands of genomes now available, there have been fewer amalgamated datasets focused on consistently processing samples created using different methods and filters. Therefore, I collated and processed a sample of 299 mostly publicly available ancient genomes sampling genetic diversity in Europe and recapitulating known clustering within ancient individuals. I made inferences of local genetic adaptation in 30 of the oldest Palaeolithic Hunter Gatherers, which were selected as they may reveal novel adaptations not detectable in younger individuals and or highlight earlier adaptations associated with the colonisation of Eurasia. I found many previously characterised candidates and one novel candidate in TCEA3. I also explored the advantage of incorporating ancient genomes in a test for Local Genetic Adaptation and observed a slight increase in candidates. Finally, I investigated functional annotations for the candidates of local genetic adaptation, highlighting some variants that may have influenced gene expression and disease risk and some which fall within Neanderthal- introgressed regions.

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