Human population history and its interplay with natural selection
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The complex demographic changes that underlie the expansion of anatomically modern humans out of Africa have important consequences on the dynamics of natural selection and our ability to detect it. In this thesis, I aimed to refine our knowledge on human population history using ancient genomes, and then used a climate-informed, spatially explicit framework to explore the interplay between complex demographies and selection.
I first analysed a high-coverage genome from Upper Palaeolithic Romania from ~37.8 kya, and demonstrated an early diversification of multiple lineages shortly after the out-of-Africa expansion (Chapter 2). I then investigated Late Upper Palaeolithic (~13.3ky old) and Mesolithic (~9.7 ky old) samples from the Caucasus and a Late Upper Palaeolithic (~13.7ky old) sample from Western Europe, and found that these two groups belong to distinct lineages that also diverged shortly after the out of Africa, ~45-60 ky ago (Chapter 3). Finally, I used East Asian samples from ~7.7ky ago to show that there has been a greater degree of genetic continuity in this region compared to Europe (Chapter 4).
In the second part of my thesis, I used a climate-informed, spatially explicit demographic
model that captures the out-of-Africa expansion to explore natural selection. I first
investigated whether the model can represent the confounding effect of demography on
selection statistics, when applied to neutral part of the genome (Chapter 5). Whilst the
overlap between different selection statistics was somewhat underestimated by the model, the
relationship between signals from different populations is generally well-captured. I then
modelled natural selection in the same framework and investigated the spatial distribution of
two genetic variants associated with a protective effect against malaria, sickle-cell anaemia
and