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Insights into human evolution from archaic introgression patterns and mutational signatures

Research output: Book/anthology/dissertation/reportPh.D. thesisResearch

Human evolutionary history is a complex narration of migrations around the globe and intricate mixtures among human populations, but also with Neanderthals and Denisovans. As a consequence, up to 2 to 6% of the genetic material of living individuals traces back to archaic humans. In this thesis, we recover archaic fragments from thousands of Icelanders and show that around half of the genome of the introgressing Neadenrthal can be pieced together. Some fragments correspond directly to Denisovans, indicative of a direct contact between Denisovans and the ancestors of West Eurasians, adding another event to the multiple interactions between Denisovans and modern humans. In sharp contrast, we find the Neanderthal admixture to Eurasian populations can be explained through a single event. Surprisingly, we find that populations in the west present shorter fragments than populations in the east. We suggest the underlying cause to be generation time differences among Eurasians during the last 40,000 years. Independently from the recombination clock, generation time can also be investigated from the mutation rate and spectrum. From pedigree studies, it is known that the parental age and sex have a direct effect on the amount of mutations and their type. In line with our hypothesis, we find both mutation accumulation and spectrum in Eurasians to correspond with their generation time inferred. Moreover, we use sex-specific mutation signatures to assess the mean maternal and paternal age independently among Eurasians. When comparing modern humans to Neanderthals with similar analysis, we observe differences in mutational patterns concordant with Neanderthals having older mothers and modern humans younger fathers. Finally, we explore the phenotypic consequences of archaic introgression and find that only 5 traits in the Icelandic population are associated by archaic variants, a smaller impact than previously thought. Moreover, we show that there is no excess of deleterious variants in archaic fragments in modern genomes, consistent with a rapid purge of deleterious effects in the first generations after introgression. However, this strong purifying selection cannot account for the reduction of archaic content in the X chromosome. Instead, we suggest that 11% of the X is under selective sweeps which are recurrent in great apes. Therefore, positive selection for human variants instead of purging against archaic ones might be responsible for the deserts of archaic ancestry in the X chromosome.
Original languageEnglish
Number of pages118
Publication statusPublished - 30 Jun 2021

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