A Genetic Record of Admixture Between Humans and Ancient Hominins
MetadataShow full item record
Recent studies showed that admixture between modern humans and ancient hominin species was a ubiquitous phenomenon in the past. We now know that modern humans admixed with Neanderthals as well as Denisovans, an extinct hominin species, existence of which we acknowledged through genetic studies. Whilst the majority of admixture events took place in Eurasia following the out-of-Africa migrations of modern humans, there is now accumulating evidence indicating that the ancestors of modern humans also admixed with ancient hominins in Africa. An emerging question following these findings is where, when and how many times modern humans admixed with ancient hominin species. In this dissertation, I studied the genetic remnants of these admixture events, that is introgression from ancient hominin species into modern humans, in a population specific manner. I started with discussing the importance of western Asia in terms of human evolution. Western Asia has been a major cross-roads of human population movements throughout the human evolutionary history. As such the region deserves more focused studies. Second, I investigated the Neanderthal ancestry proportions specifically in western Asia. Results revealed that western Asians carry slightly lower Neanderthal ancestry as compared to other Eurasian populations. Migrations from Africa into the region in more recent times likely diluted Neanderthal ancestry in western Asia. These results are based on point estimates of genome-wide Neanderthal ancestry for different human populations. I also found thousands of Neanderthal introgressed haplotypes in the genomes of western Asians as well as Europeans and East Asians. Many of these haplotypes harbored important genes, and some were found in higher frequencies. An example is a Neanderthal-introgressed haplotype carrying multiple toll-like receptor genes (TLR1, 6 and 10) which was found in moderate to high frequencies in the Turkish as well as East Asian populations but not in the European population. This is likely a result of population-specific selective forces. The method, which I employed to find Neanderthal-introgressed haplotypes in the genomes Eurasians, also helped me to verify introgression from an unsampled ancient hominin species in a salivary mucin gene, MUC7 in the genomes of sub-Saharan Africans. I used this same method, S*-statistics, as well as large deletion polymorphisms to find the source of the excess Neanderthal ancestry in present-day East Asians in comparison to Europeans. When I mapped Neanderthal-introgressed DNA found in East Asian as well as Western European genomes to the two high quality Neanderthal genomes belonging to different populations of Neanderthals, that is, early and late Neanderthals, I found that both modern human populations carry Neanderthal ancestry introgressed from late as well as early Neanderthal populations. Overall, the collection of work documented in this dissertation not only contributes to the recent attempts to rewrite the human population history but also demonstrates potentially important phenotypic effects of ancient hominin introgression into modern humans.