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Through the layers of the Ethiopian genome: a survey of human genetic variation based on genome-wide genotyping and re-sequencing data



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Pagani, Luca 


Understanding our evolutionary history as a species has since long been one of the most attracting and controversial themes of the scientific investigation. From its geographical position, outstanding fossil record and richness of human diversity, the Horn of Africa and, particularly, the Ethiopian region offers an unmatched opportunity to investigate our origins from a genetic perspective. To carry out a genome-wide survey of this region, 13 out of the estimated 80 extant Ethiopian populations were typed on an Illumina Omni 1M SNP array. The results showed a good concordance between genetic and linguistic stratification and, overall, a complex population structure placing the Ethiopians in between North and Sub Saharan Africans, due to the recent non African gene flow which was dated at around 3000 years ago. Furthermore the SNP array data unveiled putative traces of the out of Africa migrations as well as, in two of the typed populations, signatures of genetic adaptation to high altitude. To obtain an unbiased, high resolution representation of the Ethiopian genetic landscape, 25 individuals from each of five populations were newly collected and sequenced on an Illumina HiSeq platform. These populations were chosen, from among the ones typed on the SNP array, to represent the main components of Ethiopian genetic diversity. Of the 25 samples per population, 24 were sequenced at low depth to generate a broad list of genetic variants, while one sample from each was sequenced at high depth to provide a higher resolution list of variants peculiar to each analysed population. The 125 Ethiopian genomes thus sequenced, while overall consistent with the genotyping results, described the Ethiopian populations in a less biased way than the SNP array data. Furthermore estimation of past effective population size fluctuations from the individual genomes unveiled a unique pattern in the ancestry of the Ethiopian populations in the early stages of human evolution. These results provide a data resource which can be used in future analyses.





Ethiopia Genome Project, Biological Anthropology, Evolutionary Genetics


Doctor of Philosophy (PhD)

Awarding Institution

University of Cambridge
This work was supported by: Domestic Research Studentship, Cambridge European Trust and Emmanuel College.