Dottore di ricerca

ciclo: XXXVI

supervisore: Prof. Giovanni Destro Bisol

Titolo della tesi: Unraveling the impact of population structure, admixture, and adaptation on patterns of genetic diversity in distinct populations from West Central and Central Africa

West Central and Central Africa contain expansive rainforests where the world’s largest group of hunter-gatherers live near other African populations that have adopted an agriculturalist lifestyle within the last several thousand years. Given the paucity of fossil remains in this region, information regarding the prehistory of these populations has been limited. Thus, genomic studies have been employed to reconstruct the evolutionary history of these groups. This dissertation analyzes genomic variation in western rainforest hunter- gatherers (specifically, Baka, Bakola and Mbenzele) and in farmers (specifically, Bassa, Ewondo and Ngoumba) from Cameroon and the Central African Republic. Based on my analyses, I found that the ancestors of western hunter-gatherer populations diverged from the ancestors of Bantu-speaking agriculturalists ~50,000 years ago (ya), revealing an ancient age of separation between hunter-gatherer and non-hunter-gatherer populations. Moreover, the Mbenzele diverged from the other western hunter-gatherers ~10,000 ya, well before the expansion of Bantu-speakers across Africa beginning ~5,000 ya. Although the Mbenzele experienced a bottleneck event after their divergence, this population still maintained a larger effective population size compared to the other rainforest hunter- gatherers. My data also showed that there was gene flow between the ancestors of African hunter-gatherers and agriculturalists at different points in time. In addition, I uncovered evidence that the Bassa, Ewondo, and Ngoumba diverged from a common ancestor ~1,000 ya, well after the initial geographic expansion of Bantu-speaking agriculturalists. In addition to demographic history, natural selection also has shaped patterns of diversity in African populations. To investigate these patterns, I examined sequence variation at 22 bitter taste receptor genes in the Baka, Bakola, and Mbenzele hunter- gatherers and Bassa, Ewondo, and Ngoumba agriculturalists. Here, I identified 353 single nucleotide polymorphisms (SNPs) across the TAS2R genes, and among these SNPs, 34 of them have never been previously described. I also observed striking departures from neutral evolution at several TAS2R genes based on summary statistics—indicative of positive selection—in both hunter-gatherer and agriculturalist populations. To further investigate these signatures of selection, I characterized long-range linkage disequilibrium (LD) across chromosomes 5, 7, and 12 in my populations using iHS and EHH statistics. These analyses uncovered unusually long haplotype structure around alleles at the TAS2R genes. Furthermore, some of these signals of positive selection were shared between hunter-gatherer and Bantu-speaking populations. Interestingly, I observed varying proportions of ancestry originating from Bantu-speakers in hunter- gatherers (and vice versa) in genomic regions containing allelic variation under recent selection, suggesting historical gene flow and natural selection may have jointly influenced the frequency and distribution of selected alleles at some of the TAS2R genes. Additionally, a subset of these alleles was found to be correlated with levels of P. falciparum malaria infection. Overall, this study provides new insights into the evolutionary history of diverse African populations, which are still highly underrepresented in genomic studies.

Produzione scientifica

11573/1340375 - 2019 - Inter-individual genomic heterogeneity within European population isolates
Anagnostou, Paolo; Dominici, Valentina; Battaggia, Cinzia; Lisi, Alessandro; Sarno, Stefania; Boattini, Alessio; Calò, Carla; Francalacci, Paolo; Vona, Giuseppe; Tofanelli, Sergio; Vilar, Miguel G.; Colonna, Vincenza; Pagani, Luca; Destro Bisol, Giovanni - 01a Articolo in rivista
rivista: PLOS ONE (San Francisco, CA : Public Library of Science) pp. 1-15 - issn: 1932-6203 - wos: WOS:000532444100002 (4) - scopus: 2-s2.0-85073055526 (4)

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