Ecology and evolution
Authors: Goeury T, Faye N, Gerbault P, Černý V, Crubézy E, Chiaroni J, Brouk H, Brunet L, Galan M, de Groot NG, Nunes JM, Sanchez-Mazas A
African populations remain underrepresented in studies of human genetic diversity, despite a growing interest in understanding how they have adapted to the diverse environments they live in. In particular, understanding the genetic basis of immune adaptation to pathogens is of paramount importance in a continent such as Africa, where the burden of infectious diseases is a major public health challenge. In this study, we investigated the molecular variation of four Human Leukocyte Antigens () class II genes (, , and ), directly involved in the immune response to parasitic infections, in more than 1000 individuals from 23 populations across North, East, Central and West Africa. By analyzing the molecular diversity of these populations in relation to various geographical, cultural and environmental factors, we identified divergent genetic profiles for several (semi-)nomadic populations of the Sahel belt as a signature of their unique demography. In addition, we observed significant genetic structuring supporting both substantial geographic and linguistic differentiations within West Africa. Furthermore, neutrality tests suggest balancing selection has been shaping the diversity of these four class II genes, which is consistent with molecular comparisons between genes and their orthologs in chimpanzees (). However, the most striking observation comes from linear modeling, demonstrating that the prevalence of , the primary pathogen of malaria in Africa, significantly explains a large proportion of the nucleotide diversity observed at the gene. , a highly frequent allele in Burkinabé populations, is identified as a potential protective allele against malaria, suggesting that strong pathogen-driven positive selection at this gene has shaped variation in Africa. Additionally, two low-frequency alleles, and also show significant associations with prevalence, supporting resistance to malaria is determined by multigenic and/or multiallelic combinations rather than single allele effects.
Nature
Authors: Malaspinas AS, Westaway MC, Muller C, Sousa VC, Lao O, Alves I, Bergström A, Athanasiadis G, Cheng JY, Crawford JE, Heupink TH, Macholdt E, Peischl S, Rasmussen S, Schiffels S, Subramanian S, Wright JL, Albrechtsen A, Barbieri C, Dupanloup I, Eriksson A, Margaryan A, Moltke I, Pugach I, Korneliussen TS, Levkivskyi IP, Moreno-Mayar JV, Ni S, Racimo F, Sikora M, Xue Y, Aghakhanian FA, Brucato N, Brunak S, Campos PF, Clark W, Ellingvåg S, Fourmile G, Gerbault P, Injie D, Koki G, Leavesley M, Logan B, Lynch A, Matisoo-Smith EA, McAllister PJ, Mentzer AJ, Metspalu M, Migliano AB, Murgha L, Phipps ME, Pomat W, Reynolds D, Ricaut FX, Siba P, Thomas MG, Wales T, Wall CM, Oppenheimer SJ, Tyler-Smith C, Durbin R, Dortch J, Manica A, Schierup MH, Foley RA, Lahr MM, Bowern C, Wall JD, Mailund T, Stoneking M, Nielsen R, Sandhu MS, Excoffier L, Lambert DM, Willerslev E
The population history of Aboriginal Australians remains largely uncharacterized. Here we generate high-coverage genomes for 83 Aboriginal Australians (speakers of Pama-Nyungan languages) and 25 Papuans from the New Guinea Highlands. We find that Papuan and Aboriginal Australian ancestors diversified 25-40 thousand years ago (kya), suggesting pre-Holocene population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania). However, all of the studied Aboriginal Australians descend from a single founding population that differentiated ~10-32 kya. We infer a population expansion in northeast Australia during the Holocene epoch (past 10,000 years) associated with limited gene flow from this region to the rest of Australia, consistent with the spread of the Pama-Nyungan languages. We estimate that Aboriginal Australians and Papuans diverged from Eurasians 51-72 kya, following a single out-of-Africa dispersal, and subsequently admixed with archaic populations. Finally, we report evidence of selection in Aboriginal Australians potentially associated with living in the desert.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences
Authors: Gerbault P, Liebert A, Itan Y, Powell A, Currat M, Burger J, Swallow DM, Thomas MG
Niche construction is the process by which organisms construct important components of their local environment in ways that introduce novel selection pressures. Lactase persistence is one of the clearest examples of niche construction in humans. Lactase is the enzyme responsible for the digestion of the milk sugar lactose and its production decreases after the weaning phase in most mammals, including most humans. Some humans, however, continue to produce lactase throughout adulthood, a trait known as lactase persistence. In European populations, a single mutation (-13910*T) explains the distribution of the phenotype, whereas several mutations are associated with it in Africa and the Middle East. Current estimates for the age of lactase persistence-associated alleles bracket those for the origins of animal domestication and the culturally transmitted practice of dairying. We report new data on the distribution of -13910*T and summarize genetic studies on the diversity of lactase persistence worldwide. We review relevant archaeological data and describe three simulation studies that have shed light on the evolution of this trait in Europe. These studies illustrate how genetic and archaeological information can be integrated to bring new insights to the origins and spread of lactase persistence. Finally, we discuss possible improvements to these models.
