Continental-scale genomic analysis suggests shared post-admixture adaptation in the Americas

We thank the people working at the High Performance Computing Center of the University of Tartu for the help and support provided. We thank Marco Rosario Capodiferro for useful discussions. This work was supported by the European Union through the European Regional Development Fund (Project No. 20142020.4.01.16-0030 to LO, MMe, FM; Project No. 2014-2020.4.01.160271 to RF; Project No. 2014-2020.4.01.16-0125 to RF; Project No. 2014-2020.4.01.16-0024 to DM, LP). This work was supported by the Estonian Research Council grant PUT (PRG243) (to RF, MMe, LP). This work was supported by institutional research funding IUT (IUT24-1) of the EstonianMinistry of Education and Research (to TK). This research was supported by the European Union through Horizon 2020 grant no. 810645 (to MMe). This research was supported by the European Union through the Horizon 2020 research and innovation programme under grant no 810645 and through the European Regional Development Fund project no. MOBEC008 to MMo.American populations are one of the most interesting examples of recently admixed groups, where ancestral components from three major continental human groups (Africans, Eurasians and Native Americans) have admixed within the last 15 generations. Recently, several genetic surveys focusing on thousands of individuals shed light on the geography, chronology and relevance of these events. However, even though gene f low could drive adaptive evolution, it is unclear whether and how natural selection acted on the resulting genetic variation in the Americas. In this study, we analysed the patterns of local ancestry of genomic fragments in genome-wide data for ∼6000 admixed individuals from 10 American countries. In doing so, we identified regions characterized by a divergent ancestry profile (DAP), in which a significant over or under ancestral representation is evident. Our results highlighted a series of genomic regions with DAPs associated with immune system response and relevant medical traits, with the longest DAP region encompassing the human leukocyte antigen locus. Furthermore, we found that DAP regions are enriched in genes linked to cancer-related traits and autoimmune diseases. Then, analysing the biological impact of these regions, we showed that natural selection could have acted preferentially towards variants located in coding and non-coding transcripts and characterized by a high deleteriousness score. Taken together, our analyses suggest that shared patterns of post admixture adaptation occurred at a continental scale in the Americas, affecting more often functional and impactful genomic variants.European Commission 2014-2020.4.01.16-0030 2014-2020.4.01.16-0271 2014-2020.4.01.16-0125 2014-2020.4.01.16-0024 MOBEC008Estonian Research Council grant PUT PRG243institutional research funding IUT of the Estonian Ministry of Education and Research IUT24-1European Union through Horizon 2020 grant 81064

Evaluating the Impact of Sex-Biased Genetic Admixture in the Americas through the Analysis of Haplotype Data

This work was supported by the European Union through the European Regional Development Fund (Project No. 2014-2020.4.01.16-0030 to LO, LM, MM, FM; Project No. 2014-2020.4.01.16-0271 to RF; Project No. 2014-2020.4.01.16-0125 to RF; Project No. 2014-2020.4.01.16-0024 to LM, DM, LP; Project No. 2014-2020.4.01.15-0012 to MM; Project no. MOBEC008 to MM). This work was supported by the Estonian Research Council grant PUT (PRG243) to RF and MM and PUT (PRG1027) to KT. This research was supported by the European Union through Horizon 2020 research and innovation programme under grant no 810645 to MM and no 824110 to KT. AA and MRC received support from the Italian Ministry of Education, University and Research (MIUR) for Progetti PRIN2017 20174BTC4R and the Dipartimenti di Eccellenza Program (2018-2022).A general imbalance in the proportion of disembarked males and females in the Americas has been documented during the Trans-Atlantic Slave Trade and the Colonial Era and, although less prominent, more recently. This imbalance may have left a signature on the genomes of modern-day populations characterised by high levels of admixture. The analysis of the uniparental systems and the evaluation of continental proportion ratio of autosomal and X chromosomes revealed a general sex imbalance towards males for European and females for African and Indigenous American ancestries. However, the consistency and degree of this imbalance are variable, suggesting that other factors, such as cultural and social practices, may have played a role in shaping it. Moreover, very few investigations have evaluated the sex imbalance using haplotype data, containing more critical information than genotypes. Here, we analysed genome-wide data for more than 5000 admixed American individuals to assess the presence, direction and magnitude of sex-biased admixture in the Americas. For this purpose, we applied two haplotype-based approaches, ELAI and NNLS, and we compared them with a genotype-based method, ADMIXTURE. In doing so, besides a general agreement between methods, we unravelled that the post-colonial admixture dynamics show higher complexity than previously described.European Commission 2014-2020.4.01.16-0030 2014-2020.4.01.16-0271 2014-2020.4.01.16-0125 2014-2020.4.01.16-0024 2014-2020.4.01.15-0012MOBEC008Estonian Research Council grant PUT PRG243 PRG1027European Commission 810645 824110Ministry of Education, Universities and Research (MIUR) PRIN2017 20174BTC4

CMS Collaboration

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