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. 2021 Nov 1;30(22):2123-2134.
doi: 10.1093/hmg/ddab177.

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

Linda Ongaro  1 , Mayukh Mondal  1 , Rodrigo Flores  1 , Davide Marnetto  1 , Ludovica Molinaro  1 , Marta E Alarcón-Riquelme  2 , Andrés Moreno-Estrada  3 , Nedio Mabunda  4 , Mario Ventura  5 , Kristiina Tambets  1 , Garrett Hellenthal  6 , Cristian Capelli  7   8 , Toomas Kivisild  9 , Mait Metspalu  1 , Luca Pagani  1   10 , Francesco Montinaro  1   5
Affiliations

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

Linda Ongaro et al. Hum Mol Genet. .

Abstract

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 flow 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.

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Figures

Figure 1
Figure 1
An overview of divergent ancestry profile regions inferred by local ancestry profiles for all ancestries. (A) Population distribution of DAPs. The x axis shows DAPS in single populations while y axis shows DAP sharing among groups. (B) Genomic location of shared DAPs. Different colours refer to the ancestry and direction of the divergence, as indicated in the legend.
Figure 2
Figure 2
Comparison of the distribution of all the PHRED-scaled C-score values belonging to windows with divergent ancestry profiles (DAPs) with the ones from the non-divergent for European and American ancestries in the 20Pop dataset. The asterisk refers to a statistically significant P-value (Wilcoxon test, Bonferroni corrected alpha = 0.01). The number of analysed windows is reported in Supplementary Material, Table S5A.
Figure 3
Figure 3
Comparison of the distribution of Annotypes (Coding Transcript, Intergenic, Non-coding Transcript, Regulatory Feature, Transcript) belonging to divergent ancestry profiles (DAPs) windows with the ones from the non-divergent for European (A) and American (B) ancestries in the 20Pop dataset. The asterisk refers to a statistically significant P-value (Wilcoxon test, Bonferroni corrected alpha = 0.002). The number of analysed windows is reported in Supplementary Material, Table S5B.
Figure 4
Figure 4
Gene-set enrichment analysis results for the European ancestry of the 20Pop dataset (Supplementary Material, Table S6A–D). Only the first 10 enriched terms for library are shown. Libraries: Genome-wide Association Studies (GWAS) Catalog 2019, GTEx Tissue Sample Gene Expression Profiles up, Human 2019 Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) 2018.
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References

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