Showing papers by "Garrett Hellenthal published in 2020"
Harvard University1, Université de Montréal2, Broad Institute3, Howard Hughes Medical Institute4, Spanish National Research Council5, University of California, Santa Cruz6, University College London7, University of Yaoundé I8, University of Tübingen9, Pennsylvania State University10, Royal Museum for Central Africa11, University of Bordeaux12, Université libre de Bruxelles13, University of Buea14, Royal Belgian Institute of Natural Sciences15, Stony Brook University16, Katholieke Universiteit Leuven17, University of California, Santa Barbara18, Duke University19, Saint Louis University Madrid Campus20
TL;DR: An Africa-wide phylogeny is infer that features widespread admixture and three prominent radiations, including one that gave rise to at least four major lineages deep in the history of modern humans.
Abstract: Our knowledge of ancient human population structure in sub-Saharan Africa, particularly prior to the advent of food production, remains limited. Here we report genome-wide DNA data from four children—two of whom were buried approximately 8,000 years ago and two 3,000 years ago—from Shum Laka (Cameroon), one of the earliest known archaeological sites within the probable homeland of the Bantu language group1–11. One individual carried the deeply divergent Y chromosome haplogroup A00, which today is found almost exclusively in the same region12,13. However, the genome-wide ancestry profiles of all four individuals are most similar to those of present-day hunter-gatherers from western Central Africa, which implies that populations in western Cameroon today—as well as speakers of Bantu languages from across the continent—are not descended substantially from the population represented by these four people. We infer an Africa-wide phylogeny that features widespread admixture and three prominent radiations, including one that gave rise to at least four major lineages deep in the history of modern humans. Genome-wide ancestry profiles of four individuals, dating to 8,000 and 3,000 years before present, from the archaeological site of Shum Laka (Cameroon) shed light on the deep population history of sub-Saharan Africa.
75 citations
University of Pavia1, Pablo de Olavide University2, European Institute of Oncology3, University of Tartu4, Universidad del Norte, Colombia5, University of Illinois at Urbana–Champaign6, University of Florence7, University of Santiago de Compostela8, University College London9, University of Padua10, Smithsonian Tropical Research Institute11, University of Bari12
TL;DR: This article reported ten pre-Hispanic (plus two early colonial) genomes and 84 genome-wide profiles from seven groups presently living in Panama and revealed that demographic changes and isolation events contributed to create the extensive genetic structure currently seen in the area, which is also characterized by a distinctive Isthmo-Colombian Indigenous component.
Abstract: The recently enriched genomic history of Indigenous groups in the Americas is still meagre concerning continental Central America. Here, we report ten pre-Hispanic (plus two early colonial) genomes and 84 genome-wide profiles from seven groups presently living in Panama. Our analyses reveal that pre-Hispanic demographic changes and isolation events contributed to create the extensive genetic structure currently seen in the area, which is also characterized by a distinctive Isthmo-Colombian Indigenous component. This component drives these populations on a specific variability axis and derives from the local admixture of different ancestries of northern North American origin(s). Two of these ancestries were differentially associated to Pleistocene Indigenous groups that also moved into South America leaving heterogenous footprints. An additional Pleistocene ancestry was brought by UPopI, a still unsampled population that remained restricted to the Isthmian area, expanded locally during the early Holocene, and left genomic traces up to the present.
17 citations
TL;DR: Analysis of patterns of local ancestry of genomic fragments in genome-wide data for ∼6,000 admixed individuals from ten American countries suggests that shared patterns of post admixture adaptation occurred at continental scale in the Americas, affecting more often functional and impactful genomic variants.
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, despite the fact that gene-flow could drive adaptive evolution, it is not clear 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 ~6,000 admixed individuals from ten American countries. In doing so, we identified regions characterised 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 Divergent Ancestry Profiles (DAP) 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, analyzing 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 characterised by a high deleteriousness score.
Taken together, our analyses suggest that shared patterns of post admixture adaptation occurred at continental scale in the Americas, affecting more often functional and impactful genomic variants.
3 citations