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Palaeo-Eskimo genetic ancestry and the peopling of Chukotka and North America.

ABSTRACT: Much of the American Arctic was first settled 5,000 years ago, by groups of people known as Palaeo-Eskimos. They were subsequently joined and largely displaced around 1,000 years ago by ancestors of the present-day Inuit and Yup'ik^1-3. The genetic relationship between Palaeo-Eskimos and Native American, Inuit, Yup'ik and Aleut populations remains uncertain^4-6. Here we present genomic data for 48 ancient individuals from Chukotka, East Siberia, the Aleutian Islands, Alaska, and the Canadian Arctic. We co-analyse these data with data from present-day Alaskan Iñupiat and West Siberian populations and published genomes. Using methods based on rare-allele and haplotype sharing, as well as established techniques^4,7-9, we show that Palaeo-Eskimo-related ancestry is ubiquitous among people who speak Na-Dene and Eskimo-Aleut languages. We develop a comprehensive model for the Holocene peopling events of Chukotka and North America, and show that Na-Dene-speaking peoples, people of the Aleutian Islands, and Yup'ik and Inuit across the Arctic region all share ancestry from a single Palaeo-Eskimo-related Siberian source.

SUBMITTER: Flegontov P

PROVIDER: S-EPMC6942545 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature

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Palaeo-Eskimo genetic ancestry and the peopling of Chukotka and North America.

Flegontov Pavel P Altınışık N Ezgi NE Changmai Piya P Rohland Nadin N Mallick Swapan S Adamski Nicole N Bolnick Deborah A DA Broomandkhoshbacht Nasreen N Candilio Francesca F Culleton Brendan J BJ Flegontova Olga O Friesen T Max TM Jeong Choongwon C Harper Thomas K TK Keating Denise D Kennett Douglas J DJ Kim Alexander M AM Lamnidis Thiseas C TC Lawson Ann Marie AM Olalde Iñigo I Oppenheimer Jonas J Potter Ben A BA Raff Jennifer J Sattler Robert A RA Skoglund Pontus P Stewardson Kristin K Vajda Edward J EJ Vasilyev Sergey S Veselovskaya Elizaveta E Hayes M Geoffrey MG O'Rourke Dennis H DH Krause Johannes J Pinhasi Ron R Reich David D Schiffels Stephan S

Nature 20190605 7760

Much of the American Arctic was first settled 5,000 years ago, by groups of people known as Palaeo-Eskimos. They were subsequently joined and largely displaced around 1,000 years ago by ancestors of the present-day Inuit and Yup'ik<sup>1-3</sup>. The genetic relationship between Palaeo-Eskimos and Native American, Inuit, Yup'ik and Aleut populations remains uncertain<sup>4-6</sup>. Here we present genomic data for 48 ancient individuals from Chukotka, East Siberia, the Aleutian Islands, Alaska, ...[more]

PMID: 31168094

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Project description:BackgroundModern Latin American populations were formed via genetic admixture among ancestral source populations from Africa, the Americas and Europe. We are interested in studying how combinations of genetic ancestry in admixed Latin American populations may impact genomic determinants of health and disease. For this study, we characterized the impact of ancestry and admixture on genetic variants that underlie health- and disease-related phenotypes in population genomic samples from Colombia, Mexico, Peru, and Puerto Rico.ResultsWe analyzed a total of 347 admixed Latin American genomes along with 1102 putative ancestral source genomes from Africans, Europeans, and Native Americans. We characterized the genetic ancestry, relatedness, and admixture patterns for each of the admixed Latin American genomes, finding a spectrum of ancestry proportions within and between populations. We then identified single nucleotide polymorphisms (SNPs) with anomalous ancestry-enrichment patterns, i.e. SNPs that exist in any given Latin American population at a higher frequency than expected based on the population's genetic ancestry profile. For this set of ancestry-enriched SNPs, we inspected their phenotypic impact on disease, metabolism, and the immune system. All four of the Latin American populations show ancestry-enrichment for a number of shared pathways, yielding evidence of similar selection pressures on these populations during their evolution. For example, all four populations show ancestry-enriched SNPs in multiple genes from immune system pathways, such as the cytokine receptor interaction, T cell receptor signaling, and antigen presentation pathways. We also found SNPs with excess African or European ancestry that are associated with ancestry-specific gene expression patterns and play crucial roles in the immune system and infectious disease responses. Genes from both the innate and adaptive immune system were found to be regulated by ancestry-enriched SNPs with population-specific regulatory effects.ConclusionsAncestry-enriched SNPs in Latin American populations have a substantial effect on health- and disease-related phenotypes. The concordant impact observed for same phenotypes across populations points to a process of adaptive introgression, whereby ancestry-enriched SNPs with specific functional utility appear to have been retained in modern populations by virtue of their effects on health and fitness.

Dataset Information

Palaeo-Eskimo genetic ancestry and the peopling of Chukotka and North America.

Publications

Palaeo-Eskimo genetic ancestry and the peopling of Chukotka and North America.

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