Dataset Information

Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation.

ABSTRACT: Full sequencing of individual human genomes has greatly expanded our understanding of human genetic variation and population history. Here, we present a systematic analysis of 50 human genomes from 11 diverse global populations sequenced at high coverage. Our sample includes 12 individuals who have admixed ancestry and who have varying degrees of recent (within the last 500 years) African, Native American, and European ancestry. We found over 21 million single-nucleotide variants that contribute to a 1.75-fold range in nucleotide heterozygosity across diverse human genomes. This heterozygosity ranged from a high of one heterozygous site per kilobase in west African genomes to a low of 0.57 heterozygous sites per kilobase in segments inferred to have diploid Native American ancestry from the genomes of Mexican and Puerto Rican individuals. We show evidence of all three continental ancestries in the genomes of Mexican, Puerto Rican, and African American populations, and the genome-wide statistics are highly consistent across individuals from a population once ancestry proportions have been accounted for. Using a generalized linear model, we identified subtle variations across populations in the proportion of neutral versus deleterious variation and found that genome-wide statistics vary in admixed populations even once ancestry proportions have been factored in. We further infer that multiple periods of gene flow shaped the diversity of admixed populations in the Americas-70% of the European ancestry in today's African Americans dates back to European gene flow happening only 7-8 generations ago.

SUBMITTER: Kidd JM

PROVIDER: S-EPMC3484644 | biostudies-literature | 2012 Oct

REPOSITORIES: biostudies-literature

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Publications

Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation.

Kidd Jeffrey M JM Gravel Simon S Byrnes Jake J Moreno-Estrada Andres A Musharoff Shaila S Bryc Katarzyna K Degenhardt Jeremiah D JD Brisbin Abra A Sheth Vrunda V Chen Rong R McLaughlin Stephen F SF Peckham Heather E HE Omberg Larsson L Bormann Chung Christina A CA Stanley Sarah S Pearlstein Kevin K Levandowsky Elizabeth E Acevedo-Acevedo Suehelay S Auton Adam A Keinan Alon A Acuña-Alonzo Victor V Barquera-Lozano Rodrigo R Canizales-Quinteros Samuel S Eng Celeste C Burchard Esteban G EG Russell Archie A Reynolds Andy A Clark Andrew G AG Reese Martin G MG Lincoln Stephen E SE Butte Atul J AJ De La Vega Francisco M FM Bustamante Carlos D CD

American journal of human genetics 20121001 4

Full sequencing of individual human genomes has greatly expanded our understanding of human genetic variation and population history. Here, we present a systematic analysis of 50 human genomes from 11 diverse global populations sequenced at high coverage. Our sample includes 12 individuals who have admixed ancestry and who have varying degrees of recent (within the last 500 years) African, Native American, and European ancestry. We found over 21 million single-nucleotide variants that contribute ...[more]

PMID: 23040495

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Project description:The Caribbean is a genetically diverse region with heterogeneous admixture compositions influenced by local island ecologies, migrations, colonial conflicts, and demographic histories. The Commonwealth of Dominica is a mountainous island in the Lesser Antilles historically known to harbor communities with unique patterns of migration, mixture, and isolation. This community-based population genetic study adds biological evidence to inform post-colonial narrative histories in a Dominican horticultural village. High density single nucleotide polymorphism data paired with a previously compiled genealogy provide the first genome-wide insights on genetic ancestry and population structure in Dominica. We assessed family-based clustering, inferred global ancestry, and dated recent admixture by implementing the fastSTRUCTURE clustering algorithm, modeling graph-based migration with TreeMix, assessing patterns of linkage disequilibrium decay with ALDER, and visualizing data from Dominica with Human Genome Diversity Panel references. These analyses distinguish family-based genetic structure from variation in African, European, and indigenous Amerindian admixture proportions, and analyses of linkage disequilibrium decay estimate admixture dates 5-6 generations (~160 years) ago. African ancestry accounts for the largest mixture components, followed by European and then indigenous components; however, our global ancestry inferences are consistent with previous mitochondrial, Y chromosome, and ancestry marker data from Dominica that show uniquely higher proportions of indigenous ancestry and lower proportions of African ancestry relative to known admixture in other French- and English-speaking Caribbean islands. Our genetic results support local narratives about the community's history and founding, which indicate that newly emancipated people settled in the steep, dense vegetation along Dominica's eastern coast in the mid-19th century. Strong genetic signals of post-colonial admixture and family-based structure highlight the localized impacts of colonial forces and island ecologies in this region, and more data from other groups are needed to more broadly inform on Dominica's complex history and present diversity.

Dataset Information

Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation.

Publications

Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation.

Similar Datasets

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