As a companion to the collection, this review highlights recent progress and discusses future directions for the study of admixed human populations.
collection
Human Genetic Admixture
Throughout human history, large-scale migrations have facilitated the formation of populations with ancestry from multiple previously separated populations. This process leads to subsequent shuffling of genetic ancestry through recombination, producing variation in ancestry between populations, among individuals in a population, and along the genome within an individual. Recent methodological and empirical developments have elucidated the genomic signatures of this admixture process, bringing previously understudied admixed populations to the forefront of population and medical genetics.
In this collection, we present a selection of PLOS Genetics research that exemplifies recent progress in human genetic admixture and areas for future development.
Image Credit: pgen.1008385 Fig 4 by Mehrjoo et al., CC BY 4.0
Collection Review
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Image creditpgen.1009374 Fig 1 by Korunes and Goldberg, CC BY 4.0PLOS Genetics Human genetic admixture
Population history and demography
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Image creditpgen.1008204 Fig 4 by Ragsdale and Gravel, CC BY 4.0PLOS Genetics Models of archaic admixture and recent history from two-locus statistics
Shows that human evolutionary models that include archaic admixture in Africa, Asia, and Europe provide a much better description of patterns of genetic diversity across the human genome.
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Image creditpgen.1005703 Fig 1 by Bradburd et al., CC BY 4.0PLOS Genetics A Spatial Framework for Understanding Population Structure and Admixture
Introduces a statistical method for inferring, for a set of sequenced samples, a map in which the distances between population locations reflect genetic, rather than geographic, proximity.
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Image creditpgen.1008175 Fig 3 by Durvasula and Sankararaman, CC BY 4.0PLOS Genetics A statistical model for reference-free inference of archaic local ancestry
Develops a method that identifies segments of archaic ancestry in modern human genomes without the need for archaic reference genomes.
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Image creditpgen.1007385 Fig 4 by Browning et al., CC BY 4.0PLOS Genetics Ancestry-specific recent effective population size in the Americas
Develops methodology for estimating past effective population size and analyzes data from Hispanic, African-American, and European-American populations residing in the United States.
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Image creditpgen.1008895 Fig 3 by Hubisz et al., CC BY 4.0PLOS Genetics Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph
Presents ARGweaver-D, an extension of the ARGweaver algorithm which can be applied under a user-defined demographic model including population splits and migration events.
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Image creditpgen.1003925 Fig 1 by Moreno-Estrada et al., CC BY 4.0PLoS Genetics Reconstructing the Population Genetic History of the Caribbean
Investigates the population genetic history of the Caribbean basin by characterizing patterns of genome-wide variation among 330 individuals.
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Image creditpgen.1004530 Fig 1 by Verdu et al., CC BY 4.0PLoS Genetics Patterns of Admixture and Population Structure in Native Populations of Northwest North America
Collaborates with six indigenous communities in British Columbia and Southeast Alaska to generate and analyze genome-wide data for over 100 individuals.
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Image creditpgen.1008385 Fig 3 by Mehrjoo et al., CC BY 4.0PLOS Genetics Distinct genetic variation and heterogeneity of the Iranian population
Pursues Iran's genome-wide and geographic characterization based on 1021 samples from eleven ethnic groups.
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Image creditpgen.1006852 Fig 1 by Martiniano et al., CC BY 4.0PLOS Genetics The population genomics of archaeological transition in west Iberia: Investigation of ancient substructure using imputation and haplotype-based methods
Sequences Neolithic and Bronze Age samples from Portugal and compares these to other ancient and present-day individuals.
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Image creditpgen.1006059 Fig 1 by Baharian et al., CC BY 4.0PLOS Genetics The Great Migration and African-American Genomic Diversity
Presents a comprehensive assessment of genomic diversity in the African-American population by studying three genotyped cohorts.
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Image creditpgen.1008417 Fig 2 by Font-Porterias et al., CC BY 4.0PLOS Genetics European Roma groups show complex West Eurasian admixture footprints and a common South Asian genetic origin
Reveals a common South Asian origin of all European Roma, closely related to a Punjabi group from Northwestern India.
Phenotypically important loci and regions under selection
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Image creditpgen.1002641 Fig 2 by Jarvis et al., CC BY 4.0PLOS Genetics Patterns of Ancestry, Signatures of Natural Selection, and Genetic Association with Stature in Western African Pygmies
Analyzes a set of admixing Bantu-speaking agricultural and Western Pygmy hunter-gatherer populations and identifies several genomic regions that may have been targets of natural selection.
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Image creditpgen.1003372 Fig 3 by Beleza et al., CC BY 4.0PLoS Genetics Genetic Architecture of Skin and Eye Color in an African- European Admixed Population
Studies a unique population in Cape Verde in which extensive mixing between individuals of Portuguese and West African ancestry has given rise to a broad range of phenotypes.
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Image creditpgen.1007791 Fig 1 by Rajabli et al., CC BY 4.0PLOS Genetics Ancestral origin of ApoE ε4 Alzheimer disease risk in Puerto Rican and African American populations
Shows that the risk of Alzheimer disease is lower for those who inherit the genomic region surrounding the ApoE gene from an African ancestor than for those who inherit from a European ancestor.
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Image creditpgen.1004572 Fig 1 by Ruiz-Linares et al., CC BY 4.0PLoS Genetics Admixture in Latin America: Geographic Structure, Phenotypic Diversity and Self-Perception of Ancestry Based on 7,342 Individuals
Estimates individual ancestry proportions in a sample of 7,342 subjects from five countries (Brazil, Chile, Colombia, México and Perú), who were also characterized for physical appearance traits.
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Image creditpgen.1008500 S5 Fig by Kowalski et al., CC BY 4.0PLOS Genetics Use of >100,000 NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium whole genome sequences improves imputation quality and detection of rare variant associations in admixed African and Hispanic/Latino populations
Uses sequences from ~21,600 individuals of African ancestry (AAs) and ~21,700 Hispanics/Latinos and demonstrates substantially higher imputation quality for low frequency and rare variants.
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Image creditpgen.1007650 Fig 2 by Jeong et al., CC BY 4.0PLOS Genetics Detecting past and ongoing natural selection among ethnically Tibetan women at high altitude in Nepal
Uses genotype and phenotype information of 1,000 ethnically Tibetan women to show that natural selection systematically altered frequency of alleles associated with reproductive outcomes.
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Image creditpgen.1007368 Fig 5 by Yao et al., CC BY 4.0PLOS Genetics Genetic ancestry and population differences in levels of inflammatory cytokines in women: Role for evolutionary selection and environmental factors
Reveals a genetic variant implicated in low circulating levels of key chemokines regulating the migration of white blood cells, which occurs almost exclusively among Africans.
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Image creditpgen.1005052 Fig 3 by Chimusa et al., CC BY 4.0PLOS Genetics A Genomic Portrait of Haplotype Diversity and Signatures of Selection in Indigenous Southern African Populations
Identifies several signals of selection, before and after admixture, some of which involve loci associated with human diseases, including malaria, influenza, tuberculosis and HIV/AIDS.
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Image creditpgen.1007741 Fig 4 by Kim et al., CC BY 4.0PLOS Genetics Deleterious variation shapes the genomic landscape of introgression
Shows that when ancestry from a larger population is added to a smaller population, ancestry from the larger population dramatically increases in frequency as it carries fewer deleterious mutations.
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Image creditpgen.1006340 Fig 6 by Juric et al., CC BY 4.0PLOS Genetics The Strength of Selection against Neanderthal Introgression
Shows that observed patterns of Neanderthal ancestry in modern humans can be explained simply as a consequence of the difference in effective population size between Neanderthals and humans.