Detecting individual ancestry in the human genome

Detecting and quantifying the population substructure present in a sample of individuals are of main interest in the fields of genetic epidemiology, population genetics, and forensics among others. To date, several algorithms have been proposed for estimating the amount of genetic ancestry within an individual. In the present review, we introduce the most widely used methods in population genetics for detecting individual genetic ancestry. We further show, by means of simulations, the performance of popular algorithms for detecting individual ancestry in various controlled demographic scenarios. Finally, we provide some hints on how to interpret the results from these algorithms.

• Publication year

  2015

• Venue

  Investigative Genetics

• Publication date

  2015-05-01

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1186/s13323-015-0019-xPMID 25937887PMCID 4416275
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets

  2014cited by this paper
• GAGA: A New Algorithm for Genomic Inference of Geographic Ancestry Reveals Fine Level Population Substructure in Europeans

  2014cited by this paper
• A Genetic Atlas of Human Admixture History

  2014cited by this paper
• Fast and Efficient Estimation of Individual Ancestry Coefficients

  2014influential reference
• Geographic population structure analysis of worldwide human populations infers their biogeographical origins

  2014cited by this paper
• Enhanced localization of genetic samples through linkage-disequilibrium correction.

  2013cited by this paper
• Softwares and methods for estimating genetic ancestry in human populations

  2013cited by this paper
• Hierarchical and Spatially Explicit Clustering of DNA Sequences with BAPS Software

  2013cited by this paper
• Reconstructing the population history of European Romani from genome-wide data.

  2012cited by this paper
• A model-based approach for analysis of spatial structure in genetic data

  2012cited by this paper
• Reconstructing Native American Population History

  2012cited by this paper
• The genetic prehistory of southern Africa

  2012cited by this paper
• Inference of Population Structure using Dense Haplotype Data

  2012cited by this paper
• Historical Population Movements in Europe Influence Genetic Relationships in Modern Samples

  2012cited by this paper
• Anisotropic Isolation by Distance: The Main Orientations of Human Genetic Differentiation

  2012cited by this paper
• Ancient Admixture in Human History

  2012cited by this paper
• Reconstructing the Population History of European Romani from Genome-wide Data

  2012cited by this paper
• Population identification using genetic data.

  2012cited by this paper
• Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

  2012cited by this paper
• Population Genetics Models of Local Ancestry

  2012cited by this paper
• Improving human forensics through advances in genetics, genomics and molecular biology

  2011cited by this paper
• GemTools: A fast and efficient approach to estimating genetic ancestry

  2011cited by this paper
• Perspectives on human population structure at the cusp of the sequencing era.

  2011cited by this paper
• Contrasting signals of positive selection in genes involved in human skin-color variation from tests based on SNP scans and resequencing

  2011cited by this paper
• The computer program STRUCTURE does not reliably identify the main genetic clusters within species: simulations and implications for human population structure

  2011cited by this paper
• A General Mechanistic Model for Admixture Histories of Hybrid Populations

  2011cited by this paper
• Dating the age of admixture via wavelet transform analysis of genome-wide data

  2011cited by this paper
• Integrating common and rare genetic variation in diverse human populations

  2010cited by this paper
• Human genome diversity: frequently asked questions.

  2010cited by this paper
• Principal component analysis under population genetic models of range expansion and admixture.

  2010influential reference
• Discovering genetic ancestry using spectral graph theory

  2009influential reference
• Fast model-based estimation of ancestry in unrelated individuals.

  2009influential reference
• A Genealogical Interpretation of Principal Components Analysis

  2009influential reference
• Genome-wide patterns of population structure and admixture in West Africans and African Americans

  2009cited by this paper
• Laplacian Eigenfunctions Learn Population Structure

  2009influential reference
• Accurate Inference of Subtle Population Structure (and Other Genetic Discontinuities) Using Principal Coordinates

  2009cited by this paper
• Sensitive Detection of Chromosomal Segments of Distinct Ancestry in Admixed Populations

  2009cited by this paper
• Genetic markers in the playground of multivariate analysis

  2009cited by this paper
• Genes mirror geography within Europe

  2008cited by this paper
• adegenet: a R package for the multivariate analysis of genetic markers

  2008cited by this paper
• Revealing cryptic spatial patterns in genetic variability by a new multivariate method

  2008cited by this paper
• Accounting for ancestry: population substructure and genome-wide association studies.

  2008cited by this paper
• Genotype, haplotype and copy-number variation in worldwide human populations

  2008cited by this paper
• Comparing Genetic Ancestry and Self-Described Race in African Americans Born in the United States and in Africa

  2008cited by this paper
• Supplemental Information for : Interpreting principal components analyses of spatial population genetic variation

  2008influential reference
• PLINK: a tool set for whole-genome association and population-based linkage analyses.

  2007cited by this paper
• CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure

  2007influential reference
• Generalized Analysis of Molecular Variance

  2007cited by this paper
• Human evolution and its relevance for genetic epidemiology.

  2007cited by this paper
• Going the distance: human population genetics in a clinal world.

  2007cited by this paper
• Bayesian clustering algorithms ascertaining spatial population structure: a new computer program and a comparison study

  2007cited by this paper
• Dissecting racial and ethnic differences.

  2006cited by this paper
• Genomic Boundaries between Human Populations

  2006cited by this paper
• Population Structure and Eigenanalysis

  2006influential reference
• Principal components analysis corrects for stratification in genome-wide association studies

  2006cited by this paper
• Estimation of individual admixture: Analytical and study design considerations

  2005cited by this paper
• Human Races: Classifying People vs Understanding Diversity

  2005cited by this paper
• Initial sequence of the chimpanzee genome and comparison with the human genome

  2005cited by this paper
• Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa.

  2005cited by this paper
• Characterization of a likelihood based method and effects of markers informativeness in evaluation of admixture and population group assignment

  2005cited by this paper
• Detecting the number of clusters of individuals using the software structure: a simulation study

  2005cited by this paper
• Algorithms for Selecting Informative Marker Panels for Population Assignment

  2005cited by this paper
• Geneland: a computer package for landscape genetics

  2005cited by this paper
• BAPS 2: enhanced possibilities for the analysis of genetic population structure

  2004cited by this paper
• Human genetic diversity: Lewontin's fallacy.

  2003cited by this paper
• Model-Based Clustering, Discriminant Analysis, and Density Estimation

  2002cited by this paper
• Generating samples under a Wright-Fisher neutral model of genetic variation

  2002influential reference
• Estimate of the mutation rate per nucleotide in humans.

  2000cited by this paper
• Inference of population structure using multilocus genotype data.

  2000influential reference
• Inferring admixture proportions from molecular data.

  1998cited by this paper
• MAXIMUM‐LIKELIHOOD ESTIMATION OF POPULATION DIVERGENCE TIMES AND POPULATION PHYLOGENY IN MODELS WITHOUT MUTATION

  1998cited by this paper
• Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data.

  1992cited by this paper
• The genetic structure of admixed populations.

  1991cited by this paper
• ESTIMATING F‐STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE

  1984cited by this paper
• The Apportionment of Human Diversity

  1972cited by this paper
• Supporting Online Material Materials and Methods Figs. S1 to S3 Tables S1 to S5 References Worldwide Human Relationships Inferred from Genome-wide Patterns of Variation

  year unknowncited by this paper

• Revealing the range of equally likely estimates in the admixture model

  2025cites this paper
• Combining multiscale replication in network and landscape genetic analyses to assess functional connectivity and population resilience in Parnassius clodius butterflies.

  2025cites this paper
• Habitat Quality and Water Availability Affect Genetic Connectivity of Platypus Across an Urban Landscape

  2025cites this paper
• Revealing the range of maximum likelihood estimates in the admixture model

  2025cites this paper
• Recentering forensic anthropology within a multifaceted body of evolutionary theory: Strengthening method by making theory explicit

  2022cites this paper
• Short running title: Genomic patterns of four Trachemys congeners Complex genetic patterns and distribution limits mediated by native congeners of the worldwide invasive red-eared slider turtle

  2021cites this paper
• A central limit theorem concerning uncertainty in estimates of individual admixture.

  2021cites this paper
• Estimating individual admixture from finite reference databases

  2021cites this paper
• The Study of European Migration in Asia-Pacific During the Early Modern Period: San Salvador de Isla Hermosa (Keelung, Taiwan)

  2020cites this paper
• Forensic inference of biogeographical ancestry from genotype: The Genetic Ancestry Lab

  2020cites this paper
• Genome‐wide insights into introgression and its consequences for genome‐wide heterozygosity in the Mytilus species complex across Europe

  2020cites this paper
• Japan considered from the hypothesis of farmer/language spread

  2020cites this paper
• GRAF-pop: A Fast Distance-Based Method To Infer Subject Ancestry from Multiple Genotype Datasets Without Principal Components Analysis

  2019cites this paper
• Genotyping by sequencing reveals contrasting patterns of population structure, ecologically mediated divergence, and long‐distance dispersal in North American palms

  2018cites this paper
• Genome-Wide SNPs Identify Limits to Connectivity in the Extreme Freshwater Disperser, Spangled Perch Leiopotherapon unicolor (Terapontidae)

  2018cites this paper
• BITE: an R package for biodiversity analyses

  2017influential citation
• CONE: Community Oriented Network Estimation Is a Versatile Framework for Inferring Population Structure in Large-Scale Sequencing Data

  2017cites this paper
• Captive Ancestry Upwardly Biases Estimates of Relative Reproductive Success

  2017cites this paper
• Fast Inference of Individual Admixture Coefficients Using Geographic Data

  2016cites this paper
• FAST INFERENCE OF INDIVIDUAL ADMIXTURE 1 COEFFICIENTS USING GEOGRAPHIC DATA

  2016cites this paper
• TESS3: fast inference of spatial population structure and genome scans for selection

  2016cites this paper
• Immunogenomics of gastrointestinal nematode infection in ruminants – breeding for resistance to produce food sustainably and safely

  2016cites this paper
• Identifying outlier loci in admixed and in continuous populations using ancestral population differentiation statistics

  2016cites this paper
• Inference and Analysis of Population Structure Using Genetic Data and Network Theory

  2015cites this paper