Models, methods and tools for ancestry inference and admixture analysis

BackgroundGenetic admixture refers to the process or consequence of interbreeding between two or more previously isolated populations within a species. Compared to many other evolutionary driving forces such as mutations, genetic drift, and natural selection, genetic admixture is a quick mechanism for shaping population genomic diversity. In particular, admixture results in “recombination” of genetic variants that have been fixed in different populations, which has many evolutionary and medical implications.ResultsHowever, it is challenging to accurately reconstruct population admixture history and to understand of population admixture dynamics. In this review, we provide an overview of models, methods, and tools for ancestry inference and admixture analysis.ConclusionsMany methods and tools used for admixture analysis were originally developed to analyze human data, but these methods can also be directly applied and/or slightly modified to study non-human species as well.

[1]  S. Wright,et al.  Evolution in Mendelian Populations. , 1931, Genetics.

[2]  M. Kimura,et al.  The Stepping Stone Model of Population Structure and the Decrease of Genetic Correlation with Distance. , 1964, Genetics.

[3]  W. G. Hill,et al.  The effect of linkage on limits to artificial selection. , 1966, Genetical research.

[4]  Ranajit Chakraborty,et al.  Gene admixture in human populations: Models and predictions , 1986 .

[5]  K. Weiss,et al.  Admixture as a tool for finding linked genes and detecting that difference from allelic association between loci. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[6]  J. Long.  The genetic structure of admixed populations. , 1991, Genetics.

[7]  J. Stephens,et al.  Mapping by admixture linkage disequilibrium in human populations: limits and guidelines. , 1994, American journal of human genetics.

[8]  W. Ewens,et al.  The transmission/disequilibrium test: history, subdivision, and admixture. , 1995, American journal of human genetics.

[9]  Y. Yuval,et al.  Dominant inheritance in two families with familial Mediterranean fever (FMF). , 1995, American journal of medical genetics.

[10]  P. McKeigue,et al.  Mapping genes underlying ethnic differences in disease risk by linkage disequilibrium in recently admixed populations. , 1997, American journal of human genetics.

[11]  I. Barrai,et al.  Isolation by distance in Germany , 1997, Human Genetics.

[12]  P. McKeigue,et al.  Mapping genes that underlie ethnic differences in disease risk: methods for detecting linkage in admixed populations, by conditioning on parental admixture. , 1998, American journal of human genetics.

[13]  P. Donnelly,et al.  Inference of population structure using multilocus genotype data. , 2000, Genetics.

[14]  E. Boerwinkle,et al.  Population structure in admixed populations: effect of admixture dynamics on the pattern of linkage disequilibrium. , 2001, American journal of human genetics.

[15]  Peter Beerli,et al.  Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[16]  R. Kittles,et al.  Ancestral proportions and admixture dynamics in geographically defined African Americans living in South Carolina. , 2001, American journal of physical anthropology.

[17]  M. Feldman,et al.  Genetic Structure of Human Populations , 2002, Science.

[18]  K. Benirschke.  The Evolution and Genetics of Latin American Populations , 2002 .

[19]  M. Stephens,et al.  Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. , 2003, Genetics.

[20]  M. Stephens,et al.  Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. , 2003, Genetics.

[21]  Xiaofeng Zhu,et al.  Linkage analysis of a complex disease through use of admixed populations. , 2004, American journal of human genetics.

[22]  C. Hoggart,et al.  Design and analysis of admixture mapping studies. , 2004, American journal of human genetics.

[23]  M. Daly,et al.  Methods for high-density admixture mapping of disease genes. , 2004, American journal of human genetics.

[24]  Giovanni Montana,et al.  Statistical tests for admixture mapping with case-control and cases-only data. , 2004, American journal of human genetics.

[25]  N. Risch,et al.  Estimation of individual admixture: Analytical and study design considerations , 2005, Genetic epidemiology.

[26]  W. Guo,et al.  On the Formula for Admixture Linkage Disequilibrium , 2006, Human Heredity.

[27]  D. Reich,et al.  Population Structure and Eigenanalysis , 2006, PLoS genetics.

[28]  N. Risch,et al.  Reconstructing genetic ancestry blocks in admixed individuals. , 2006, American journal of human genetics.

[29]  Vincent Plagnol,et al.  Possible Ancestral Structure in Human Populations , 2006, PLoS genetics.

[30]  W. Guo,et al.  The admixture linkage disequilibrium and genetic linkage inference on the gradual admixture population. , 2006, Yi chuan xue bao = Acta genetica Sinica.

[31]  L. Xiangjun,et al.  ? Higher Education Press and Springer-Verlag 2007 , 2007 .

[32]  E. Halperin,et al.  Estimating Local Ancestry in Admixed Populations , 2022 .

[33]  Li Jin,et al.  Analysis of genomic admixture in Uyghur and its implication in mapping strategy. , 2008, American journal of human genetics.

[34]  Shuhua Xu,et al.  A genome-wide analysis of admixture in Uyghurs and a high-density admixture map for disease-gene discovery. , 2008, American journal of human genetics.

[35]  Chuong B. Do,et al.  Effect of genetic divergence in identifying ancestral origin using HAPAA. , 2008, Genome research.

[36]  Michael I. Jordan,et al.  On the Inference of Ancestries in Admixed Populations , 2008, RECOMB.

[37]  Chad Huff,et al.  Linkage Disequilibrium Between Loci With Unknown Phase , 2009, Genetics.

[38]  Eduardo Barrientos,et al.  Analysis of genomic diversity in Mexican Mestizo populations to develop genomic medicine in Mexico , 2009, Proceedings of the National Academy of Sciences.

[39]  Eran Halperin,et al.  Inference of locus-specific ancestry in closely related populations , 2009, Bioinform..

[40]  D. Absher,et al.  Characterizing the admixed African ancestry of African Americans , 2009, Genome Biology.

[41]  David H. Alexander,et al.  Fast model-based estimation of ancestry in unrelated individuals. , 2009, Genome research.

[42]  Alkes L. Price,et al.  Reconstructing Indian Population History , 2009, Nature.

[43]  R. Nielsen,et al.  Inference of Historical Changes in Migration Rate From the Lengths of Migrant Tracts , 2009, Genetics.

[44]  Stephen L. Hauser,et al.  Genome-wide patterns of population structure and admixture in West Africans and African Americans , 2009, Proceedings of the National Academy of Sciences.

[45]  M. Stephens,et al.  Inferring weak population structure with the assistance of sample group information , 2009, Molecular ecology resources.

[46]  D. Reich,et al.  Sensitive Detection of Chromosomal Segments of Distinct Ancestry in Admixed Populations , 2009, PLoS genetics.

[47]  Kirk E Lohmueller,et al.  Detecting ancient admixture and estimating demographic parameters in multiple human populations. , 2009, Molecular biology and evolution.

[48]  C. Winkler,et al.  Admixture mapping comes of age. , 2010, Annual review of genomics and human genetics.

[49]  Philip L. F. Johnson,et al.  Genetic history of an archaic hominin group from Denisova Cave in Siberia , 2010, Nature.

[50]  Philip L. F. Johnson,et al.  A Draft Sequence of the Neandertal Genome , 2010, Science.

[51]  F. Ayala,et al.  Genome-wide Patterns of Population Structure and Admixture Among Hispanic/Latino Populations , 2010 .

[52]  M. Stoneking,et al.  Dating the age of admixture via wavelet transform analysis of genome-wide data , 2011, Genome Biology.

[53]  Sharon R Grossman,et al.  Integrating common and rare genetic variation in diverse human populations , 2010, Nature.

[54]  H. Ostrer,et al.  The History of African Gene Flow into Southern Europeans, Levantines, and Jews , 2011, PLoS genetics.

[55]  Loren Gragert,et al.  The Shaping of Modern Human Immune Systems by Multiregional Admixture with Archaic Humans , 2011, Science.

[56]  Nicholas A. Johnson,et al.  Ancestral Components of Admixed Genomes in a Mexican Cohort , 2011, PLoS genetics.

[57]  C. Bustamante,et al.  Inferring genome-wide patterns of admixture in Qataris using fifty-five ancestral populations , 2012, BMC Genetics.

[58]  Thomas Mailund,et al.  Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection. , 2011, Genome research.

[59]  Noah A. Rosenberg,et al.  A General Mechanistic Model for Admixture Histories of Hybrid Populations , 2011, Genetics.

[60]  David Reich,et al.  Testing for ancient admixture between closely related populations. , 2011, Molecular biology and evolution.

[61]  Xiaofeng Zhu,et al.  The landscape of recombination in African Americans , 2011, Nature.

[62]  S. Gravel.  Population Genetics Models of Local Ancestry , 2012, Genetics.

[63]  Jake K. Byrnes,et al.  PCAdmix: Principal Components-Based Assignment of Ancestry Along Each Chromosome in Individuals with Admixed Ancestry from Two or More Populations , 2012, Human biology.

[64]  D. Falush,et al.  Inference of Population Structure using Dense Haplotype Data , 2012, PLoS genetics.

[65]  M. Hammer,et al.  Global genetic variation at OAS1 provides evidence of archaic admixture in Melanesian populations. , 2012, Molecular biology and evolution.

[66]  Adrian W. Briggs,et al.  A High-Coverage Genome Sequence from an Archaic Denisovan Individual , 2012, Science.

[67]  M. Hammer,et al.  A haplotype at STAT2 Introgressed from neanderthals and serves as a candidate of positive selection in Papua New Guinea. , 2012, American journal of human genetics.

[68]  Li Jin,et al.  Exploring population admixture dynamics via empirical and simulated genome-wide distribution of ancestral chromosomal segments. , 2012, American journal of human genetics.

[69]  Swapan Mallick,et al.  Ancient Admixture in Human History , 2012, Genetics.

[70]  Jia Li,et al.  Efficient inference of local ancestry , 2013, Bioinform..

[71]  C. Bustamante,et al.  RFMix: a discriminative modeling approach for rapid and robust local-ancestry inference. , 2013, American journal of human genetics.

[72]  Philip L. F. Johnson,et al.  The complete genome sequence of a Neanderthal from the Altai Mountains , 2013 .

[73]  Joseph K. Pickrell,et al.  Inferring Admixture Histories of Human Populations Using Linkage Disequilibrium , 2012, Genetics.

[74]  Serafim Batzoglou,et al.  Ancestry Inference in Complex Admixtures via Variable-length Markov Chain Linkage Models , 2013, J. Comput. Biol..

[75]  J. Marchini,et al.  Multiway Admixture Deconvolution Using Phased or Unphased Ancestral Panels , 2013, Genetic epidemiology.

[76]  Wenfei Jin,et al.  Distribution of ancestral chromosomal segments in admixed genomes and its implications for inferring population history and admixture mapping , 2013, European Journal of Human Genetics.

[77]  Joshua M. Akey,et al.  Resurrecting Surviving Neandertal Lineages from Modern Human Genomes , 2014, Science.

[78]  Swapan Mallick,et al.  The genomic landscape of Neanderthal ancestry in present-day humans. , 2016 .

[79]  M. Stephens,et al.  fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets , 2014, Genetics.

[80]  Shuhua Xu,et al.  Neanderthal introgression at chromosome 3p21.31 was under positive natural selection in East Asians. , 2014, Molecular biology and evolution.

[81]  Robert Brown,et al.  Enhanced Methods for Local Ancestry Assignment in Sequenced Admixed Individuals , 2014, PLoS Comput. Biol..

[82]  Badri Padhukasahasram,et al.  Inferring ancestry from population genomic data and its applications , 2014, Front. Genet..

[83]  D. Falush,et al.  A Genetic Atlas of Human Admixture History , 2014, Science.

[84]  Michael C. Westaway,et al.  Genomic structure in Europeans dating back at least 36,200 years , 2014, Science.

[85]  T. Mailund,et al.  Lineage sorting in apes. , 2014, Annual review of genetics.

[86]  R. Mägi,et al.  Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans , 2013, Nature.

[87]  Asan,et al.  Altitude adaptation in Tibet caused by introgression of Denisovan-like DNA , 2014, Nature.

[88]  Bonnie Berger,et al.  Ancient west Eurasian ancestry in southern and eastern Africa , 2013, Proceedings of the National Academy of Sciences.

[89]  J. Akey,et al.  Resurrecting Surviving Neandertal Lineages from Modern Human , 2014 .

[90]  S. Scherer,et al.  The population genomic landscape of human genetic structure, admixture history and local adaptation in Peninsular Malaysia , 2014, Human Genetics.

[91]  Yongtao Guan.  Detecting Structure of Haplotypes and Local Ancestry , 2014, Genetics.

[92]  Michael F. Siebauer,et al.  Patterns of coding variation in the complete exomes of three Neandertals , 2014, Proceedings of the National Academy of Sciences.

[93]  Shuhua Xu,et al.  Neanderthal origin of the haplotypes carrying the functional variant Val92Met in the MC1R in modern humans. , 2014, Molecular biology and evolution.

[94]  Guillaume Bouchard,et al.  Fast and Efficient Estimation of Individual Ancestry Coefficients , 2014, Genetics.

[95]  Anders Eriksson,et al.  Upper Palaeolithic genomes reveal deep roots of modern Eurasians , 2015, Nature Communications.

[96]  R. Nielsen,et al.  Evidence for archaic adaptive introgression in humans , 2015, Nature Reviews Genetics.

[97]  Shuhua Xu,et al.  Reintroduction of a Homocysteine Level-Associated Allele into East Asians by Neanderthal Introgression. , 2015, Molecular biology and evolution.

[98]  Length Distribution of Ancestral Tracks under a General Admixture Model and Its Applications in Population History Inference , 2015 .

[99]  M. Stoneking,et al.  Denisovan Ancestry in East Eurasian and Native American Populations , 2015, bioRxiv.

[100]  Matthew Stephens,et al.  Visualizing spatial population structure with estimated effective migration surfaces , 2014, Nature Genetics.

[101]  Wei Guo,et al.  Corrigendum: Length Distribution of Ancestral Tracks under a General Admixture Model and Its Applications in Population History Inference , 2016, Scientific reports.

[102]  Length Distribution of Ancestral Tracks under a General Admixture Model and Its Applications in Population History Inference , 2016, Scientific reports.

[103]  Li Jin,et al.  Ancestral Origins and Genetic History of Tibetan Highlanders. , 2016, American journal of human genetics.

[104]  M. Stoneking,et al.  The Complex Admixture History and Recent Southern Origins of Siberian Populations , 2015, bioRxiv.

[105]  David Posada,et al.  Multilocus inference of species trees and DNA barcoding , 2016, Philosophical Transactions of the Royal Society B: Biological Sciences.

[106]  Ziheng Yang,et al.  Challenges in Species Tree Estimation Under the Multispecies Coalescent Model , 2016, Genetics.

[107]  Hongxiang Qiu,et al.  Modeling Continuous Admixture Using Admixture-Induced Linkage Disequilibrium , 2017, Scientific Reports.

[108]  E P Xing,et al.  Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with polynomial functions , 2016, Heredity.

[109]  X. Ni,et al.  Inference of multiple-wave admixtures by length distribution of ancestral tracks , 2016, Heredity.