Alexander DH, Novembre J, Lange K (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19:1655–1664
CAS
PubMed
PubMed Central
CrossRef
Google Scholar
Balding DJ, Nichols RA (1994) DNA profile match probability calculation: how to allow for population stratification, relatedness, database selection and single bands. Forensic Sci Int 64:125–140
CAS
PubMed
CrossRef
Google Scholar
Balding DJ, Nichols RA (1995) A method for quantifying differentiation between populations at multi-allelic loci and its implications for investigating identity and paternity. Genetica 96:3–12
CAS
PubMed
CrossRef
Google Scholar
Beaumont MA, Zhang W, Balding DJ (2002) Approximate Bayesian computation in population genetics. Genetics 162:2025–2035
PubMed
PubMed Central
Google Scholar
Becquet C, Przeworski M (2007) A new approach to estimate parameters of speciation models with application to apes. Genome Res 17:1505–1519
CAS
PubMed
PubMed Central
CrossRef
Google Scholar
Bhatia G, Patterson N, Sankararaman S, Price AL (2013) Estimating and interpreting FST: the impact of rare variants. Genome Res 23:1514–1521
CAS
PubMed
PubMed Central
CrossRef
Google Scholar
Bradburd GS, Ralph PL, Coop GM (2016) A spatial framework for understanding population structure and admixture. PLoS Genet 12:e1005703
PubMed
PubMed Central
CrossRef
CAS
Google Scholar
Cann RL, Stoneking M, Wilson AC (1987) Mitochondrial DNA and human evolution. Nature 325:31–36
CAS
PubMed
CrossRef
Google Scholar
Cann HM, de Toma C, Cazes L, Legrand MF, Morel V et al (2002) A human genome diversity cell line panel. Science 296:261–262
CAS
PubMed
CrossRef
Google Scholar
Cavalli-Sforza LL, Edwards AWF (1967) Phylogenetic analysis -models and estimation procedures. Am J Hum Gen 19:233–257
CAS
Google Scholar
Cavalli-Sforza LL, Menozzi P, Piazza A (1994) The History and Geography of Human Genes. Princeton University Press, Princeton, NJ
Google Scholar
Chakraborty R, Jin L (1993) A unified approach to study hypervariable polymorphisms: statistical considerations of determining relatedness and population distances. In: DNA fingerprinting: state of the science. Birkhäuser, Basel, pp 153–175
Google Scholar
Chen C, Durand E, Forbes F, François O (2007) Bayesian clustering algorithms ascertaining spatial population structure: a new computer program and a comparison study. Mol Ecol Notes 7:747–756
CrossRef
Google Scholar
Corander J, Waldmann P, Sillanpää MJ (2003) Bayesian analysis of genetic differentiation between populations. Genetics 163:367–374
CAS
PubMed
PubMed Central
Google Scholar
Csilléry K, Blum MGB, Gaggiotti OE, François O (2010) Approximate Bayesian computation in practice. Trends Ecol Evol 25:410–418
PubMed
CrossRef
Google Scholar
Csilléry K, François O, Blum MGB (2012) abc: an R package for approximate Bayesian computation (ABC). Methods Ecol Evol 3:475–479
CrossRef
Google Scholar
Duforet-Frebourg N, Blum MGB (2014) Nonstationary patterns of isolation-by-distance: inferring measure of local genetic differentiation with Bayesian kriging. Evolution 68:1110–1123
PubMed
PubMed Central
CrossRef
Google Scholar
Ewens WJ, Spielman RS (1995) The transmission/disequilibrium test: history, subdivision, and admixture. Am J Hum Genet 57:455–464
CAS
PubMed
PubMed Central
CrossRef
Google Scholar
Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Res 10:564–567
CrossRef
Google Scholar
Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567–1587
CAS
PubMed
PubMed Central
Google Scholar
Felsenstein, J (1983) Parsimony in systematics: biological and statistical issues. Annu Rev Ecol Syst 14:313–333
Google Scholar
Foreman L, Smith A, Evett I (1997) Bayesian analysis of DNA profiling data in forensic identification applications. J R Stat Soc A 160:429–469
CrossRef
Google Scholar
Goldstein DB, Ruiz Linares A, Cavalli-Sforza LL, Feldman MW (1995) Genetic absolute dating based on microsatellites and the origin of modern humans. Proc Natl Acad Sci USA 92:6723–6727
CAS
PubMed
CrossRef
PubMed Central
Google Scholar
Green RE, Krause J, Briggs AW, Maricic T, Stenzel U et al (2010) A draft sequence of the Neandertal genome. Science 328:710–722
CAS
PubMed
PubMed Central
CrossRef
Google Scholar
Guillot G, Estoup A, Mortier F, Cosson JF (2005) A spatial statistical model for landscape genetics. Genetics 170:1261–1280
CAS
PubMed
PubMed Central
CrossRef
Google Scholar
Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD (2009) Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet 5:e1000695
PubMed
PubMed Central
CrossRef
CAS
Google Scholar
Hey J, Nielsen R (2004) Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 167:747–760
CAS
PubMed
PubMed Central
CrossRef
Google Scholar
Hey J, Nielsen R (2007) Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proc Natl Acad Sci USA 104:2785–2790
CAS
PubMed
CrossRef
PubMed Central
Google Scholar
Holsinger KE, Weir BS (2009) Genetics in geographically structured populations: defining, estimating and interpreting F(ST). Nat Rev Genet 10:639–650
CAS
PubMed
PubMed Central
CrossRef
Google Scholar
Jakobsson M, Rosenberg NA (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23:1801–1806
CAS
PubMed
CrossRef
Google Scholar
Jakobsson M, Scholz SW, Scheet P, Gibbs JR, VanLiere JM et al (2008) Genotype, haplotype and copy-number variation in worldwide human populations. Nature 451:998–1003
CAS
PubMed
CrossRef
Google Scholar
Jay F, Sjödin P, Jakobsson M, Blum MGM (2013) Anisotropic isolation by distance: the main orientations of human genetic differentiation. Mol Biol Evol 30:513–525
CAS
PubMed
CrossRef
Google Scholar
Jolliffe I (2005) Principal component analysis. Wiley, New York
Google Scholar
Jost L (2008) G(ST) and its relatives do not measure differentiation. Mol Ecol 17:4015–4026
PubMed
CrossRef
Google Scholar
Katti MV, Rajekar PK, Gupta VS (2001) Differential distribution of simple sequence repeats in eukaryotic genome sequences. Mol Biol Evol 18:1161–1167
CAS
PubMed
CrossRef
Google Scholar
Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874
CAS
PubMed
CrossRef
PubMed Central
Google Scholar
Landsteiner K, Weiner AS (1940) An agglutinable factor in human blood recognized by immune sera for rhesus blood. Proc Soc Exp Biol NY 43:223
CAS
CrossRef
Google Scholar
Lawson DJ, Hellenthal G, Myers S, Falush D (2011) Inference of population structure using dense haplotype data. PLoS Genet 8:e1002453
CrossRef
CAS
Google Scholar
Lewontin RC, Hubby JL (1966) A molecular approach to the study of genetic heterozygosity in natural populations. II. Amount of variation and degree of heterozygosity in natural populations of Drosophila pseudoobscura. Genetics 54:595–609
CAS
PubMed
PubMed Central
CrossRef
Google Scholar
Li N, Stephens M (2003) Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics 165:2213–2233
CAS
PubMed
PubMed Central
Google Scholar
Li JZ, Absher DM, Tang H, Southwick AM, Casto AM et al (2008) Worldwide human relationships inferred from genome-wide patterns of variation. Science 319:1100–1104
CAS
PubMed
CrossRef
Google Scholar
Li J, Li H, Jakobsson M, Li S, Sjödin P, Lascoux M (2012) Joint analysis of demography and selection in population genetics: where do we stand and where could we go? Mol Ecol 21:28–44
CAS
PubMed
CrossRef
Google Scholar
Lipson M, Loh PR, Levin A, Reich D, Patterson N, Berger B (2013) Efficient moment-based inference of population admixture parameters and sources of gene flow. Mol Biol Evol 30:1788–1802
CAS
PubMed
PubMed Central
CrossRef
Google Scholar
Lopes JS, Balding D, Beaumont MA (2009) PopABC: a program to infer historical demographic parameters. Bioinformatics 25:2747–2749
CAS
PubMed
CrossRef
Google Scholar
Mallick S, Li H, Lipson M, Mathieson I, Gymrek M et al (2016) The Simons genome diversity project: 300 genomes from 142 diverse populations. Nature 538:201–206
CAS
PubMed
PubMed Central
CrossRef
Google Scholar
McVean G (2009) A genealogical interpretation of principal components analysis M. PLoS Genetics 5:e1000686
Google Scholar
Nei M (1972) Genetic distance between populations. Am Nat 106:283–292
CrossRef
Google Scholar
Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA 70:3321–3323
CAS
PubMed
CrossRef
PubMed Central
Google Scholar
Nei M, Tajima F, Tateno Y (1983) Accuracy of estimated phylogenetic trees from molecular data. II Gene frequency data. J Mol Evol 19:153–170
CAS
PubMed
CrossRef
Google Scholar
Nicholson G, Smith AV, Jónsson F, Gústafsson Ó, Stefánsson K, Donnelly P (2002) Assessing population differentiation and isolation from single nucleotide polymorphism data. J R Stat Soc B 64:695–715
CrossRef
Google Scholar
Nielsen R, Wakeley J (2001) Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics 158:885–896
CAS
PubMed
PubMed Central
Google Scholar
Patterson N, Price AL, Reich D (2006) Population structure and eigen analysis. PLoS Genetics 2:e190
Google Scholar
Patterson N, Moorjani P, Luo Y, Mallick S, Rohland N et al (2012) Ancient admixture in human history. Genetics 192:1065–1093
PubMed
PubMed Central
CrossRef
Google Scholar
Petkova D, Novembre J, Stephens M (2016) Visualizing spatial population structure with estimated effective migration surfaces. Nat Genet 48:94–100
CAS
PubMed
CrossRef
Google Scholar
Pickrell JK, Pritchard JK (2012) Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet 8:e1002967
CAS
PubMed
PubMed Central
CrossRef
Google Scholar
Prevosti A, Ocana J, Alonzo G (1975) Distances between populations for Drosophila subobscura based on chromosome arrangement frequencies. Theor Appl Genet 45:231–241
CAS
PubMed
CrossRef
Google Scholar
Price AL, Tandon A, Patterson N, Barnes KC, Rafaels N et al (2009) Sensitive detection of chromosomal segments of distinct ancestry in admixed populations. PLoS Genet 5:e1000519
PubMed
PubMed Central
CrossRef
CAS
Google Scholar
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959
CAS
PubMed
PubMed Central
Google Scholar
Pudlo P, Marin JM, Estoup A, Cornuet JM, Gautier M, Robert CP (2016) Reliable ABC model choice via random forests. Bioinformatics 32:859–866
CAS
PubMed
CrossRef
Google Scholar
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR et al (2007) PLINK: a toolset for whole-genome association and population-based linkage analysis. Am Hum Genet 81:559–575
CAS
CrossRef
Google Scholar
Quinn GP, Keough MJ (2002) Experimental design and data analysis for biologists. Cambridge University Press, Cambridge
CrossRef
Google Scholar
Reich D, Thangaraj K, Patterson N, Price AL, Singh L (2009) Reconstructing Indian population history. Nature 461:489–494
CAS
PubMed
PubMed Central
CrossRef
Google Scholar
Reich D, Green RE, Kircher M, Krause J, Patterson N et al (2010) Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468:1053–1060
CAS
PubMed
PubMed Central
CrossRef
Google Scholar
Reynolds J, Weir BS, Cockerham CC (1983) Estimation of the coancestry coefficient: basis for a short-term genetic distance. Genetics 105:767–779
CAS
PubMed
PubMed Central
CrossRef
Google Scholar
Roeder K, Escobar M, Kadane JB, Balazs I (1998) Measuring heterogeneity in forensic databases using hierarchical Bayes models. Biometrika 85:269–287
CrossRef
Google Scholar
Rogers JS (1972) Measures of similarity and genetic distance. In: Studies in genetics VII. University of Texas Publication 7213. Austin, Texas, pp 145−153
Google Scholar
Rosenberg NA (2004) Distruct: a program for the graphical display of population structure. Mol Ecol Notes 4:137–138
CrossRef
Google Scholar
Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK et al (2002) Genetic structure of human populations. Science 298:2381–2385
CAS
PubMed
CrossRef
Google Scholar
Rousset F (2013) Exegeses on maximum genetic differentiation. Genetics 194:557–559
PubMed
PubMed Central
CrossRef
Google Scholar
Ryman N, Leimar O (2009) G(ST) is still a useful measure of genetic differentiation – a comment on Jost’s D. Mol Ecol 18:2084–2087
PubMed
CrossRef
Google Scholar
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
CAS
PubMed
Google Scholar
Schlebusch CM, Skoglund P, Sjödin P, Gattepaille LM, Hernandez D et al (2012) Genomic variation in seven Khoe-San groups reveals adaptation and complex African history. Science 338:374–379
CAS
PubMed
CrossRef
PubMed Central
Google Scholar
Shriver M, Jin L, Boerwinkle E, Deka R, Ferrell RE et al (1995) A novel measure of genetic distance for highly polymorphic tandem repeat loci. Mol Biol Evol 12:914–920
CAS
PubMed
Google Scholar
Slatkin M (1995) A measure of population subdivision based on microsatellite allele frequencies. Genetics 139:457–462
CAS
PubMed
PubMed Central
CrossRef
Google Scholar
Tang H, Peng J, Wang P, Risch NJ (2005) Estimation of individual admixture: analytical and study design considerations. Genet Epidemiol 28:289–301
PubMed
CrossRef
Google Scholar
Tellier A, Pfaffelhuber P, Haubold B, Naduvilezhath L, Rose LE et al (2011) Estimating parameters of speciation models based on refined summaries of the joint site-frequency spectrum. PLoS One 6:e18155
CAS
PubMed
PubMed Central
CrossRef
Google Scholar
Veeramah KR, Hammer MF (2014) The impact of whole-genome sequencing on the reconstruction of human population history. Nat Rev Genet 15:149–162
CAS
PubMed
CrossRef
Google Scholar
Venter JC, Adams MD, Myers EW, Li PW, Mural RJ et al (2001) The sequence of the human genome. Science 291(5507):1304–51. https://doi.org/10.1126/science.1058040. Erratum in: Science 292(5523):1838 (2001). PMID: 11181995.
Weir BS (1996) Genetic data analysis II. Sinauer Associates, Sunderland
Google Scholar
Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370
CAS
PubMed
Google Scholar
Wright S (1949) The genetical structure of populations. Ann Hum Gen 15:323–354
Google Scholar