3 Analysis of Population Structure
67
Jolliffe I (2005) Principal component analysis. Wiley, New York
Jost L (2008) G(ST) and its relatives do not measure differentiation. Mol Ecol 17:4015–4026
Katti MV, Rajekar PK, Gupta VS (2001) Differential distribution of simple sequence repeats in
eukaryotic genome sequences. Mol Biol Evol 18:1161–1167
Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version
7.0 for bigger datasets. Mol Biol Evol 33:1870–1874
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
Lawson DJ, Hellenthal G, Myers S, Falush D (2011) Inference of population structure using dense
haplotype data. PLoS Genet 8:e1002453
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
Li N, Stephens M (2003) Modeling linkage disequilibrium and identifying recombination hotspots
using single-nucleotide polymorphism data. Genetics 165:2213–2233
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
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
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
Lopes JS, Balding D, Beaumont MA (2009) PopABC: a program to infer historical demographic
parameters. Bioinformatics 25:2747–2749
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
McVean G (2009) A genealogical interpretation of principal components analysis M. PLoS
Genetics 5:e1000686
Nei M (1972) Genetic distance between populations. Am Nat 106:283–292
Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA
70:3321–3323
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
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
Nielsen R, Wakeley J (2001) Distinguishing migration from isolation: a Markov chain Monte Carlo
approach. Genetics 158:885–896
Patterson N, Price AL, Reich D (2006) Population structure and eigen analysis. PLoS Genetics
2:e190
Patterson N, Moorjani P, Luo Y, Mallick S, Rohland N et al (2012) Ancient admixture in human
history. Genetics 192:1065–1093
Petkova D, Novembre J, Stephens M (2016) Visualizing spatial population structure with estimated
effective migration surfaces. Nat Genet 48:94–100
Pickrell JK, Pritchard JK (2012) Inference of population splits and mixtures from genome-wide
allele frequency data. PLoS Genet 8:e1002967
Prevosti A, Ocana J, Alonzo G (1975) Distances between populations for Drosophila subobscura
based on chromosome arrangement frequencies. Theor Appl Genet 45:231–241
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
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus
genotype data. Genetics 155:945–959
67
Jolliffe I (2005) Principal component analysis. Wiley, New York
Jost L (2008) G(ST) and its relatives do not measure differentiation. Mol Ecol 17:4015–4026
Katti MV, Rajekar PK, Gupta VS (2001) Differential distribution of simple sequence repeats in
eukaryotic genome sequences. Mol Biol Evol 18:1161–1167
Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version
7.0 for bigger datasets. Mol Biol Evol 33:1870–1874
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
Lawson DJ, Hellenthal G, Myers S, Falush D (2011) Inference of population structure using dense
haplotype data. PLoS Genet 8:e1002453
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
Li N, Stephens M (2003) Modeling linkage disequilibrium and identifying recombination hotspots
using single-nucleotide polymorphism data. Genetics 165:2213–2233
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
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
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
Lopes JS, Balding D, Beaumont MA (2009) PopABC: a program to infer historical demographic
parameters. Bioinformatics 25:2747–2749
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
McVean G (2009) A genealogical interpretation of principal components analysis M. PLoS
Genetics 5:e1000686
Nei M (1972) Genetic distance between populations. Am Nat 106:283–292
Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA
70:3321–3323
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
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
Nielsen R, Wakeley J (2001) Distinguishing migration from isolation: a Markov chain Monte Carlo
approach. Genetics 158:885–896
Patterson N, Price AL, Reich D (2006) Population structure and eigen analysis. PLoS Genetics
2:e190
Patterson N, Moorjani P, Luo Y, Mallick S, Rohland N et al (2012) Ancient admixture in human
history. Genetics 192:1065–1093
Petkova D, Novembre J, Stephens M (2016) Visualizing spatial population structure with estimated
effective migration surfaces. Nat Genet 48:94–100
Pickrell JK, Pritchard JK (2012) Inference of population splits and mixtures from genome-wide
allele frequency data. PLoS Genet 8:e1002967
Prevosti A, Ocana J, Alonzo G (1975) Distances between populations for Drosophila subobscura
based on chromosome arrangement frequencies. Theor Appl Genet 45:231–241
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
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus
genotype data. Genetics 155:945–959