8 Inferring Human Demographic History from Genetic Data
199
Bryc K, Auton A, Nelson MR, Oksenberg JR, Hauser SL, Williams S, Froment A, Bodo JM,
Wambebe C, Tishkoff SA et al (2010) Genome-wide patterns of population structure and
admixture in West Africans and African Americans. Proc Natl Acad Sci USA 107:786–791
Caballero A (1994) Developments in the prediction of effective population size. Heredity 73:657–
679
Cann RL, Stoneking M, Wilson AC (1987) Mitochondrial DNA and human evolution. Nature
325:31–36
Cavalli-Sforza LL, Menozzi P, Piazza A (1994) The history and geography of human genes.
Princeton University Press, Princeton, NJ
Chen H, Hey J, Chen K (2015) Inferring very recent population growth rate from population-scale
sequencing data: using a large-sample coalescent estimator. Mol Biol Evol 32:2996–3011
Choudhry S, Coyle NE, Tang H, Salari K, Lind D, Clark SL, Tsai HJ, Naqvi M, Phong A, Ung
N et al (2006) Population stratification confounds genetic association studies among Latinos.
Hum Genet 118:652–664
Conrad DF, Jakobsson M, Coop G, Wen X, Wall JD, Rosenberg NA, Pritchard JK (2006) A
worldwide survey of haplotype variation and linkage disequilibrium in the human genome. Nat
Genet 38:1251–1260
Coon CS (1962) The origins of races. Alfred A. Knopf, New York
Coventry A, Bull-Otterson LM, Liu X, Clark AG, Maxwell TJ, Crosby J, Hixson JE, Rea TJ,
Muzny DM, Lewis LR et al (2010) Deep resequencing reveals excess rare recent variants
consistent with explosive population growth. Nat Commun 1:131
DeGiorgio M, Jakobsson M, Rosenberg NA (2009) Out of Africa: modern human origins special
feature: explaining worldwide patterns of human genetic variation using a coalescent-based
serial founder model of migration outward from Africa. Proc Natl Acad Sci USA 106:16057–
16062
Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees.
BMC Evol Biol 7:214
Durvasula A, Sankararaman S (2020) Recovering signals of ghost archaic introgression in African
populations. Sci Adv 6(7):eaax5097. https://doi.org/10.1126/sciadv.aax5097
Edwards AWF, Cavalli-Sforza LL (1964) Reconstruction of evolutionary trees. In: Heywood VH,
McNeill J (eds) Phenetic and phylogenetic classification (systematics association pub. #6).
London, pp 67–76
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
Fay JC, Wu CI (1999) A human population bottleneck can account for the discordance between
patterns of mitochondrial versus nuclear DNA variation. Mol Biol Evol 16:1003–1005
Fischer A, Pollack J, Thalmann O, Nickel B, Paabo S (2006) Demographic history and genetic
differentiation in apes. Curr Biol 16:1133–1138
Frisse L, Hudson RR, Bartoszewicz A, Wall JD, Donfack J, Di Rienzo A (2001) Gene conversion
and different population histories may explain the contrast between polymorphsim and linkage
disequilibrium levels. Am J Hum Genet 69:831–843
Fu Q, Meyer M, Gao X, Stenzel U, Burbano HA, Kelso J, Paabo S (2013) DNA analysis of an
early modern human from Tianyuan cave, China. Proc Natl Acad Sci USA 110:2223–2227
Gao F, Keinan A (2016) Inference of super-exponential human population growth via efficient
computation of the site frequency spectrum for generalized models. Genetics 202:235–245
Garrigan D (2009) Composite likelihood estimation of demographic parameters. BMC Genet 10:72
Garrigan D, Mobasher Z, Severson T, Wilder JA, Hammer MF (2005) Evidence for archaic Asian
ancestry on the human X chromosome. Mol Biol Evol 22:189–192
Gazave E, Ma L, Chang D, Coventry A, Gao F, Muzny D, Boerwinkle E, Gibbs RA, Sing CF,
Clark AG et al (2014) Neutral genomic regions refine models of recent rapid human population
growth. Proc Natl Acad Sci USA 111:757–762
GenomeAsia100K Consortium (2019) The GenomeAsia 100K project enables genetic discoveries
across Asia. Nature 576:106–111
Gibbons A (1993) Pleistocene population explosions. Science 262:27–28
199
Bryc K, Auton A, Nelson MR, Oksenberg JR, Hauser SL, Williams S, Froment A, Bodo JM,
Wambebe C, Tishkoff SA et al (2010) Genome-wide patterns of population structure and
admixture in West Africans and African Americans. Proc Natl Acad Sci USA 107:786–791
Caballero A (1994) Developments in the prediction of effective population size. Heredity 73:657–
679
Cann RL, Stoneking M, Wilson AC (1987) Mitochondrial DNA and human evolution. Nature
325:31–36
Cavalli-Sforza LL, Menozzi P, Piazza A (1994) The history and geography of human genes.
Princeton University Press, Princeton, NJ
Chen H, Hey J, Chen K (2015) Inferring very recent population growth rate from population-scale
sequencing data: using a large-sample coalescent estimator. Mol Biol Evol 32:2996–3011
Choudhry S, Coyle NE, Tang H, Salari K, Lind D, Clark SL, Tsai HJ, Naqvi M, Phong A, Ung
N et al (2006) Population stratification confounds genetic association studies among Latinos.
Hum Genet 118:652–664
Conrad DF, Jakobsson M, Coop G, Wen X, Wall JD, Rosenberg NA, Pritchard JK (2006) A
worldwide survey of haplotype variation and linkage disequilibrium in the human genome. Nat
Genet 38:1251–1260
Coon CS (1962) The origins of races. Alfred A. Knopf, New York
Coventry A, Bull-Otterson LM, Liu X, Clark AG, Maxwell TJ, Crosby J, Hixson JE, Rea TJ,
Muzny DM, Lewis LR et al (2010) Deep resequencing reveals excess rare recent variants
consistent with explosive population growth. Nat Commun 1:131
DeGiorgio M, Jakobsson M, Rosenberg NA (2009) Out of Africa: modern human origins special
feature: explaining worldwide patterns of human genetic variation using a coalescent-based
serial founder model of migration outward from Africa. Proc Natl Acad Sci USA 106:16057–
16062
Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees.
BMC Evol Biol 7:214
Durvasula A, Sankararaman S (2020) Recovering signals of ghost archaic introgression in African
populations. Sci Adv 6(7):eaax5097. https://doi.org/10.1126/sciadv.aax5097
Edwards AWF, Cavalli-Sforza LL (1964) Reconstruction of evolutionary trees. In: Heywood VH,
McNeill J (eds) Phenetic and phylogenetic classification (systematics association pub. #6).
London, pp 67–76
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
Fay JC, Wu CI (1999) A human population bottleneck can account for the discordance between
patterns of mitochondrial versus nuclear DNA variation. Mol Biol Evol 16:1003–1005
Fischer A, Pollack J, Thalmann O, Nickel B, Paabo S (2006) Demographic history and genetic
differentiation in apes. Curr Biol 16:1133–1138
Frisse L, Hudson RR, Bartoszewicz A, Wall JD, Donfack J, Di Rienzo A (2001) Gene conversion
and different population histories may explain the contrast between polymorphsim and linkage
disequilibrium levels. Am J Hum Genet 69:831–843
Fu Q, Meyer M, Gao X, Stenzel U, Burbano HA, Kelso J, Paabo S (2013) DNA analysis of an
early modern human from Tianyuan cave, China. Proc Natl Acad Sci USA 110:2223–2227
Gao F, Keinan A (2016) Inference of super-exponential human population growth via efficient
computation of the site frequency spectrum for generalized models. Genetics 202:235–245
Garrigan D (2009) Composite likelihood estimation of demographic parameters. BMC Genet 10:72
Garrigan D, Mobasher Z, Severson T, Wilder JA, Hammer MF (2005) Evidence for archaic Asian
ancestry on the human X chromosome. Mol Biol Evol 22:189–192
Gazave E, Ma L, Chang D, Coventry A, Gao F, Muzny D, Boerwinkle E, Gibbs RA, Sing CF,
Clark AG et al (2014) Neutral genomic regions refine models of recent rapid human population
growth. Proc Natl Acad Sci USA 111:757–762
GenomeAsia100K Consortium (2019) The GenomeAsia 100K project enables genetic discoveries
across Asia. Nature 576:106–111
Gibbons A (1993) Pleistocene population explosions. Science 262:27–28