30
J. Wakeley
Slatkin M (1991) Inbreeding coefficients and coalescence times. Genet Res Camb 58:167–175
Slatkin M, Hudson RR (1991) Pairwise comparisons of mitochondrial DNA sequences in stable
and exponentially growing populations. Genetics 129:555–562
Speidel L, Forest M, Sinan S, Myers SR (2019) A method for genome-wide genealogy estimation
for thousands of samples. Nat Genet 51:1321–1329
Spence JP, Steinrücken M, Terhorst J, Song YS (2018) Inference of population history using
coalescent HMMs: review and outlook. Curr Op Genet Devel 53:70–76
Stephens M, Donnelly P (2000) Inference in molecular population genetics. J R Stat Soc Ser B
62:605–655
Stephens M, Donnelly P (2003) Ancestral inference in population genetics models with selection.
Aust N Z J Stat 45:395–430
Stephens JC, Schneider JA, Tanguay DA, Choi J, Acharya T, Stanley SE, Jiang R, Messer CJ, Chew
A, Han J-H, Duan J, Carr JL, Lee MS, Koshy B, Kumar AM, Zhang G, Newell W, Windemuth
A, Xu C, Kalbfleisch TS, Shaner SL, Arnold K, Schultz V, Drysdale CM, Nandabalan K, Judson
RS, Ruaño G, Vovis GF (2001) Haplotype variation and linkage disequilibrium in 313 human
genes. Science 293:489–493
Strobeck C (1987) Average number of nucleotide differences in a sample from a single subpopulation: a test for population subdivision. Genetics 117:149–153
Tajima F (1983) Evolutionary relationship of DNA sequences in finite populations. Genetics
105:437–460
Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA. Genetics
123:585–595
Tajima F (1997) Estimation of the amount of DNA polymorphism and statistical tests of the neutral
mutation hypothesis based on DNA polymorphism. In: Donnelly P, Tavaré S (eds) Progress in
population genetics and human evolution. Springer, New York, pp 149–164
Takahata N (1988) The coalescent in two partially isolated diffusion populations. Genet Res Camb
53:213–222
Takahata N, Nei M (1985) Gene genealogy and variance of interpopulational nucleotide differences. Genetics 110:325–344
Tavaré S (1984) Lines-of-descent and genealogical processes, and their application in population
genetic models. Theor Popul Biol 26:119–164
The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation.
Nature 526:68–74
Valdes AM, Slatkin M, Freimer NB (1993) Allele frequencies at microsatellite loci: the stepwise
mutation model revisited. Genetics 133:737–749
Wakeley J (1999) Non-equilibrium migration in human history. Genetics 153:1863–1871
Wakeley J (2009) Coalescent theory: an introduction. Macmillan Learning, Macmillan, New York
Wakeley J, Hey J (1997) Estimating ancestral population parameters. Genetics 145:847–855
Wakeley J, King L, Low BS, Ramachandran S (2012) Gene genealogies within a fixed pedigree,
and the robustness of Kingman’s coalescent. Genetics 190:1433–1445
Wakeley J, King L, Wilton P (2016) Effects of the population pedigree on genetic signatures of
historical demographic events. Proc Natl Acad Sci USA 113:7994–8001
Watterson GA (1975) On the number of segregating sites in genetical models without recombination. Theoret Pop Biol 7:256–276
Watterson GA (1982) Mutant substitutions at linked nucleotide sites. Adv Appl Probab 14:166–205
Wilkinson-Herbots HM (2008) The distribution of the coalescence time and the number of pairwise
nucleotide differences in the “isolation with migration” model. Theoret Pop Biol 73:277–288
Wilton PR, Baduel P, Landon MM, Wakeley J (2017) Population structure and coalescence in
pedigrees: comparisons to the structured coalescent and a framework for inference. Theoret
Pop Biol 115:1–12
Winther GW, Giordano R, Edge MD, Nieslen R (2015) The mind, the lab, and the field: three kinds
of populations in scientific practice. Stud Hist Phil Biol Biomed Sci 52:12–21
Wright S (1931) Evolution in Mendelian populations. Genetics 16:97–159
Wu Y (2010) Exact computation of coalescent likelihood for panmictic and subdivided populations
under the infinite sites model. IEEE/ACM Trans Comput Biol Bioinform 7:611–618
J. Wakeley
Slatkin M (1991) Inbreeding coefficients and coalescence times. Genet Res Camb 58:167–175
Slatkin M, Hudson RR (1991) Pairwise comparisons of mitochondrial DNA sequences in stable
and exponentially growing populations. Genetics 129:555–562
Speidel L, Forest M, Sinan S, Myers SR (2019) A method for genome-wide genealogy estimation
for thousands of samples. Nat Genet 51:1321–1329
Spence JP, Steinrücken M, Terhorst J, Song YS (2018) Inference of population history using
coalescent HMMs: review and outlook. Curr Op Genet Devel 53:70–76
Stephens M, Donnelly P (2000) Inference in molecular population genetics. J R Stat Soc Ser B
62:605–655
Stephens M, Donnelly P (2003) Ancestral inference in population genetics models with selection.
Aust N Z J Stat 45:395–430
Stephens JC, Schneider JA, Tanguay DA, Choi J, Acharya T, Stanley SE, Jiang R, Messer CJ, Chew
A, Han J-H, Duan J, Carr JL, Lee MS, Koshy B, Kumar AM, Zhang G, Newell W, Windemuth
A, Xu C, Kalbfleisch TS, Shaner SL, Arnold K, Schultz V, Drysdale CM, Nandabalan K, Judson
RS, Ruaño G, Vovis GF (2001) Haplotype variation and linkage disequilibrium in 313 human
genes. Science 293:489–493
Strobeck C (1987) Average number of nucleotide differences in a sample from a single subpopulation: a test for population subdivision. Genetics 117:149–153
Tajima F (1983) Evolutionary relationship of DNA sequences in finite populations. Genetics
105:437–460
Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA. Genetics
123:585–595
Tajima F (1997) Estimation of the amount of DNA polymorphism and statistical tests of the neutral
mutation hypothesis based on DNA polymorphism. In: Donnelly P, Tavaré S (eds) Progress in
population genetics and human evolution. Springer, New York, pp 149–164
Takahata N (1988) The coalescent in two partially isolated diffusion populations. Genet Res Camb
53:213–222
Takahata N, Nei M (1985) Gene genealogy and variance of interpopulational nucleotide differences. Genetics 110:325–344
Tavaré S (1984) Lines-of-descent and genealogical processes, and their application in population
genetic models. Theor Popul Biol 26:119–164
The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation.
Nature 526:68–74
Valdes AM, Slatkin M, Freimer NB (1993) Allele frequencies at microsatellite loci: the stepwise
mutation model revisited. Genetics 133:737–749
Wakeley J (1999) Non-equilibrium migration in human history. Genetics 153:1863–1871
Wakeley J (2009) Coalescent theory: an introduction. Macmillan Learning, Macmillan, New York
Wakeley J, Hey J (1997) Estimating ancestral population parameters. Genetics 145:847–855
Wakeley J, King L, Low BS, Ramachandran S (2012) Gene genealogies within a fixed pedigree,
and the robustness of Kingman’s coalescent. Genetics 190:1433–1445
Wakeley J, King L, Wilton P (2016) Effects of the population pedigree on genetic signatures of
historical demographic events. Proc Natl Acad Sci USA 113:7994–8001
Watterson GA (1975) On the number of segregating sites in genetical models without recombination. Theoret Pop Biol 7:256–276
Watterson GA (1982) Mutant substitutions at linked nucleotide sites. Adv Appl Probab 14:166–205
Wilkinson-Herbots HM (2008) The distribution of the coalescence time and the number of pairwise
nucleotide differences in the “isolation with migration” model. Theoret Pop Biol 73:277–288
Wilton PR, Baduel P, Landon MM, Wakeley J (2017) Population structure and coalescence in
pedigrees: comparisons to the structured coalescent and a framework for inference. Theoret
Pop Biol 115:1–12
Winther GW, Giordano R, Edge MD, Nieslen R (2015) The mind, the lab, and the field: three kinds
of populations in scientific practice. Stud Hist Phil Biol Biomed Sci 52:12–21
Wright S (1931) Evolution in Mendelian populations. Genetics 16:97–159
Wu Y (2010) Exact computation of coalescent likelihood for panmictic and subdivided populations
under the infinite sites model. IEEE/ACM Trans Comput Biol Bioinform 7:611–618