28
J. Wakeley
Ferretti L, Perez-Enciso M, Ramos-Onsins S (2010) Optimal neutrality tests based on the
frequency spectrum. Genetics 186:353–365
Fisher RA (1930) The genetical theory of natural selection. Clarendon, Oxford
Fu Y-X (1995) Statistical properties of segregating sites. Theoret Pop Biol 48:172–197
Fu Y-X (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking
and background selection. Genetics 147:915–925
Fu Y-X, Li W-H (1993) Statistical tests of neutrality of mutations. Genetics 133:693–709
Griffiths RC, Tavaré S (1994) Simulating probability distributions in the coalescent. Theoret Pop
Biol 46:131–159
Griffiths RC, Tavaré S (1996) Monte Carlo inference methods in population genetics. Math Comput
Modelling 23:141–158
Hanski I, Gaggiotti OE (2004) Ecology, genetics, and evolution of metapopulations. Elsevier
Academic, London
Harris K (2019) From a database of genomes to a forest of evolutionary trees. Nat Genet 51:1304–
1307
Hasegawa M, Kishino H, Yano H (1985) Dating of the human-ape splitting by a molecular clock
of mitochondrial DNA. J Mol Evol 22:160–174
Hawks J. “Coalescent Gene Genealogies” from the Wolfram Demonstrations Project. http://
demonstrations.wolfram.com/CoalescentGeneGenealogies/
Hein J, Schierup MH, Wiuf C (2005) Gene genealogies, variation and evolution: a primer in
coalescent theory. Oxford University Press, Oxford
Herbots HM (1997) The structured coalescent. In: Donnelly P, Tavaré S (eds) Progress in
population genetics and human evolution, IMA volumes in mathematics and its applications,
vol 87. Springer, New York, pp 231–255
Hey J (2010) Isolation with migration models for more than two populations. Mol Biol Evol
27:905–920
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
Hey J, Nielsen R (2007) Integration within the Felsenstein equation for improved Markov chain
Monte Carlo methods in population genetics. Proc Natl Acad Sci U S A 104:2785–2790
Hochman A (2019) Race and reference. Biology & Philosophy 34:32
Hodgkinson A, Eyre-Walker A (2010) Human triallelic sites: evidence for a new mutational
mechanism? Genetics 184:233–241
Hudson RR (1983) Testing the constant-rate neutral allele model with protein sequence data.
Evolution 37:203–217
Hudson RR (1990) Gene genealogies and the coalescent process. In: Futuyma DJ, Antonovics J
(eds) Oxford surveys in evolutionary biology, vol 7. Oxford University Press, Oxford, pp 1–44
Huff CD, Xing J, Rogers AR, Witherspoon D, Jorde LB (2010) Mobile elements reveal small
population size in the ancient ancestors of Homo sapiens. Proc Natl Acad Sci USA 107:2147–
2152
Keinan A, Clark AG (2012) Recent explosive human population growth has resulted in an excess
of rare genetic variants. Science 336:740–743
Kelleher J, Wong Y, Wohns AW, Fadil C, Albers PK, McVean G (2019) Inferring whole-genome
histories in large population datasets. Nat Genet 51:1330–1338
Kingman JFC (1982a) On the genealogy of large populations. J Appl Probab 19A:27–43
Kingman JFC (1982b) The coalescent. Stoch Process Appl 13:235–248
Kingman JFC (1982c) Exchangeability and the evolution of large populations. In: Koch G,
Spizzichino F (eds) Exchangeability in probability and statistics. North-Holland, Amsterdam,
pp 97–112
Ko A, Nielsen R (2019) Joint estimation of pedigrees and effective population size using Markov
chain Monte Carlo. Genetics 212:855–868
Kuhner MK (2006) LAMARC 2.0: maximum likelihood and Bayesian estimation of population
parameters. Bioinformatics 22:768–770
J. Wakeley
Ferretti L, Perez-Enciso M, Ramos-Onsins S (2010) Optimal neutrality tests based on the
frequency spectrum. Genetics 186:353–365
Fisher RA (1930) The genetical theory of natural selection. Clarendon, Oxford
Fu Y-X (1995) Statistical properties of segregating sites. Theoret Pop Biol 48:172–197
Fu Y-X (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking
and background selection. Genetics 147:915–925
Fu Y-X, Li W-H (1993) Statistical tests of neutrality of mutations. Genetics 133:693–709
Griffiths RC, Tavaré S (1994) Simulating probability distributions in the coalescent. Theoret Pop
Biol 46:131–159
Griffiths RC, Tavaré S (1996) Monte Carlo inference methods in population genetics. Math Comput
Modelling 23:141–158
Hanski I, Gaggiotti OE (2004) Ecology, genetics, and evolution of metapopulations. Elsevier
Academic, London
Harris K (2019) From a database of genomes to a forest of evolutionary trees. Nat Genet 51:1304–
1307
Hasegawa M, Kishino H, Yano H (1985) Dating of the human-ape splitting by a molecular clock
of mitochondrial DNA. J Mol Evol 22:160–174
Hawks J. “Coalescent Gene Genealogies” from the Wolfram Demonstrations Project. http://
demonstrations.wolfram.com/CoalescentGeneGenealogies/
Hein J, Schierup MH, Wiuf C (2005) Gene genealogies, variation and evolution: a primer in
coalescent theory. Oxford University Press, Oxford
Herbots HM (1997) The structured coalescent. In: Donnelly P, Tavaré S (eds) Progress in
population genetics and human evolution, IMA volumes in mathematics and its applications,
vol 87. Springer, New York, pp 231–255
Hey J (2010) Isolation with migration models for more than two populations. Mol Biol Evol
27:905–920
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
Hey J, Nielsen R (2007) Integration within the Felsenstein equation for improved Markov chain
Monte Carlo methods in population genetics. Proc Natl Acad Sci U S A 104:2785–2790
Hochman A (2019) Race and reference. Biology & Philosophy 34:32
Hodgkinson A, Eyre-Walker A (2010) Human triallelic sites: evidence for a new mutational
mechanism? Genetics 184:233–241
Hudson RR (1983) Testing the constant-rate neutral allele model with protein sequence data.
Evolution 37:203–217
Hudson RR (1990) Gene genealogies and the coalescent process. In: Futuyma DJ, Antonovics J
(eds) Oxford surveys in evolutionary biology, vol 7. Oxford University Press, Oxford, pp 1–44
Huff CD, Xing J, Rogers AR, Witherspoon D, Jorde LB (2010) Mobile elements reveal small
population size in the ancient ancestors of Homo sapiens. Proc Natl Acad Sci USA 107:2147–
2152
Keinan A, Clark AG (2012) Recent explosive human population growth has resulted in an excess
of rare genetic variants. Science 336:740–743
Kelleher J, Wong Y, Wohns AW, Fadil C, Albers PK, McVean G (2019) Inferring whole-genome
histories in large population datasets. Nat Genet 51:1330–1338
Kingman JFC (1982a) On the genealogy of large populations. J Appl Probab 19A:27–43
Kingman JFC (1982b) The coalescent. Stoch Process Appl 13:235–248
Kingman JFC (1982c) Exchangeability and the evolution of large populations. In: Koch G,
Spizzichino F (eds) Exchangeability in probability and statistics. North-Holland, Amsterdam,
pp 97–112
Ko A, Nielsen R (2019) Joint estimation of pedigrees and effective population size using Markov
chain Monte Carlo. Genetics 212:855–868
Kuhner MK (2006) LAMARC 2.0: maximum likelihood and Bayesian estimation of population
parameters. Bioinformatics 22:768–770