1 Coalescent Models
27
described. These models aid in the interpretation of genetic data and express our
understanding of how evolutionary forces produce and maintain variation at a single
locus without recombination.
References
Achaz G (2009) Frequency spectrum neutrality tests: one for all and all for one. Genetics 183:249–
258
Alvarado-Serrano DF, Hickerson MJ (2016) Spatially explicit summary statistics for historical
population genetic inference. Methods Ecol Evol 7:418–427
Alvarez G, Ceballos FC, Quinteiro C (2009) The role of inbreeding in the extinction of a European
royal dynasty. PLoS One 4(4):e5174
Beaumont MA (2010) Approximate Bayesian computation in evolution and ecology. Annu Rev
Ecol Evol Syst 41:379–406
Beerli P (2006) Comparison of Bayesian and maximum-likelihood inference of population genetic
parameters. Bioinformatics 22:341–345
Bycro C et al (2018) The UK biobank resource with deep phenotyping and genomic data. Nature
562:203–209
Cannings C (1974) The latent roots of certain Markov chains arising in genetics: a new approach.
I. Haploid models. Adv Appl Probab 6:260–290
Cannings C, Thompson EA, Skolnick MH (1978) Probability functions on complex pedigrees.
Adv Appl Probab 10:26–61
Cargill M, Altshuler D, Ireland J, Sklar P, Ardlie K, Patil N, Lane CR, Lim EP, Kalyanaraman N,
Nemesh J, Ziaugra L, Friedland L, Rolfe A, Warrington J, Lipshutz R, Daly GQ, Lander ES
(1999) Characterization of single-nucleotide polymorphisms in coding regions of human genes.
Nat Genet 22:231–237
Chang JT (1999) Recent common ancestors of all present-day individuals. Adv Appl Probab
31:1002–1026
de Iorio M, Griffiths RC, Leblois R, Rousset F (2005) Stepwise mutation likelihood computation
by sequential importance sampling in subdivided population models. Theoret Pop Biol 68:41–
53
Donnelly P, Tavaré S (1995) Coalescents and genealogical structure under neutrality. Annu Rev
Genet 29:401–421
Drummond AJ, Suchard MA, Xie D, Rambaut A (2012) Bayesian phylogenetics with BEAUti and
the BEAST 1.7. Mol Biol Evol 29:1969–1973
Durrett R, Schweinsberg J (2004) Approximating selective sweeps. Theoret Pop Biol 66:129–138
Etheridge AM, Pfaffelhuber P, Wakolbinger A (2006) An approximate sampling formula under
genetic hitchhiking. Ann Appl Probab 16:685–729
Ewens WJ (1972) The sampling theory of selectively neutral alleles. Theoret Pop Biol 3:87–112
Ewens WJ (1974) A note on the sampling theory for infinite alleles and infinite sites models.
Theoret Pop Biol 6:143–148
Ewens WJ (1990) Population genetics theory—the past and the future. In: Lessard S (ed) Mathematical and statistical developments of evolutionary theory. Kluwer Academic, Amsterdam, pp
177–227
Ewens WJ (2004) Mathematical population genetics, vol I: theoretical foundations. Springer,
Berlin
Fay JC, Wu C-I (2000) Hitchhiking under positive Darwinian selection. Genetics 155:1405–1413
Fearnhead P (2006) Perfect simulation from nonneutral population genetic models: variable
population size and population subsdivision. Genetics 174:1397–1406
Felsenstein J (2006) Accuracy of coalescent likelihood estimates: do we need more sites, more
sequences, or more loci? Mol Biol Evol 23:691–700
27
described. These models aid in the interpretation of genetic data and express our
understanding of how evolutionary forces produce and maintain variation at a single
locus without recombination.
References
Achaz G (2009) Frequency spectrum neutrality tests: one for all and all for one. Genetics 183:249–
258
Alvarado-Serrano DF, Hickerson MJ (2016) Spatially explicit summary statistics for historical
population genetic inference. Methods Ecol Evol 7:418–427
Alvarez G, Ceballos FC, Quinteiro C (2009) The role of inbreeding in the extinction of a European
royal dynasty. PLoS One 4(4):e5174
Beaumont MA (2010) Approximate Bayesian computation in evolution and ecology. Annu Rev
Ecol Evol Syst 41:379–406
Beerli P (2006) Comparison of Bayesian and maximum-likelihood inference of population genetic
parameters. Bioinformatics 22:341–345
Bycro C et al (2018) The UK biobank resource with deep phenotyping and genomic data. Nature
562:203–209
Cannings C (1974) The latent roots of certain Markov chains arising in genetics: a new approach.
I. Haploid models. Adv Appl Probab 6:260–290
Cannings C, Thompson EA, Skolnick MH (1978) Probability functions on complex pedigrees.
Adv Appl Probab 10:26–61
Cargill M, Altshuler D, Ireland J, Sklar P, Ardlie K, Patil N, Lane CR, Lim EP, Kalyanaraman N,
Nemesh J, Ziaugra L, Friedland L, Rolfe A, Warrington J, Lipshutz R, Daly GQ, Lander ES
(1999) Characterization of single-nucleotide polymorphisms in coding regions of human genes.
Nat Genet 22:231–237
Chang JT (1999) Recent common ancestors of all present-day individuals. Adv Appl Probab
31:1002–1026
de Iorio M, Griffiths RC, Leblois R, Rousset F (2005) Stepwise mutation likelihood computation
by sequential importance sampling in subdivided population models. Theoret Pop Biol 68:41–
53
Donnelly P, Tavaré S (1995) Coalescents and genealogical structure under neutrality. Annu Rev
Genet 29:401–421
Drummond AJ, Suchard MA, Xie D, Rambaut A (2012) Bayesian phylogenetics with BEAUti and
the BEAST 1.7. Mol Biol Evol 29:1969–1973
Durrett R, Schweinsberg J (2004) Approximating selective sweeps. Theoret Pop Biol 66:129–138
Etheridge AM, Pfaffelhuber P, Wakolbinger A (2006) An approximate sampling formula under
genetic hitchhiking. Ann Appl Probab 16:685–729
Ewens WJ (1972) The sampling theory of selectively neutral alleles. Theoret Pop Biol 3:87–112
Ewens WJ (1974) A note on the sampling theory for infinite alleles and infinite sites models.
Theoret Pop Biol 6:143–148
Ewens WJ (1990) Population genetics theory—the past and the future. In: Lessard S (ed) Mathematical and statistical developments of evolutionary theory. Kluwer Academic, Amsterdam, pp
177–227
Ewens WJ (2004) Mathematical population genetics, vol I: theoretical foundations. Springer,
Berlin
Fay JC, Wu C-I (2000) Hitchhiking under positive Darwinian selection. Genetics 155:1405–1413
Fearnhead P (2006) Perfect simulation from nonneutral population genetic models: variable
population size and population subsdivision. Genetics 174:1397–1406
Felsenstein J (2006) Accuracy of coalescent likelihood estimates: do we need more sites, more
sequences, or more loci? Mol Biol Evol 23:691–700