1 Coalescent Models
29
Kuhner MK, Yamato J, Felsenstein J (1995) Estimating effective population size and mutation rate
from sequence data using Metropolis-Hastings sampling. Genetics 140:1421–1430
Leffler EM, Bullaughey K, Matute DR, Meyer WK, Ségurel L, Venkat A, Andolfatto P, Przeworski
M (2012) Revisiting an old riddle: what determines genetic diversity levels within species?
PLoS Biol 10(9):e1001388
Li W-H (1976) Distribution of nucleotide difference between two randomly chosen cistrons in a
subdivided population: the finite island model. Theoret Pop Biol 10:303–308
Li H, Durbin R (2011) Inference of population history from individual whole-genome sequences.
Nature 475:493–496
Li N, Stephens M (2003) Modeling linkage disequilibrium and identifying recombination hotspots
using single-nucleotide polymorphism data. Genetics 165:2213–2233
Malécot G (1946) La consaguinite dans une population limitee. Comp Rendus Acad Sci Paris
222:841–843
Mallick S et al (2016) The Simons genome diversity project: 300 genomes from 142 diverse
populations. Nature 538:201–206
Möhle M (1998a) Robustness results for the coalescent. J Appl Probab 35:438–447
Möhle M (1998b) A convergence theorem for Markov chains arising in population genetics and
the coalescent with partial selfing. Adv Appl Probab 30:493–512
Möhle M (1998c) Coalescent results for two-sex population models. Adv Appl Probab 30:513–520
Möhle M (1999) The concept of duality and applications to Markov processes arising in neutral
population genetics models. Bernoulli 5:761–777
Möhle M, Sagitov S (2001) A classification of coalescent processes for haploid exchangeable
population models. Ann Appl Probab 29:1547–1562
Notohara M (1990) The coalescent and the genealogical process in geographically structured
population. J Math Biol 9:59–75
Ott J (1999) Analysis of human genetic linkage, 3rd edn. Johns Hopkins University Press,
Baltimore
Pfaffelhuber P, Wakolbinger A (2005) The process of most recent common ancestors in an evolving
coalescent. Stoch Proc App 116:1836–1859
Pluzhnikov A, Donnelly P (1996) Optimal sequencing strategies for surveying molecular genetic
diversity. Genetics 144:1247–1262
Polanski A, Kimmel M (2003) New explicit expressions for relative frequencies of singlenucleotide polymorphisms with application to statistical inference on population growth.
Genetics 165:427–436
Rauch EM, Bar-Yam Y (2004) Theory predicts the uneven distribution of genetic diversity within
species. Nature 431:449–452
Rohde DLT, Olsen S, Chang JT (2003) Modeling the recent common ancestry of all living humans.
Nature 425:798–804
Rosenberg NA (2006) Standardized subsets of the HGDP-CEPH human genome diversity cell line
panel, accounting for atypical and duplicated samples and pairs of close relatives. Ann Hum
Genet 70:841–847
Rosenberg NA, Mahajan S, Ramachandran S, Zhao C, Pritchard JK, Feldman MW (2005) Clines,
clusters, and the effect of study design on the inference of human population structure. PLoS
Genet 1:e70
Sainudiin R, Véber A (2018) Full likelihood inference from the site frequency spectrum based on
the optimal tree resolution. Theoret Pop Biol 124:1–15
Sargsyan O, Wakeley J (2008) A coalescent process with simultaneous multiple mergers for
approximating the gene genealogies of many marine organisms. Theoret Pop Biol 74:104–114
Simonsen KL, Churchill GA, Aquadro CF (1995) Properties of statistical tests of neutrality for
DNA polymorphism data. Genetics 141:413–429
Sjödin P, Kaj I, Krone S, Lascoux M, Nordborg M (2005) On the meaning and existence of an
effective population size. Genetics 169:1061–1070
Slatkin M (1987) The average number of sites separating DNA sequences drawn from a subdivided
population. Theoret Pop Biol 32:42–49
29
Kuhner MK, Yamato J, Felsenstein J (1995) Estimating effective population size and mutation rate
from sequence data using Metropolis-Hastings sampling. Genetics 140:1421–1430
Leffler EM, Bullaughey K, Matute DR, Meyer WK, Ségurel L, Venkat A, Andolfatto P, Przeworski
M (2012) Revisiting an old riddle: what determines genetic diversity levels within species?
PLoS Biol 10(9):e1001388
Li W-H (1976) Distribution of nucleotide difference between two randomly chosen cistrons in a
subdivided population: the finite island model. Theoret Pop Biol 10:303–308
Li H, Durbin R (2011) Inference of population history from individual whole-genome sequences.
Nature 475:493–496
Li N, Stephens M (2003) Modeling linkage disequilibrium and identifying recombination hotspots
using single-nucleotide polymorphism data. Genetics 165:2213–2233
Malécot G (1946) La consaguinite dans une population limitee. Comp Rendus Acad Sci Paris
222:841–843
Mallick S et al (2016) The Simons genome diversity project: 300 genomes from 142 diverse
populations. Nature 538:201–206
Möhle M (1998a) Robustness results for the coalescent. J Appl Probab 35:438–447
Möhle M (1998b) A convergence theorem for Markov chains arising in population genetics and
the coalescent with partial selfing. Adv Appl Probab 30:493–512
Möhle M (1998c) Coalescent results for two-sex population models. Adv Appl Probab 30:513–520
Möhle M (1999) The concept of duality and applications to Markov processes arising in neutral
population genetics models. Bernoulli 5:761–777
Möhle M, Sagitov S (2001) A classification of coalescent processes for haploid exchangeable
population models. Ann Appl Probab 29:1547–1562
Notohara M (1990) The coalescent and the genealogical process in geographically structured
population. J Math Biol 9:59–75
Ott J (1999) Analysis of human genetic linkage, 3rd edn. Johns Hopkins University Press,
Baltimore
Pfaffelhuber P, Wakolbinger A (2005) The process of most recent common ancestors in an evolving
coalescent. Stoch Proc App 116:1836–1859
Pluzhnikov A, Donnelly P (1996) Optimal sequencing strategies for surveying molecular genetic
diversity. Genetics 144:1247–1262
Polanski A, Kimmel M (2003) New explicit expressions for relative frequencies of singlenucleotide polymorphisms with application to statistical inference on population growth.
Genetics 165:427–436
Rauch EM, Bar-Yam Y (2004) Theory predicts the uneven distribution of genetic diversity within
species. Nature 431:449–452
Rohde DLT, Olsen S, Chang JT (2003) Modeling the recent common ancestry of all living humans.
Nature 425:798–804
Rosenberg NA (2006) Standardized subsets of the HGDP-CEPH human genome diversity cell line
panel, accounting for atypical and duplicated samples and pairs of close relatives. Ann Hum
Genet 70:841–847
Rosenberg NA, Mahajan S, Ramachandran S, Zhao C, Pritchard JK, Feldman MW (2005) Clines,
clusters, and the effect of study design on the inference of human population structure. PLoS
Genet 1:e70
Sainudiin R, Véber A (2018) Full likelihood inference from the site frequency spectrum based on
the optimal tree resolution. Theoret Pop Biol 124:1–15
Sargsyan O, Wakeley J (2008) A coalescent process with simultaneous multiple mergers for
approximating the gene genealogies of many marine organisms. Theoret Pop Biol 74:104–114
Simonsen KL, Churchill GA, Aquadro CF (1995) Properties of statistical tests of neutrality for
DNA polymorphism data. Genetics 141:413–429
Sjödin P, Kaj I, Krone S, Lascoux M, Nordborg M (2005) On the meaning and existence of an
effective population size. Genetics 169:1061–1070
Slatkin M (1987) The average number of sites separating DNA sequences drawn from a subdivided
population. Theoret Pop Biol 32:42–49