Lineage sorting in apes

Annual Review of Genetics

Volumn 48, Issue , 2014, Pages 519-535

  Mailund, Thomas ^a   Munch, Kasper ^a   Schierup, Mikkel Heide ^a  

^a AARHUS UNIVERSITY   (Denmark)

Author keywords

great apes evolution; incomplete lineage sorting; phylogenetics; population genomics; speciation

Indexed keywords

APE; ARTICLE; DNA SEQUENCE; EFFECTIVE POPULATION SIZE; GENE DUPLICATION; GENE SEQUENCE; GENEALOGY; GENETIC RECOMBINATION; GENETIC VARIABILITY; GENOME ANALYSIS; HOMOPLASY; HUMAN; HUMAN GENOME; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; NATURAL SELECTION; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENOMICS; PHYLOGENY; PLESIOMORPHY; POPULATION BIOLOGY; POPULATION GENETICS; POPULATION SIZE; SPECIES DIFFERENTIATION; ANIMAL; GENETIC SELECTION; GENETICS; GENOME; HOMINID;

HOMINIDAE;

ANIMALS; EVOLUTION, MOLECULAR; GENETIC SPECIATION; GENOME; HOMINIDAE; PHYLOGENY; RECOMBINATION, GENETIC; SELECTION, GENETIC;

EID: 84913585432     PISSN: 00664197     EISSN: 15452948     Source Type: Book Series    
DOI: 10.1146/annurev-genet-120213-092532     Document Type: Article

References (87)

1. Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, et al. 2010. A map of human genome variation from population-scale sequencing. Nature 467(7319):1061-73
2. Andersen LN, Mailund T, Hobolth A. 2014. Efficient computation in the IM model. J. Math. Biol. 68(6):1423-51
3. Andrés AM, Hubisz MJ, Indap A, Torgerson DG, Degenhardt JD, et al. 2009. Targets of balancing selection in the human genome. Mol. Biol. Evol. 26(12):2755-64
4. Barreiro L, Quintana-Murci L. 2010. From evolutionary genetics to human immunology: how selection shapes host defence genes. Nat. Rev. Genet. 11(1):17-30
5. Barton NH. 2006. Evolutionary biology:How did the human species form? Curr. Biol. 16(16):R647-50
6. Becquet C, Przeworski M. 2007. A new approach to estimate parameters of speciation models with application to apes. Genome Res. 17(10):1505-19
7. Blanchette M, Diallo AB, Green ED, Miller W, Haussler D. 2008. Computational reconstruction of ancestral DNA sequences. Methods Mol. Biol. 422:171-84
8. Burgess R, Yang Z. 2008. Estimation of hominoid ancestral population sizes under Bayesian coalescent models incorporating mutation rate variation and sequencing errors. Mol. Biol. Evol. 25(9):1979-94
9. Chen FC, Li WH. 2001. Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees. Am. J. Hum. Genet. 68(2):444-56
10. Chen GK, Marjoram P, Wall JD. 2009. Fast and flexible simulation of DNA sequence data. Genome Res. 19(1):136-42
11. DeGiorgio M, Lohmueller KE, Nielsen R. 2014. A model-based approach for identifying signatures of ancient balancing selection in genetic data. PLOS Genet. 10(8):e1004561
12. Degnan JH, Rosenberg NA. 2006. Discordance of species trees with their most likely gene trees. PLOS Genet. 2(5):e68
13. Degnan JH, Rosenberg NA. 2009. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol. Evol. 24(6):332-40
14. Ding Q, Hu Y, Xu S, Wang J, Jin L. 2014. Neanderthal introgression at chromosome 3p21. 31 was under positive natural selection in East Asians. Mol. Biol. Evol. 31(3):683-95
15. Dutheil JY, Ganapathy G, Hobolth A, Mailund T, Uyenoyama MK, Schierup MH. 2009. Ancestral population genomics: the coalescent hidden Markov model approach. Genetics 183(1):259-74.
16. Dutheil JY, Hobolth A. . 2012. Ancestral population genomics. Methods Mol. Biol. 856:293-13
17. Fabre P-H, Rodrigues A, Douzery EJP. 2009. Patterns of macroevolution among Primates inferred from a supermatrix of mitochondrial and nuclear DNA. Mol. Phylogenet. Evol. 53(3):808-25
18. Glazko GV, Nei M. 2003. Estimation of divergence times for major lineages of primate species. Mol. Biol. Evol. 20(3):424-34
19. Hein J, Schierup M, Wiuf C. 2005. Gene Genealogies, Variation and Evolution: A Primer in Coalescent Theory. Oxford: Oxford Univ. Press
20. Hellmann I, Ebersberger I, Ptak SE, Paäbo S, Przeworski M. 2003. A neutral explanation for the correlation of diversity with recombination rates in humans. Am. J. Hum. Genet. 72(6):1527-35
21. Hey J. 2010. The divergence of chimpanzee species and subspecies as revealed in multipopulation isolation-with-migration analyses. Mol. Biol. Evol. 27(4):921-33
22. Hobolth A, Andersen LN, Mailund T. 2011. On computing the coalescence time density in an isolationwith-migration model with few samples. Genetics 187(4):1241-43
23. Hobolth A, Christensen OF, Mailund T, Schierup MH. 2007. Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hiddenMarkovmodel. PLOS Genet. 3(2):e7
24. Hobolth A, Jensen JL. 2014. Markovian approximation to the finite loci coalescent with recombination along multiple sequences. Theor. Popul. Biol. In press
25. Hudson RR. 1983. Properties of a neutral allele model with intragenic recombination. Theor. Popul. Biol. 23(2):183-201
26. Hvilsom C, Qian Y, Bataillon T, Li Y, Mailund T, et al. 2012. Extensive X-linked adaptive evolution in central chimpanzees. Proc. Natl. Acad. Sci. USA 109(6):2054-59
27. Innan H, Watanabe H. 2006. The effect of gene flow on the coalescent time in the human-chimpanzee ancestral population. Mol. Biol. Evol. 23(5):1040-47
28. Kong A, Thorleifsson G, Gudbjartsson DF, Masson G, Sigurdsson A, et al. 2010. Fine-scale recombination rate differences between sexes, populations and individuals. Nature 467(7319):1099-103
29. Krause J, Fu Q, Good JM, Viola B, Shunkov MV, et al. 2010. The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature 464(7290):894-97
30. Leffler EM, Gao Z, Pfeifer S, Ségurel L, Auton A, et al. 2013. Multiple instances of ancient balancing selection shared between humans and chimpanzees. Science 339(6127):1578-82
31. Li H, Durbin R. 2011. Inference of human population history from individualwhole-genome sequences. Nature 475(7357):493-96
32. Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, et al. 2011. Comparative and demographic analysis of orangutan genomes. Nature 469(7331):529-33
33. Maddison WP. 1997. Gene trees in species trees. Syst. Biol. 46(3):523-36
34. Mailund T, Dutheil JY, Hobolth A, Lunter G, Schierup MH. 2011. Estimating divergence time and ancestral effective population size of Bornean and Sumatran orangutan subspecies using a coalescent hidden Markov model. PLOS Genet. 7(3):e1001319
35. Mailund T, Halager AE, Westergaard M, Dutheil JY, Munch K, et al. 2012. A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species. PLOS Genet. 8(12):e1003125
36. Marjoram P, Wall JD. 2006. Fast "coalescent" simulation. BMC Genet. 7:16.
37. Matsudaira K, Ishida T. 2010. Phylogenetic relationships and divergence dates of the whole mitochondrial genome sequences among three gibbon genera. Mol. Phylogenet. Evol. 55(2):454-59
38. McVean GA, Cardin NJ. 2005. Approximating the coalescent with recombination. Philos. Trans. R. Soc. Lond. Ser. B 360(1459):1387-93
39. Meyer M, Fu Q, Aximu-Petri A, Glocke I, Nickel B, et al. 2014. A mitochondrial genome sequence of a hominin from Sima de los Huesos. Nature 505(7483):403-6
40. Meyer M, Kircher M, Gansauge M-T, Li H, Racimo F, et al. 2012. A high-coverage genome sequence from an archaic Denisovan individual. Science 338(6104):222-26
41. Munch K, Mailund T, Dutheil JY, Schierup MH. 2014. A fine-scale recombination map of the humanchimpanzee ancestor reveals faster change in humans than in chimpanzees and a strong impact of GC-biased gene conversion. Genome Res. 24(3):467-74
42. Osada N, Wu C-I. 2005. Inferring the mode of speciation from genomic data: a study of the great apes. Genetics 169(1):259-64
43. Pamilo P, Nei M. 1988. Relationships between gene trees and species trees. Mol. Biol. Evol. 5(5):568-83
44. Patterson N, Richter DJ, Gnerre S, Lander ES, Reich D. 2006. Genetic evidence for complex speciation of humans and chimpanzees. Nature 441(7097):1103-8
45. Paul JS, Steinrucken M, Song YS. 2011. An accurate sequentially Markov conditional sampling distribution for the coalescent with recombination. Genetics 187(4):1115-28
46. Pease JB, Hahn MW. 2013. More accurate phylogenies inferred from low-recombination regions in the presence of incomplete lineage sorting. Evol. Int. J. Org. Evol. 67(8):2376-84
47. Perelman P, Johnson WE, Roos C, Seuánez HN, Horvath JE, et al. 2011. A molecular phylogeny of living primates. PLOS Genet. 7(3):e1001342
48. Prado-Martinez J, Sudmant PH, Kidd JM, Li H, Kelley JL, et al. 2013. Great ape genetic diversity and population history. Nature 499(7459):471-75
49. Presgraves DC, Yi SV. 2009. Doubts about complex speciation between humans and chimpanzees. Trends Ecol. Evol. 24(10):533-40
50. Prufer K, Munch K, Hellmann I, Akagi K, Miller JR, et al. 2012. The bonobo genome compared with the chimpanzee and human genomes. Nature 486(7404):527-31
51. Prufer K, Racimo F, Patterson N, Jay F, Sankararaman S, et al. 2014. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505(7481):43-49
52. Rannala B, Yang Z. 2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164(4):1645-56
53. Rasmussen MD, Kellis M. 2012. Unified modeling of gene duplication, loss, and coalescence using a locus tree. Genome Res. 22(4):755-65
54. Rasmussen MD, Hubisz MJ, Gronau I, Siepel A. 2014. Genome-wide inference of ancestral recombination graphs. PLOS Genet. 10(5):e1004342
55. Reich D, Green RE, Kircher M, Krause J, Patterson N, et al. 2010. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468(7327):1053-60
56. Rokas A, Williams BL, King N, Carroll SB. 2003. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425(6960):798-804
57. Salichos L, Rokas A. 2013. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature 497(7449):327-31
58. Samson M, Libert F, Doranz BJ, Rucker J, Liesnard C, et al. 1996. Resistance to HIV-1 infection in Caucasian individuals bearingmutant alleles of the CCR-5 chemokine receptor gene. Nature 382(6593):722-25
59. Sankararaman S, Mallick S, Dannemann M, Prufer K, Kelso J, et al. 2014. The genomic landscape of Neanderthal ancestry in present-day humans. Nature 507(7492):354-57
60. Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, et al. 2012. Insights into hominid evolution from the gorilla genome sequence. Nature 483(7388):169-75
61. Schierup MH, Mikkelsen AM, Hein J. 2001. Recombination, balancing selection and phylogenies in MHC and self-incompatibility genes. Genetics 159(4):1833-44
62. Ségurel L, Thompson EE, Flutre T, Lovstad J, Venkat A, et al. 2012. The ABO blood group is a trans-species polymorphism in primates. Proc. Natl. Acad. Sci. USA 109(45):18493-98
63. Sheehan S, Harris K, Song YS. 2013. Estimating variable effective population sizes from multiple genomes: a sequentially Markov conditional sampling distribution approach. Genetics 194(3):647-62
64. Simonsen KL, Churchill GA. 1997. A Markov chain model of coalescence with recombination. Theor. Popul. Biol. 52(1):43-59
65. Steinrucken M, Paul JS, Song YS. 2013. A sequentially Markov conditional sampling distribution for structured populations with migration and recombination. Theor. Popul. Biol. 87:51-61
66. Steinrucken M, Wang YX, Song YS. 2013. An explicit transition density expansion for a multi-Allelic Wright-Fisher diffusion with general diploid selection. Theor. Popul. Biol. 83:1-14
67. Steiper ME, Young NM. 2006. Primatemolecular divergence dates. Mol. Phylogenet. Evol. 41(2):384-94
68. Takahata N, Satta Y, Klein J. 1992. Polymorphism and balancing selection at major histocompatibility complex loci. Genetics 130(4):925-38
69. Takahata N, Satta Y, Klein J. 1995. Divergence time and population size in the lineage leading to modern humans. Theor. Popul. Biol. 48(2):198-221
70. Thalmann O, Fischer A, Lankester F, Paäbo S, Vigilant L. 2007. The complex evolutionary history of gorillas: insights from genomic data. Mol. Biol. Evol. 24(1):146-58
71. Wakeley J. 2008. Complex speciation of humans and chimpanzees. Nature 452(7184):E3-4; discussion E4
72. Wakeley J. 2009. Coalescent Theory: An Introduction. Greenwood Village, CO: Roberts & Company Publ.
73. Wall JD. 2003. Estimating ancestral population sizes and divergence times. Genetics 163(1):395-404
74. Wang Y, Hey J. 2010. Estimating divergence parameters with small samples from a large number of loci. Genetics 184(2):363-79
75. Wegmann D, Excoffier L. 2010. Bayesian inference of the demographic history of chimpanzees. Mol. Biol. Evol. 27(6):1425-35
76. Wilkinson-Herbots HM. 2012. The distribution of the coalescence time and the number of pairwise nucleotide differences in a model of population divergence or speciation with an initial period of gene flow. Theor. Popul. Biol. 82(2):92-108
77. Wiuf C, Hein J. 1999. Recombination as a point process along sequences. Theor. Popul. Biol. 55(3):248-59
78. Won YJ, Hey J. 2005. Divergence population genetics of chimpanzees. Mol. Biol. Evol. 22(2):297-307
79. Wu CI. 1991. Inferences of species phylogeny in relation to segregation of ancient polymorphisms. Genetics 127(2):429-35
80. Wu C-I, Ting C-T. 2004. Genes and speciation. Nat. Rev. Genet. 5(2):114-22
81. WuY-C, Rasmussen MD, Bansal MS, Kellis M. 2013. Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees. Genome Res. 24(3):475-86
82. Yamamichi M, Gojobori J, Innan H. 2012. An autosomal analysis gives no genetic evidence for complex speciation of humans and chimpanzees. Mol. Biol. Evol. 29(1):145-56
83. Yang Z. 1997. On the estimation of ancestral population sizes ofmodern humans. Genet. Res. 69(2):111-16
84. Yang Z. 2002. Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci. Genetics 162(4):1811-23
85. Yang Z. 2010. A likelihood ratio test of speciation with gene flow using genomic sequence data. Genome Biol. Evol. 2:200-11
86. Yang Z, Nielsen R. 2000. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol. 17(1):32-43
87. Zhu T, Yang Z. 2012. Maximum likelihood implementation of an isolation-with-migration model with three species for testing speciation with gene flow. Mol. Biol. Evol. 29(10):3131-42