1932

Abstract

Recombination allows different parts of the genome to have different genealogical histories. When a species splits in two, allelic lineages sort into the two descendant species, and this lineage sorting varies along the genome. If speciation events are close in time, the lineage sorting process may be incomplete at the second speciation event and lead to gene genealogies that do not match the species phylogeny. We review different recent approaches to model lineage sorting along the genome and show how it is possible to learn about population sizes, natural selection, and recombination rates in ancestral species from application of these models to genome alignments of great ape species.

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2014-11-23
2024-10-10
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Literature Cited

  1. Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM. 1.  et al. 2010. A map of human genome variation from population-scale sequencing. Nature 467:73191061–73 [Google Scholar]
  2. Andersen LN, Mailund T, Hobolth A. 2.  2014. Efficient computation in the IM model. J. Math. Biol. 68:61423–51 [Google Scholar]
  3. Andrés AM, Hubisz MJ, Indap A, Torgerson DG, Degenhardt JD. 3.  et al. 2009. Targets of balancing selection in the human genome. Mol. Biol. Evol. 26:122755–64 [Google Scholar]
  4. Barreiro L, Quintana-Murci L. 4.  2010. From evolutionary genetics to human immunology: how selection shapes host defence genes. Nat. Rev. Genet. 11:117–30 [Google Scholar]
  5. Barton NH. 5.  2006. Evolutionary biology: How did the human species form?. Curr. Biol. 16:16R647–50 [Google Scholar]
  6. Becquet C, Przeworski M. 6.  2007. A new approach to estimate parameters of speciation models with application to apes. Genome Res. 17:101505–19 [Google Scholar]
  7. Blanchette M, Diallo AB, Green ED, Miller W, Haussler D. 7.  2008. Computational reconstruction of ancestral DNA sequences. Methods Mol. Biol. 422:171–84 [Google Scholar]
  8. Burgess R, Yang Z. 8.  2008. Estimation of hominoid ancestral population sizes under Bayesian coalescent models incorporating mutation rate variation and sequencing errors. Mol. Biol. Evol. 25:91979–94 [Google Scholar]
  9. Chen FC, Li WH. 9.  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. 68:2444–56 [Google Scholar]
  10. Chen GK, Marjoram P, Wall JD. 10.  2009. Fast and flexible simulation of DNA sequence data. Genome Res. 19:1136–42 [Google Scholar]
  11. DeGiorgio M, Lohmueller KE, Nielsen R. 11.  2014. A model-based approach for identifying signatures of ancient balancing selection in genetic data.. PLOS Genet 10:8e1004561 [Google Scholar]
  12. Degnan JH, Rosenberg NA. 12.  2006. Discordance of species trees with their most likely gene trees. PLOS Genet. 2:5e68 [Google Scholar]
  13. Degnan JH, Rosenberg NA. 13.  2009. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol. Evol. 24:6332–40 [Google Scholar]
  14. Ding Q, Hu Y, Xu S, Wang J, Jin L. 14.  2014. Neanderthal introgression at chromosome 3p21.31 was under positive natural selection in East Asians. Mol. Biol. Evol. 31:3683–95 [Google Scholar]
  15. Dutheil JY, Ganapathy G, Hobolth A, Mailund T, Uyenoyama MK, Schierup MH. 15.  2009. Ancestral population genomics: the coalescent hidden Markov model approach. Genetics 183:1259–74 [Google Scholar]
  16. Dutheil JY, Hobolth A.15a.  2012. Ancestral population genomics. Methods Mol. Biol. 856:293–13 [Google Scholar]
  17. Fabre P-H, Rodrigues A, Douzery EJP. 16.  2009. Patterns of macroevolution among Primates inferred from a supermatrix of mitochondrial and nuclear DNA. Mol. Phylogenet. Evol. 53:3808–25 [Google Scholar]
  18. Glazko GV, Nei M. 17.  2003. Estimation of divergence times for major lineages of primate species. Mol. Biol. Evol. 20:3424–34 [Google Scholar]
  19. Hein J, Schierup M, Wiuf C. 18.  2005. Gene Genealogies, Variation and Evolution: A Primer in Coalescent Theory Oxford: Oxford Univ. Press [Google Scholar]
  20. Hellmann I, Ebersberger I, Ptak SE, Pääbo S, Przeworski M. 19.  2003. A neutral explanation for the correlation of diversity with recombination rates in humans. Am. J. Hum. Genet. 72:61527–35 [Google Scholar]
  21. Hey J. 20.  2010. The divergence of chimpanzee species and subspecies as revealed in multipopulation isolation-with-migration analyses. Mol. Biol. Evol. 27:4921–33 [Google Scholar]
  22. Hobolth A, Andersen LN, Mailund T. 21.  2011. On computing the coalescence time density in an isolation-with-migration model with few samples. Genetics 187:41241–43 [Google Scholar]
  23. Hobolth A, Christensen OF, Mailund T, Schierup MH. 22.  2007. Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model. PLOS Genet. 3:2e7 [Google Scholar]
  24. Hobolth A, Jensen JL. 23.  2014. Markovian approximation to the finite loci coalescent with recombination along multiple sequences. Theor. Popul. Biol. In press [Google Scholar]
  25. Hudson RR. 24.  1983. Properties of a neutral allele model with intragenic recombination. Theor. Popul. Biol. 23:2183–201 [Google Scholar]
  26. Hvilsom C, Qian Y, Bataillon T, Li Y, Mailund T. 25.  et al. 2012. Extensive X-linked adaptive evolution in central chimpanzees. Proc. Natl. Acad. Sci. USA 109:62054–59 [Google Scholar]
  27. Innan H, Watanabe H. 26.  2006. The effect of gene flow on the coalescent time in the human-chimpanzee ancestral population. Mol. Biol. Evol. 23:51040–47 [Google Scholar]
  28. Kong A, Thorleifsson G, Gudbjartsson DF, Masson G, Sigurdsson A. 27.  et al. 2010. Fine-scale recombination rate differences between sexes, populations and individuals. Nature 467:73191099–103 [Google Scholar]
  29. Krause J, Fu Q, Good JM, Viola B, Shunkov MV. 28.  et al. 2010. The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature 464:7290894–97 [Google Scholar]
  30. Leffler EM, Gao Z, Pfeifer S, Ségurel L, Auton A. 29.  et al. 2013. Multiple instances of ancient balancing selection shared between humans and chimpanzees. Science 339:61271578–82 [Google Scholar]
  31. Li H, Durbin R. 30.  2011. Inference of human population history from individual whole-genome sequences. Nature 475:7357493–96 [Google Scholar]
  32. Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV. 31.  et al. 2011. Comparative and demographic analysis of orangutan genomes. Nature 469:7331529–33 [Google Scholar]
  33. Maddison WP. 32.  1997. Gene trees in species trees. Syst. Biol. 46:3523–36 [Google Scholar]
  34. Mailund T, Dutheil JY, Hobolth A, Lunter G, Schierup MH. 33.  2011. Estimating divergence time and ancestral effective population size of Bornean and Sumatran orangutan subspecies using a coalescent hidden Markov model. PLOS Genet. 7:3e1001319 [Google Scholar]
  35. Mailund T, Halager AE, Westergaard M, Dutheil JY, Munch K. 34.  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. 8:12e1003125 [Google Scholar]
  36. Marjoram P, Wall JD. 35.  2006. Fast “coalescent” simulation. BMC Genet. 7:16 [Google Scholar]
  37. Matsudaira K, Ishida T. 35a.  2010. Phylogenetic relationships and divergence dates of the whole mitochondrial genome sequences among three gibbon genera. Mol. Phylogenet. Evol. 55:2454–-59 [Google Scholar]
  38. McVean GA, Cardin NJ. 36.  2005. Approximating the coalescent with recombination. Philos. Trans. R. Soc. Lond. Ser. B 360:14591387–93 [Google Scholar]
  39. Meyer M, Fu Q, Aximu-Petri A, Glocke I, Nickel B. 37.  et al. 2014. A mitochondrial genome sequence of a hominin from Sima de los Huesos. Nature 505:7483403–6 [Google Scholar]
  40. Meyer M, Kircher M, Gansauge M-T, Li H, Racimo F. 38.  et al. 2012. A high-coverage genome sequence from an archaic Denisovan individual. Science 338:6104222–26 [Google Scholar]
  41. Munch K, Mailund T, Dutheil JY, Schierup MH. 39.  2014. A fine-scale recombination map of the human-chimpanzee ancestor reveals faster change in humans than in chimpanzees and a strong impact of GC-biased gene conversion. Genome Res. 24:3467–74 [Google Scholar]
  42. Osada N, Wu C-I. 40.  2005. Inferring the mode of speciation from genomic data: a study of the great apes. Genetics 169:1259–64 [Google Scholar]
  43. Pamilo P, Nei M. 41.  1988. Relationships between gene trees and species trees. Mol. Biol. Evol. 5:5568–83 [Google Scholar]
  44. Patterson N, Richter DJ, Gnerre S, Lander ES, Reich D. 42.  2006. Genetic evidence for complex speciation of humans and chimpanzees. Nature 441:70971103–8 [Google Scholar]
  45. Paul JS, Steinrücken M, Song YS. 43.  2011. An accurate sequentially Markov conditional sampling distribution for the coalescent with recombination. Genetics 187:41115–28 [Google Scholar]
  46. Pease JB, Hahn MW. 44.  2013. More accurate phylogenies inferred from low-recombination regions in the presence of incomplete lineage sorting. Evol. Int. J. Org. Evol. 67:82376–84 [Google Scholar]
  47. Perelman P, Johnson WE, Roos C, Seuánez HN, Horvath JE. 45.  et al. 2011. A molecular phylogeny of living primates. PLOS Genet. 7:3e1001342 [Google Scholar]
  48. Prado-Martinez J, Sudmant PH, Kidd JM, Li H, Kelley JL. 46.  et al. 2013. Great ape genetic diversity and population history. Nature 499:7459471–75 [Google Scholar]
  49. Presgraves DC, Yi SV. 47.  2009. Doubts about complex speciation between humans and chimpanzees. Trends Ecol. Evol. 24:10533–40 [Google Scholar]
  50. Prüfer K, Munch K, Hellmann I, Akagi K, Miller JR. 48.  et al. 2012. The bonobo genome compared with the chimpanzee and human genomes. Nature 486:7404527–31 [Google Scholar]
  51. Prüfer K, Racimo F, Patterson N, Jay F, Sankararaman S. 49.  et al. 2014. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505:748143–49 [Google Scholar]
  52. Rannala B, Yang Z. 50.  2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164:41645–56 [Google Scholar]
  53. Rasmussen MD, Kellis M. 51.  2012. Unified modeling of gene duplication, loss, and coalescence using a locus tree. Genome Res. 22:4755–65 [Google Scholar]
  54. Rasmussen MD, Hubisz MJ, Gronau I, Siepel A. 52.  2014. Genome-wide inference of ancestral recombination graphs. PLOS Genet. 10:5e1004342 [Google Scholar]
  55. Reich D, Green RE, Kircher M, Krause J, Patterson N. 53.  et al. 2010. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468:73271053–60 [Google Scholar]
  56. Rokas A, Williams BL, King N, Carroll SB. 54.  2003. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425:6960798–804 [Google Scholar]
  57. Salichos L, Rokas A. 55.  2013. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature 497:7449327–31 [Google Scholar]
  58. Samson M, Libert F, Doranz BJ, Rucker J, Liesnard C. 56.  et al. 1996. Resistance to HIV-1 infection in Caucasian individuals bearing mutant alleles of the CCR-5 chemokine receptor gene. Nature 382:6593722–25 [Google Scholar]
  59. Sankararaman S, Mallick S, Dannemann M, Prüfer K, Kelso J. 57.  et al. 2014. The genomic landscape of Neanderthal ancestry in present-day humans. Nature 507:7492354–57 [Google Scholar]
  60. Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I. 58.  et al. 2012. Insights into hominid evolution from the gorilla genome sequence. Nature 483:7388169–75 [Google Scholar]
  61. Schierup MH, Mikkelsen AM, Hein J. 59.  2001. Recombination, balancing selection and phylogenies in MHC and self-incompatibility genes. Genetics 159:41833–44 [Google Scholar]
  62. Ségurel L, Thompson EE, Flutre T, Lovstad J, Venkat A. 60.  et al. 2012. The ABO blood group is a trans-species polymorphism in primates. Proc. Natl. Acad. Sci. USA 109:4518493–98 [Google Scholar]
  63. Sheehan S, Harris K, Song YS. 61.  2013. Estimating variable effective population sizes from multiple genomes: a sequentially Markov conditional sampling distribution approach. Genetics 194:3647–62 [Google Scholar]
  64. Simonsen KL, Churchill GA. 62.  1997. A Markov chain model of coalescence with recombination. Theor. Popul. Biol. 52:143–59 [Google Scholar]
  65. Steinrücken M, Paul JS, Song YS. 63.  2013. A sequentially Markov conditional sampling distribution for structured populations with migration and recombination. Theor. Popul. Biol. 87:51–61 [Google Scholar]
  66. Steinrücken M, Wang YX, Song YS. 64.  2013. An explicit transition density expansion for a multi-allelic Wright-Fisher diffusion with general diploid selection. Theor. Popul. Biol. 83:1–14 [Google Scholar]
  67. Steiper ME, Young NM. 65.  2006. Primate molecular divergence dates. Mol. Phylogenet. Evol. 41:2384–94 [Google Scholar]
  68. Takahata N, Satta Y, Klein J. 66.  1992. Polymorphism and balancing selection at major histocompatibility complex loci. Genetics 130:4925–38 [Google Scholar]
  69. Takahata N, Satta Y, Klein J. 67.  1995. Divergence time and population size in the lineage leading to modern humans. Theor. Popul. Biol. 48:2198–221 [Google Scholar]
  70. Thalmann O, Fischer A, Lankester F, Pääbo S, Vigilant L. 68.  2007. The complex evolutionary history of gorillas: insights from genomic data. Mol. Biol. Evol. 24:1146–58 [Google Scholar]
  71. Wakeley J. 69.  2008. Complex speciation of humans and chimpanzees. Nature 452:7184E3–4 discussion E4 [Google Scholar]
  72. Wakeley J. 70.  2009. Coalescent Theory: An Introduction Greenwood Village, CO: Roberts & Company Publ. [Google Scholar]
  73. Wall JD. 71.  2003. Estimating ancestral population sizes and divergence times. Genetics 163:1395–404 [Google Scholar]
  74. Wang Y, Hey J. 72.  2010. Estimating divergence parameters with small samples from a large number of loci. Genetics 184:2363–79 [Google Scholar]
  75. Wegmann D, Excoffier L. 73.  2010. Bayesian inference of the demographic history of chimpanzees. Mol. Biol. Evol. 27:61425–35 [Google Scholar]
  76. Wilkinson-Herbots HM. 74.  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. 82:292–108 [Google Scholar]
  77. Wiuf C, Hein J. 75.  1999. Recombination as a point process along sequences. Theor. Popul. Biol. 55:3248–59 [Google Scholar]
  78. Won YJ, Hey J. 76.  2005. Divergence population genetics of chimpanzees. Mol. Biol. Evol. 22:2297–307 [Google Scholar]
  79. Wu CI. 77.  1991. Inferences of species phylogeny in relation to segregation of ancient polymorphisms. Genetics 127:2429–35 [Google Scholar]
  80. Wu C-I, Ting C-T. 78.  2004. Genes and speciation. Nat. Rev. Genet. 5:2114–22 [Google Scholar]
  81. Wu Y-C, Rasmussen MD, Bansal MS, Kellis M. 79.  2013. Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees. Genome Res. 24:3475–86 [Google Scholar]
  82. Yamamichi M, Gojobori J, Innan H. 80.  2012. An autosomal analysis gives no genetic evidence for complex speciation of humans and chimpanzees. Mol. Biol. Evol. 29:1145–56 [Google Scholar]
  83. Yang Z. 81.  1997. On the estimation of ancestral population sizes of modern humans. Genet. Res. 69:2111–16 [Google Scholar]
  84. Yang Z. 82.  2002. Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci. Genetics 162:41811–23 [Google Scholar]
  85. Yang Z. 83.  2010. A likelihood ratio test of speciation with gene flow using genomic sequence data. Genome Biol. Evol. 2:200–11 [Google Scholar]
  86. Yang Z, Nielsen R. 84.  2000. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol. 17:132–43 [Google Scholar]
  87. Zhu T, Yang Z. 85.  2012. Maximum likelihood implementation of an isolation-with-migration model with three species for testing speciation with gene flow. Mol. Biol. Evol. 29:103131–42 [Google Scholar]
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