Identifying hybridization events in the presence of coalescence via model selection

Systematic Biology

Volumn 58, Issue 5, 2009, Pages 478-488

  Kubatko, Laura Salter ^a  

^a OHIO STATE UNIVERSITY   (United States)

Author keywords

Deep coalescence; Gene trees; Hybridization; Incomplete lineage sorting; Multilocus data; Species phylogeny

Indexed keywords

ARTICLE; BIOLOGICAL MODEL; BIOLOGY; CLASSIFICATION; COMPUTER SIMULATION; HYBRIDIZATION; METHODOLOGY; MOLECULAR EVOLUTION; PHYLOGENY; SPECIES DIFFERENCE; STATISTICAL MODEL; PROCEDURES;

CLASSIFICATION; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; HYBRIDIZATION, GENETIC; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; PHYLOGENY; SPECIES SPECIFICITY;

ANIMALIA;

EID: 70450277249     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syp055     Document Type: Article

References (74)

1. Akaike H. 1974. A new look at the statistical model identification. IEEE Trans Automat Contr 19:716-723.
2. Ané C., Larget B., Baum D., Smith S., Rokas A. 2007. Bayesian estimation of concordance among gene trees. Mol. Biol. Evol. 24:412-426.
3. Arnold M.L. 1997. Natural hybridization and evolution. New York: Oxford University Press.
4. Baack E., Rieseberg L. 2007. A genomic view of introgression and hybrid speciation. Curr. Opin. Genet. Dev. 17:1-6.
5. Bossu C.M., Near T.J. 2009. Gene trees reveal repeated instances of mi-tochondrial DNA introgression in orangethroat darters (Percidae: Etheostoma). Syst. Biol. 58:114-129.
6. Bryant D., Moulton V. 2004. Neighbor-Net: an agglomerative method for the construction of phylogenetic networks. Mol. Biol. Evol. 21:255-265.
7. Buckley T., Cordeiro M., Marshall D., Simon C. 2006. Differentiating between hypotheses of lineage sorting and introgression in New Zealand cicadas (Maoricicada dugdale). Syst. Biol. 55:411-425.
8. Buerkle C.A., Morris R., Asmussen M., Rieseberg L. 2000. The likelihood of homoploid hybrid speciation. Heredity. 84:441-451.
9. Bullini L. 1994. Origin and evolution of animal hybrid species. Trends Ecol. Evol. 9:422-426.
10. Burnham K.P., Anderson D.R. 2002. Model selection and multi-model inference: a practical-theoretic approach. 2nd ed. New York: Springer-Verlag.
11. Carstens B.C., Knowles L.L. 2007. Estimating phylogeny from gene tree probabilities in Melanoplus grasshoppers despite incomplete lineage sorting. Syst. Biol. 56:400-411.
12. Degnan J.H., Rosenberg N.A. 2006. Discordance of species trees with their most likely gene trees. PLoS Genet. 3:762-768.
13. Degnan J.H., Salter L. 2005. Gene tree distributions under the coales-cent process. Evolution. 59:24-37.
14. DeMarais B.D., Dowling T., Douglas M., Minckley W., Marsh P. 1992. Origin of Gila seminuda (Teleostei: Cyprinidae) through introgres-sive hybridization: implications for evolution and conservation. Proc. Natl. Acad. Sci. USA. 89:2747-2751.
15. Dowling T.E., DeMarais B.D. 1993. Evolutionary significance of intro-gressive hybridization in cyprinid fishes. Nature. 362:444-446.
16. Dowling T.E., Secor C.L. 1997. The role of hybridization and intro-gression in the diversification of animals. Annu. Rev. Ecol. Syst. 28: 593-619.
17. Edwards S., Liu L., Pearl D. 2007. High-resolution species trees without concatenation. Proc. Natl. Acad. Sci. USA. 104:5936-5941.
18. Gauthier O., Lapointe F.J. 2007. Hybrid and phylogenetics revisited: a statistical test of hybridization using quartets. Syst. Bot. 32:8-15.
19. Gompert Z., Fordyce J., Forister M., Shapiro A., Nice C. 2006. Ho-moploid hybrid speciation in an extreme habitat. Science. 314: 1923-1925.
20. Gonçalvesa H., Mart́inez-Solanod I., Ferranda N., Garćia-Paŕisc M. 2007. Conflicting phylogenetic signal of nuclear vs mitochondrial DNA markers in midwife toads (Anura, Discoglossidae, Alytes): Deep coalescence or ancestral hybridization? Mol. Phylogenet. Evol. 44:494-500.
21. Good J.M., Dembroski J.R., Nagorsen D.W., Sullivan J. 2003. Phy-logeography and introgressive hybridization: Chipmunks (Genus Tamias) in the northern Rocky mountains. Evolution. 57:1900-1916.
22. Grant P.R., Grant B.R., Markert J.A., Keller L.F., Petren K. 2004. Convergence evolution of Darwin?s finches caused by introgressive hybridization and selection. Evolution. 58:1588-1599.
23. Gross B., Rieseberg L. 2005. The ecological genetics of homoploid hybrid speciation. J. Hered. 96:241-252.
24. Hennig W. 1966. Phylogenetic systematics. Urbana-Champaign (IL): Illinois Press.
25. Holder M., Anderson J., Holloway A. 2001. Difficulties in detecting hybridization. Syst. Biol. 50:978-982.
26. Jin G., Nakhleh L., Snir S., Tuller T. 2006. Maximum likelihood of phy-logenetic networks. Bioinformatics. 22:2604-2611.
27. Joly S., McLenachan P.A., Lockhart P.J. 2009. A statistical approach for distinguishing hybridization and incomplete lineage sorting. Am. Nat. 174:E54-E70.
28. Kingman J.F.C. 1982. The coalescent. Stoch. Proc. Appl. 13:235-248.
29. Kubatko L., Carstens B., Knowles L. 2009. STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics. 25:971-973.
30. Kubatko L., Degnan J. 2007. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst. Biol. 56:17-24.
31. Legendre P., Makarenkov V. 2002. Reconstruction of biogeographic and evolutionary networks using reticulograms. Syst. Biol. 51: 199-216.
32. Linnen C., Farrell B. 2007. Mitonuclear discordance is caused by rampant mitochondrial introgression in Neodiprion (Hymenoptera: Diprionidae) sawflies. Evolution. 61:1417-1438.
33. Liu L., Pearl D. 2007. Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Syst. Biol. 56:504-514.
34. Liu L., Yu L., Pearl D.K. 2009. Maximum tree: a consistent estimator of the species tree. J. Math. Biol. doi:10.1007/s00285-009-0260-0.
35. Maddison W.P. 1997. Gene trees in species trees. Syst. Biol. 46: 523-536.
36. Maddison W., Knowles L. 2006. Inferring phylogeny despite incomplete lineage sorting. Syst. Biol. 55:21-30.
37. Mallet J. 2005. Hybridization as an invasion of the genome. Trends Ecol. Evol. 20:229-237.
38. Mallet J. 2007. Hybrid speciation. Nature 446:279-283.
39. Maureira-Butler I.J., Pfeil B.E., Muangprom A., Osborn T.C., Doyle J.J. 2008. The reticulate history of Medicago (Fabaceae). Syst. Biol. 57:466-482.
40. Mavárez J., Salazar C.A., Bermingham E., Salcedo C., Jiggins C.D., Linares M. 2006. Speciation by hybridization in Heliconius butterflies. Nature. 441:868-871.
41. Meng C., Kubatko L.S. 2009. Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: a model. Theor. Popul. Biol. 75:35-45.
42. Meyer A., Salzburger W., Schartl M. 2006. Hybrid origin of a swordtail species (Teleostei: Xiphophorus clemenciae) driven by sexual selection. Mol. Ecol. 15:721-730.
43. Mossel E., Roch S. 2007. Incomplete lineage sorting: consistent phy-logeny estimation from multiple loci. Available from: http://arxiv. org/pdf/0710.0262.
44. Nolte A.W., Freyhof J., Stemshorn K., Tautz D. 2005. An invasive lineage of sculpins, Cottus sp. (Pisces, Teleostei) in the Rhine with new habitat adaptations has originated from hybridization between old phylogeographic groups. Proc. R. Soc. Lond. B. 272:2379-2387.
45. Pamilo P., Nei M. 1988. Relationships between gene trees and species trees. Mol. Biol. Evol. 5:568-583.
46. Posada D. 2002. Evaluation of methods for detecting recombination from DNA sequences: empirical data. Mol. Biol. Evol. 19: 708-717.
47. Posada D., Buckley T.R. 2004. Model selection and model averaging in phylogenetics: advantages of Akaike Information Criterion and Bayesian approaches over likelihood ratio tests. Syst. Biol. 53: 793-808.
48. Rambaut A., Grassly N. 1997. SeqGen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13:235-238. (Pubitemid 27249927)
49. Rannala B., Yang Z. 2003. Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci. Genetics. 164:1645-1656.
50. Rieseberg L. 1997. Hybrid origins of plant species. Annu. Rev. Ecol. Syst. 28:359-389.
51. Rieseberg L., Wendel J. 1993. Introgression and its consequences in plants. In: R.G. Harrison, editor. Hybrid zones and the evolutionary process. New York: Oxford University Press. p. 70-109.
52. Rieseberg L.H., Morefield J.D. 1995. Character expression, phyloge-netic reconstruction, and the detection of reticulate evolution. In: Hoch P., Stephenson A.G., editors. Experimental and molecular approaches to plant biosystematics. St. Louis (MO): Missouri Botanical Garden.
53. Roques S., Sevigny J.-M., Bernatchez L. 2001. Evidence for a broadscale introgressive hybridization between two redfish (genus Sebastes) in the North-west Atlantic: a rare marine example. Mol. Ecol. 10: 149-165.
54. Rosenberg N.A. 2002. The probability of topological concordance of gene trees and species trees. Theor. Popul. Biol. 61:225-247.
55. Rosenberg N.A. 2003. The shapes of neutral gene genealogies in two species: probabilities of monophyly, paraphyly, and polyphyly in a coalescent model. Evolution. 57:1465-1477.
56. Rosenberg N.A., Tao R. 2008. Discordance of species trees with their most likely gene trees: the case of five taxa. Syst. Biol. 57:131-140.
57. Salzburger W., Baric S., Sturmbauer C. 2002. Speciation via intro-gressive hybridization in East African cichilds? Mol. Ecol. 11: 619-625.
58. Sang T., Zhong Y. 2000. Testing hybridization hypotheses based on in-congruent gene trees. Syst. Biol. 49:422-434.
59. Schwarz G.E. 1978. Estimating the dimension of a model. Ann. Stat. 6:461-464.
60. Schwarz D., Matta B., Shakir-Botteri N., McPheron B. 2005. Host shift to an invasive plant triggers rapid animal hybrid speciation. Nature. 436:546-549.
61. Seehausen O. 2004. Hybridization and adaptive radiation. Trends Ecol. Evol. 19:198-206.
62. Shaw K.L. 2002. Conflict between nuclear and mitochondrial DNA phylogenies of a recent species radiation: what mtDNA reveals and conceals about modes of speciation in Hawaiian crickets. Proc. Natl. Acad. Sci. USA. 99:16122-16127.
63. Spinks P.Q., Shaffer H.B. 2009. Conflicting mitochondrial and nuclear phylogenies for the widely disjunct Emys (Testudines: Emydidae) species complex, and what they tell us about biogeography and hybridization. Syst. Biol. 58:1-20.
64. Strimmer K., Moulton V. 2000. Likelihood analysis of phylogenetic networks using directed graphical models. Mol. Biol. Evol. 17: 875-881.
65. Tajima F. 1983. Evolutionary relationship of DNA sequences in finite populations. Genetics. 105:437-460.
66. Takahata N., Nei M. 1985a. Gene genealogy and variance of interpop-ulational nucleotide differences. Genetics. 110:325-344.
67. Takahata N., Nei M. 1985b. Gene genealogy and variance of interpop-ulational nucleotide differences. Genetics. 110:325-344.
68. Tavaré S. 1984. Line-of-descent and genealogical processes, and their applications in population genetics models. Theor. Popul. Biol. 26:119-164.
69. Than C., Ruths D., Innan H., Nakhleh L. 2007. Confounding factors in HGT detection: statistical error, coalescent effects, and multiple solutions. J. Comput. Biol. 14:517-535.
70. Thorsson A., Salmela E., Anamthawat-Jonsson K. 2001. Morphological, cytogenetic, and molecular evidence for inrogressive hybridization in birch. J. Hered. 92:404-408.
71. Wakeley J. 2008. Coalescent theory: an introduction. Greenwood Village (CO): Roberts and Company.
72. Weigel D.E., Peterson J.T., Spruell P. 2002. A model using pheno-typic characteristics to detect introgressive hybridizations in wild westslope cutthroat trout and rainbow trout. Trans. Am. Fish. Soc. 141:389-403.
73. Xu S. 2000. Phylogenetic analysis under reticulate evolution. Mol. Biol. Evol. 17:897-907.
74. Yang Z. 2002. Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci. Genetics. 162:1811-1823.