Resolving species phylogenies of recent evolutionary radiations

Annals of the Missouri Botanical Garden

Volumn 95, Issue 2, 2008, Pages 224-231

  Knowles, L Lacey ^a   Chan, Yat Hei ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

Coalescence; Divergence time; Genealogical discord; Incomplete lineage sorting; Radiation; Speciation; Statistical phylogeography

Indexed keywords

EID: 45849088450     PISSN: 00266493     EISSN: None     Source Type: Journal    
DOI: 10.3417/2006102     Document Type: Conference Paper

References (43)

1. Arbogast, B., S. V. Edwards, J. Wakeley, P. Beerli & J. B. Slowinski. 2002. Estimating divergence times from molecular data on phylogenetic and population genetic time scales. Annual Rev. Ecol. Syst. 33: 707-740.
2. Avise, J. C., J. F. Shapiro, S. W. Daniel, C. F. Aquadro & R. A. Lansman. 1983. Mitochondrial DNA differentiation during the speciation process in Peromyscus. Molec. Biol. Evol. 1: 38-56.
3. Carstens, B. C. & L. L. Knowles. 2007. Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: An example from Melanoplus grasshoppers. Syst. Biol. 56: 1-12.
4. Degnan, J. H. & L. A. Salter. 2005. Gene tree distributions under the coalescent process. Evolution 59: 24-37.
5. Edwards, S. V. & P. Beerli. 2000. Perspective: Gene divergence, population divergence, and the variance in coalescence time in phylogeography studies. Evolution 54: 1839-1854.
6. _, L. Liu & D. K. Pearl. 2007. High-resolution species trees without concatenation. Proc. Natl. Acad. Sci. U.S.A. 104: 5936-5941.
7. Felsenstein, J. 2004. Inferring Phylogenies. Sinauer Associates, Sunderland, Massachusetts.
8. _. 2006. Accuracy of coalescent likelihood estimates: Do we need more sites, more sequences, or more loci? Molec. Biol. Evol. 23: 691-700.
9. Hasegawa, M., H. Kishino & T. Yano. 1985. Dating of the humanape splitting by a molecular clock of mitochondrial DNA. J. Molec. Evol. 22: 160-174.
10. Hewitt, G. M. 2004. Genetic consequences of climatic oscillations in the Quaternary. Philos. Trans., Ser. B. 359: 183-195.
11. Hey, J. & C. A. Machado. 2003. The study of structured populations - New hope for a difficult and divided science. Nat. Rev. Genet. 4: 535-543.
12. Hudson, R. 1990. Gene genealogies and the coalescent process. Oxford Surv. Evol. Biol. 7: 1-14.
13. _ & J. A. Coyne. 2002. Mathematical consequences of the genealogical species concept. Evolution 56: 1557-1565.
14. Jackman, T. R., A. Larson, K. de Queiroz & J. B. Losos. 1999. Phylogenetic relationships and tempo of early diversification in Anolis lizards. Syst. Biol. 48: 254-285.
15. Jennings, W. B. & S. V. Edwards. 2005. Speciational history of Australian grass finches (Poephila) inferred from thirty gene trees. Evolution 59: 2033-2047.
16. Kingman, J. F. C. 1982. The coalescent. Stochastic Process Applic. 13: 235-248.
17. Knowles, L. L. 2000. Tests of Pleistocene speciation in montane grasshoppers from the sky islands of western North America (genus Melanoplus). Evolution 54: 1337-1348.
18. _. 2001. Did the Pleistocene glaciations promote divergence? Tests of explicit refugial models in montane grasshoppers. Molec. Ecol. 10: 691-701.
19. _. 2004. The burgeoning field of statistical phylogeography. J. Evol. Biol. 17: 1-10.
20. _ & W. P. Maddison. 2002. Statistical phylogeography. Molec. Ecol. 11: 2623-2635.
21. _ & B. C. Carstens. 2007a. Estimating a geographically explicit model of population divergence. Evolution 61: 477-493.
22. _ & _. 2007b. Delimiting species without monophyletic gene trees. Syst. Biol. 56: 887-895.
23. Liu, L. & D. K. Pearl. 2007. Species trees from gene trees: Reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Syst. Biol. 56: 504-514.
24. Maddison, W. P. 1997. Gene trees in species trees. Syst. Biol. 46: 523-536.
25. _ & D. R. Maddison. 2004. Mesquite: A modular system for evolutionary analysis. Version 1.01. 〈http://mesquiteproject.org〉, accessed 28 February 2008.
26. _ & L. L. Knowles. 2006. Inferring phylogeny despite incomplete lineage sorting. Syst. Biol. 55: 21-30.
27. Masta, S. E. & W. P. Maddison. 2002. Sexual selection driving diversification in jumping spiders. Proc. Natl. Acad. Sci. U.S.A. 99: 4442-4447.
28. Mendelson, T. & K. L. Shaw. 2005. Rapid speciation in an arthropod. Nature 433: 375.
29. Miyamoto, M. M. & W. M. Fitch. 1995. Testing species phylogenies and phylogenetic methods with congruence. Syst. Biol. 44: 64-76.
30. Nikaido, M. H., H. Hamilton, H. Makino, T. Sasaki, K. Takahashi, M. Goto, N. Kanda, L. A. Pastene & N. Okada. 2006. Generating single-copy nuclear gene data for a recent adaptive radiation. Molec. Phylogen. Evol. 39: 124-134.
31. Pamilo, P. & M. Nei. 1988. Relationships between gene trees and species trees. Molec. Biol. Evol. 5: 568-583.
32. Poe, S. & A. L. Chubb. 2004. Birds in a bush: Five genes indicate explosive evolution of avian orders. Evolution 58: 404-415.
33. Rieseberg, L. H., T. E. Wood & E. J. Baack. 2006. The nature of plant species. Nature 440: 524-527.
34. Rokas, A., B. L. Williams, N. King & S. B. Carrol. 2003. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425: 798-804.
35. Rosenberg, N. A. 2002. The probability of topological concordance of gene trees and species trees. Theor. Populat. Biol. 61: 225-247.
36. _. 2003. The shapes of neutral gene genealogies in two species: Probabilities of monophyly, paraphyly, and polyphyly in a coalescent model. Evolution 61: 225-247.
37. Shedlock, A. M., K. Takahashi & N. Okada. 2004. SINEs of speciation: Tracking lineages with retroposons. Trends Ecol. Evol. 19: 545-553.
38. Slowinski, J. B. 2001. Molecular polytomies. Molec. Phylogen. Evol. 19: 114-120.
39. Tajima, F. 1983. Evolutionary relationship of DNA sequences in finite populations. Genetics 105: 437-460.
40. Takahata, N. 1989. Gene genealogy in 3 related populations - Consistency probability between gene and population trees. Genetics 122: 957-966.
41. _ & M. Nei. 1985. Gene genealogy and variance of interpopulational nucleotide differences. Genetics 110: 325-344.
42. Tateno, Y., M. Nei & F. Tajima. 1982. Accuracy of estimated phylogenetic trees from molecular data. I. Distantly related species. J. Molec. Evol. 18: 387-404.
43. Walsh, H. E., M. G. Kidd, T. Moum & V. L. Friesen. 1999. Polytomies and the power of phylogenetic inference. Evolution 53: 932-937.