Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: An example from melanoplus grasshoppers

Systematic Biology

Volumn 56, Issue 3, 2007, Pages 400-411

  Carstens, Bryan C ^a   Knowles, L Lacey ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

Coalescent; Gene trees; Incomplete lineage sorting; Species phylogeny

Indexed keywords

ANIMAL; ARTICLE; BIOLOGICAL MODEL; CLASSIFICATION; COMPUTER SIMULATION; GENETIC VARIABILITY; GENETICS; GRASSHOPPER; PHYLOGENY; SPECIES DIFFERENCE; SPECIES DIFFERENTIATION; STATISTICAL MODEL;

ANIMALS; COMPUTER SIMULATION; GENETIC SPECIATION; GRASSHOPPERS; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; PHYLOGENY; SPECIES SPECIFICITY; VARIATION (GENETICS);

MELANOPLUS;

EID: 34249700809     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1080/10635150701405560     Document Type: Article

References (65)

1. Anderson, F. E., and D. L. Swofford. 2004. Should we be worried about long-branch attraction in real data sets? Investigations using metazoan 18S rDNA. Mol. Phylogenet. Evol. 33:440-451.
2. Anisimova, M., and O. Gascucl. 2006. Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. Syst. Biol. 55:539-552.
3. Arvestad, L., A.-C. Berglund, B. Sennblad, and J. Lagergren. 2004. Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution. RECOMB 04:326-335.
4. Avise, J. C., C. D. Ankney, and W. S. Nelson. 1990. Mitochondrial gene trees and evolutionary relationships of mallard and black ducks. Evolution 44:1109-1119.
5. Bruno, W. J., and A. L. Halpern. 1999. Topological bias and inconsistency of maximum likelihood using wrong models. Mol. Biol. Evol. 16:564-566.
6. Buckley, T., M. Cordeiro, D. Marshall, and C. Simon. 2006. Differentiating between hypotheses of lineage sorting and introgression in New Zealand alpine cicadas (Maoricicada Dugdale). Syst. Biol. 55:411-425.
7. Carstens, B. C., and L. L. Knowles. 2007. Shifting distributions and speciation: genomic resolution of species divergence during rapid climate change. Mol. Ecol. 16:619-627.
8. Carstens, B. C., and L. L. Knowles. 2006. Variable nuclear markers for Melanoplus oregonensis identified from the screening of a genomic library. Mol. Ecol. Notes 6:683-685.
9. Crews, S. C., and M. Hedin. 2006. Studies of morphological and molecular phylogenetic divergence in spiders (Araneae: Homalonychus) from the American southwest, including divergence along the Baja California peninsula. Mol. Phylogenet. Evol. 38:470-487.
10. Cummings, M. P. 1994. Transmission patterns of eukaryotic transposable elements: Arguments for and against horizontal transfer. Trends Ecol. Evol. 9:141-145.
11. Degnan, J. H., and L. M. Salter. 2005. Gene tree distributions under the coalescent process. Evolution 9:24-37.
12. Felsenstein, J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27:401-410.
13. Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.
14. Felsenstein, J. 1992. Estimating effective population size from samples of sequences: a bootstrap Monte Carlo integration approach. Genet. Res. 60:209-220.
15. Felsenstein, J. 2004. Inferring phylogenies. Sinauer Associates, Sunderland, Massachusetts.
16. Fitch, W. M. 1970. Distinguishing homologous from analogous proteins. Syst. Zool. 19:99-113.
17. Ford, V. S., J. Lee, B. G. Baldwin, and L. D. Gottlieb. 2006. Species divergence and relationships in Stephanomeria (Compositae): PgiC phyleny compared to prior biosystematic studies. Am. J. Bot. 93:480-490.
18. Funk, D. J., and K. E. Omland. 2003. Species-level paraphyly and polyphyly: Frequency, causes, and consequences, with insights from animal mitochondrial DNA. Ann. Rev. Ecol. Syst. 34:397-423.
19. Gibbard, P., and T. Van Kolfschoten. 2004. The Pleistocene and Holocene Epochs. Pages 441-452 in A geologic time scale (F. M. Gradstein, J. G. Ogg, and A. G. Smith, eds.). Cambridge University Press, London.
20. Hillis, D. M., J. P. Huelsenbeck, and C. W. Cunningham. 1994. Application and accuracy of molecular phylogenies. Science 264:671-677.
21. Hillis, D. M., B. K. Mable, and C. Moritz. 1996. Applications of molecular systematics: The state of the field and a look into the future. Pages 515-543 m Molecular systematics, 2nd edition (D. M. Hillis, C. Moritz, and B. K. Mable, eds.). Sinauer Associates, Sunderland, Massachusetts.
22. Hudson, R. R. 1992. Gene trees, species trees and the segregation of ancestral alleles. Genetics 131:509-512.
23. Hudson, R. R., and J. A. Coyne, 2002. Mathematical consequences of the genealogical species concept. Evolution 56:1557-1565.
24. Hudson, R. R., and M. Turelli. 2003. Stochasticity overrules the "threetimes" rule: Genetic drift, genetic draft, and coalescence times for nuclear loci versus mitochondrial DNA. Evolution 57:182-190.
25. Huelsenbeck, J. P., D. M. Hillis, and R. Jones. 1996. Parametric boot-strapping in molecular phylogenetics: Applications and performance. Pages 19-45 in Molecular zoology: Advances, strategies, and protocols (J. D. Ferraris and S. R. Palumbi, eds.). Wiley-Liss, New York.
26. Hughes, J., and A. P. Vogler. 2004. The phylogeny of acorn weevils (genus Curculio) from mitochondrial and nuclear DNA sequences: The problem of incomplete data. Mol. Phylogenet. Evol. 32:601-615.
27. Jennings, W. B., and S. V. Edwards. 2005. Speciational history of Australian grass finches (Pocphila) inferred from thirty gene trees. Evolution 59:2033-2047.
28. Kingman, J. F. C. 1982. The coalescent. Stochastic Process Appl. 13:235248.
29. Knowles, L. L. 2000. Tests of Pleistocene speciation in montane grasshoppers (genus Melanoplus) from the sky islands of western North America. Evolution 54:1337-1348.
30. Knowles, L. L. 2001a. Did the Pleistocene glaciations promote divergence? Tests of explicit refugial models in montane grasshoppers. Mol. Ecol. 10:691-701.
31. Knowles, L. L. 2001b. Genealogical portraits of speciation in montane grasshoppers (genus Melanoplus) from the sky islands of the Rocky Mountains. Proc. Roy. Soc. Lond. B 268:319-324.
32. Knowles, L. L., and B. C. Carstens. 2007. Inferring a population-divergence model for statistical phylogeographic tests in montane grasshoppers. Evolution 61:477-493.
33. Knowles, L. L., B. C. Carstens, and M. L. Keat. 2007. Coupling genetic and ecological-niche models to examine how past population distributions contribute to divergence. Current Biol. 17:1-7.
34. Knowles, L. L., and W. P. Maddison. 2002. Statistical phylogeography. Mol. Ecol. 11:2623-2635.
35. Knowles, L. L., and D. Otte. 2000. Phylogenetic analysis of montane grasshoppers from western North America (genus Melanoplus, Acrididae, Melanoplinae) Ann. Ent. Soc. Am. 93:421-431.
36. Kubatko, L. S., and J. H. Degnan. 2007. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst. Biol. 56:17-24.
37. Liu, L., and D. K. Pearl. 2006. Species trees from gene trees: Reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Technical report #53, Ohio State University.
38. Lundrigan, B. L., S. A. Jansa, and P. K. Tucker. 2002. Phylogenetic relationships in the genus Mus, based on paternally, maternally, and biparentally inherited characters. Syst. Biol. 51:410-431.
39. Maddison, W. P. 1997. Gene trees in species trees. Syst. Biol. 46:523-536.
40. Maddison, W. P., and L. L. Knowles. 2006. Inferring phylogeny despite incomplete lineage sorting. Syst. Biol. 55:21-30.
41. Maddison W. P., and D. R. Maddison. 2004. Mesquite: A modular system for evolutionary analysis. Version 1.01. Available at http://mesquiteproject.org
42. Minin, V., Z. Abdo, P. Joyce, and J. Sullivan. 2003. Performance-based selection of likelihood models for phylogeny estimation. Syst. Biol 52:674-683.
43. Morando, M. L. J. Avila, J. Baker, and J. W. Sites. 2004. Phylogeny and phylogeography of the Liolaemus darwinii complex (Squamata: Liolaemidae): Evidence for introgression and incomplete lineage sorting. Evolution 58:842-861.
44. Pamilo, P., and M. Nei. 1988. Relationships between gene trees and species trees. Mol. Biol. Evol. 5:568-583.
45. Parker, A., and I. Kornfield. 2000. Evolution of the mitochondrial DNA control region in the mbuna (Cichlidae) species flock of Lake Malawi, East Africa. J. Mol. Evol. 45:70-83.
46. Rannala, B., and Z. Yang. 2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164:1645-1656.
47. Rieseberg, L. H. 2001. Chromosomal rearrangements and speciation. TREE 16:351-358.
48. Robert, C., and G. Casella. 1999. Monte Carlo statistical methods. Springer, New York.
49. Rokas, A., D. Kruger, and S. B. Carroll. 2005. Animal evolution and the molecular signature of radiations compressed in time. Science 310:1933-1938.
50. Rokas, A., B. L. Williams, N. King, and S. B. Carrol. 2003. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425:798-804.
51. Rosenberg, N. A. 2002. The probability of topological concordance of gene trees and species trees. Theor. Pop. Biol. 61:225-247.
52. 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.
53. Slowinski, J. B., and R. D. M. Page. 1999. How should species phylogenies be inferred from sequence data? Syst. Biol. 48:814-825.
54. Steppan, S. J., R. M. Adkins, and J. Anderson. 2004. Phylogeny and divergence-date estimates of rapid radiations in muroid rodents based on multiple nuclear genes. Syst. Biol. 53:533-553.
55. Steppan, S. J., R. M. Adkins, P. Q. Spinks, and C. Hale. 2005. Multi-gene phylogeny of the Old World mice, Murinae, reveals distinct geographic lineages and the declining utility of mitochondrial genes compared to nuclear genes. Mol. Phyl. Evol. 37:370-388.
56. Stephens, M., and P. Donnelly. 2003. A comparison of bayesian methods for haplotype reconstruction. Am. J. Human. Genet. 73:1162-1169.
57. Sullivan, J., and P. Joyce. 2005. Model selection in phylogenetics. Ann. Rev. Ecol. Evol. Syst. 36:445-466.
58. Sullivan, J., and D. L. Swofford. 1997. Are guinea pigs rodents? The importance of adequate models in molecular phylogenetics. J. Mamm. Evol. 4:77-86.
59. Sullivan, J., and D. L. Swofford. 2001. Should we use model-based methods for phylogenetic inference when we know that the assumptions about among-site rate variation and nucleotide substitution pattern are violated? Syst. Biol. 50:723-729.
60. Swofford, D. L. 2002. Paup": Phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland, Massachusetts.
61. Swofford, D. L., G. P. Olsen, P. J. Waddell, and D. M. Hillis. 1996. Phylogenetic inference. Pages 407-514 in Molecular systematics, 2nd edition (D. M. Hillis, C. Moritz, and B. K. Mable, eds.). Sinauer Associates, Sunderland, Massachusetts.
62. Tajima, F. 1983. Evolutionary relationships of DNA sequences in finite populations. Genetics 105:437-460.
63. Takahata, N. 1989. Gene genealogy in three related populations: consistency probability between gene and population trees. Genetics 122:957-966.
64. Takahata, N., and M. Nei. 1985. Gene genealogy and variance of interpopulational nucleotide differences. Genetics 110:325-344.
65. Wakeley, J., R. Nielsen, S. N. Liu-Cordero, and K. Ardlie. 2001. The discovery of single-nucleotide polymorphisms and inferences about human demographic history. Am. J. Hum. Genet. 69:1332-1347.