A genealogical approach to quantifying lineage divergence

Evolution

Volumn 62, Issue 9, 2008, Pages 2411-2422

  Cummings, Michael P ^a   Neel, Maile C ^a   Shaw, Kerry L ^a,b  

^a Bldg 142   (United States)

^b Department of Obstetrics Gynecology   (United States)

Author keywords

Ancestral polymorphism; Congruence; Exclusivity; Genealogy; Lineage sorting; Monophyly; Paraphyly; Phylogeny; Polyphyly; Speciation; Species

Indexed keywords

DIVERGENCE; GENETIC ANALYSIS; HYPOTHESIS TESTING; PHYLOGENETICS; POLYMORPHISM; SPECIATION (BIOLOGY); STATISTICAL ANALYSIS;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; COMPUTER SIMULATION; DOLPHIN; EVALUATION; GENETICS; GRYLLIDAE; PHYLOGENY; SPECIES DIFFERENTIATION; STATISTICAL MODEL;

ANIMALS; COMPUTER SIMULATION; DOLPHINS; GENETIC SPECIATION; GRYLLIDAE; MODELS, GENETIC; MODELS, STATISTICAL; PHYLOGENY;

EID: 51549089796     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1111/j.1558-5646.2008.00442.x     Document Type: Article

References (52)

1. Avise, J. C., and R. M. Ball, Jr. 1990. Principles of genealogical concordance in species concepts and biological taxonomy. Oxf. Surv. Evol. Biol. 7 : 45 67.
2. Avise, J. C., R. A. Lansman, and R. O. Shade. 1979. Use of restriction endonucleases to measure mitochondrial-DNA sequence relatedness in natural populations.1. Population structure and evolution in the genus Peromyscus. Genetics 92 : 279 295.
3. Baum, D. A., and K. L. Shaw. 1995. Genealogical perspectives on the species problem. Pp. 289 303 in P. C. Hock, and A. G. Stevenson, ed., Experimental and molecular approaches to plant biosystematics. Missouri Botanical Garden, St. Louis.
4. Bazinet, A. L., and M. P. Cummings. 2008. The Lattice Project: a grid research and production environment combining multiple grid computing models In press in M. H. W. Weber, ed. Distributed & Grid Computing - Science Made Transparent for Everyone. Rechenkraft.net, Marburg.
5. Bazinet, A. L., D. S. Myers, J. Fuetsch, and M. P. Cummings. 2007. Grid services base library: a high-level, procedural application program interface for writing Globus-based grid services. Future Gener. Comp. Sy. 23 : 517 522.
6. Bickel, P. J., and Van Zwet, W. R. 1978. Asymptotic expansion for the power of distribution free tests in the two-sample problem. Ann. Stat. 6 : 987 1007.
7. Broughton, R. E., and R. G. Harrison. 2003. Nuclear gene genealogies reveal historical, demographic and selective factors associated with speciation in field crickets. Genetics 163 : 1389 1401.
8. Cummings, M. P., and J. C. Huskamp. 2005. Grid computing. Educause Review 40 : 116 117.
9. Cummings, M. P., S. A. Handley, D. S. Myers, D. L. Reed, A. Rokas, and K. Winka. 2003. Comparing bootstrap and posterior probability values in the four-taxon case. Syst. Biol. 52 : 477 487.
10. Degnan, J. H., and N. A. Rosenberg. 2006. Discordance of species trees with their most likely gene trees. Plos Genet. 2 : 762 768.
11. Edwards, S. V., S. B. Kingan, J. D. Calkins, C. N. Balakrishnan, W. B. Jennings, W. J. Swanson, and M. D. Sorenson. 2005. Speciation in birds: genes, geography, and sexual selection. Proc. Natl. Acad. Sci. USA 102 : 6550 6557.
12. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 : 783 791.
13. Funk, D. J., and K. E. Omland. 2003. Species-level paraphyly and polyphyly: frequency, causes and consequences with insights from animal mitochondrial DNA. Annu. Rev. Ecol. Syst. 34 : 397 423.
14. Gu, X., Y.-X. Fu, and W.-H. Li. 1995. Maximum likelihood estimation of the heterogeneity of substitution rates among nucleotide sites. Mol. Biol. Evol. 12 : 546 557.
15. Hare, M. P., F. Cipriano, and S. R. Palumbi. 2002. Genetic evidence on the demography of speciation in allopatric dolphin species. Evolution 56 : 804 816.
16. Hudson, R. R. 1990. Gene genealogies and the coalescent process. Oxf. Surv. Evol. Biol. 7 : 1 44.
17. Hudson, R. R. 2002. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18 : 337 338.
18. Hudson, R. R., and J. A. Coyne. 2002. Mathematical consequences of the genealogical species concept. Evolution 56 : 1557 1565.
19. Hudson, R. R., and M. Turelli. 2003. Stochasticity overrules the "three-times rule": genetic drift, genetic draft, and coalescence times for nuclear loci versus mitochondrial DNA. Evolution 57 : 182 190.
20. Hudson, R. R., M. Slatkin, and W. P. Maddison. 1992. Estimation of levels of gene flow from DNA-sequence data. Genetics 132 : 583 589.
21. Kingman, J. F. C. 1982. The coalescent. Stochas. Proc. Appl. 13 : 235 248.
22. Knowles, L. L., and B. C. Carstens. 2007. Delimiting species without monophyletic gene trees. Syst Biol 56 : 887 895.
23. Knowles, L. L., and W. P. Maddison. 2002. Statistical phylogeography. Mol. Ecol. 11 : 2623 2635.
24. Larget, B., and D. L. Simon. 1999. Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol. 16 : 750 759.
25. Liu, L., and 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.
26. Machado, C. A., and J. Hey. 2003. The causes of phylogenetic conflict in a classic Drosophila species group. Proc. R Soc. Lond. B. 270 : 1193 1202.
27. Maddison, W. P. 1997. Gene trees in species trees. Syst. Biol. 46 : 523 536.
28. Maddison, W. P., and D. R. Maddison. 1989. Interactive analysis of phylogeny and character evolution using the computer program MacClade. Folia Primatol. 53 : 190 202.
29. Maddison, W. P., and M. Slatkin. 1991. Null models for the number of evolutionary steps in a character on a phylogenetic tree. Evolution 45 : 1184 1197.
30. Mau, B., M. Newton, and B. Larget. 1999. Bayesian phylogenetic inference via Markov chain Monte Carlo methods. Biometrics 55 : 1 12.
31. Mayr, E. 1963. Animal species and evolution. Harvard Univ. Press, Cambridge, MA.
32. Moore, W. S. 1995. Inferring phylogenies from mtDNA variation: mitochondrial-gene trees. Evolution 49 : 718 726.
33. Myers, D. S., and M. P. Cummings. 2003. Necessity is the mother of invention: a simple grid computing system using commodity tools. J. Parallel Distrib. Comput. 63 : 578 589.
34. Pollard, D. A., V. N. Iyer, A. M. Moses, and M. B. Eisen. 2006. Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting. PLoS Genet. 2 : e173.
35. Rannala, B., and Z. Yang. 1996. Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J. Mol. Evol. 43 : 304 311.
36. 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.
37. Rosenberg, N. A. 2007. Statistical tests for taxonomic distinctiveness from observations of monophyly. Evolution 61 : 317 323.
38. Shaw, K. L. 1998. Species and the diversity of natural groups. Pp. 44 56 in D. J. Howard, and S. H. Berlocher, eds. Endless forms: species and speciation. Oxford Univ. Press, Oxford, England.
39. Shaw, K. L. 2002. Conflict between mitochondrial and nuclear DNA phylogenies of a recent species radiation: what mitochondrial DNA reveals and conceals about modes of speciation in Hawaiian crickets. Proc. Natl. Acad. Sci. USA 99 : 16122 16127.
40. Sites, J. W., and J. C. Marshall. 2003. Delimiting species: a Renaissance issue in systematic biology. Trends Ecol. Evol. 18 : 462 470.
41. Sites, J. W., Jr., and J. C. Marshall. 2004. Empirical criteria for delimiting species. Annu. Rev. Ecol. Evol. Syst. 35 : 199 229.
42. Slatkin, M., and W. P. Maddison. 1990. Detecting isolation by distance using phylogenies of genes. Genetics 126 : 249 260.
43. Slatkin, M., and J. L. Pollack. 2006. The concordance of gene trees and species trees at two linked loci. Genetics 172 : 1979 1984.
44. Swofford, D. L. 2003. PAUP*. Phylogenetic analysis using parsimony (*and Other Methods). Sinauer Associates, Sunderland, MA.
45. Swofford, D. L., and J. Sullivan. 2003. Phylogeny inference based on parsimony and other methods using PAUP*, Practice. Pp. 182 206 in M. Salemi, and A.-M. Vandamme, eds. The Phylogenetic handbook, a practical approach to DNA and protein phylogeny. Cambridge Univ. Press, Cambridge, England.
46. Tajima, F. 1983. Evolutionary relationship of DNA sequences in finite populations. Genetics 105 : 437 460.
47. Takahata, N. 1989. Gene genealogy in three related populations: consistency probability between gene and population trees. Genetics 122 : 957 966.
48. Tavare, S. 1986. Some probabilistic and statistical problems in the analysis of DNA sequences. Lect. Math Life. Sci. 17 : 57 86.
49. Templeton, A. R. 2001. Using phylogeographic analyses of gene trees to test species status and processes. Mol. Ecol. 10 : 779 791.
50. Wright, S. 1951. The genetical structure of populations. Annals Eugen. 15 : 323 354.
51. Yang, Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39 : 306 314.
52. Yang, Z., and B. Rannala. 1997. Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method. Mol. Biol. Evol. 14 : 717 724.