Test for simultaneous divergence using approximate Bayesian computation

Evolution

Volumn 60, Issue 12, 2006, Pages 2435-2453

  Hickerson, Michael J ^a,d   Stahl, Eli A ^b   Lessios, H A ^c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF MASSACHUSETTS DARTMOUTH   (United States)

^c SMITHSONIAN TROPICAL RESEARCH INSTITUTE   (Panama)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Approximate Bayesian computation; Coalescent; Comparative phylogeography; Echinoid; Hierarchical model; Meta analysis; Vicariance

Indexed keywords

BAYESIAN ANALYSIS; COMPARATIVE STUDY; DATA SET; DEMOGRAPHIC HISTORY; DIVERGENCE; DNA; ECHINODERM; HIERARCHICAL SYSTEM; ISOLATED POPULATION; ISOLATION EFFECT; META-ANALYSIS; MUTATION; NATURAL BARRIER; PHYLOGEOGRAPHY; RECOMBINATION; VICARIANCE;

ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; EVOLUTION; PANAMA; SEA URCHIN; TIME;

ANIMALS; BAYES THEOREM; EVOLUTION; MODELS, BIOLOGICAL; PANAMA; SEA URCHINS; TIME FACTORS;

ECHINOIDA;

EID: 33846875227     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1554/05-578.1     Document Type: Article

References (67)

1. Arbogast, B. S., and G. J. Kenagy. 2001. Comparative phylogeography as an integrative approach to historical biogeography. J. Biogeogr. 28:819-825.
2. Arbogast, B. S., S. V. Edwards, J. Wakeley, P. Beerli, and J. B. Slowinski. 2002. Estimating divergence times from molecular data on phylogenetic and population genetic timescales. Annu. Rev. Ecol. and Sys. 33:707-740.
3. Avise, J. C. 2000. Phylogeography: the history and formation of species. Harvard Univ. Press, Cambridge, MA.
4. Avise, J. C., D. Walker, and G. C. Johns. 1998. Speciation durations and Pleistocene effects on vertebrate phylogeography. Proc. R. Soc. Lond. B 265:1707-1712.
5. Beaumont, B. A. 2004. Recent developments in genetic data analysis: What can they tell us about human demographic history? Heredity 92:365-379.
6. Beaumont, B. A., and B. Rannala. 2004. The Bayesian revolution in genetics. Nat. Rev. Genet. 5:251-261.
7. Beaumont, M. A., W. Zhang, and D. J. Balding. 2002. Approximate Bayesian computation in population genetics. Genetics 162:2025-2035.
8. Bermingham, E., and C. Moritz. 1998. Comparative phylogeography: concepts and applications. Mol. Ecol. 7:367-369.
9. Bermingham, E., S. S. McCafferty, and A. P. Martin. 1997. Fish biogeography and molecular clocks: perspectives from the Panamanian Isthmus. Pp. 113-128 in T. D. Kocher and C. A. Stepien, eds. Molecular systematics of fishes. Academic Press, San Diego.
10. Carstens, B. C., S. J. Brunsfeld, J. R. Demboski, J. D. Good, and J. Sullivan. 2005. Investigating the evolutionary history of the Pacific Northwest mesic forest ecosystem: hypothesis testing within a comparative phylogeographic framework. Evolution 59:1639-1652.
11. Chesher, P. H. 1972. The status of knowledge of Panamainian echinoids. Bull. Biol. Soc. Wash 2:139-158.
12. Coates, A. G., J. B. C. Jackson, L. S. Collins, T. M. Cronin, H. J. Dowsett, L. M. Bybell, P. Jung, and J. A. Obando. 1992. Closure of the Isthmus of Panama: the near-shore marine record of Costa Rica and western Panama. Geol. Soc. Am. Bull. 104:814-828.
13. Coyne, J. A., and H. A. Orr. 2004. Speciation. Sinauer Associates, Sunderland, MA.
14. Cronin, T. M., and T. M. Dowsett. 1996. Biotic and oceanographic response to the Pliocene closing of the central American Isthmus. Pp. 76-104 in J. B. C. Jackson, A. F. Budd, and A. G. Coates, eds. Evolution and environment in tropical America. Univ. of Chicago Press, Chicago.
15. Cunningham, C. W., and T. M. Collins. 1998. Beyond area relationships: extinction and recolonization in molecular marine biogeography. Pp. 297-322 in B. Schierwater, B. Streit, G. Wagner, and R. DeSalle, eds. Molecular ecology and evolution: approaches and applications. Birkhauser Verlag, Basel, Switzerland.
16. Cunningham, C. W., H. Zhu, and D. M. Hillis. 1998. Best-fit maximum likelihood models for phylogenetic inference: empirical tests with known phylogenies. Evolution 52:978-987.
17. DeSalle, R., T. Freedman, E. M. Prager, and A. C. Wilson. 1987. Tempo and mode of sequence evolution in mitochondrial DNA of Hawaiian Drosophila. J. Mol. Evol. 26:157-164.
18. Edwards, S. V., and P. Beerli. 2000. Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution 54:1839-1854.
19. Estoup, A., B. A. Beaumont, F. Sennedot, C. Moritz, and J.-M. Cornuet. 2004. Genetic analysis of complex demographic scenarios: spatially expanding populations of the cane toad, Bufo marinus. Evolution 58:2021-2036.
20. Excoffier, L., A. Estoup, and J.-M. Cornuet. 2005. Bayesian analysis of an admixture model with mutations and arbitrarily linked markers. Genetics 169:1727-1738.
21. Felsenstein, J. 2006. Accuracy of coalescent likelihood estimates: Do we need more sites, more sequences, or more loci? Mol. Biol. Evol. 23:691-700.
22. Fitzpatrick, B. M. 2002. Molecular correlates of reproductive isolation. Evolution 56:191-198.
23. Fu, Y.-X., and W.-H. Li. 1997. Estimating the common ancestor of a sample of DNA sequences. Mol. Biol. Evol. 14:195-199.
24. Gavrilets, S. 2004. Models of speciation: What have we learned in 40 years? Evolution 57:2197-2215.
25. Gelman, A., J. B. Carlin, H. S. Stern, and D. B. Rubin. 1995. Bayesian data analysis. Chapman and Hall/CRC, London.
26. _. 2004. Bayesian data analysis. 2nd ed. Chapman and Hall/CRC, Boca Raton, FL.
27. Gillespie, J. H. 1984. Molecular evolution over the mutational landscape. Evolution 38:1116-1129.
28. Graham, C. H., S. R. Ron, J. C. Santos, C. J. Schneider, and C. Moritz. 2004. Integrating phylogeographic and environmental niche models to explore speciation mechanisms in dendrobatid frogs. Evolution 58:1781-1793.
29. Hasegawa, M., H. Kishino, and T. A. Yano. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:160-174.
30. Hey, J., and R. Nielsen. 2004. Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 167:747-760.
31. Hickerson, M. J., M. A. Gilchrist, and N. Takebayashi. 2003. Calibrating a molecular clock from phylogeographic data: moments and likelihood estimators. Evolution 57:2216-2225.
32. Hickerson, M. J., G. Dolman, and C. Moritz. 2006. Comparative phylogeographic summary statistics for testing simultaneous vicariance across taxon-pairs. Mol. Ecol. 15:209-224.
33. Hubbell, S. P. 2001. The unified neutral theory of biodiversity and biogeography. Princeton Univ. Press, Princeton, NJ.
34. Hudson, R. R. 2002. ms: a program for generating samples under neutral models. Bioinformatics 18:337-338.
35. Hugall, A., C. Moritz, A. Moussalli, and J. Stanisic. 2002. Reconciling paleodistribution models and comparative phylogeography in the wet tropics rainforest land snail Gnarosophia bellendenkerensis (Brazier 1875). Proc. Natl. Acad. Sci. USA 99:6112-6117.
36. James, W., and C. Stein. 1960. Estimation with quadradic loss. Proceedings of the fourth Berkeley symposium on mathematical statistics and probability, Berkeley, CA.
37. Jeffreys, H. 1961. Theory of probability. Clarendon Press, Oxford, U.K.
38. Jordan, D. S. 1908. The law of geminate species. Am. Nat. 42:73-80.
39. Kass, R. E., and A. Raftery. 1995. Bayesian factors. J. Am. Stat. Assoc. 90:773-795.
40. Knowles, L. L., and W. P. Maddison. 2002. Statistical phylogeography. Mol. Ecol. 11:2623-2635.
41. Knowlton, N., and L. A. Weigt. 1998. New dates and new rates for divergence across the Isthmus of Panama. Proc. R. Soc. Lond. B 265:2257-2263.
42. Lessios, H. A. 1979. Use of Panamanian sea-urchins to test the molecular clock. Nature 280:599-601.
43. Lessios, H. A., B. D. Kessing, D. R. Robertson, and G. Paulay. 1999. Phylogeography of the pantropical sea urchin Eucidaris in relation to land barriers and ocean currents. Evolution 53:806-817.
44. Lessios, H. A., B. D. Kessing, and J. S. Pearse. 2001. Population structure and speciation in tropical seas: global phylogeography of the sea urchin Diadema. Evolution 55:955-975.
45. Lessios, H. A., J. Kane, and D. R. Robertson. 2003. Phylogeography of the pantropical sea urchin Tripneustes: contrasting patterns of population structure between oceans. Evolution 57:2026-2036.
46. Loader, C. 1996. Local likelihood density estimation. Ann. Stat. 24:1602-1618.
47. Marko, P. B. 2002. Fossil calibration of molecular clocks and the divergence times of geminate species pairs separated by the Isthmus of Panama. Mol. Biol. Evol. 19:2005-2021.
48. Mayr, E. 1954. Geographic speciation in tropical echinoids. Evolution 8:1-18.
49. McCartney, M. A., G. Keller, and H. A. Lessios. 2000. Dispersal barriers in tropical oceans and speciation in Atlantic and eastern Pacific sea urchins of the genus Echinometra. Mol. Ecol. 9:1391-1400.
50. Moritz, C., J. L. Patton, C. J. Schneider, and T. B. Smith. 2000. Diversification of rainforest faunas: an integrated molecular approach. Annu. Rev. Ecol. Syst. 31:533-563.
51. Nei, M., and W. Li. 1979. Mathematical model for studying variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. USA 76:5269-5273.
52. Nielsen, R., and J. Wakeley. 2001. Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics 158:885-896.
53. Plagnol, V., and S. Tavare. 2002. Approximate Bayesian computation and MCMC. Pp. 99-114 in H. Neiderreiter, ed. Monte Carlo and quasi-Monte Carlo methods. Springer Verlag, Berlin.
54. Pritchard, J. K., M. T. Seielstad, A. Perez-Lezaun, and M. W. Feldman. 1999. Population growth of human Y chromosomes: a study of Y chromosome microsatellites. Mole. Biol. Evol. 16:1791-1798.
55. R Development Core Team. 2004. R: a language and environment for statistical computing. R Development Core Team, Vienna. Available via http://www.R-project.org
56. Ricklefs, R. E. 2003. Genetics, evolution, and ecological communities. Ecology 84:185-192.
57. Schneider, C. J., M. Cunningham, and C. Moritz. 1998. Comparative phylogeography and the history of endemic vertebrates in the wet tropics rainforests of Australia. Mol. Ecol. 7:487-498.
58. Tajima, F. 1983. Evolutionary relationship of DNA sequences in finite populations. Genetics 105:437-460.
59. _. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595.
60. Takahata, N. 1986. An attempt to estimate the effective size of the ancestral species common to two extant species from which homologous genes are sequenced. Genet. Res. 48:187-190.
61. Takahata, N., and M. Nei. 1985. Gene genealogy and variance of intrapopulational nucleotide differences. Genetics 110:325-344.
62. Tallmon, D. A., G. Luikart, and B. A. Beaumont. 2004. Comparative evaluation of a new effective population size estimator based on approximate Bayesian computation. Genetics 167:977-988.
63. Thorne, J. L., and H. Kishino. 2002. Divergence time and evolutionary rate estimation with multilocus data. Syst. Biol. 51:689-702.
64. Wakeley, J., and J. Hey. 1997. Estimating ancestral population parameters. Genetics 145:847-855.
65. Watterson, G. A. 1975. On the number of segregating sites in genetic models without recombination. Theor. Popul. Biol. 7:256-276.
66. Weiss, G., and A. von Haeseler. 1998. Inference of population history using a likelihood approach. Genetics 149:1539-1546.
67. Zigler, K. S., and H. A. Lessios. 2004. Speciation on the coasts of the New World: phylogeography, reproductive isolation, and the evolution of bindin in the sea urchin genus Lytechinus. Evolution 58:1225-1241.