Rapid diversification, incomplete isolation, and the "speciation clock" in North American salamanders (genus Plethodon): Testing the hybrid swarm hypothesis of rapid radiation

Evolution

Volumn 60, Issue 12, 2006, Pages 2585-2603

  Wiens, John J ^a   Engstrom, Tag N ^c   Chippindale, Paul T ^b  

^a STONY BROOK UNIVERSITY   (United States)

^b UNIVERSITY OF TEXAS AT ARLINGTON   (United States)

^c CALIFORNIA STATE UNIVERSITY   (United States)

Author keywords

Amphibians; Diversification; Hybridization; Phylogeny; Reproductive isolation; Salamanders; Speciation

Indexed keywords

ADAPTIVE RADIATION; AMPHIBIAN; EVOLUTION; GENE FLOW; HYBRID; HYBRIDIZATION; HYPOTHESIS TESTING; INTROGRESSION; LIFE HISTORY; MITOCHONDRIAL DNA; PHYLOGENY; REPRODUCTIVE ISOLATION; SPECIATION (BIOLOGY);

AMPHIBIA; ANIMAL; ARTICLE; BIODIVERSITY; EVOLUTION; GENETICS; HYBRIDIZATION; TIME; UNITED STATES;

ANIMALS; APPALACHIAN REGION; BIODIVERSITY; EVOLUTION; HYBRIDIZATION, GENETIC; TIME FACTORS; URODELA;

NORTH AMERICA;

AMPHIBIA; PLETHODON; SALAMANDROIDEA;

EID: 33846877190     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1554/06-138.1     Document Type: Article

References (77)

1. Alfaro, M. E., S. Zoller, and F. Lutzoni. 2003. Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. Mol. Biol. Evol. 20:255-266.
2. AmphibiaWeb: Information on amphibian biology and conservation. [web application]. 2006. AmphibiaWeb, Berkeley, CA. Available at: http://amphibiaweb.org/. (Accessed: August 4, 2006).
3. Arévalo, E., S. K. Davis, and J. W. Sites, Jr. 1994. Mitochondrial DNA sequence divergence and phylogenetic relationships among eight chromosome races of the Sceloporus grammicus complex (Phrynosomatidae) in Central Mexico. Syst. Biol. 43: 387-418.
4. Barnosky, A. D. 2001. Distinguishing the effects of the Red Queen and Court Jester on Miocene mammal evolution in the northern Rocky Mountains. J. Vert. Paleontol. 21:172-185.
5. Bolnick, D. I., and T. J. Near. 2005. Tempo of hybrid inviability in centrarchid fishes (Teleostei: Centrarchidae). Evolution 59: 1754-1767.
6. Carr, D. E. 1996. Morphological variation among species and populations of salamanders in the Plethodon glutinosus complex. Herpetologica 52:56-65.
7. Chippindale, P. T., R. M. Bonett, A. S. Baldwin, and J. J. Wiens. 2004. Phylogenetic evidence for a major reversal in life history evolution in plethodontid salamanders. Evolution 58: 2809-2822.
8. Clark, J. M. 1985. Fossil plethodontid salamanders from the latest Miocene of California. J. Herpetol. 19:41-47.
9. Conant, R., and J. T. Colllins. 1991. A field guide to reptiles and amphibians. Eastern and Central North America. Houghton Mifflin, Boston, MA.
10. Coyne, J. A., and H. A. Orr. 1989. Patterns of speciation in Drosophila. Evolution 43:362-381.
11. _. 1997. "Patterns of speciation in Drosophila" revisited. Evolution 51:295-303.
12. _. 2004. Speciation. Sinauer, Sunderland, MA.
13. Dawley, E. M. 1984. Recognition of individual, sex, and species odours by salamanders of the Plethodon glutinosus-P. jordani complex. Anim. Behav. 32:353-361.
14. _. 1986. Behavioral isolating mechanisms in sympatric terrestrial salamanders. Herpetologica 42:156-164.
15. Erixon, P., B. Svennblad, T. Britton, and B. Oxelman. 2003. Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics. Syst. Biol. 52:665-673.
16. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
17. Frost, D. R. 2004. Amphibian species of the world: an online reference. Vers. 3.0 (checked 24 August 2006). Electronic database accessible at http://research.amnh.org/herpetology/amphibia/ index.html. American Museum of Natural History, New York.
18. Frost, D. R., and D. M. Hillis. 1990. Species in concept and practice: herpetological applications. Herpetologica 46:87-104.
19. Gardner, J. D. 2003. The fossil salamander Proamphiuma cretacea Estes (Caudata: Amphiumidae) and relationships within the Amphiumidae. J. Vert. Paleontol. 23:769-782.
20. Grant, P. R., and B. R. Grant. 1992. Hybridization in bird species. Science 256:193-197.
21. _. 2002. Adaptive radiation of Darwin's finches. Am. Sci. 90: 130-139.
22. Grant, P. R., B. R. Grant, and K. Petren. 2005. Hybridization in the recent past. Am. Nat. 166:56-67.
23. Greenhalgh, P., C. E. Olesen, and L. A. Steiner. 1993. Characterization and expression of recombination activating genes (RAG-1 and RAG-2) in Xenopus laevis. J. Immunol. 151:3100-3110.
24. Gu, X., Y. X. Fu, and W. H. Li. 1995. Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Mol. Biol. Evol. 12:546-557.
25. Highton, R. 1989. Biochemical evolution in the slimy salamanders of the Plethodon glutinosus complex in the eastern United States. Part 1. Geographic protein variation. Ill. Biol. Monogr. 57:1-78.
26. _. 1995. Speciation in eastern North American salamanders of the genus Plethodon. Annu. Rev. Ecol. Syst. 26:579-600.
27. _. 2004. A new species of Woodland Salamander of the Plethodon cinereus group from the Blue Ridge Mountains of Virginia. Jeffersoniana 14:1-22.
28. Highton, R., and A. Larson. 1979. The genetic relationships of the salamanders of the genus Plethodon. Syst. Zool. 28:579-599.
29. Highton, R., and R. B. Peabody. 2000. Geographic protein variation and speciation in salamanders of the Plethodon jordani and Plethodon glutinosus complexes in the southern Appalachian mountains with the description of four new species. Pp. 31-75 in R. C. Bruce, R. G. Jaeger, and L. D. Houck, eds. The biology of plethodontid salamanders. Kluwer Academic/Plenum. New York.
30. Hillis, D. M. 1988. Systematics of the Rana pipiens complex: puzzle and paradigm. Annu. Rev. Ecol. Syst. 19:39-63.
31. Hillis, D. M., and J. J. Bull. 1993. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst. Biol. 42:182-192.
32. Huelsenbeck, J. P., and B. Rannala. 2004. Frequentist properties of Bayesian posterior probabilities. Syst. Biol. 53:904-913.
33. Huelsenbeck, J. P., and F. Ronquist. 2001. MrBayes: Bayesian inference of phylogeny. Bioinformatics 17:754-755.
34. IUCN, Conservation International, and NatureServe. 2004. Global amphibian assessment. www.globalamphibians.org.
35. Kozak, K. H., and J. J. Wiens. 2006. Does niche conservatism promote speciation? A case study in North American salamanders. Evolution 60:2604-2621.
36. Kozak, K. H., D. W. Weisrock, and A. Larson. 2006. Rapid lineage accumulation in a non-adaptive radiation: phylogenetic analysis of diversification rates in eastern North American woodland salamanders (Plethodontidae: Plethodon). Proc. R. Soc. Lond. 273: 539-546.
37. Lewis, P. O. 2001. A likelihood approach to inferring phylogeny from discrete morphological characters. Syst. Biol. 50:913-925.
38. Maddison, D. R., and W. P. Maddison. 2001. MacClade 4.02. Sinauer, Sunderland, MA.
39. Mahoney, M. J. 2001. Molecular systematics of Plethodon and Aneides (Caudata: Plethodontidae: Plethodontini): phylogenetic analysis of an old and rapid radiation. Mol. Phylogenet. Evol. 18: 174-188.
40. Mendelson, T. C. 2003. Sexual isolation evolves faster than hybrid inviability in a diverse and sexually dimorphic genus of fish (Percidae: Etheostoma). Evolution 57:317-327.
41. Mendelson, T. C., and K. L. Shaw. 2005. Sexual behavior: rapid speciation in an arthropod. Nature 433:375-376.
42. Min, M. S., S. Y. Yang, R. M. Bonett, D. R. Vieites, R. A. Brandon, and D. B. Wake. 2005. Discovery of the first Asian plethodontid salamander. Nature 435:87-90.
43. Moritz, C., C. J. Schneider, and D. B. Wake. 1992. Evolutionary relationships within the Ensatina eschscholtzii complex confirm the ring species interpretation. Syst. Biol. 41:273-291.
44. Nee, S., R. M. May, and P. H. Harvey. 1994. The reconstructed evolutionary process. Philos. Trans. R. Soc. Lond. B 344: 305-311.
45. Nikoh, N., N. Iwabe, K-I. Kuma, M. Ohno, T. Sugiyama, Y. Watanabe, K. Yasui, Z. Shi-cui, K. Hori, Y. Shimura, and T. Miyata. 1997. An estimate of divergence time of Parazoa and Eumetazoa and that of Cephalochordata and Vertebrata by aldolase and triose phosphate isomerase clocks. J. Mol. Evol. 45:97-106.
46. Nylander, J. A. A. 2004. MrModeltest 2.0. Program distributed by the author. Evolutionary Biology Centre, Uppsala University. (http://www.ebc.uu.se/ systzoo/staff/nylander.html).
47. Nylander, J. A. A., F. Ronquist, J. P. Huelsenbeck, and J. L. Nieves-Aldrey. 2004. Bayesian phylogenetic analysis of combined data. Syst. Biol. 53:47-67.
48. Palmer, C., R. A. Watts, R. Gregg, M. McCall, L. D. Houck, R. Highton, and S. J. Arnold. 2005. Lineage-specific differences in evolutionary mode in a salamander courtship pheromone. Mol. Biol. Evol. 22:2243-2256.
49. Petranka, J. W. 1998. Salamanders of the United States and Canada. Smithsonian Institution Press, Washington, DC.
50. Presgraves, D. C. 2002. Patterns of postzygotic isolation in Lepidoptera. Evolution 56:1168-1183.
51. 1 postzygotic incompatibilities in birds. Evolution 56:2083-2089.
52. Rambaut, A., P. H. Harvey, and S. Nee. 1997. End-Epi: an application for reconstructing phylogenetic and population processes from molecular sequences. Comput. Appl. Biosci. 13:303-306.
53. Rodriguez, J., L. Oliver, A. Martin, and R. Medina. 1990. The general stochastic model of nucleotide substitution. J. Theor. Biol. 142:485-501.
54. Rollman, S. M., L. D. Houck, and R. C. Feldhoff. 2003. Conspecific and heterospecific effects on female receptivity. Anim. Behav. 66:857-861.
55. Sanderson, M. J. 2002. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol. Biol. Evol. 19:101-109.
56. _. 2003. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 19:301-302.
57. Sasa, M., P. T. Chippindale, and N. A. Johnson. 1998. Patterns of postzygotic isolation in frogs. Evolution 52:1811-1820.
58. Schluter, D. 2000. The ecology of adaptive radiation. Oxford Univ. Press, Oxford, U.K.
59. Seehausen, O. 2004. Hybridization and adaptive radiation. Trends Ecol. Evol. 19:198-207.
60. Seehausen, O., and J. J. M. van Alphen. 1999. Can sympatric speciation by disruptive sexual selection explain rapid evolution of cichlid fish diversity in Lake Victoria? Ecol. Lett. 2:262-271.
61. Seehausen, O., J. J. M. van Alphen, and F. Witte. 1997. Cichlid fish diversity threatened by eutrophication that curbs sexual selection. Science 277:1808-1811.
62. Shaw, K. L. 2002. Conflict between mitochondrial and nuclear 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. Simmons, M. P., and H. Ochoterena. 2000. Gaps as characters in sequence-based phylogenetic analyses. Syst. Biol. 49:369-381.
64. Sites, J. W., Jr., M. Morando, R. Highton, F. Huber, and R. E. Jung. 2004. Phylogenetic relationships of the endangered Shenandoah salamander (Plethodon shenandoah) and other salamanders of the Plethodon cinereus group (Caudata Plethodontidae). J. Herp. 38:96-105.
65. Swofford, D. L. 2002. PAUP*: Phylogenetic analysis using parsimony*, version 4.0b10. Sinauer, Sunderland, MA.
66. Tihen, J. A., and D. B. Wake. 1981. Vertebrae of plethodontid salamanders from the Lower Miocene of Montana. J. Herpetol. 15:35-40.
67. Ventakesh, B., M. V. Erdmann, and S. Brenner. 2001. Molecular synapomorphies resolve evolutionary relationships of extant jawed vertebrates. Proc. Natl. Acad. Sci. USA 98:11382-11387.
68. Watts, R., C. Palmer, R. Feldhoff, P. Feldhoff, L. D. Houck, A. Jones, M. Pfrender, S. Rollmann, and S. J. Arnold. 2004. Stabilizing selection on behavior and morphology masks positive selection on the signal in a salamander pheromone signaling complex. Mol. Biol. Evol. 21:1032-1041.
69. Weisrock, D. W., K. H. Kozak, and A. Larson. 2005. Phylogeographic analysis of mitochondrial gene flow and introgression in the salamander, Plethodon shermani. Mol. Ecol. 14: 1457-1472.
70. Wiens, J. J. 1998a. Combining data sets with different phylogenetic histories. Syst. Biol. 47:568-581.
71. _. 1998b. Does adding characters with missing data increase or decrease phylogenetic accuracy? Syst. Biol. 47:625-640.
72. _. 2004a. Speciation and ecology revisited: phylogenetic niche conservatism and the origin of species. Evolution 58: 193-197.
73. _. 2004b. What is speciation and how should we study it? Am. Nat. 163:914-923.
74. Wiens, J. J., J. W. Fetzner, C. L. Parkinson, and T. W. Reeder. 2005a. Hylid frog phylogeny and sampling strategies for speciose clades. Syst. Biol. 54:719-748.
75. Wiens, J. J., R. M. Bonett, and P. T. Chippindale. 2005b. Ontogeny discombobulates phylogeny: paedomorphosis and higher-level salamander relationships. Syst. Biol. 54:91-110.
76. Wilcox, T. P., D. J. Zwickl, T. A. Heath, and D. M. Hillis. 2002. Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support. Mol. Phylogenetic. Evol. 25:361-371.
77. Yang, Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39:306-314.