A multilocus test of simultaneous divergence across the isthmus of panama using snapping shrimp in the genus Alpheus

Evolution

Volumn 63, Issue 2, 2009, Pages 514-530

  Hurt, Carla ^a   Anker, Arthur ^b   Knowlton, Nancy ^c  

^a UNIVERSITY OF MIAMI   (United States)

^b University of Florida ^*  (United States)

^c DEPARTMENT OF PALEOBIOLOGY   (United States)

Author keywords

Alpheus; Coalescent theory; Isthmus of Panama; Molecular evolution; Speciation

Indexed keywords

CYTOCHROME C OXIDASE;

BAYESIAN ANALYSIS; COALESCENCE; CRUSTACEAN; EVOLUTIONARY BIOLOGY; GENE FLOW; MOLECULAR ECOLOGY; POLYMORPHISM; SPECIATION (BIOLOGY); TAXONOMY;

ANIMAL; ARTICLE; BAYES THEOREM; CLASSIFICATION; DECAPODA (CRUSTACEA); GENETICS; PANAMA; PHYLOGENY; SPECIES DIFFERENTIATION;

ANIMALS; BAYES THEOREM; DECAPODA (CRUSTACEA); ELECTRON TRANSPORT COMPLEX IV; GENETIC SPECIATION; PANAMA; PHYLOGENY;

CENTRAL AMERICA; ISTHMUS OF PANAMA; PANAMA [CENTRAL AMERICA];

ALPHEIDAE; ALPHEUS; DECAPODA (CRUSTACEA);

EID: 58849105855     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1111/j.1558-5646.2008.00566.x     Document Type: Article

References (47)

1. Anker, A., C. Hurt, and N. Knowlton. 2007a. Revision of the Alpheus nuttingi (Schmitt) species complex, with description of a new species from the tropical eastern Pacific (Crustacea: Decapoda: Alpheidae). Zootaxa 1577 : 41 60.
2. Anker, A., C. Hurt, and N. Knowlton. 2007b. Three transisthmian snapping shrimps (Crustacea: Decapoda: Alpheidae: Alpheus) associated with innkeeper worms (Echiura: Thalassematidae). Zootaxa 1626 : 1 23.
3. Anker, A., C. Hurt, and N. Knowlton. 2008a. Revision of the Alpheus websteri Kingsley, 1880 species complex (Crustacea: Decapoda: Alpheidae), with revalidation of A. arenensis (Chace, 1937). Zootaxa 1694 : 51 68.
4. Anker, A., C. Hurt, and N. Knowlton. 2008b. Revision of the Alpheus formosus Gibbes 1850 species complex, with redescription of A. formosus and description of a new species from the tropical western Atlantic (Crustacea: Decapoda: Alpheidae). Zootaxa 1707 : 1 22.
5. Anker, A., C. Hurt, and N. Knowlton. 2008c. Revision of the Alpheus cristulifrons Rathbun species complex, with description of a new species from the tropical eastern Atlantic (Crustacea: Decapoda: Alpheidae). J Mar Biol Ass UK 88 : 543 562 2004. Molecular markers, natural history, and evolution. 2nd ed. Sinauer Associates Inc Sunderland, MA
6. Beaumont, M. A., W. Zhang, and D. J. Balding. 2002. Approximate Bayesian computation in population genetics. Genetics 162 : 2025 2035.
7. Bermingham, E., and H. A. Lessios. 1993. Rate variation of protein and mtDNA evolution as revealed by sea urchins separated by the Isthmus of Panama. PNAS 90 : 2434 2738.
8. 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, CA.
9. Coates, A. G., and J. A. Obando. 1996. The geological evolution of the Central American Isthmus. Pp. 21 56, in J. B. C. Jackson, A. F. Budd, and A. G. Coates, eds. Evolution and environment in tropical America. Univ. of Chicago Press, Chicago, IL.
10. Coates, A. G., J. G. C. Jackson, L. S. Collins, T. M. Cronin, H. 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.
11. Collins T. M. 1996. Molecular comparisons of transisthmian species pairs: rates and patterns of evolution. Pp. 303 334, in J. B. C. Jackson, A. F. Budd and A. G. Coates, eds. Evolution and environment in tropical America. Univ. of Chicago Press, Chicago, IL.
12. Collins, L. S., A. F. Budd, and A. G. Coates. 1996. Earliest evolution associated with closure of the Tropical American Seaway. Proc. Natl. Acad. Sci. USA 93 : 6069 6072.
13. Edwards, S. V., and P. Beerli. 2000. Perspective: Gene divergence, population divergence, and variance in coalescent time in phylogeographic studies. Evolution 54 : 1839 1854.
14. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 : 783 791.
15. Folmer, O., M. Black, W. Hoeh, R. Lutz, and R. Vrijenhoek. 1994. DNA primers for amplification of mitochondrial cytochrome C oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol. 3 : 294 299.
16. Hasegawa, M., H. Kishino, and T. Yano. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22 : 160 174.
17. Hey, J. and R. Nielsen. 2004. MuLTilocus method for estimating population sizes, migration rates, and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 167 : 747 760.
18. Hasegawa, M., H. Kishino, and T. Yano. 2007. Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proc. Natl. Acad. Sci. USA 104 : 2785 2790.
19. 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.
20. Hickerson, M. J., E. A. Stahl, and H. A. Lessios 2006. Test for simultaneous divergence using approximate Bayesian computation. Evolution 60 : 2435 2453.
21. Hickerson, M. J., E. A. Stahl, and N. Takebayashi. 2007. MsBayes: pipeline for testing comparative phylogeographic histories using hierarchical approximate Bayesian computation. BMC Bioinform. 2007 : 268 274.
22. Hudson, R. R., and N. Kaplan. 1985. Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111 : 147 164.
23. Hudson, R. R., M. Kreitman, and M. Aguadé. 1987. A test of neutral molecular evolution based on nucleotide data. Genetics 116 : 153 159.
24. Jackson, J. B. C., P. Jung, A. G. Coates, and L. S. Collins 1993. Diversity and extinction of tropical American mollusks and emergence of the Isthmus of Panama. Science 260 : 1624 1626.
25. Jordan, D. S. 1908. The law of the geminate species. Am. Nat. 42 : 73 80.
26. Jung, P. 1989. Revision of the Strombina-group (Gastropoda: Columbellidae), fossil and living: distribution, biostratigraphy, and systematics. Schweiz. Paleontol. Abh. 111 : 1 298.
27. Keigwin, L. D. 1982. Isotopic paleoceanography of the Caribbean and east Pacific: role of Panama uplift in Late Neogene time. Science 217 : 350 353.
28. Kimura, M. 1969. The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations. Genetics 61 : 893 903.
29. 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.
30. Knowlton, N., L. A. Weigt, L. A. Solorzano, D. K. Mills, and E. Bermingham. 1993. Divergence in proteins, mitochondrial DNA, and reproductive compatibility across the Isthmus of Panama. Science 260 : 1629 1632.
31. Kim, W., and L. G. Abele. 1988. The snapping shrimp genus Alpheus from the eastern Pacific (Decapoda: Caridea: Alpheidae). Smithson. Contrib. Zool. 454 : 1 119.
32. Kumar, S., and S. Subramanian. 2002. Mutation rates in mammalian genomes. Proc. Natl. Acad. Sci. USA 99 : 803 808.
33. Kumar, S., T. Koichiro, and M. Nei. 2005. MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers. Bioinformatics 10 : 198 191.
34. Lessios, H. A. 1979. Use of Panamanian sea urchins to test the molecular clock. Nature 280 : 599 601.
35. Moriyama, E. N., and T. Gojobori. 1992. Rates of synonymous substitution and base composition of nuclear genes in Drosophila. Genetics 130 : 855 864.
36. Pamilo P. and M. Nei. 1988. Relationships between gene trees and species trees. Mol. Biol. Evol. 5 : 568 583.
37. 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.
38. Regier, J. C. 2007. Protocols, Concepts, and Reagents for preparing DNA sequencing templates. Version 8/30/05. http://www.umbi.umd.edu/users/jcrlab/PCR- primers.pdf.
39. Regier, J. C., and R. Schultz. 1997. Molecular phylogeny of the major arthropod groups indicates polyphyly of Crustaceans and a new hypothesis for the origin of Hexapods. Mol. Biol. Evol. 14 : 902 913.
40. Rozas, J., J. C. Sanchez-DelBarrio, X. Messeguer, and R. Rozas. 2003. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 10 : 2496 2497.
41. Saitou, N., and M. Nei. 1986. The number of nucleotides required to determine the branching order of three species, with special reference to the human-chimpanzee-gorilla divergence. J. Mol. Evol. 24 : 189 204.
42. Stephens, M., N. Smith, and P. Donnelly 2001. A new statistical method for haplotype reconstruction from population data. Am. J. Hum. Genet. 68 : 978 989.
43. Vawter, A. T., R. H. Rosenblatt, and G. C. Gorman. 1980. Genetic divergence among fishes of eastern Pacific and Caribbean: Support for the molecular clock. Evolution 34 : 705 711.
44. Wakeley, J., and J. Hey. 1997. Estimating ancestral population parameters. Genetics 145 : 847 855.
45. Williams, S. T., and N. Knowlton. 2001. Mitochondrial pseudogenes are pervasive and often insidious in the snapping shrimp genus Alpheus. Mol. Biol. Evol. 18 : 1484 1493.
46. Williams, S. T., N. Knowlton, L. A. Weigt, and J. A. Jara. 2001. Evidence of three major clades within the snapping shrimp genus Alpheus inferred from nuclear and mitochondrial gene sequence data. Mol. Phylogenet. Evol. 20 : 375 389.
47. Yang, Z. 2002. Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci. Genetics 162 : 1811 1823.