The Pleistocene history of the sheepshead minnow (Cyprinodon variegatus): Non-equilibrium evolutionary dynamics within a diversifying species complex

Molecular Phylogenetics and Evolution

Volumn 43, Issue 3, 2007, Pages 743-754

  Haney, Robert A ^a   Silliman, Brian R ^b   Fry, Adam J ^c   Layman, Craig A ^d   Rand, David M ^a  

^a BROWN UNIVERSITY   (United States)

^b University of Florida ^*  (United States)

^c UNIVERSITY OF CONNECTICUT   (United States)

^d YALE UNIVERSITY   (United States)

Author keywords

Cyprinodon; Demography; Gene flow; Mitochondrial control region; Phylogeography

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; CLASSIFICATION; CYPRINODONTIFORMES; DNA SEQUENCE; GENETICS; GEOGRAPHY; MEXICO; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY;

ANIMALS; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GEOGRAPHY; KILLIFISHES; MEXICO; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

CYPRINODON; CYPRINODON VARIEGATUS; VERTEBRATA;

EID: 34248993677     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2006.08.022     Document Type: Article

References (49)

1. Adams S.M., Lindmeier J.B., and Duvernell D.D. Microstaellite analysis of the phylogeography, Pleistocene history and secondary contact hypotheses for the killifish, Fundulus heteroclitus. Mol. Ecol. 15 (2006) 1109-1123
2. Avise J.C., Arnold J., Ball R.M., Bermingham E., Lamb T., Neigel J.E., Reeb C.A., and Saunders N.C. Intraspecific phylogeography: the mitochondrial bridge between population genetics and systematics. Ann. Rev. Ecol. Syst. 18 (1987) 489-522
3. Avise J.C., Reeb C.A., and Saunders N.C. Geographic population structure and species differences in mitochondrial DNA of mouthbrooding marine catfishes (Ariidae) and demersal spawning toadfishes (Batrachiodidae). Evolution 41 (1987) 991-1002
4. Avise J.C. Phylogeography (2000), Harvard University Press, Cambridge, MA
5. Bernardi G., Sordino P., and Powers D.A. Concordant mitochondrial and nuclear DNA phylogenies for populations of the teleost fish Fundulus heteroclitus. Proc. Natl. Acad. Sci. USA 90 (1993) 9271-9274
6. Briggs J.C. Marine Zoogeography (1974), McGraw-Hill, New York
7. Briggs J.C. Global Biogeography (1995), Elsevier, Amsterdam
8. Caudill C.C., and Bucklin A. Molecular phylogeography and evolutionary history of the estuarine copepod, Acartia tonsa, on the Northwest Atlantic coast. Hydrobiologia 511 (2004) 91-102
9. Collin R. The effects of mode of development on phylogeography and population structure of North Atlantic Crepidula (Gastropoda: Calyptraeidae). Mol. Ecol. 10 (2001) 2249-2262
10. Daiber F.C. Animals of the Tidal Marsh (1982), Van Nostrand Reinhold Company, New York, NY
11. Darling, J.D.S., 1976. Electrophoretic variation in Cyprinodon variegatus and systematics of some fishes of the subfamily Cyprinodontinae. Unpubl. M.S. thesis, Yale University, New Haven, Connecticut.
12. Echelle A.A., Carson E.W., Echelle A.F., Van Den Bussche R.A., Dowling T.E., and Meyer A. Historical biogeography of the New-World pupfish genus Cyprinodon (Teleostei: Cyprinodontidae). Copeia 2005 (2005) 320-339
13. Echelle A.A., Fuselier L., Van Den Bussche R.A., Rodriguez C.M.L., and Smith M.L. Molecular systematics of Hispaniolan pupfishes (Cyprinodontidae: Cyprinodon): implications for the biogeography of insular Caribbean fishes. Mol. Phylogenet. Evol. 39 (2006) 855-864
14. Elder J.F., and Turner B.J. Concerted evolution at the population level: pupfish hindIII satellite DNA sequences. Proc. Natl. Acad. Sci. USA 91 (1994) 994-998
15. Engle V.D., and Summers J.K. Latitudinal gradients in benthic community composition in Western Atlantic estuaries. J. Biogeogr. 26 (1999) 1007-1023
16. Finne, K.L., 2001. Phylogeographic structure of the Atlantic pupfish, Cyprinodon variegatus (Cyprinodontidae), along the eastern coast of North America. Unpubl. M.S. thesis, Virginia Polytechnic Institute and State University, Blacksburg, Virginia.
17. Fu Y.X. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics. 147 (1997) 915-925
18. Gonzalez-Villasenor L.I., and Powers D.A. Mitochondrial-DNA restriction-site polymorphisms in the teleost Fundulus heteroclitus support secondary intergradation. Evolution 44 (1990) 27-37
19. Gurgel C.F.D., Fredericq S., and Norris J.N. Phylogeography of Gracilaria tikvahiae (Gracilariaceae, Rhodophyta): a study of genetic discontinuity in a continuously distributed species based on molecular evidence. J. Phycol. 40 (2004) 748-758
20. Hall, T., 1999. Bioedit sequence alignment editor. Department of Microbiology, North Carolina State University. URL http://www.mbio.ncsu.edu/BioEdit/bioedit.html.
21. Hewitt G. The genetic legacy of the Quaternary ice ages. Nature. 405 (2000) 907-913
22. Holtmeier C.L. Heterochrony, maternal effects and phenotypic variation among sympatric pupfishes. Evolution 55 (2001) 330-338
23. Hrbek T., and Meyer A. Closing of the Tethys Sea and the phylogeny of Eurasian killifishes (Cyprinodontiformes: Cyprinodontidae). J. Evol. Biol. 16 (2003) 17-36
24. Hubbs C.L. Fishes of the Yucatan Peninsula. Carnegie Institution of Washington Publication 457 (1936) 157-287
25. Hudson R.R. A new statistic for detecting genetic differentiation. Genetics. 155 (2000) 2011-2014
26. Hudson R.R., Slatkin M., and Maddison W.P. Estimation of levels of gene flow from DNA sequence data. Genetics. 132 (1992) 583-589
27. Huelsenbeck J.P., and Ronquist F. MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17 (2001) 754-755
28. Kass R.E., and Raftery A.E. Bayes factors. Jour. Am. Stat. Assoc. 90 (1995) 773-795
29. Kelly D.W., MacIsaac H.J., and Heath D.D. Vicariance and dispersal effects on phylogeographic structure and speciation in a widespread estuarine invertebrate. Evolution 60 (2006) 257-267
30. Kuhner M.K., Yamato J., and Felsenstein J. Maximum likelihood estimation of population growth rates based on the coalescent. Genetics. 149 (1998) 429-434
31. Kumar S., Tamura K., Jakobsen I.B., and Nei M. MEGA2: Molecular Evolutionary Genetics Analysis software. Bioinformatics 17 (2001) 1244-1245
32. Lee W., Conroy J., Howell W.H., and Kocher T.D. Structure and evolution of teleost mitochondrial control region. J. Mol. Evol. 41 (1995) 54-66
33. Lee T., and O' Foighil D. Hidden Floridian biodiversity: mitochondrial and nuclear gene trees reveal four cryptic species within the scorched mussel, Brachidontes exustus, species complex. Mol. Ecol. 13 (2004) 3527-3542
34. McMillen-Jackson A.L., and Bert T.M. Disparate patterns of population genetic structure and population history in two sympatric penaeid shrimp species (Farfantepenaeus aztecus and Litopenaeus setiferus) in the eastern United States. Mol. Ecol. 12 (2003) 2895-2905
35. Miya M., and Nishida M. Organization of the mitochondrial genome of a deep-sea fish Gonostoma gracile (Teleostei: Stomiiformes): the first example of transfer RNA gene rearrangements in bony fishes. Mar. Biotechnol. 1 (1999) 416-426
36. Perdices A., Carmona J.A., Fernandez-Delgado C., and Doadrio I. Nuclear and mitochondrial data reveal high genetic divergence among Atlantic and Mediterranean populations of the Iberian killifish Aphanius iberus (Teleostei: Cyprinodontidae). Heredity. 87 (2001) 314-324
37. Posada D., and Crandall K.A. MODELTEST: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
38. Ramos-Onsins S.E., and Rozas J. Statistical properties of new neutrality tests against population growth. Mol. Biol. Evol. 19 (2002) 2092-2100
39. Reeb C.A., and Avise J.C. A genetic discontinuity in a continuously distributed species: mitochondrial DNA in the American Oyster, Crassostrea virginica. Genetics. 124 (1990) 397-406
40. Ronquist F., and Huelsenbeck J.P. MrBayes3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
41. Rozas J., and Rozas R. DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15 (1999) 174-175
42. Sanderson M.J. nonparametric approach to estimating divergence times in the absence of rate constancy. Mol. Biol. Evol. 14 (1997) 1218-1231
43. Smith M.W., Chapman R.W., and Powers D.A. Mitochondrial DNA analysis of Atlantic coast, Chesapeake Bay, and Delaware Bay populations of the teleost Fundulus heteroclitus indicates temporally unstable distributions over geologic time. Mol. Mar. Biol. Biotechnol. 7 (1998) 79-87
44. Swofford D.L. PAUP* Phylogenetic analysis using parsimony (*and other methods). Version 4.04b10 (1998), Sinauer Associates, Sunderland, Massachusetts
45. Turner B.J., and Liu R.K. Extensive interspecific genetic compatibility in the New World killifish genus Cyprinodon. Copeia 1977 (1977) 259-269
46. Wares J.P., and Cunningham C.W. Phylogeography and historical ecology of the North Atlantic intertidal. Evolution 55 (2001) 2455-2469
47. Watterson G.A. On the number of segregating sites in genetical models without recombination. Theor. Pop. Biol. 7 (1975) 256-276
48. Weinberg J.R., Dahlgren T.G., Trowbridge N., and Halanych K.M. Genetic differences within and between species of deep-sea crabs (Chaceon) from the North Atlantic Ocean. Biol. Bull. 204 (2003) 318-326
49. Young A.M., Torres C., Mack J.E., and Cunningham C.W. Morphological and genetic evidence for vicariance and refugium in Atlantic and Gulf of Mexico populations of the hermit crab Pagurus longicarpus. Mar. Biol. 140 (2002) 1059-1066