Population structure of the dusky pipefish (Syngnathus floridae) from the Atlantic and Gulf of Mexico, as revealed by mitochondrial DNA and microsatellite analyses

Journal of Biogeography

Volumn 37, Issue 7, 2010, Pages 1363-1377

  Mobley, Kenyon B ^a   Small, Clayton M ^a   Jue, Nathaniel K ^b   Jones, Adam G ^a  

^a TEXAS A AND M UNIVERSITY   (United States)

^b FLORIDA STATE UNIVERSITY   (United States)

Author keywords

Atlantic Ocean; Biogeographical barriers; Control region; Cytochrome b; Gulf of Mexico; Microsatellites; Phylogeography; Pipefish; Population genetics; Syngnathus floridae

Indexed keywords

BAYESIAN ANALYSIS; CLUSTER ANALYSIS; CYTOCHROME; FISH; GENE EXPRESSION; GENE FLOW; GENETIC DIFFERENTIATION; GENETIC MARKER; LIFE HISTORY TRAIT; MIGRATION; MITOCHONDRIAL DNA; MOLECULAR ANALYSIS; NUMERICAL MODEL; PHYLOGENETICS; PHYLOGEOGRAPHY; PLEISTOCENE; POPULATION STRUCTURE; RANGE EXPANSION;

ATLANTIC COAST [NORTH AMERICA]; ATLANTIC OCEAN; GULF OF MEXICO;

SYNGNATHUS FLORIDAE;

EID: 77954779932     PISSN: 03050270     EISSN: 13652699     Source Type: Journal    
DOI: 10.1111/j.1365-2699.2010.02288.x     Document Type: Article

References (72)

1. Avise JC. Molecular population structure and the biogeographic history of a regional fauna: a case-history with lessons for conservation biology. Oikos 1992, 63:62-76.
2. Avise JC. Phylogeography: the history and formation of species 2000, Harvard University Press, Cambridge, MA
3. Avise JC, Jones AG, Walker D, Dewoody JA. Genetic mating systems and reproductive natural histories of fishes: lessons for ecology and evolution. Annual Review of Genetics 2002, 36:19-45.
4. Bagley MJ, Lindquist DG, Geller JB. Microsatellite variation, effective population size, and population genetic structure of vermilion snapper, Rhomboplites aurorubens, off the southeastern USA. Marine Biology 1999, 134:609-620.
5. Beerli P. Comparison of Bayesian and maximum-likelihood inference of population genetic parameters. Bioinformatics 2006, 22:341-345.
6. Beerli P. MIGRATE v.3.0: a maximum likelihood and Bayesian estimator of gene flow using the coalescent 2008, http://popgen.sc.fsu.edu/Migrate-n.html, Available at:
7. Bernatchez L, Wilson CC. Comparative phylogeography of Nearctic and Palearctic fishes. Molecular Ecology 1998, 7:431-452.
8. Bowen BW, Avise JC. Genetic structure of Atlantic and Gulf of Mexico populations of sea bass, menhaden, and sturgeon: influence of zoogeographic factors and life-history patterns. Marine Biology 1990, 107:371-381.
9. Bowen BW, Bass AL, Rocha LA, Grant WS, Robertson DR. Phylogeography of the trumpetfish (Aulostomus spp.): ring species complex on a global scale. Evolution 2001, 55:1029-1039.
10. Bowen BW, Muss A, Rocha LA, Grant WS. Shallow mtDNA coalescence in Atlantic pygmy angelfishes (genus Centropyge) indicates a recent invasion from the Indian Ocean. Journal of Heredity 2006, 96:1-12.
11. Briggs JC. Marine zoogeography 1974, McGraw-Hill, New York
12. Brown J. A comparative life history study of four species of pipefishes (family Syngnathidae) in Florida 1972, PhD Thesis, University of Florida, Gainesville, FL
13. Buonaccorsi VP, Starkey E, Graves JE. Mitochondrial and nuclear DNA analysis of population subdivision among young-of-the-year Spanish mackerel (Scomberomorus maculatus) from the western Atlantic and Gulf of Mexico. Marine Biology 2001, 138:37-45.
14. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Research 2003, 31:3497-3500.
15. Chenoweth SF, Hughes JM, Connolly RC. Phylogeography of the pipefish, Urocampus carinirostris, suggests secondary intergradation of ancient lineages. Marine Biology 2002, 141:541-547.
16. Clement M, Posada D, Crandall KA. TCS: a computer program to estimate gene genealogies. Molecular Ecology 2000, 9:1657-1659.
17. Craig MT, Hastings PA, Pondella DJI, Robertson DR, Rosales-Casian JA. Phylogeography of the flag cabrilla Epinephelus labriformis (Serranidae): implications for the biogeography of the Tropical Eastern Pacific and the early stages of speciation in a marine shore fish. Journal of Biogeography 2006, 33:969-979.
18. Cunningham CW, Buss LW, Anderson CW. Molecular and geological evidence of shared history between hermit crabs and their symbiotic genus Hydractinia. Evolution 1991, 45:1301-1316.
19. Dawson CE. Fishes of the Western North Atlantic, Part 8, Order Gasterosteiformes, Suborder Syngnathoidei 1982, Sears Foundation for Marine Research, Yale University, New Haven, CT
20. Evanno G, Regnaut S, Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 2005, 14:2611-2620.
21. Excoffier L, Smouse PE, Quattro JM. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 1992, 131:479-491.
22. Fu YX. Statistical tests of neutrality of mutations against population growth, hitchhiking and backgroud selection. Genetics 1997, 147:915-925.
23. Gold JR, Richardson LR. Mitochondrial DNA diversification and population structure in fishes from the Gulf of Mexico and western Atlantic. Journal of Heredity 1998, 89:404-414.
24. Gold JR, Pak E, Devries DA. Population structure of king mackerel (Scomberomorus cavalla) around peninsular Florida, as revealed by microsatellite DNA. Fishery Bulletin 2002, 100:491-509.
25. Grant WS, Bowen BW. Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation. Journal of Heredity 1998, 89:415-426.
26. Guindon S, Lethiec F, Duroux P, Gascuel O. PHYML Online - a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Research 2005, 33:W557-W559.
27. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium 1999, 41:95-98.
28. Hardy OJ, Vekemans X. SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Molecular Ecology Notes 2002, 2:618-620.
29. Hardy OJ, Charbonnel N, Freville H, Heuertz M. Microsatellite allele sizes: a simple test to assess their significance on genetic differentiation. Genetics 2003, 163:1467-1482.
30. Herald ES. Studies on the Atlantic American pipefishes with descriptions of new species. Proceedings of the California Academy of Sciences 1965, 32:363-375.
31. Jones AG, Avise JC. Polygynandry in the dusky pipefish Syngnathus floridae revealed by microsatellite DNA markers. Evolution 1997a, 51:1611-1622.
32. Jones AG, Avise JC. Microsatellite analysis of maternity and the mating system in the Gulf pipefish Syngnathus scovelli, a species with male pregnancy and sex-role reversal. Molecular Ecology 1997b, 6:203-213.
33. Jones AG, Rosenqvist G, Berglund A, Avise JC. The genetic mating system of a sex-role-reversed pipefish (Syngnathus typhle): a molecular inquiry. Behavioral Ecology and Sociobiology 1999, 46:357-365.
34. Keeney DB, Heupel MR, Hueter RE, Heist EJ. Microsatellite and mitochondrial DNA analyses of the genetic structure of blacktip shark (Carcharhinus limbatus) nurseries in the northwestern Atlantic, Gulf of Mexico, and Caribbean Sea. Molecular Ecology 2005, 14:1911-1923.
35. Kocher TD, K TW, Meyer A, Edwards SV, Pääbo S, Villablan CA, Villablan FX, Wilson AC. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proceedings of the National Academy of Sciences USA 1989, 74:5436-5467.
36. Lee T, Ó Foighil D. Placing the Floridian marine genetic disjunction into a regional evolutionary context using the scorched mussel, Brachidontes exustus, species complex. Evolution 2005, 59:2139-2158.
37. Livingstone RJ. Trophic organization of fishes in a coastal seagrass system. Marine Ecology Progress Series 1982, 7:1-12.
38. Lourie SA, Vincent ACJ. A marine fish follows Wallace's Line: the phylogeography of the three-spot seahorse (Hippocampus trimaculatus, Syngnathidae, Teleostei) in Southeast Asia. Journal of Biogeography 2004, 31:1975-1985.
39. Mercer LP. The comparative ecology of two species of pipefish (Syngnathidae) in the York River, Virginia 1973, The College of William and Mary, Williamsburg, VA
40. Meyer A, Kocher TD, Basasibwaki P, Wilson AC. Monophyletic origin of Lake Victoria cichlid fishes suggested by mitochondrial DNA sequences. Nature 1990, 347:550-553.
41. Mobley KB, Jones AG. Geographical variation in the mating system of the dusky pipefish (Syngnathus floridae). Molecular Ecology 2007, 16:2596-2606.
42. Mobley KB, Jones AG. Environmental, demographic and genetic mating system variation among five geographically distinct dusky pipefish (Syngnathus floridae) populations. Molecular Ecology 2009, 18:1476-1490.
43. Nei M, Tajima F, Tateno Y. Accuracy of estimated phylogenetic trees from molecular data. Journal of Molecular Evolution 1983, 19:153-170.
44. Olsen JL, Stam WT, Coyer JA, Reusch TBH, Billingham M, Bostrom C, Clavert E, Cristie H, Granger S, La Lumiere R, Milchakova N, Oudot-Lesecq M, Procaccini G, Sanjabi B, Serrao E, Veldsink J, Widdicombe S, Wyllie-Echeverria S. North Atlantic phylogeography and large-scale population differentiation of the seagrass Zostera marina L. Molecular Ecology 2004, 13:1923-1941.
45. Ota T. DISPAN: genetic distance and phylogenetic analysis 1993, http://homes.bio.psu.edu/people/Faculty/Nei/Lab/Programs.html, Available at: (accessed December 2007
46. Pääbo S, Thomas WK, Whitfield KM, Kumazawa Y, Wilson AC. Rearrangements of mitochondrial transfer RNA genes in marsupials. Journal of Molecular Evolution 1991, 33:426-430.
47. Page RDM. TreeView v1.4 1997, http://taxonomy.zoology.gla.ac.uk/rod/rod.html, Available at:
48. Palumbi SR. Genetic divergence, reproductive isolation, and marine speciation. Annual Review of Ecology and Systematics 1994, 25:547-572.
49. Piry S, Luikart JL, Cornuet JM. BOTTLENECK: a computer program for detecting recent reduction in the effective size using allele frequency data. Journal of Heredity 1999, 90:502-503.
50. Posada D. COLLAPSE 2007, http://darwin.uvigo.es, Available at: (accessed March 2007
51. Posada D, Crandall KA. MODELTEST: testing the model of DNA substitution. Bioinformatics 1998, 14:817-818.
52. Prichard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics 2000, 155:945-959.
53. Raymond M, Rousset F. GENEPOP v1.2: population genetics software for exact tests and ecumenicism. Journal of Heredity 1995, 86:248-249.
54. Reeb CA, Avise JC. A genetic discontinuity in a continuously distributed species: mitochondrial DNA in the American oyster, Crassostrea virginica. Genetics 1990, 124:397-406.
55. Rice WR. Analyzing tables of statistical tests. Evolution 1989, 43:223-225.
56. Rocha-Olivares A, Garber NM, Stuck KC. High genetic diversity, large inter-oceanic divergence and historical demography of the striped mullet. Journal of Fish Biology 2000, 57:1134-1149.
57. Rogers AR, Harpending H. Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution 1992, 9:552-569.
58. Saillant E, Gold JR. Population structure and variance effective size of red snapper (Lutjanus campechanus) in the northern Gulf of Mexico. Fishery Bulletin 2006, 104:136-148.
59. Schneider S, Roessli D, Excoffier L. ARLEQUIN v2.1: an integrated software for population genetics data analysis 2000, Genetics and Biometry Laboratory, Department of Anthropology, University of Geneva, Geneva
60. Shokri MR, Gladstone W, Jelbart J. The effectiveness of seahorses and pipefish (Pisces: Syngnathidae) as a flagship group to evaluate the conservation value of estuarine seagrass beds. Aquatic Conservation: Marine and Freshwater Ecosystems 2009, 19:588-595.
61. Short F, Carruthers T, Dennison W, Waycott M. Global seagrass distribution and diversity: a bioregional model. Journal of Experimental Marine Biology and Ecology 2007, 350:3-20.
62. Slatkin M. Gene flow and the geographic structure of natural populations. Science 1987, 236:787-792.
63. Soltis DE, Morris AB, McLachlan JS, Manos PS, Soltis PS. Comparative phylogeography of unglaciated eastern North America. Molecular Ecology 2006, 15:4261-4293.
64. Swofford DL. PAUP*. Phylogenetic analysis using parsimony (*and other methods) 2003, Sinauer Associates, Sunderland, MA
65. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 1989a, 123:585-595.
66. Tajima F. The effect of change in population size on DNA polymorphism. Genetics 1989b, 123:597-601.
67. Teske PR, Cherry MI, Matthee CA. Population genetics of the endangered Knysna seahorse, Hippocampus capensis. Molecular Ecology 2003, 12:1703-1715.
68. Teske PR, Hamilton H, Palsboll PJ, Choo CK, Gabr H, Lourie SA, Santos M, Sreepada A, Cherry MI, Matthee CA. Molecular evidence for long-distance colonization in an Indo-Pacific seahorse lineage. Marine Ecology - Progress Series 2005, 286:249-260.
69. Wares JP, Cunningham CW. Phylogeography and historical ecology of the North Atlantic intertidal. Evolution 2001, 55:2455-2469.
70. Waycott M, Duarte CM, Carruthers TJB, Orth RJ, Dennison WC, Olyarnik S, Calladine A, Fourqurean JW, Heck KL, Hughes AR, Kendrick GA, Kenworthy WJ, Short FT, Williams SL. Accelerating loss of seagrasses across the globe threatens coastal ecosystems. Proceedings of the National Academy of Sciences USA 2009, 106:12377-12381.
71. Wilson AB. Genetic signature of recent glaciation on populations of a near-shore marine fish species (Syngnathus leptorhynchus). Molecular Ecology 2006, 15:1857-1871.
72. Wilson AB, Vincent A, Ahnesjö I, Meyer A. Male pregnancy in seahorses and pipefishes (Family Syngnathidae): rapid diversification of paternal brood pouch morphology inferred from a molecular phylogeny. Journal of Heredity 2001, 92:159-166.