Placing the Floridian marine genetic disjunction into a regional evolutionary context using the scorched mussel, Brachidontes exustus, species complex

Evolution

Volumn 59, Issue 10, 2005, Pages 2139-2158

  Lee, Taehwan ^a   Foighil, Diarmaid Ó ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

Bivalvia; Caribbean; Cryptic species; Genetic disjunction; Phylogeny; Pseudocongruence

Indexed keywords

BIVALVE; CLADISTICS; CRYPSIS; PHYLOGENY;

ANIMAL; ARTICLE; ATLANTIC OCEAN; CENTRAL AMERICA; DNA SEQUENCE; GENETICS; GENOTYPE; GEOGRAPHY; MOLECULAR EVOLUTION; MYTILIDAE; PACIFIC OCEAN; PANAMA; PHYLOGENY; UNITED STATES;

ANIMALS; ATLANTIC OCEAN; CARIBBEAN REGION; EVOLUTION, MOLECULAR; FLORIDA; GENOTYPE; GEOGRAPHY; MYTILIDAE; PACIFIC OCEAN; PANAMA; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

BIVALVIA; HORMOMYA EXUSTUS;

EID: 27644451791     PISSN: 00143820     EISSN: None     Source Type: Journal    
DOI: 10.1554/05-193.1     Document Type: Article

References (114)

1. Abbott, R. T. 1960. The genus Strombus in the Indo-Pacific. Indo-Pac. Mollusca 1:33-146.
2. _. 1974. American seashells. Van Nostrand Reinhold, New York.
3. Abbott, R. T., and R. H. Jensen. 1967. Molluscan faunal changes around Bermuda. Science 155:687-688.
4. Avise, J. C. 1992. Molecular population structure and the biogeographic history of a regional fauna: a case history with lessons for conservation biology. Oikos 63:62-76.
5. _. 2000. Phylogeography: the history and formation of species. Harvard Univ. Press, Cambridge, MA.
6. Avise, J. C., C. A. Reeb, and N. C. Saunders. 1987. Geographic population structure and species differences in mitochondrial DNA of mouthbrooding marine catfishes (Ariidae) and demersal spawning toadfishes (Battrachoididae). Evolution 41:991-1002.
7. Barber, P. H., S. R. Palumbi, M. V. Erdmann, and M. K. Moosa. 2002. Sharp genetic breaks among populations of Haptosquilla pulchella (Stomatopoda) indicate limits to larval transport: patterns, causes and consequences. Mol. Ecol. 11:659-674.
8. Beerli, P., and J. Felsenstein. 2001. Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proc. Natl. Acad. Sci. USA 98:4563-4568.
9. Bert, T. M. 1986. Speciation in western Atlantic stone crabs (genus Menippe): the role of geological processes and climatic events in the formation and distribution of species. Mar. Biol. 93:157-170.
10. Bert, T. M., and W. S. Arnold. 1995. An empirical test of predictions of two competing models for the maintenance and fate of hybrid zones: both models are supported in a hard-clam hybrid zone. Evolution 49:276-289.
11. Bert, T. M., and R. G. Harrison. 1988. Hybridization in western Atlantic stone crabs (genus Menippe): evolutionary history and ecological context influence species interactions. Evolution 42:528-544.
12. Bieler, R., and P. M. Mikkelsen. 2004. Marine bivalves of the Florida Keys: a qualitative faunal analysis based on original collections, museum holdings and literature data. Malacologia 46:503-544.
13. Borsa, P., M. Naciri, L. Bahiri, L. Chikhi, F. J. García de León, G. Kotoulas, and F. Bonhomme. 1997. Infraspecific zoogeography of the Mediterranean: population genetic analysis on sixteen Atlanto-Mediterranean species (fishes and invertebrates). Vie Milieu 47:295-305.
14. Briggs, J. C. 1970. A faunal history of the North Atlantic Ocean. Syst. Zool. 19:19-34.
15. _. 1974. Marine zoogeography. McGraw Hill, New York.
16. Campos, B., and L. Ramorino. 1980: Larval and early benthic stages of Brachidontes granulata (Bivalvia: Mytilidae). Veliger 22:277-281.
17. Chase, M. R., R. J. Etter, M. A. Rex, and J. M. Quattro. 1998. Bathymetric patterns of genetic variation in a deep-sea proto-branch bivalve, Demninucula atacellana. Mar. Biol. 131:301-308.
18. Clement, M., D. Posada, and K. A. Crandall. 2000. TCS: a computer program to estimate gene genealogies. Mol. Ecol. 9:1657-1660.
19. Coan, E. V., P. V. Scott, and F. R. Bernard. 2000. Bivalve seashells of North America. Santa Barbara Museum of Natural History, Santa Barbara, CA.
20. 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.
21. Colborn, J., R. E. Crabtree, J. B. Shaklee, E. Pfeiler, and B. W. Bowen. 2001. The evolutionary enigma of bonefishes (Albula spp.): cryptic species and ancient separations in a globally distributed shorefish. Evolution 55:807-820.
22. Colin, P. L. 2003. Larvae retention: Genes or oceanography? Science 300:1657-1659.
23. Collin, R. 2001. The effects of mode of development on phylogeography and population structure of North Atlantic Crepidula (Gastropoda: Calyptraeidae). Mol. Ecol. 10:2249-2262.
24. _. 2002. Another last word on Crepidula convexa with a description of C. ustulatulina n. sp. (Gastropoda: Calyptraeidae) from the Gulf of Mexico and southern Florida. Bull. Mar. Sci. 70:177-184.
25. Collins, L. S. 1996. Environmental changes in Caribbean shallow waters relative to the closing tropical American seaway. Pp. 130-167 in J. B. Jackson, A. F. Budd, and A. G. Coates, eds. Evolution and environment in tropical America. Univ. of Chicago Press, Chicago.
26. Collins, T. M. 1996. Molecular comparisons of transisthmian species pairs: rates and patterns of evolution. Pp. 303-330 in J. B. Jackson, A. F. Budd, and A. G. Coates, eds. Evolution and environment in tropical America. Univ. of Chicago Press, Chicago.
27. Cowen, R. K., K. M. M. Lwiza, S. Sponaugle, C. B. Paris, and D. B. Olson. 2000. Connectivity of marine populations: Open or closed? Science 287:857-859.
28. Cronin, T. M. 1988. Evolution of marine climates of the US Atlantic coast during the past four million years. Philos. Trans. R. Soc. B. 318:661-678.
29. Cunningham, C. W., and T. M. Collins. 1994. Developing model systems for molecular biogeography: vicariance and interchange in marine invertebrates. Pp. 405-433 in B. Schierwater, B. Streit, G. P. Wagner, and R. DeSalle, eds. Molecular ecology and evolution: approaches and applications. Birkhauser Verlag, Basel, Switzerland.
30. _. 1998. Beyond area relationships: extinction and reclonization in molecular marine biogeography. Pp. 279-321 in R. DeSalle and B. Schierwater, eds. Molecular approaches to ecology and evolution. Birkhauser Verlag, Basel, Switzerland.
31. Cunningham, C. W., L. W. Buss, and C. W. Anderson. 1991. Molecular and geological evidence of shared history between hermit crabs and the symbiotic genus Hydractinia. Evolution 458:1301-1316.
32. Distel, D. L. 2000. Phylogenetic relationships among Mytilidae (Bivalvia): 18S rRNA data suggest convergence in mytilid body plans. Mol. Phylogenet. Evol. 15:25-33.
33. Droxler, A. W., K. Burke, A. D. Cunningham, A. C. Hine, E. Rosencrantx, D. Duncan, P. Hallock, and E. Robinson. 1998. Caribbean constraints on circulation between Atlantic and Pacific Oceans over the past 40 million years. Pp. 160-191 in T. Crowley and K. Burke, eds. Tectonic boundary conditions for climate reconstruction. Oxford Univ. Press, Oxford, U.K.
34. Duggins, C. F., A. A. Karlin, T. A. Mousseau, and K. G. Relyea. 1995. Analysis of a hybrid zone in Fundulus majalis in a northeastern Florida ecotone. Heredity 74:117-128.
35. Edwards, S., and P. Beerli. 2000. Gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution 54:1839-1854.
36. Excoffier, L., P. E. Smouse, and J. M. Quattro. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:45479-45491.
37. Farris, J. S., M. Källersjö, A. G. Kluge, and C. Bult. 1995. Testing significance of congruence. Cladistics 10:315-319.
38. Felder, D. L., and J. L. Staton. 1994. Genetic differentiation in the Gulf-Atlantic species complexes of Sesarma and Uca (Crustacea: Decapoda: Brachyura). J. Crustacean Biol. 14:191-209.
39. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 32:79-81.
40. _. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
41. Fields, A., and E. Moore. 1983. The larval biology of Brachidontes modiolus (Linné, 1767) Bivalvia: Mytilidae). Veliger 26:52-61.
42. Folmer, O., M. Black, W. Hoeh, R. Lutz, and R. Vrijenhork. 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol. 3:294-299.
43. Gold, J. R., and L. R. Richardson. 1998. Mitochondrial DNA diversification and population structure in fishes from the Gulf of Mexico and western Atlantic. J. Hered. 89:404-414.
44. Gopurenko, D., J. M. Hughes, and C. P. Keenan. 1999. Mitochondrial DNA evidence for rapid colonization of the Indo-West Pacific by the mudcrab Scylla serrata. Mar. Biol. 134:227-233.
45. Grosberg, R., and C. W. Cunningham. 2001. Genetic structure in the sea from populations to communities. Pp. 61-84 in M. D. Bertness, S. D. Gaines, and M. E. Hay, eds. Marine community ecology. Sinauer Associates, Sunderland, MA.
46. Hare, M. P., and J. C. Avise. 1996. Molecular genetic analysis of a stepped multilocus cline in the American oyster (Crassostrea virginica). Evolution 50:2305-2315.
47. _. 1998. Population structure in the American oyster as inferred by nuclear gene genealogies. Mol. Biol. Evol. 15:119-128.
48. Hare, M. P., S. A. Karl, and J. C. Avise. 1996. Anonymous nuclear DNA markers in the American oyster and their implications for the heterozygote deficiency phenonemon in marine bivalves. Mol. Biol. Evol. 13:334-345.
49. Hateley, J. G., and T. D. Sleeter. 1993. A biochemical genetic investigation of spiny lobster (Panulirus argus) stock replenishment in Bermuda. Bull. Mar. Sci. 52:993-1006.
50. Hillis, D. M., B. K. Mable, and C. Moritz. 1996. Applications of molecular systematics. Pp. 515-530 in D. M. Hillis, C. Moritz, and B. K. Mable, eds. Molecular systematics. 2nd ed. Sinauer Associates, Sunderland, MA.
51. Iturralde-Vinent, M. A., and R. D. E. MacPhee. 1999. Paleogeography of the Caribbean region: implications for Cenozoic biogeography. Bull. Am. Mus. Nat. Hist. 283:1-95.
52. Jackson, J. B. C. 1986. Modes of dispersal of clonal benthic invertebrates: consequences for species' distributions and genetic structure of local populations. Bull. Mar. Sci. 39:588-606.
53. Karl, S. A., and J. C. Avise. 1992. Balancing selection at allozyme loci in oysters: implications from nuclear RFLPs. Science 256:100-102.
54. Kirkendale, L. A., and C. P. Meyer. 2004. Phylogeography of the Patelloida profunda group (Gastropoda: Lottidae): diversification in a dispersal-driven marine system. Mol. Ecol. 13:2749-2762.
55. Kirkendale, L. A., T. Lee, P. Baker, and D. Ó Foighil. 2004. Oysters of the Conch Republic (Florida Keys): a molecular phylogenetic study of Parahyotissa mcgintyi, Teskeyostrea weberi and Ostreola equestris. Malacologia 46:309-326.
56. Knowlton, N. 2000. Molecular genetic analyses of species boundaries in the sea. Hydrobiologia 420:73-90.
57. 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.
58. Kuhner, M. K., J. Yamato, and J. Felsenstein. 1998. Maximum likelihood estimation of population growth rates based on the coalescent. Genetics 149:429-434.
59. Lacson, J. M. 1992. Minimal genetic variation among samples of six species of coral reef fishes collected at La Parguera, Puerto Rico, and Discovery Bay, Jamaica. Mar. Biol. 112:327-331.
60. Lavery, S., C. Moritz, and D. R. Fielder. 1996. Genetic patterns suggest exponential population growth in a declining species. Mol. Biol. Evol. 13:1106-1113.
61. Lee, T., and D. Ó Foighil. 2004. Hidden Floridian biodiversity: mitochondrial and nuclear gene trees reveal four cryptic species within the scorched mussel, Brachidontes exustus, species complex. Mol. Ecol. 13:3527-3542.
62. Lessios, H. A., B. D. Kessing, and J. S. Pearse. 2001. Phylogeography of the pantropical sea urchin Eucidaris in relation to land barriers and ocean currents. Evolution 53:955-975.
63. 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.
64. 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.
65. _. 2004. "What's larvae got to do with it?" Disparate patterns of post-glacial population structure in two benthic marine gastropods with identical dispersal potential. Mol. Ecol. 13:597-611.
66. Marshall, L. G. 1988. Land mammals and the Great American Interchange. Am. Sci. 76:380-388.
67. McDonald, J. H., B. C. Verrelli, and L. B. Geyer. 1996. Lack of geographic variation in anonymous nuclear polymorphisms in the American oyster, Crassostrea virginica. Mol. Biol. Evol. 13:1114-1118.
68. Meyer, C. P. 2003. Molecular systematics of cowries (Gastropoda: Cypraeidae) and diversification patterns in the tropics. Biol. J. Linn. Soc. 79:401-459.
69. Meyer, C. P., J. B. Geller, and G. Paulay. 2005. Fine scale endemism on coral reefs: archipelagic differentiation in turbinid gastropods. Evolution 59:113-125.
70. Mikkelsen, P. M., and R. Bieler. 2000. Marine bivalves of the Florida Keys: discovered biodiversity. Pp. 367-387 in E. M. Harper, J. D. Taylor, and J. A. Crame, eds. The evolutionary biology of the Bivalvia. Geological Society of London, Special Publication no. 177.
71. Mitton, J. B., C. J. Berg Jr.,and K. S. Orr. 1989. Population structure, larval dispersal, and gene flow in the queen conch, Strombus gigas, of the Caribbean. Biol. Bull. 177:356-362.
72. Mora, C., and P. F. Sale. 2002. Are populations of coral reef fish open or closed? Trends Ecol. Evol. 17:422-428.
73. Morton, B. 1988. The population dynamics and reproductive cycle of Brachidontes variabilis (Bivalvia: Mytilidae) in a Hong Kong mangrove. Malacol. Rev. 21:109-117.
74. Nei, M. 1987. Molecular evolutionary genetics. Columbia Univ. Press, New York.
75. Nei, M., and W.-H. Li. 1979. Mathematical model for studying genetic variation in terms of restriction endonuclease. Proc. Natl. Acad. Sci. USA 76:5269-5273.
76. Ó Foighil, D., T. J. Hilbish, and R. M. Showman. 1996. Mitochondrial gene variation in Mercenaria clam sibling species reveals a relict secondary contact zone in the western Gulf of Mexico. Mar. Biol. 126:675-683.
77. Palumbi, S. R. 1994. Genetic divergence, reproductive isolation, and marine speciation. Annu. Rev. Ecol. Syst. 25:547-572.
78. _. 1996. Nucleic acids. II. The polymerase chain reaction. Pp. 205-247 in D. M. Hillis, C. Moritz, and B. K. Mable, eds. Molecular systematics. 2nd ed. Sinauer Associates, Sunderland, MA.
79. Park, J.-K., and D. Ó Foighil. 2000. Sphaeriid and corbiculid clams represent separate heterodont bivalve radiations into freshwater environments. Mol. Phylogenet. Evol. 14:75-88.
80. Paulay, G., and C. Meyer. 2002. Diversification in the tropical Pacific: comparisons between marine and terrestrial systems and the importance of founder speciation. Integr. Comp. Biol. 42:922-934.
81. Pielou, E. C. 1991. After the ice age. Univ. of Chicago Press, Chicago.
82. Posada, D., and K. A. Crandall. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817-818.
83. Quesada, H., D. A. G. Skibinski, and D. O. F. Skibinski. 1996. Sex-biased heteroplasmy and mitochondrial DNA inheritance in the mussel Mytilus galloprovincialis Lmk. Curr. Genet. 29:423-426.
84. Randazzo, A. F., and D. S. Jones. 1997. The geology of Florida. Univ. Press of Florida, Gainesville.
85. Rawson, P. D., and T. J. Hilbish. 1995. Evolutionary relationships among the male and female mitochondrial DNA lineages in the Mytilus edulis species complex. Mol. Biol. Evol. 12:893-901.
86. Reeb, C. A., and J. C. Avise. 1990. A genetic discontinuity in a continuously distributed species: mitochondrial DNA in the American oyster, Crassostrea virginica. Genetics 124:397-406.
87. Richards, H. G., R. T. Abbott, and T. Skymer. 1969. The marine Pleistocene mollusks of Bermuda. Not. Nat. 425:1-10.
88. Rocha, L. A., A. L. Bass, D. R. Robertson, and B. W. Bowen. 2002. Adult habitat preferences, larval dispersal, and the comparative phylogeography of three Atlantic surgeonfishes (Teleostei: Acanthuridae). Mol. Ecol. 11:243-252.
89. Rocha, L. A., D. R. Robertson, J. Roman, and B. W. Bowen. 2005. Ecological speciation in tropical reef fishes. Proc. R. Soc. B 272:573-579.
90. Ronquist, F., and J. P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
91. Sarver, S. K., M. C. Landrum, and D. W. Foltz. 1992. Genetics and taxonomy of ribbed mussels (Geukensia spp.). Mar. Biol. 113:385-390.
92. Saunders, N. C., L. G. Kessler, and J. C. Avise. 1986. Genetic variation and geographic differentiation in mitochondrial DNA of the horseshoe crab, Limulus polyphemus. Genetics 112:613-627.
93. Schizas, N. V., G. T. Street, B. C. Coul, G. T. Chandler, and J. M. Quattro. 1999. Molecular population structure of the marine benthic copepod Microarthridion littorale along the southeastern and Gulf coasts of the USA. Mar. Biol. 135:399-405.
94. Schneider, S., D. Roessli, and L. Excoffier. 2000. Arlequin: a software for population genetics data analysis. Ver. 2.000. Genetics and Biometry Laboratory, University of Geneva, Switzerland.
95. Shulman, M. J., and E. Bermingham. 1995. Early life histories, ocean currents, and the population genetics of Caribbean reef fishes. Evolution 49:897-910.
96. Sterrer, W. 1986. Marine fauna and flora of Bermuda. Wiley and Sons, New York.
97. _. 1998. How many species are there in Bermuda? Bull. Mar. Sci. 62:809-840.
98. Swofford, D. L. 2003. PAUP*: phylogenetic analysis using parsimony (*and other methods). Ver. 4. Sinauer Associates, Sunderland, MA.
99. Tajima, F. 1983. Evolutioanry relationship of DNA sequences in finite populations. Genetics 105:437-460.
100. _. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595.
101. Taylor, M. S., and M. E. Hellberg. 2003a. Genetic evidence for local retention of pelagic larvae in a Caribbean reef fish. Science 299:107-109.
102. _. 2003b. Larvae retention: Genes or oceanography? Science 300:1657-1659.
103. Templeton, A. R., K. A. Crandall, and C. F. Sing. 1992. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics 132:619-633.
104. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The CLUSTAL X window interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876-4882.
105. Thorpe, J. P., A. M. Sole-Cava, and P. C. Watts. 2000. Exploited marine invertebrates: genetics and fisheries. Hydrobiologia 420:165-184.
106. Vermeij, G. J. 1987. The dispersal barrier in the tropical Pacific: implications for molluscan speciation and extinction. Evolution 41:1046-1058.
107. _. 2001. Distribution, history, and taxonomy of the Thais clade (Gastropoda: Muricidae) in the Neogene of tropical America. J. Paleontol. 75:697-705.
108. Wares, J. P. 2002. Community genetics in the northwestern Atlantic intertidal. Mol. Ecol. 11:1131-1144.
109. Wares, J. P., and C. W. Cunningham. 2001. Phylogeography and historical ecology of the North Atlantic intertidal. Evolution 55:2455-2469.
110. Warner, R. R., and S. R. Palumbi. 2003. Larvae retention: Genes or oceanography? Science 300:1657-1659.
111. Webb, S. D. 1990. Historical biogeography. Pp. 70-100 in R. I. Myers and J. J. Ewel, eds. Ecosystems of Florida. Univ. of Central Florida Press, Orlando.
112. White, L. R., B. A. McPherson, and J. R. Stauffer. 1996. Molecular genetic identification tools for the unionids of French Creek, Pennsylvania. Malacologia 38:181-202.
113. Williams, D., D. Dunkerley, P. DeDekker, P. Kershaw, and M. Chappel. 1998. Quaternary environments. Arnold, London.
114. Williams, S. T., and D. G. Reid. 2004. Speciation and diversity on tropical rocky shores: a global phylogeny of snails of the genus Echinolittorina. Evolution 58:2227-2251.