Phylogenetic relationships of tropical eastern Pacific snappers (Lutjanidae) inferred from mitochondrial DNA sequences

Systematics and Biodiversity

Volumn 13, Issue 6, 2015, Pages 916-927

  Gold, J R ^a   Willis, S C ^a   Renshaw, M A ^b   Buentello, A ^c   Walker, H J ^d   Puritz, J B ^a   Hollenbeck, C M ^a   Voelker, G ^e  

^a TEXAS A AND M UNIVERSITY CORPUS CHRISTI   (United States)

^b UNIVERSITY OF NOTRE DAME   (United States)

^c Schillinger Genetics and Navita Premium Feed Ingredients   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e TEXAS A AND M UNIVERSITY   (United States)

Author keywords

dispersal; Isthmus of Panama; Lutjanidae; phylogenetics; phylogeography

Indexed keywords

EID: 84949088688     PISSN: 14772000     EISSN: 14780933     Source Type: Journal    
DOI: 10.1080/14772000.2015.1078857     Document Type: Article

References (78)

1. Allen, G. R. (1985). Snappers of the world: An annotated and illustrated catalogue of lutjanid species known to date. In FAO Fisheries Synopsis No. 125 (vol. 6, pp. 1-208). Rome: Food and Agriculture Organization of the United States.
2. Bacon, C. D., Silvestrob, D., Jaramilloa, C., Smith, B. T., Chakrabarty, P., & Antonelli, A. (2015). Biological evidence supports an early and complex emergence of the Isthmus of Panama. In Proceedings of the National Academy of Sciences USA, http://www.pnas.org/content/112/19/6110.full.pdf (accessed 15 May 2015).
3. Banford, H. M., Bermingham, E., & Collette, B. B. (2004). Molecular phylogenetics and biogeography of transisthmian and amphi-Atlantic needlefishes (Belonidae: Strongylura and Tylosurus): Perspectives on New World marine speciation. Molecular Phylogenetics and Evolution, 31, 833-851.
4. Banford, H. M., Bermingham, E., Collette, B. B., & McCafferty, S. S. (1999). Phylogenetic systematics of the Scomberomorus regalis (Teleostei: Scombridae) species group: Molecules, morphology and biogeography of Spanish mackerels. Copeia, 1999, 596-613.
5. Bartoli, G., Sarnthein, M., Weinelt, M., Erlenkeuser, H., Garbe-Schönberg, D., & Lea, D. W. (2005). Final closure of Panama and the onset of northern hemisphere glaciation. Earth and Planetary Science Letters, 237, 33-44.
6. Bermingham, E., McCafferty, S. S., & Martin, A. P. (1997). Fish biogeography and molecular clocks: Perspectives from the Panamanian Isthmus. In T. D. Kocher, & C. A. Stepien (Eds.), Molecular systematics of fishes (pp. 113-128). San Diego, CA: Academic Press.
7. Betancur, R. R., Broughton, R. E., Wiley, E. O., Carpenter, K., López, J. A., Li, C., ⋯, Ortí, G. (2013). The tree of life and a new classification of bony fishes. Public Library of Science Currents Tree of Life Edition, 1. doi:10.1371/currents. tol.53ba26640df0ccaee75bb165c8c26288
8. Blaber, S. J. M., Dichmont, C. M., Buckworth, R. C., Badrudin, Sumiono, B., Nurhakim, S., Iskandar, B., Fegan, B., ⋯ Salini, J. P. (2005). Shared stocks of snappers (Lutjanidae) in Australia and Indonesia: Integrating biology, population dynamics and socio-economics to examine management scenarios. Reviews in Fish Biology and Fisheries, 15, 111-127.
9. Brandley, M. C., Schmitz, A., & Reeder, T. W. (2005). Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards. Systematic Biology, 54, 373-390.
10. Brasier, M. D. (1975). An outline history of seagrass communities. Paleontology, 18, 681-702.
11. Chu, C., Rizman-Idid, M., & Ching, C. V. (2013). Phylogenetic relationships of selected genera of Lutjanidae inferred from mitochondrial regions, with a note on the taxonomic status of Pinjalo pinjalo. Ciencias Marinas, 39, 349-361.
12. Coates, A. G., Collins, L. S., Aubry, M. P., & Berggren, W. A. (2004). The geology of the Darien, Panama, and the Miocene-Pliocene collision of the Panama arc with northwestern South America. Geological Society of America Bulletin, 116, 1327-1344.
13. Coleman, F. C., Koenig, C. C., Huntsman, G. R., Musick, J. A., Eklund, A. M., McGovern, J., ⋯ Grimes, C. B. (2000). Long-lived reef fishes: The grouper-snapper complex. Fisheries, 25, 14-21.
14. Collins, L. S., Budd, A. F., & Coates, A. G. (1996). Earliest evolution associated with closure of the Tropical American Seaway. Proceedings of the National Academy of Sciences USA, 93, 6069-6072.
15. Collins, L. S., Coates, A. G., Berggren, W. A., Aubry, M-P., & Zhang, J. (1996). The late Miocene Panama isthmian strait. Geology, 24, 687-690.
16. Cowman, P. F., & Bellwood, D. R. (2011). Coral reefs as drivers of cladogenesis: Expanding coral reefs, cryptic extinction events, and the development of biodiversity hotspots. Journal of Evolutionary Biology, 24, 2543-2562.
17. Cronin, T. M. (2011). Geographical isolation in marine species: Evolution and speciation in Ostracoda, I. In N. Ikeya, K. Ishizaki, & T. Hanai (Eds.), Evolutionary biology of Ostracoda: Its fundamentals and applications (pp. 871-889). Amsterdam: Elsevier.
18. Dayton, P. K., Thrush, S. F., Agardy, M. T., & Hofman, R. J. (1995). Environmental effects of marine fishing. Aquatic Conservation: Marine and Freshwater Ecosystems, 5, 205-232.
19. Domning, D. P. (2001). Sirenians, seagrasses, and Cenozoic ecological change in the Caribbean. Palaeogeography, Palaeoclimatology, Palaeoecology, 166, 27-50.
20. Duque-Caro, H. (1990). Neogene stratigraphy, paleoceanography and paleobiology in northwest South America and the evolution of the Panama Seaway. Paleogeography, Paleoclimatology, and Paleoecology, 77, 203-234.
21. Eschmeyer, W. N., & Fong, J. D. (2015). Species by family/subfamily in the Catalog of Fishes. http://researcharchive.calaca demy.org/research/ichthyology/catalog/SpeciesByFamily. asp (accessed 13 May 2015).
22. Fisher-Reid, M. C., & Wiens, J. J. (2011). What are the consequences of combining nuclear and mitochondrial data for phylogenetic analysis? Lessons from Plethodon salamanders and 13 other vertebrate clades. Bio Med Central Evolutionary Biology, 11, 300.
23. Gaither, M. R., Toonen, R. J., Robertson, D. R., Planes, S., & Bowen, B. W. (2010). Genetic evaluation of marine biogeographical barriers: Perspectives from two widespread Indo-Pacific snappers (Lutjanus kasmira and Lutjanus fulvus). Journal of Biogeography, 37, 133-147.
24. Glynn, P. W. (1972). Observations on the ecology of the Caribbean and Pacific coasts of Panama. Bulletin of the Biological Society of Washington, 2, 13-30.
25. Gold, J. R., Voelker, G., & Renshaw, M. A. (2011). Phylogenetic relationships of tropical western Atlantic snappers in Subfamily Lutjaninae (Lutjanidae; Perciformes) inferred from mitochondrial DNA sequences. Biological Journal of the Linnean Society, 102, 915-929.
26. Gomes, G., Sampaio, I., & Schneider, H. (2012). Population structure of Lutjanus purpureus (Lutjanidae - Perciformes) on the Brazilian coast: Further existence evidence of a single species of red snapper in the western Atlantic. Anais da Academia Brasileira de Ciências, 84, Retrieved from http://dx. doi.org/10.1590/S0001-37652012000400013 (accessed 15 May 2015).
27. Gomes, G., Santos, S., Vallinoto, M., Schneider, H., Orti, G., & Sampaio, I. (2008). Can Lutjanus purpureus (south red snapper) be "legally" considered a red snapper (Lutjanus campechanus)? Genetics and Molecular Biology, 31, 372-376.
28. Guindon, S., Dufayard, J. F., Lefort, V., Anisimova, M., Hordijk, W., & Gascuel, O. (2010). New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0. Systematic Biology, 59, 307-321, 2010.
29. Hasegawa, M., Kishino, H., & Yano, T. (1985). Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution, 22, 160-174.
30. Hastings, P. A., Walker, H. J. Jr., & Galland, G. R. (2014). Fishes: A guide to their diversity. Oakland, CA: University of California Press.
31. Haug, G. H., Tiedemann, R., Zahn, R., & Ravelo, A. C. (2001). Role of Panama uplift on oceanic freshwater balance. Geology, 29, 207-210.
32. Ho, S. Y. W. (2009). An examination of phylogenetic models of substitution rate variation among lineages. Biology Letters, 5, 421-424.
33. Ho, S. (2008). The molecular clock and estimating species divergence. Nature Education, 1, 168.
34. Ivany, L. C., Patterson, W. P., & Lohmann, K. C. (2000). Cooler winters as a possible cause of mass extinctions at the Eocene/Oligocene boundary. Nature, 407, 887-890.
35. Jackson, J. B. C., & Herrera Cubilla, A. (2000). Adaptation and constraint as determinants of zooid and ovicell size among encrusting ascophoran cheilostome Bryozoa from opposite sides of the Isthmus of Panama. In A. Herrera, J. B. C., & Cubilla, & J. B. C.. Jackson (Eds.), Proceedings of the 11th international bryozoology association conference (pp. 249-258). Balboa, Republic of Panama: Smithsonian Tropical Research Institute.
36. Jackson, J. B. C., Jung, P., Coates, A. G., & Collins, L. S. (1993). Diversity and extinction of tropical American mollusks and emergence of the Isthmus of Panama. Science, 260, 1624-1626.
37. Jackson, J. B. C., & O'Dea, A. (2013). Timing of the oceanographic and biological isolation of the Caribbean Sea from the tropical eastern Pacific Ocean. Bulletin of Marine Science, 89, 779-800.
38. Johnson, G. D. (1980). The limits and relationships of the Lutjanidae and associated families. Bulletin of the Scripps Institution of Oceanography, 24, 1-114.
39. Johnson, G. D. (1993). Percomorph phylogeny: Progress and problems. Bulletin of Marine Science, 52, 3-28.
40. Jordan, D. S. (1908). The Law of geminate species. American Naturalist, 42, 73-80.
41. Keller, G., & Barron, J. A. (1983). Paleoceanographic implications of Miocene deep-sea hiatuses. Geological Society of America Bulletin, 94, 590-613.
42. Lanfear, R., Welch, J. J., & Bromham, L. (2010). Watching the clock: Studying variation in rates of molecular evolution between species. Trends in Ecology and Evolution, 25, 495-503.
43. Larkum, A. W. D., & den Hartog, C. (1989). Evolution and biogeography of seagrasses. In A. W. D. Larkum, A. J. McComb, & S. A. Shepherd (Eds.), Biology of seagrasses: A treatise on the biology of seagrasses with special reference to the Australian region (pp. 112-156). Amsterdam: Elsevier.
44. Leigh, E. G., O'Deal, A., & Vermeij, G. J. (2014). Historical biogeography of the Isthmus of Panama. Biological Reviews, 89, 148-172.
45. Leis, J. M. (1987). Review of early like history of tropical groupers (Serranidae) and snapper (Lutjanidae). In J. Polovina, & S. Ralston (Eds.), Tropical snappers and groupers: Biology and fisheries management (pp. 189-237). Boulder, CO: Westview Press.
46. Leis, J. M. (2005). A larva of the eteline lutjanid, Randallichthys filamentosus (Pisces: Perciformes), with comments on phylogenetic implications of larval morphology of basal lutjanids. Zootaxa, 1008, 57-64.
47. Lessios, H. A. (1990). Adaptation and phylogeny as determinants of egg size in echinoderms from the two sides of the Isthmus of Panama. American Naturalist, 135, 1-13.
48. Lessios, H. A., & Weinberg, J. R. (1994). Genetic and morphological divergence of the isopod Excirolana on the two sides of the Isthmus of Panama. Evolution, 48, 530-548.
49. Maddison, W. P., & Maddison, D. R. (2001). Mesquite: A modular system for evolutionary analysis. Version 0.98. Retrieved from http://mesquiteproject.org (accessed 15 May 2015).
50. Marko, P. B., & Jackson, J. B. C. (2001). Patterns of morphological diversity among and within arcid bivalve species pairs separated by the Isthmus of Panama. Journal of Paleontology, 75, 590-606.
51. Mayr, E. (1970). Populations, species, and evolution. Cambridge, MA: Harvard University Press.
52. Mihaljević, M., Renema, W., Welsh, K., & Pandolfi, J. M. (2014). Eocene-Miocene shallow-water carbonate platforms and increased habitat diversity in Sarawak, Malaysia. Palaios, 29, 378-391.
53. Miller, K. G., Fairbanks, R. G., & Mountain, G. S. (1987). Tertiary oxygen isotope synthesis, sea level history, and continental margin erosion. Paleoceanography, 2, 1-19.
54. Miller, T. L., & Cribb, T. H. (2007). Phylogenetic relationships of some common Indo-Pacific snappers (Perciformes: Lutjanidae) based on mitochondrial DNA sequences, with comments on the taxonomic position of the Caesioninae. Molecular Phylogenetics and Evolution, 44, 450-460.
55. Montes, C., Cardona, A., Jaramillo, C., Pardo, A., Silva, J. C., Valencia, V., ⋯ Niño, H. (2015). Middle Miocene closure of the Central American Seaway. Science, 348, 226-229.
56. Musick, J. A. (1999). Ecology and conservation of long-lived marine animals. American Fisheries Society Symposium, 23, 1-10.
57. Muths, D., Gouwsb, G., Mwale, M., Tessierc, E., & Bourjea, J. (2012). Genetic connectivity of the reef fish Lutjanus kasmira at the scale of the western Indian Ocean. Canadian Journal of Fisheries and Aquatic Sciences, 69, 842-853.
58. Near, T. J., & Cheng, C.-H. C. (2008). Phylogenetics of notothenioid fishes (Teleostei: Acanthomorpha): Inferences from mitochondrial and nuclear gene sequences. Molecular Phylogenetics and Evolution, 47, 832-840.
59. Nylander, J. A. A. (2004). MrModeltest v2. Program distributed by the author. Evolutionary Biology Centre, Uppsala University.
60. Reader, S. E., & Leis, J. M. (1996). Larval development in the lutjanid subfamily Caesioninae (Pisces): The genera Caesio, Dipterygonotus, Gymnocaesio and Pterocaesio. Bulletin of Marine Science, 59, 310-369.
61. Roch, L. A., Lindeman, K. C., Rocha, C. R., & Lessios, H. A. (2008). Historical biogeography and speciation in the reef fish genus Haemulon (Teleostei: Haemulidae). Molecular Phylogenetics and Evolution, 48, 918-928.
62. Rosen, D. E. (1975). A vicariance model of Caribbean biogeography. Systematic Zoology, 24, 431-464.
63. Russ, G. R., & Alcala, A. C. (1989). Effects of intense fishing pressure on an assemblage of coral reef fishes. Marine Ecology Progress Series, 56, 13-27.
64. Schneider, B., & Schmittner, A. (2006). Simulating the impact of the Panamanian seaway closure on ocean circulation, marine productivity and nutrient cycling. Earth and Planetary Science Letters, 246, 367-380.
65. Sepulchre, P., Arsouze, T., Donnadieu, Y., Dutay, J.-C., Jaramillo, C., Le Bras, J., Martin, E., Montes, C., & Waite, A. J. (2014). Consequences of shoaling of the Central American Seaway determined from modeling Nd isotopes. Paleoceanography, 29, 176-189.
66. Seutin, G., White, B. N., & Boag, P. T. (1991). Preservation of avian blood and tissue samples for DNA analysis. Canadian Journal of Zoology, 69, 82-90.
67. Soubrier, J., Steel, M., Lee, M. S. Y., Sarkissian, C. D., Guindon, S., Ho, S. W. Y., & Cooper, A. (2012). The influence of rate heterogeneity among sites on the time dependence of molecular rates. Molecular Biology and Evolution, 29, 3345-3358
68. Streelman, J. T., Alfaro, M., Westneat, M. W., Bellwood, D. R., & Karl, S. A. (2002). Evolutionary history of the parrotfishes: Biogeography, ecomorphology, and comparative diversity. Evolution, 56, 961-971.
69. Sumata, H., Minobe, S., Motoi, T., & Chan, W-L. (2004). Impact of Panamanian Gateway opening on the global ocean circulation. In S. F. Mawatari & H. Okada (Eds.), Neo-science of natural history: Integration of geoscience and biodiversity studies. Proceedings of the International Symposium on 'Dawn of a New Natural History (pp. 93-101). Sapporo: Hokkaido University.
70. Tavaré, S. (1986). Some probabilistic and statistical problems in the analysis of DNA sequences. Lectures on Mathematics in the Life Sciences, 17, 57-86.
71. Tavera, J. J., & De la Cruz-Agüero, J. C. (2006). Rediscovery of the golden snapper Lutjanus inermis (Peters, 1869) (Perciformes: Lutjanidae) in the Gulf of California. Ocean Science Journal, 41, 191-193.
72. Teske, P. R., Hamilton, H., Matthee, C. A., & Barker, N. P. (2007). Signatures of seaway closures and founder dispersal in the phylogeny of a circumglobally distributed seahorse lineage. Bio Med Central Evolutionary Biology, 7, 138.
73. Tringali, M. D., Bert, T. M., Seyoum, S., Bermingham, E., & Bartolacci, D. (1999). Molecular phylogenetics and ecological diversification of the transisthmian fish genus Centropomus (Perciformes: Centropomidae). Molecular Phylogenetics and Evolution, 13, 193-207.
74. USCFF (United States Commission of Fish and Fisheries). (1893). Report of the Commissioner for 1889-1891. Washington, D.C.: Government Printing Office.
75. von der Heydt, A., & Dijkstra, H. A. (2005). Flow reorganizations in the Panama Seaway: A cause for the demise of Miocene corals? Geophysical Research Letters, 32, L02609.
76. von der Heydt, A., & Dijkstra, H. A. (2006). Effect of ocean gateways on the global ocean circulation in the late Oligocene and early Miocene. Paleoceanography, 21, PA1011, doi:10.1029/2005PA001149.
77. Wellington, G. M., & Robertson, D. R. (2001). Variation in larval life history traits among reef fishes across the Isthmus of Panama. Marine Biology, 138, 11-22.
78. Zink, R. M., & Barrowclough, G. F. (2008). Mitochondrial DNA under siege in avian phylogeography. Molecular Ecology, 17, 2107-2121.