Population structure, long-term connectivity, and effective size of mutton snapper (Lutjanus analis) in the Caribbean Sea and Florida keys

Fishery Bulletin

Volumn 109, Issue 4, 2011, Pages 416-428

  Carson, Evan W ^a   Saillant, Eric ^b   Renshaw, Mark A ^a   Cummings, Nancie J ^c   Gold, John R ^a  

^a TEXAS A AND M UNIVERSITY   (United States)

^b UNIVERSITY OF SOUTHERN MISSISSIPPI   (United States)

^c NATIONAL MARINE FISHERIES SERVICE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LUTJANUS ANALIS;

EID: 80053365404     PISSN: 00900656     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (79)

1. Abdo, Z., K. A. Crandall, and P. Joyce. 2004. Evaluating the performance of likelihood methods for detecting population structure and migration. Mol. Ecol. 13:837-851.
2. Allendorf, F. W., P. A. Hohenlohe, and G. Luikart. 2010. Genomics and the future on conservation genetics. Nature Rev. Genetics 11:697-709.
3. e from temporally spaced samples using a coalescentbased likelihood. Genetics 170:955-967.
4. Arevalo, E., S. Davis, and J. Sites Jr. 1994. Mitochondrial DNA sequence divergence and phylogenetic relationships among eight chromosome races of the Sceloporus grammicus complex (Phrynosomatidae) in Central Mexico. Syst. Biol. 43:387-418.
5. Bagley, M. J., and J. B. Geller. 1998. Characterization of microsatellite loci in vermillion snapper Rhomboplites aurorubens (Percoidei: Lutjanidae). Mol. Ecol. Notes 7:1089-1090.
6. Beaumariage, D. S. 1969. Returns from the 1965 Schlitz tagging program including a cumulative analysis of previous results. Florida Dept. Nat. Res. Tech. Ser. No. 59:1-38.
7. Beaumont, M. A. 1999. Detecting population expansion and decline using microsatellites. Genetics 153:2013-2029.
8. Beerli, P., and J. Felsenstein. 2001. Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations using a coalescent approach. Proc. Nat. Acad. Sci. USA 98:4563-4568.
9. Bekkevold, D., M. M. Hansen, and V. Loeschke. 2002. Male reproductive competition in spawning aggregations of cod (Gadus morhua, L.). Mol. Ecol. 11:91-102.
10. Bielawski, J. P., and J. R. Gold. 2002. Mutation patterns of mitochondrial H- and L-strand DNA in closely related cyprinid fishes. Genetics 161:1589-1597.
11. Boehlert, G. W. 1996. Larval dispersal and survival in tropical reef fishes. In Tropical reef fisheries (N. V. C. Polunin and C. M. Roberts, eds.), p. 61-84. Chapman Hall, London.
12. Burton, M. L., K. J. Brennan, R. C. Múñoz, and R. O. Parker Jr. 2006. Preliminary evidence of increased spawning aggregations of mutton snapper (Lutjanus analis) at Riley's Hump two years after establishment of the Tortugas South Ecological Reserve. Fish. Bull.103:404-410.
13. Carvalho, G. R., and L. Hauser. 1995. Molecular genetics and the stock concept in fisheries. In Molecular genetics in fisheries (G. R. Carvalho and T. J. Pitcher, eds.), p. 55-80. Chapman and Hall, London.
14. Charlesworth, B. 2009. Effective population size and patterns of molecular evolution and variation. Nature Rev. Genetics 10:195-205.
15. Claro, R. 1981. Ecología y ciclo de vida del pargo criollo, Lutjanus analis (Cuvier), en la plataforma cubana. nf. Ceint.-Téc., Acad. Cienc. Cuba 186:1-83.
16. Claro, R., and K. C. Lindeman. 2003. Spawning aggregation sites of snapper and grouper species (Lutjanidae and Serrandidae) on the insular shelf of Cuba. Proc. Gulf Carib. Res. Inst. 14:91-106.
17. Conover, D. O., S. A. Arnott, M. R. Walsh, and S. B. Munch. 2005. Darwinian fishery science: lessons from the Atlantic silverside. Can. J. Fish. Aquat. Sci. 62:730-737.
18. 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.
19. Cowen, R. K., C. B. Paris, and A. Srinivasan. 2006. Scaling of connectivity in marine populations. Science 311:522-527.
20. Cummings, N. J. 2007a. Updated commercial catch per unit effort indices for mutton snapper line and pot fisheries in Puerto Rico, 1983-2006. Sustainable Fisheries Division, Southeast Fisheries Science Center, NMFS, NOAA, Miami, FL, contribution no. SFD-2007-18, SEDAR14-AW-01. 9 p. [Available at: http://www.sefsc.noaa.gov/sedar/, accessed July 2011.]
21. Cummings, N. J. 2007b. An examination of mutton snapper, Lutjanus analis, commercial catch per unit of effort in Puerto Rico from 1983-2005 available for use in developing estimates of abundance. Sustainable Fisheries Division, Southeast Fisheries Science Center, NMFS, NOAA, Miami, FL, contribution no. SFD-2007-18, SEDAR 14 assessment workshop report no. 1, SEDAR14-AW-01-Addendum 1, 44 p. [Available at http://www.sefsc.noaa.gov/sedar/, accessed July 2011.]
22. Domeier, M. L. 2004. A potential larval recruitment pathway originating from a Florida marine protected area. Fish. Oceanog. 13:287-294.
23. Domeier, M. L., and P. L. Colin. 1997. Tropical reef fish spawning aggregations: defined and reviewed. Bull. Mar. Sci. 60:698-726.
24. Domeier, M. L., C. Koenig, and F Coleman. 1996. Reproductive biology of the gray snapper (Lutjanus griseus), with notes on spawning for other western Atlantic snappers (Lutjanidae). In Biology, fisheries and culture of tropical groupers and snappers (F. Arreguin-Sanchez, J. L. Munro, M. C. Balgos, and D. Pauly, eds.), p. 189-201. Int. Cent. Living Aquat. Res. Mgmt. (ICLARM), Makati City, Philippines, and EPOMEX/ Univ. Autónoma de Campeche, Campeche, Mexico.
25. Dowling, T. E., W. L. Minckley, P. C. Marsh, and E. S. Goldstein. 1996. Mitochondrial DNA variability in the endangered razorback sucker (Xyrauchen texanus): analysis of hatchery stocks and implications for captive propagation. Conserv. Biol. 10:120-127.
26. El Mousadik, A., and R. J. Petit. 1996. High level of genetic differentiation for allelic richness among population of the argan tree (Argania spinosa (L.) Skeels) endemic to Morocco. Theoret. Appl. Genet. 92:832-839.
27. Esteves, R. F. 2005. Dispersal of reef fish larvae from known spawning sites in La Parguera. M.S. thesis, 53 p. Univ. Puerto Rico, Mayaguez. Excoffier, L., and H. E. L. Lischer.
28. Esteves, R. F. 2010. Arlequinsuite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Res. 10:564-567.
29. Farmer, N. A. 2009. Reef fish movements and marine reserve designs. Ph.D. diss., 217 p. Univ. Miami, Coral Gables, FL. Federal Register.
30. Farmer, N. A. 2005. Fisheries of the Caribbean, Gulf of Mexico, and South Atlantic; Comprehensive Amendment to the Fishery Management Plans of the U.S. Caribbean; final rule. vol. 70, no. 208, October 28, p. 62073-62084. GPO, Washington, D.C.
31. Fischer, A. J., M. S. Baker Jr., and C. A. Wilson. 2004. Red snapper, Lutjanus campechanus, demographic structure in the northern Gulf of Mexico based on spatial patterns in growth rates and morphometrics. Fish. Bull. 102:593-603.
32. Frankham, R. 1995. Effective population-size adult-population size ratios in wildlife: a review. Genet. Res. 66:95-107.
33. Franklin, I. R. 1980. Evolutionary change in small populations. In Conservation biology: an evolutionary-ecological perspective (M. E. Soulé and B. A. Wilcox, eds.), p. 135-149. Sinauer, Sunderland, MA. Fu Y.-X.
34. Franklin, I. R. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking, and background selection. Genetics 147:915-925.
35. Fu Y.-X, and W.-H. Li. 1993. Statistical tests of neutral mutations. Genetics 133:693-709.
36. Gold, J. R., E. Pak, and L. R. Richardson. 2001. Microsatellite variation among red snapper (Lutjanus campechanus) from the Gulf of Mexico. Mar. Biotech. 3:293-304.
37. Goudet, J. 1995. F-stat, a computer program to calculate F-statistics. J. Hered. 86 485-486.
38. Goudet, J., M. Raymond, T. de-Meeus, and F. Rousset. 1996. Testing dif ferentiation in diploid populations. Genetics 144:1933-1940.
39. Graham R. T., R. Carcamo, K. L. Rhodes, C. M. Roberts, and N. Requena. 2008. Historical and contemporary evidence of a mutton snapper (Lutjanus analis Cuvier, 1828) spawning aggregation fishery in decline. Coral Reefs 27:311-319.
40. Guo, S., and E. Thompson. 1992. Performing the exact test of Hardy-Weinberg proportion from multiple alleles. Biometrics 48:361-372.
41. Hare, M. P., L. Nunney, M. K. Schwartz, D. E. Ruzzante, M. Burford, R. S. Waples, K. Ruegg, and F. Palstraa. 2011. Understanding and estimating effective population size for practical application in marine species management. Conserv. Biol. 25:438-449.
42. Hastings, A. 1993. Complex interactions between dispersal and dynamics: lessons from coupled logistical equations. Ecology 74:1362-1372.
43. Hauser, L., and G. R. Carvalho. 2008. Paradigm shifts in marine fisheries genetics: ugly hypotheses slain by beautiful facts. Fish Fish. 9:333-362.
44. Hauser, L., and R. D. Ward. 1998. Population identification in pelagic fish: the limits of molecular markers. In Advances in molecular mycology (G. R. Carvalho, ed.), p. 2191-2242. IOS Press, Amsterdam.
45. Hellberg, M. E., R. S. Burton, J. E. Neigel, and S. R. Palumbi. 2002. Genetic assessment of connectivity among marine populations. Bull. Mar. Sci. 70 (suppl.):273-290.
46. Johns, W. E., T. L. Townsend, D. M. Fratantoni, and W. D. Wilson. 2002. On the Atlantic inflow to the Caribbean Sea. Deep- Sea Res., pt. I, 49:211-243.
47. Kritzer, J. P., and P. F. Sale. 2004. Metapopulation ecology in the sea: from Levin's model to marine ecology and fisheries science. Fish Fish. 5:131-140.
48. Matos-Caraballo, D., M. Cartagena-Haddock, and N. Peña- Alvarado. 2004. Historical landings and biostatistical CFSP data analysis for five important species. Portrait of the fishery of mutton snapper Lutjanus analis in Puerto Rico during 1988-2001. [Available from Dept. Nat. Environ. Res. Fish. Res. Lab., Mayaguez, Puerto Rico.]
49. Mueller, K. W. 1994. Gregarious behavior in mutton snapper in the Exuma Cays. Bahamas J. Sci. 5:17-22.
50. Mueller, K. W. 1995. Size structure of mutton snapper, Lutjanus analis, associated with unexploited artificial patch reefs in the central Bahamas. Fish. Bull. 93:573-576.
51. Østergaard, S., M. M. Hansen, V. Loeschcke, and E. E. Nielsen. 2003. Long-term temporal changes of genetic composition in brown trout (Salmo trutta L.) populations inhabiting an unstable environment. Mol. Ecol. 12:3123-3135.
52. Palstra, F. P., M. F. O'Connell, and D. E. Ruzzante. 2007. Population structure and gene f low reversals in Atlantic salmon (Salmo salar) over contemporary and long-term temporal scales: effects of population size and life history. Mol. Ecol. 16:4504-4522.
53. Raymond, M., and F. Rousset. 1995. Genepop(vers. 2.1): Population genetics software for exact tests and ecumenicism. J. Hered. 86:248-249.
54. Renshaw, M. A., S. Karlsson, and J. R. Gold. 2007. Isolation and characterization of microsatellites in lane snapper (Lutjanus synagris), mutton snapper (Lutjanus analis), and yellowtail snapper (Ocyurus chrysurus). Mol. Ecol. Notes 7:1084-1087.
55. Renshaw, M. A., E. Saillant, S. C. Bradfield, and J. R. Gold. 2006. Microsatellite multiplex panels for genetic studies of three species of marine fishes: red drum (Sciaenops ocellatus), red snapper (Lutjanus campechanus), and cobia (Rachycentron canadum). Aquaculture 253:731-735.
56. Rice, W. R. 1989. Analyzing tables of statistical tests. Evolution 43:223-225.
57. Rieman, B. E., and F. E. Allendorf. 2001. Effective population size and genetic conservation criteria for bull trout. N. Am. J. Fish. Manage. 21:756-764.
58. Rhodes, K.L., R. I. Lewis, R. W. Chapman, and Y. Sadovy. 2003. Genetic structure of camouflage grouper, Epinephelus polyphekadion (Pisces: Serranidae), in the western central Pacific. Mar. Biol. 142:771-776.
59. Roberts, C. M. 1997. Connectivity and management of Caribbean coral reefs. Science 278:1454-1457.
60. 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.
61. Rozas, J., J. C. Sanchez-DelBarrio, X. Messeguer, and R. Rozas. 2003. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496-2497.
62. Sadovey de Mitcheson, Y., A. Cornish, M. Doreier, P. L. Colin, M. Russell, and K. C. Lindeman. 2008. A global baseline for spawning aggregations of reef fishes. Conserv. Biol. 22:1233-1244.
63. Saillant, E., and J. R. Gold. 2006. Population structure and variance effective size of red snapper (Lutjanus campechanus) in the northern Gulf of Mexico. Fish. Bull. 104:136-148.
64. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning. A laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
65. Schultz, S. T., and M. Lynch. 1997. Mutation and extinction: the role of variable mutational effects, synergistic epistasis, beneficial mutations, and degree of outcrossing. Evolution 51:1363-1371.
66. Shulman, M. J., and E. Bermingham. 1995. Early life histories, ocean currents, and the population genetics of Caribbean reef fishes. Evolution, 49:897-910.
67. Shulzitski, K., M. A. McCartney, and M. L. Burton. 2009. Population connectivity among Dry Tortugas, Florida, and Caribbean populations of mutton snapper (Lutjanus analis), inferred from multiple microsatellite loci. Fish. Bull. 107:501-509.
68. SEDAR (Southeast Data, Assessment, and Review). 2007. SEDAR 14: Caribbean mutton snapper. Stock assessment report 2. [Available at http://www.sefsc.noaa.gov/sedar/, accessed July 2011.]
69. Seutin, G., B. N. White, and P. T. Boag. 1991. Preservation of avian blood and tissue samples for DNA analyses. Can. J. Zool. 69:82-90.
70. Storz, J., and M. A. Beaumont. 2002. Testing for genetic evidence of population expansion and contraction: an empirical analysis of microsatellite DNA variation using a hierarchical Bayesian model. Evolution 56:154-166
71. Swearer, S. E., J. E. Caselle, D. W. Lea, and R. R. Warner. 1999. Larval retention and recruitment in an island population of a coral-reef fish. Nature 402:799-802.
72. Taylor, M. S., and M. E. Hellberg. 2003. Genetic evidence for local retention of pelagic larvae in a Caribbean reef fish. Science 299:107-109.
73. van Oosterhout, C., W. Hutchinson, D. Will, and P. Shipley. 2004. Micro-checker: software for identifying and correcting genotyping errors in microsatellite data. Mol. Ecol. Notes 4:535-538.
74. Waples, R. S. 2010. Spatial-temporal stratifications in natural populations and how they affect understanding and estimation of effective population size. Mol. Ecol. Res. 10:785-796.
75. Wares, J. P., and P. M. Pringle. 2008. Drift by drift: effective population size is limited by advection. BMC Evol. Biol. 8:235.
76. Watanabe, W. O. 2001. Species profile: mutton snapper. SRAG Publication 725, 9 p. Southern Regional Aquaculture Center, Stoneville, MS.
77. Weir, B. S., and C. C. Cockerham. 1984. Estimating F-statistics for the analysis of population structure. Evolution 38:1358-1370.
78. Woods, M. K., A. J. Fischer, J. H. Cowan Jr., and D. L. Nieland. 2003. Size and age of female red snapper Lutjanus campechanus in the northern Gulf of Mexico. Proc. Gulf Caribb. Fish. Inst. 54:526-537.
79. Wright, S. 1931. Evolution in Mendelian populations. Genetics 16:97-159.