Landscape genetics reveals population subdivision in bering sea and aleutian islands pacific cod

Transactions of the American Fisheries Society

Volumn 141, Issue 6, 2012, Pages 1557-1573

  Spies, Ingrid ^a,b  

^a ALASKA FISHERIES SCIENCE CENTER   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84891660692     PISSN: 00028487     EISSN: 15488659     Source Type: Journal    
DOI: 10.1080/00028487.2012.711265     Document Type: Article

References (90)

1. Ancelet, S., and G. Guillot. 2006. Geneclust program documentation. Institut National de la Recherche Agronomique, Technical Report, Paris. Available: cran.rproject.org/web/packages/Geneclust/Geneclust.pdf. (January 2012).
2. Bakkala, R., S. Westrheim, S. Mishima, C. Zhang, and E. Brown. 1984. Distribution of Pacific cod (Gadus macrocephalus) in the North Pacific Ocean. International North Pacific Fisheries Commission 42:111-115.
3. Beaumont, M. A., and R. A. Nichols. 1996. Evaluating loci for use in the genetic analysis of population structure. Proceedings of the Royal Society of London B 263:1619-1626.
4. Belkhir, K., P. Borsa, L. Chikhi, N. Raufaste, and F. Bonhomme. 2000. GENETIX 4.02: logiciel sous Windows™ pourla genetique des populations. Laboratoire Genome, Populations, Interactions, CNRS UPR 9060, Universite de Montpellier II, Montpellier, France.
5. Bentzen, P. 1998. Seeking evidence of local stock structure using molecular genetic methods. Pages 20-30 in I. Hunt von Herbing, I. Kornfield, M. Tupper, and J. Wilson, editors. The implications oflocalized fishery stocks. Northeast Regional Agricultural Engineering Service, Cooperative Extension, Ithaca, New York.
6. Bentzen, P., C. T. Taggart, D. E. Ruzzante, and D. Cook. 1996. Microsatellite polymorphism and the population structure of Atlantic cod (Gadus morhua) inthe northwestAtlantic. Canadian Journal ofFisheries andAquatic Sciences 53:2706-2721.
7. Brodeur, R. D., S. J. Picquelle, D. M. Blood, and N. Merati. 1996. Walleye pollock egg distribution and mortality in the western Gulf of Alaska. Fisheries Oceanography 5(Supplement 1):92-111.
8. Canino, M. F., I. B. Spies, K. M. Cunningham, L. Hauser, and W. S. Grant. 2010. Multiple ice-age refugia in Pacific cod, Gadus macrocephalus. Molecular Ecology 19:4339-4351.
9. Canino, M. F., I. B. Spies, and L. Hauser. 2005. Development and characterization of novel di- and tetranucleotide microsatellite markers in Pacific cod (Gadus macrocephalus). Molecular Ecology Notes 5:908-910.
10. Carvajal-Rodríguez, A., J. de Uña-Alvarez, and E. Rolan-Alvarez. 2009. A new multitest correction (SGoF) that increases its statistical power when increasing the number of tests. BMC Bioinformaticss [online serial] 10:209.
11. Crawford, N. G. 2010. SMOGD: software for the measurement of genetic diversity. Molecular Ecology Resources 10:556-557.
12. Crida, A., and S. Manel. 2007. WOMBSOFT: an R package that implements the Wombling method to identify genetic boundary. Molecular Ecology Notes 7:588-591.
13. Cunningham, K. M., M. F. Canino, I. B. Spies, and L. Hauser. 2009. Genetic isolation by distance and localized fjord population structure in Pacific cod (Gadus macrocephalus): limited effective dispersal in the northeastern Pacific Ocean. Canadian Journal ofFisheries and Aquatic Sciences 66:153-166.
14. Gaylord, B., and S. D. Gaines. 2000. Temperature or transport? range limits in marine species mediated solely by flow. American Naturalist 155:769-789.
15. Gharrett, A. J., R. J. Riley, and P. D. Spencer. 2012. Genetic analysis reveals restricted dispersal of northern rockfish along the continental margin of the Bering Sea and Aleutian Islands. Transactions of the American Fisheries Society 141:370-382.
16. Goudet, J. 2001. FSTAT: a program to estimate and test gene diversities and fixation indices, version 2.9.3. Universite de Lausanne, Lausanne, Switzerland. Available: www2.unil.ch/popgen/softwares/fstat.htm. (January 2012).
17. Green, J. M., and J. S. Wroblewski. 2000. Movement patterns of Atlantic cod in Gilbert Bay, Labrador: evidence for bay residency and spawning site fidelity. Journal of the Marine Biological Association of the United Kingdom 80:1077-1085.
18. Guillot, G., A. Estoup, F. Mortier, and J. F. Cosson. 2005. A spatial statistical model for landscape genetics. Genetics 170:1261-1280.
19. Gustafson, R. G., W. H. Lenarz, B. B. McCain, C. C. Schmitt, W. S. Grant, T. L. Builder, and R. D. Methot. 2000. Status review of Pacific hake, Pacific cod, and walleye pollock from Puget Sound, Washington. NOAA Technical Memorandum NMFS-NWFSC-44.
20. Hauser, L., G. J. Adcock, P. J. Smith, J. H. Bernal Ramirez, and G. R. Carvalho. 2002. Loss of microsatellite diversity and low effective population size in an overexploited population of New Zealand snapper (Pagrus auratus). Proceedings of the National Academy of Sciences of the USA 99:11742-11747.
21. Hess, J. E., R. D. Vetter, and P. Moran. 2011. A steep genetic cline in yellow-tail rockfish, Sebastes flavidus, suggests regional isolation across the Cape Mendocino faunal break. Canadian Journal ofFisheries and Aquatic Sciences 68:89-104.
22. Hiatt, T., M. Dalton, R. Felthoven, B. Fissel, B. Garber-Yonts, A. Haynie, S. Kasperski, D. Lew, C. Package, J. Sepez, and C. Seung. 2010. Stock assessment and fishery evaluation report for the groundfish fisheries of the Gulf of Alaska and Bering Sea/Aleutian Islands area: Economic status of the groundfish fisheries off Alaska, 2009. North Pacific Fishery Management Council, Anchorage, Alaska. Available: www.afsc.noaa.gov/refm/docs/2010/economic.pdf. (July 2011).
23. Hilborn, R., J. M. Orensanz, and A. M. Parma. 2005. Institutions, incentives and the future of fisheries. Philosophical Transactions of the Royal Society ofLondon B 360:47-57.
24. Hinckley, S., K. M. Bailey, S. J. Picquelle, J. D. Schumacher, and P. J. Stabeno. 1991. Transport, distribution, and abundance of larval and juvenile walleye pollock (Theragra chalcogramma) in the western Gulf of Alaska. Canadian Journal of Fisheries and Aquatic Sciences 48:91-98.
25. Hunt, G. L, Jr., and P. J. Stabeno. 2005. Oceanography and ecology of the Aleutian Archipelago: spatial and temporal variation. Fisheries Oceanography 14(Supplement 1):292-306.
26. Hurst, T. P., D. W. Cooper, J. S. Scheingross, E. M. Seale, B. J. Laurel, and M. L. Spencer. 2009. Effects of ontogeny, temperature, and light on vertical movements of larval Pacific cod (Gadus macrocephalus). Fisheries Oceanography 18:301-311.
27. Hutchinson, W. F., C. van Oosterhout, S. I. Rogers, and G. R. Carvalho. 2003. Temporal analysis of archived samples indicates marked genetic changes in declining North Sea cod (Gadus morhua). Proceedings of the Royal Society of London B 270:2125-2132.
28. Hyde, J. R., and R. D. Vetter. 2009. Population genetic structure in the redefined vermilion rockfish (Sebastes miniatus) indicates limited larval dispersal and reveals natural management units. Canadian Journal ofFisheries and Aquatic Sciences 66:1569-1581.
29. Jensen, J. L., A. J. Bohonak, and S. T. Kelley. 2005. Isolation by distance, web service. BMC Geneticss [online serial] 6:13.
30. Jorde, P. E., H. Knutsen, S. H. Espeland, and N. C. Stenseth. 2007. Spatial scale of genetic structuring in coastal cod Gadus morhua and geographic extent of local populations. Marine Ecology Progress Series 343:229-237.
31. Jost, L. 2008. GST and its relatives do not measure differentiation. Molecular Ecology 17:4015-4026.
32. Kinzey, D., and A. E. Punt. 2009. Multispecies and single-species models of fish population dynamics: comparing parameter estimates. Natural Resource Modeling 22:67-104.
33. Knutsen, H., P. E. Jorde, C. Andre, and N. C. Stenseth. 2003. Fine-scaled geographical population structuring in a highly mobile marine species: the Atlantic cod. Molecular Ecology 12:385-394.
34. Knutsen, H., E. M. Olsen, L. Ciannelli, S. H. Espeland, J. A. Knutsen, J. H. Simonsen, S. Skreslet, and N. C. Stenseth. 2007. Egg distribution, bottom topography and small-scale cod population structure in a coastal marine system. Marine Ecology Progress Series 333:249-255.
35. Lacy, R. C. 1987. Loss of genetic diversity from managed populations: interacting effects of drift, mutation, immigration, selection, and population subdivision. Conservation Biology 1:143-158.
36. Ladd, C., G. L. Hunt Jr., C. W. Mordy, S. A. Salo, and P. J. Stabeno. 2005. Marine environment of the eastern and central Aleutian Islands. Fisheries Oceanography 14(Supplement 1):22-38.
37. Laikre, L., S. Palm, and N. Ryman. 2005. Genetic population structure of fishes: implications for coastal zone management. Ambio 34:111-119.
38. Lang, G. M., and P. A. Livingston. 1996. Food habits of key groundfish species in the eastern Bering Sea slope region. NOAA Technical Memorandum NMFS-AFSC-67. Available: www.afsc.noaa.gov/publications/AFSC-TM/NOAA-TM-AFSC-67.pdf. (July 2011).
39. Lanksbury, J. A., J. T. Duffy-Anderson, K. L. Mier, M. S. Busby, and P. J. Stabeno. 2007. Distribution and transport patterns of the northern rock sole, Lepidopsetta polyxystra, larvae in the southeastern Bering Sea. Progress in Oceanography 72:39-62.
40. Laurel, B. J., T. P. Hurst, L. A. Copeman, and M. W. Davis. 2008. The role of temperature on the growth and survival of early and late hatching Pacific cod larvae (Gadus macrocephalus). Journal of Plankton Research 30:1051-1060.
41. Leberg, P. L. 2002. Estimating allelic richness: effects of sample size and bottlenecks. MolecularEcology 11:2445-2449.
42. Logerwell, E. A., K. Aydin, S. Barbeaux, E. Brown, M. E. Conners, S. Lowe, J. W. Orr, I. Ortiz, R. Reuter, and P. Spencer. 2005. Geographic patterns in the demersal ichthyofauna of the Aleutian Islands. Fisheries Oceanography 14(Supplement 1):93-112.
43. Logerwell, E. A., and S. Neidetcher. 2008. Spatial and temporal patterns in Pacific cod, Gadus macrocephalus, reproductive maturity in the Bering Sea. North Pacific Research Board, Project618, Final Report, Anchorage, Alaska. Available: doc.nprb.org/web/06_prjs/618_Final%20Report.pdf. (July 2011).
44. Lough, R. G., P. C. Valentine, D. C. Potter, P. J. Auditore, G. R. Bolz, J. D. Neilson, and R. I. Perry. 1989. Ecology and distribution of juvenile cod and haddock in relation to sediment type and bottom currents on eastern Georges Bank. Marine Ecology Progress Series 56:1-12.
45. Manel, S., M. K. Schwartz, G. Luikart, and P. Taberlet. 2003. Landscape genetics: combining landscape ecology and population genetics. Trends in Ecology and Evolution 18:189-197.
46. Manni, F., E. Guerard, and E. Heyer. 2004. Geographic patterns of (genetic, morphologic, linguistic) variation: how barriers can be detected by using Monmonier’s algorithm. Human Biology 76:173-190.
47. McQuinn, I. H. 1997. Metapopulations and the Atlantic herring. Reviews in Fish Biology and Fisheries 7:297-329.
48. Miller, K. M., K. D. Le, and T. D. Beacham. 2000. Development of tri- and tetranucleotide repeat microsatellite loci in Atlantic cod (Gadus morhua). Molecular Ecology 9:238-239.
49. Monmonier, M. S. 1973. Maximum-differencebarriers: analternativenumerical regionalization method. Geographical Analysis 5:245-261.
50. Mordy, C. W., P. J. Stabeno, C. Ladd, S. Zeeman, D. P. Wisegarver, S. A. Salo, and G. L. Hunt Jr. 2005. Nutrients and primary production along the eastern Aleutian Island archipelago. Fisheries Oceanography 14(Supplement 1):55-76.
51. Munk, K. M. 2001. Maximum ages of groundfishes in waters off Alaska and British Columbia and considerations of age determination. Alaska Fishery Research Bulletin 8:12-21.
52. Narimatsu, Y., T. Hattori, Y. Ueda, H. Matsuzaka, and M. Shiogaki. 2007. Somatic growth and otolith microstructure of larval and juvenile Pacific cod Gadus macrocephalus. Fisheries Science 73:1257-1264.
53. Neigel, J. E. 2002. Is Fst obsolete? Conservation Genetics 3:167-173.
54. Nichol, D. G., T. Honkalehto, and G. G. Thompson. 2007. Proximity of Pacific cod to the sea floor: using archival tags to estimate fish availability to research bottom trawls. Fisheries Research 86:129-135.
55. Olsen, J. B., S. E. Merkouris, and J. E. Seeb. 2002. An examination of spatial and temporal genetic variation in walleye pollock (Theragra chalcogramma) using allozyme, mitochondrial DNA, and microsatellite data. U.S. National Marine Fisheries Service Fishery Bulletin 100:752-764.
56. O’Reilly, P. T., M. F. Canino, K. M. Bailey, and P. Bentzen. 2000. Isolation of twenty low stutter di- and tetranucleotide microsatellites for population analyses of walleye pollock and other gadoids. Journal of Fish Biology 56:1074-1086.
57. O’Reilly, P. T., M. F. Canino, K. M. Bailey, and P. Bentzen. 2004. Inverse relationship between FST and microsatellite polymorphism in the marine fish, walleye pollock (Theragra chalcogramma): implications for resolving weak population structure. Molecular Ecology 13:1799-1814.
58. Overland, J. E., and P. J. Stabeno. 2004. Is the climate of the Bering Sea warming and affecting the ecosystem? EOS, Transactions, American Geophysical Union 85:309-316.
59. Palof, K. J., J. Heifetz, and A. J. Gharrett. 2011.Geographic structure in Alaskan Pacific ocean perch (Sebastes alutus) indicates limited lifetime dispersal. Marine Biology 158:779-792.
60. Pampoulie, C., D. E. Ruzzante, V. Chosson, T. D. Jorundsdottir, L. Taylor, V. Thorsteinsson, A. K. Danielsdottir, and G. Marteinsdottir. 2006. The genetic structure of Atlantic cod (Gadus morhua) around Iceland: insight from microsatellites, the Pan I locus, and tagging experiments. Canadian Journal of Fisheries and Aquatic Sciences 63:2660-2674.
61. Pritchard, J. K., M. Stephens, and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945-959.
62. R Develoment Core Team. 2011. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. Available: www.R-project.org. (January 2012).
63. Reiss, H., G. Hoarau, M. Dickey-Collas, and W. J. Wolff. 2009. Genetic population structure of marine fish: mismatch between biological and fisheries management units. Fish and Fisheries 10:361-395.
64. Robichaud, D., and G. A. Rose. 2001. Multiyear homing of Atlantic cod to a spawning ground. Canadian Journal of Fisheries and Aquatic Sciences 58:2325-2329.
65. Rocha-Olivares, A., and R. D. Vetter. 1999. Effects of oceanographic circulation on the gene flow, genetic structure, and phylogeography of the rosethorn rock-fish (Sebastes helvomaculatus). Canadian Journal of Fisheries and Aquatic Sciences 56:803-813.
66. Rousset, F. 1997. Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145:1219-1228.
67. Rugen, W. C., and A. C. Matarese. 1988. Spatial and temporal distribution and relative abundance of Pacific cod (Gadus macrocephalus) larvae in the western Gulf of Alaska. National Marine Fisheries Service, Northwest and Alaska Fisheries Center, Processed Report 88-18, Seattle. Available: www.afsc.noaa.gov/Publications/ProcRpt/PR1988-18.pdf. (August 2011).
68. Ryman, N., and S. Palm. 2006. POWSIM: a computer program for assessing statistical power when testing for genetic differentiation. Molecular Ecology Notes 6:600-602.
69. Sakurai, Y., and T. Hattori. 1996. Reproductive behavior of Pacific cod in captivity. Fisheries Science 62:222-228.
70. Schindler, D. E., R. Hilborn, B. Chasco, C. P. Boatright, T. P. Quinn, L. A. Rogers, and M. S. Webster. 2010. Population diversity and the portfolio effect in an exploited species. Nature 465:609-612.
71. Schuller, M. 2011. Evidence for a role of bathymetry and emergence in spe-ciation in the genus Glycera (Glyceridae, Polychaeta) from the deep eastern Weddell Sea. Polar Biology 34:549-564.
72. Shimada, A. M., and D. K. Kimura. 1994. Seasonal movements of Pacific cod, Gadus macrocephalus, in the eastern Bering Sea and adjacent waters based on tag-recapture data. U.S. National Marine Fisheries Service Fishery Bulletin 92:800-816.
73. Sinclair, E. H., and T. K. Zeppelin. 2002. Seasonal and spatial differences in diet in the western stock of Steller sea lions (Eumetopias jubatus). Journal of Mammalogy 83:973-990.
74. Skirinsdottir, S., C. Pampoulie, S. Hauksdottir, I. Schulte, K. Olafsson, G. O. Hreggvidsson, and S. Hjorleifsdottir. 2008. Characterization of 18 new microsatellite loci in Atlantic cod (Gadus morhua L). Molecular Ecology Resources 8:1503-1505.
75. Sotka, E. E., J. P. Wares, J. A. Barth, R. K. Grosberg, and S. R. Palumbi. 2004. Strong genetic clines and geographical variation in gene flow in the rocky intertidal barnacle Balanus glandula. Molecular Ecology 13:2143-2156.
76. Spies, I. B., D. E. Stevenson, J.W. Orr, and G. R. Hoff. 2011. Molecularsystem-atics of the skate subgenus Arctoraja (Bathyraja: Rajidae) and support for an undescribed species, the leopard skate, with comments on the phylogenetics of Bathyraja. Ichthyological Research 58:77-83.
77. Stabeno, P. J., J. D. Schumacher, and K. Ohtani. 1999. The physical oceanography of the Bering Sea. Pages 1-28 in T. R. Loughlin and K. Ohtani, editors. Dynamics of the Bering Sea: a summary of physical, chemical, and biological characteristics, and a synopsis of research on the Bering Sea. University of Alaska Sea Grant, AK-SG-99-03, Fairbanks.
78. Stark, J. W. 2007. Geographic and seasonal variations in maturation and growth of female Pacific cod (Gadus macrocephalus) in the Gulf of Alaska and Bering Sea. U.S. National Marine Fisheries Service Fishery Bulletin 105:396-407.
79. Stenseth, N. C., P. E. Jorde, K. S. Chan, E. Hansen, H. Knutsen, C. Andre, M. D. Skogen, and K. Lekve. 2006. Ecological and genetic impact of Atlantic cod larval drift in the Skagerrak. Proceedings of the Royal Society B 273:1085-1092.
80. Stenvik, J., M. S. Wesmajervi, K. T. Fjalestad, B. Damsgard, and M. Delghandi. 2006. Development of 25 gene-associated microsatellite markers of Atlantic cod (Gadus morhua L.). Molecular Ecology Notes 6:1105-1107.
81. Sterner, T. 2007. Unobserved diversity, depletion and irreversibility: the importance of subpopulations for management of cod stocks. Ecological Economics 61:566-574.
82. Taylor, B. 1997. Defining “population” to meet management objectives for marine mammals. Pages 49-65 in A. E. Dizon, S. J. Chivers, and W. F. Perrin, editors. Molecular genetics of marine mammals: incorporating the proceedings of a workshop on the analysis of genetic data to address problems of stock identity as related to management of marine mammals. Society for Marine Mammalogy, Lawrence, Kansas.
83. Thompson, G. G., J. N. Ianelli, and R. Lauth. 2010. Assessment of Pacific cod stock in the eastern Bering Sea and Aleutian Islands area. North Pacific Fishery Management Council, Anchorage, Alaska. Available: www.afsc.noaa.gov/REFM/docs/2010/BSAIpcod.pdf. (July 2011).
84. Van Oosterhout, C., W. F. Hutchinson, D. P. M. Wills, and P. Shipley. 2004. MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes 4:535-538.
85. Waples, R. S., and O. Gaggiotti. 2006. What is a population? an empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity. Molecular Ecology 15:1419-1439.
86. Weir, B. S., and C. C. Cockerham. 1984. Estimating F-statistics for the analysis of population structure. Evolution 38:1358-1370.
87. Wesmajervi, M. S., T. Tafese, J. Stenvik, K. T. Fjalestad, B. Damsgard, and M. Delghandi. 2007. Eight new microsatellite markers in Atlantic cod (Gadus morhua L.) derived from an enriched genomic library. Molecular Ecology Notes 7:138-140.
88. Wright, P. J., E. Galley, I. M. Gibb, and F. C. Neat. 2006. Fidelity of adult cod to spawning grounds in Scottish waters. Fisheries Research 77:148-158.
89. Wright, S. 1931. Evolution in Mendelian populations. Genetics 16:97-159.
90. Wyllie-Echeverria, T. 1995. Sea-ice conditions and the distribution of walleye pollock (Theragra chalcogramma) on the Bering and Chukchi shelf. Canadian Special Publication of Fisheries and Aquatic Sciences 121:131-136.