Fine-scale spatial and temporal genetic structure of Atlantic cod off the Atlantic coast of the USA

Marine Ecology Progress Series

Volumn 410, Issue , 2010, Pages 177-195

  Kovach, Adrienne I ^a   Breton, Timothy S ^b   Berlinsky, David L ^b   Maceda, Lorraine ^c   Wirgin, Isaac ^c  

^a Department of Natural Resources and the Environment ^*  (United States)

^b UNIVERSITY OF NEW HAMPSHIRE   (United States)

^c NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Atlantic cod; Gadus morhua; Microsatellite DNA; Population genetic structure; Single nucleotide polymorphism; Stock identification

Indexed keywords

DIVERGENCE; GADOID; GENETIC MARKER; GENETIC STRUCTURE; JUVENILE; LOCAL ADAPTATION; MANAGEMENT PRACTICE; MITOCHONDRIAL DNA; POLYMORPHISM; SPATIOTEMPORAL ANALYSIS; SPAWNING; STOCK ASSESSMENT; STOCK IDENTIFICATION;

ATLANTIC COAST [NORTH AMERICA]; ATLANTIC COAST [UNITED STATES]; UNITED STATES;

GADUS MORHUA;

EID: 77955861786     PISSN: 01718630     EISSN: None     Source Type: Journal    
DOI: 10.3354/meps08612     Document Type: Article

References (92)

1. Anderson EC, Waples RS, Kalinowski ST (2008) An improved method for predicting the accuracy of genetic stock identification. Can J Fish Aquat Sci 65:1475-1486
2. Antao T, Lopes A, Lopes RJ, Beja-Pereira A, Luikart G (2008) LOSITAN: a workbench to detect molecular adaptation based on an Fst-outlier method. BMC Bioinformatics 9: 323-327
3. Árnason E, Hernandez UB, Kristinsson K (2009) Intense habitatspecific fisheries-induced selection at the molecular PanI locus predicts imminent collapse of a major cod fishery. PLoS ONE 45(5):e5529
4. Beacham TD, Brattey J, Millar KM, Withler RE (2002) Multiple stock structure of Atlantic cod (Gadus morhua) off Newfoundland and Labrador determined from genetic variation. ICES J Mar Sci 59:650-655
5. Beaumont MA, Balding DJ (2004) Identifying adaptive genetic divergence among populations from genome scans. Mol Ecol 13:969-980
6. Beaumont MA, Nichols RA (1996) Evaluating loci for use in the genetic analysis of population structure. Proc Biol Sci 263:1619-1626
7. Bradbury IR, Laurel BJ, Robichaud D, Rose GA and others (2008) Discrete spatial dynamics in a marine broadcast spawner: re-evaluating scales of connectivity and habitat associations in Atlantic cod (Gadus morhua L.) in coastal Newfoundland. Fish Res 91:299-309
8. Brooker AL, Cook D, Bentzen P, Wright JM, Doyle RW (1994) Organization of microsatellites differs between mammals and cold-water teleost fishes. Can J Fish Aquat Sci 51: 1959-1966
9. Cadrin SX, Secor DH (2009) Accounting for spatial population structure in stock assessment: past, present and future. In: Beamish RJ, Rothschild BJ (eds) The future of fisheries science in North America. Fish and Fisheries Series, Vol 31. Springer, Heidelberg, p 405-426
10. Cano JM, Mäkinen HS, Leinonen T, Freyhof J, Merilä J (2008) Extreme neutral genetic and morphological divergence supports classification of Adriatic three-spined stickleback (Gasterosteus aculeatus) populations as distinct conservation units. Biol Conserv 141:1055-1066
11. Case RA, Hutchinson WF, Hauser L, van Oosterhout C, Carvalho GR (2005) Macro- and micro-geographic variation in pantophysin (PanI) allele frequencies in NE Atlantic cod Gadus morhua. Mar Ecol Prog Ser 301:267-278
12. Case RA, Hutchinson WF, Hauser L, Buehler V and others (2006) Association between growth and Pan I* genotype within Atlantic cod full-sibling families. Trans Am Fish Soc 135:241-250
13. Churchill J (2009) What maintains the western Gulf of Maine stock? In: Proceedings of exploring fine-scale ecology for groundfish in the Gulf of Maine and Georges Bank. Gulf of Maine Research Institute, Portland, ME. www.gmri.org/ community (accessed 24 July 2009)
14. Collette BB, Klein-MacPhee G (2002) Bigelow and Schroeder's fishes of the Gulf of Maine. Smithsonian Institute Press, Washington, DC
15. Conover DO, Clarke LM, Munch SB, Wagner GN (2006) Spatial and temporal scales of adaptive divergence in marine fishes and the implications for conservation. J Fish Biol 69:21-47
16. Crandall KA, Bininda-Emonds ORP, Mace GM, Wayne RK (2000) Considering evolutionary processes in conservation biology. Trends Ecol Evol 15:290-295
17. Delghandi M, Stenvik J, Nilsen F, Wesmajervi MS, Fjalestad KT, Damsgård B (2008) Identification and characterisation of nine new gene-associated microsatellite markers for Atlantic cod (Gadus morhua L.). Conserv Genet 9:747-749
18. Dieringer D, Schlötterer C (2003) Micrsoatellite analyser (MSA): a platform independent analysis tool for large microsatellite data sets. Mol Ecol Notes 3:167-169
19. Endler JA (1986) Natural selection in the wild. Princeton University Press, Princeton, NJ
20. Goudet J (1995) FSTAT (version 1.2): a computer program to calculate F-statistics. J Hered 86:485-486
21. Gröger JP, Rountree RA, Thygesen UH, Jones D, Martins D, Xu Q, Rothchild BJ (2007) Geolocation of Atlantic cod (Gadus morhua) movements in the Gulf of Maine using tidal information. Fish Oceanogr 16:317-335
22. Haass NK, Kartenbeck J, Leube RE (1996) Pantophysin is a ubiquitously expressed synaptophysin homologue and defines constitutive transport vesicles. J Cell Biol 134: 731-746
23. Hauser L, Carvalho GR (2008) Paradigm shifts in marine fisheries genetics: ugly hypotheses slain by beautiful facts. Fish Fish 9:333-362
24. Hedrick PW (2005) A standardized genetic differentiation measure. Evolution 59:1633-1638
25. Howell WH, Morin M, Rennels N, Goethal D (2008) Residency of adult Atlantic cod (Gadus morhua) in the western Gulf of Maine. Fish Res 91:123-132
26. Huret M, Runge JA, Chen C, Cowles G, Xu Q, Pringle JM (2007) Dispersal modeling of fish early life stages: sensitivity with application to Atlantic cod in the western Gulf of Maine. Mar Ecol Prog Ser 347:261-274
27. Hutchings JA, Swain DP, Rowe S, Eddington JD, Velmurugu P, Brown JA (2007) Genetic variation in life-history reaction norms in a marine fish. Proc Biol Sci 274:1693-1699
28. Hutchinson WF, Carvalho GR, Rogers SI (2001) Marked genetic structuring in localised spawning populations of cod Gadus morhua in the North Sea and adjoining waters, as revealed by microsatellites. Mar Ecol Prog Ser 223: 251-260
29. ICES (2009) Report of the working group on the application of genetics in fisheries and mariculture (WGAGFM). ICES CM 2009/MCC:03, Copenhagen Iles TD, Sinclair M (1982) Atlantic herring: stock discreteness and abundance. Science 215:627-633
30. Jakobsdóttir KB, Jörundsdóttir PD, Skínidóttir S, Hjörleifsdóttir S, Hreggvidsson GO, Daníelsdóttir AK, Pampoulie C (2006) Nine new polymorphic microsatellite loci for the amplification of archived otolith DNA of Atlantic cod, Gadus morhua L. Mol Ecol Notes 6:337-339
31. Jones GP, Milicich MJ, Emslie MJ, Lunow C (1999) Selfrecruitment in a coral reef fish population. Nature 402: 802-804
32. Jones GP, Planes S, Thorrold SR (2005) Coral reef fish larvae settle close to home. Curr Biol 15:1314-1318
33. Jorde PE, Knutsen H, Espeland SH, Stenseth NC (2007) Spatial scale of genetic structuring in coastal cod Gadus morhua and geographic extent of local populations. Mar Ecol Prog Ser 343:229-237
34. Kerr LA, Cadrin SX, Secor DH (2009a) Consequences of spatial structure and connectivity to productivity and persistence of local and regional populations. ICES CM 2009/ H:02, Copenhagen
35. Kerr LA, Secor DH, Piccoli PM (2009b) Partial migration of fishes as exemplified by the estuarine-dependent white perch. Fisheries 34:114-123
36. Knutsen H, Jorde PE, Andre C, Stenseth NC (2003) Finescaled geographic population structuring in a highly mobile marine species: the Atlantic cod. Mol Ecol 12: 385-394
37. Knutsen H, Olsen EM, Ciannelli L, Espeland SH and others (2007) Egg distribution, bottom topography and smallscale cod population structure in a coastal marine system. Mar Ecol Prog Ser 333:249-255
38. Lage C, Kuhn K, Kornfield I (2004) Genetic differentiation among Atlantic cod (Gadus morhua) from Browns Bank, Georges Bank, and Nantucket Shoals. Fish Bull 102: 289-297
39. Larkin PA (1977) An epitaph for the concept of maximum sustained yield. Trans Am Fish Soc 106:1-11
40. Lewis PO, Zaykin D (2001) Genetic data analysis: computer program for the analysis of allelic data. Version 1.0 (dl6c). lewis.eeb.uconn.edu/lewishome/ software.html
41. Lough RG, Hanna CG, Berrien P, Brickman D, Loder JW, Quinlan JA (2006) Spawning pattern variability and its effect on retention, larval growth and recruitment in Georges Bank cod and haddock. Mar Ecol Prog Ser 310: 193-212
42. Manni F, Guérard E, Heyer E (2004) Geographic patterns of (genetic, morphologic, linguistic) variation: how barriers can be detected by using Monmonier's algorithm. Hum Biol 76:173-190
43. Mayo RK, Col LA (2006) The 2005 assessment of the Gulf of Maine Atlantic cod stock. US Department of Commerce, Northeast Fisheries Science Center Reference Document 02-6, Woods Hole, MA
44. McIntyre TM, Hutchings JA (2003) Small-scale temporal and spatial variation in Atlantic cod (Gadus morhua) life history. Can J Fish Aquat Sci 60:1111-1121
45. Meirmans PG (2006) Using the AMOVA framework to estimate a standardised genetic differentiation measure. Evolution 60:2399-2402
46. Metcalfe JD (2006) Fish population structuring in the North Sea: understanding processes and mechanisms from studies of the movements of adults. J Fish Biol 69(Suppl C):48-65
47. Miller KM, Le KD, Beacham TD (2000) Development of triand tetranucleotide repeat microsatellite loci in Atlantic cod (Gadus morhua). Mol Ecol 9:238-239
48. Moen T, Hayes B, Nilsen F, Delghandi M and others (2008) Identification and characterisation of novel SNP markers in Atlantic cod: evidence for directional selection. BMC Genetics 9:18
49. NeiM(1987) Molecular evolutionary genetics. Columbia University Press, New York
50. Nielsen EE, Hansen MM, Ruzzante DE, Meldrup D, Grønkjær P (2003) Evidence of a hybrid zone in Atlantic cod (Gadus morhua) in the Baltic and the Danish Belt Sea revealed by individual admixture analysis. Mol Ecol 12:1497-1508
51. Nielsen EE, Hansen MM, Meldrup D (2006) Evidence of microsatellite hitch-hiking selection in Atlantic cod (Gadus morhua L.): implications for inferring population structure in nonmodel organisms. Mol Ecol 15:3219-3229
52. O'Brien L, Burnett J, Mayo RK (1993) Maturation of nineteen species of finfish off the northeast coast of the United States, 1985-1990. NOAA Tech Rep NIMFS 113
53. Otterlei E, Nyhammer G, Folkvord A, Steffansson SO (1999) Temperature- and size-dependent growth of larval and early juvenile Atlantic cod (Gadus morhua): a comparative study of Norwegian coastal cod and northeast Arctic cod. Can J Fish Aquat Sci 56:2099-2111
54. Palumbi SR (2003) Population genetics, demographic connectivity, and the design of marine reserves. Ecol Appl 13(Suppl Mar Reserv):146-158
55. Pampoulie C, Ruzzante DE, Chosson V, Jörundsdóttir TD and others (2006) The genetic structure of Atlantic cod (Gadus morhua) around Iceland: insight from microsatellites, the Pan I locus, and tagging experiments. Can J Fish Aquat Sci 63:2660-2674
56. Pampoulie C, Stefánsson MO, Jörundsdóttir TD, Danilowicz BS, Daníelsdóttir AK (2008a) Recolonization history and large-scale dispersal in the open sea: the case study of the North Atlantic cod, Gadus morhua L. Biol J Linn Soc 94: 315-329
57. Pampoulie C, Steingrund P, Stefánsson MO, Daníelsdó ttir AK (2008b) Genetic divergence among East Icelandic and Faroese populations of Atlantic cod provides evidence for historical imprints at neutral and non-neutral markers. ICES J Mar Sci 65:65-71
58. Pampoulie C, Jakobsdótttir K, Marteinsdóttir G, Thorsteinsson V (2008c) Are vertical behaviour patterns related to the Pantophysin locus in the Atlantic cod (Gadus morhua L.)? Behav Genet 38:76-81
59. Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288-295
60. Pogson GH (2001) Nucleotide polymorphism and natural selection at the Pantophysin I (Pan I) locus in Atlantic cod, Gadus morhua (L.). Genetics 157:317-330
61. Raymond M, Rousset F (1995) GENEPOP (version 1.2) population genetic software for exact tests and ecumenicism. J Hered 86:248-249
62. Reiss H, Haloarau G, Dickey-Collas M, Wolff WJ (2009) Genetic population structure of marine fish: mismatch between biological and fisheries management units. Fish Fish 10:361-395
63. Rice WR (1989) Analyzing tables of statistical tests. Evolution 43:223-225
64. Robichaud D, Rose GA (2004) Migratory behaviour and range in Atlantic cod: inference from a century of tagging. Fish Fish 5:185-214
65. Ruzzante DE, Taggart CT, Cook D (1996a) Spatial and temporal variation in the genetic composition of a larval cod (Gadus morhua) aggregation: cohort contribution and genetic stability. Can J Fish Aquat Sci 53:2695-2705
66. Ruzzante DE, Taggart CT, Cook D, Goddard S (1996b) Genetic differentiation between inshore and offshore Atlantic cod (Gadus morhua) off Newfoundland: microsatellite DNA variation and antifreeze level. Can J Fish Aquat Sci 53:634-645
67. Ruzzante DE, Taggart CT, Cook D (1998) A nuclear DNA basis for shelf- and bank-scale population structure in northwest Atlantic cod (Gadus morhua): Labrador to Georges Bank. Mol Ecol 7:1663-1680
68. Ruzzante DE, Taggart CT, Cook D (1999) A review of the evidence for genetic structure of cod (Gadus morhua) populations in the NW Atlantic and population affinities of larval cod off Newfoundland and the Gulf of St. Lawrence. Fish Res 43:79-97
69. Ruzzante DE, Wroblewski JS, Taggart CT, Smedbol RK, Cook D, Goddard SV (2000) Bay-scale population structure in coastal Atlantic cod in Labrador and Newfoundland. J Fish Biol 56:431-447
70. Ruzzante DE, Mariani S, Bekkevold D, André C and others (2006) Biocomplexity in a highly migratory pelagic marine fish, Atlantic herring. Proc R Soc B Biol Sci 273:1459-1464
71. Sarvas TH, Fevolden SE (2005) Pantophysin (Pan I) locus divergence between inshore v. offshore and northern v. southern populations of Atlantic cod in the north-east Atlantic. J Fish Biol 67:444-469
72. Schneider S, Roessli D, Excoffier L (2000) Arlequin ver. 2.000: A software for population genetics data analysis. Genetics and Biometry Laboratory, University of Geneva, Geneva
73. Siceloff L (2009) Fine-scale activity, distribution, and habitat utilization of Atlantic cod (Gadus morhua) on the Ipswich Bay spawning ground. MS thesis, University of New Hampshire, Durham, NH
74. Skarstein TH, Westgaard JI, Fevolden SE (2007) Comparing microsatellite variation in north-east Atlantic cod (Gadus morhua L.) to genetic structuring as revealed by the pantophysin (PanI) locus. J Fish Biol 70C:271-290
75. Smedbol RK, Stephenson R (2001) The importance of managing within-species diversity in cod and herring fisheries of the north-western Atlantic. J Fish Biol 59:109-128
76. Stenvik J, Wesmajervi MS, Damsgård B, Delghandi M (2006a) Genotyping of pantophysin I (PanI) of Atlantic cod (Gadus morhua L.) by allele-specific PCR. Mol Ecol Notes 6:272-275
77. Stenvik J, Wesmajervi MS, Fjalestad KT, Damsgård B, Delghandi M (2006b) Development of 25 gene-associated microsatellite markers of Atlantic cod (Gadus morhua L.). Mol Ecol Notes 6:1105-1107
78. Svedäng H, Righton D, Jonsson P (2007) Migratory behavior of Atlantic cod Gadus morhua: natal homing is the prime stock-separating mechanism. Mar Ecol Prog Ser 345: 1-12
79. Taggart CT (1997) Bank-scale migration patterns in northern cod. N Atl Fish Org Sci Counc Stud 29:51-60
80. Tallack SML (ed) (2009) Proceedings from a workshop to identify future research priorities for cod tagging in the Gulf of Maine, 12 February 2009. Northeast Fisheries Science Center Reference Document 09-09, Woods Hole, MA
81. Templeman W (1974) Migrations and intermingling of Atlantic cod (Gadus morhua) stocks of the Newfoundland area. J Fish Res Board Can 31:1073-1092
82. Thorrold SR, Latkoczy C, Swart PK, Jones CM (2001) Natal homing in a marine fish metapopulation. Science 291: 297-299
83. Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535-538
84. Waples RS (1998) Separating the wheat from the chaff: patterns of genetic differentiation in high gene flow species. J Hered 89:438-450
85. Waples RS, Punt AE, Cope JM (2008) Integrating genetic data into management of marine resources: How can we do it better? Fish Fish 9:423-449
86. Ward RD, Woodwark M, Skibinski DOF (1994) A comparison of genetic diversity levels in marine, fresh-water, and anadromous fishes. J Fish Biol 44:213-232
87. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358-1370
88. Wesmajervi MS, Tafese T, Stenvik J, Fjalestad KJ, Damsgård B, Delghandi M (2007) Eight new microsatellite markers in Atlantic cod (Gadus morhua L.) derived from an enriched genomic library. Mol Ecol Notes 7:138-140
89. Westgaard JI, Fevolden SE (2007) Atlantic cod (Gadus morhua L.) in inner and outer coastal zones of northern Norway display divergent genetic signature at non-neutral loci. Fish Res 85:306-315
90. Wirgin I, Waldman JR (2005) Use of nuclear DNA in stock identification: single copy and repetitive sequence markers. In: Cadrin SX, Friedland KD, Waldman JR (eds) Stock identification methods: applications in fisheries science. Elsevier Academic Press, Burlington, MA, p 331-370
91. Wirgin I, Kovach A, Maceda L, Roy NK, Waldman J, Berlinsky D (2007) Stock identification of Atlantic cod in U.S. waters using microsatellite and single nucleotide polymorphism DNA analyses. Trans Am Fish Soc 136:375-391
92. Jónsdóttir IG, Marteinsdóttir G, Pampoulie C (2008) Relation of growth and condition with the Pan I locus in Atlantic cod (Gadus morhua L.) around Iceland. Mar Biol 154: 867-874