Microgeographical population structure of cod Gadus morhua in the North Sea and west of Scotland: The role of sampling loci and individuals

Marine Ecology Progress Series

Volumn 376, Issue , 2009, Pages 213-225

  Nielsen, Einar Eg ^a   Wright, Peter John ^b   Hemmer Hansen, Jakob ^a   Poulsen, Nina Aagaard ^a,c   Gibb, Iain Monro ^b   Meldrup, Dorte ^a  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^b MARINE LABORATORY   (United Kingdom)

^c AARHUS UNIVERSITY   (Denmark)

Author keywords

Atlantic cod; Genetic; Microsatellites; Population structure; Selection

Indexed keywords

GADOID; GENETIC DIFFERENTIATION; GENETIC MARKER; GEOGRAPHICAL DISTRIBUTION; POPULATION STRUCTURE;

ATLANTIC OCEAN; EURASIA; EUROPE; NORTH SEA; SCOTLAND; UNITED KINGDOM; WESTERN EUROPE;

GADUS MORHUA;

EID: 62149096423     PISSN: 01718630     EISSN: None     Source Type: Journal    
DOI: 10.3354/meps07798     Document Type: Article

References (51)

1. Allendorf FW, Phelps SR (1981) Use of allelic frequencies to describe population structure. Can J Fish Aquat Sci 38:1507-1514
2. Beaumont MA, Nichols RA (1996) Evaluating loci for use in the genetic analysis of population structure. Proc R Soc Lond B 263:1619-1626
3. Beerli P, Felsenstein J (1999) Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach. Genetics 152:763-773
4. Bentzen P, Taggart CT, Ruzzante DE, Cook D (1996) Microsatellite polymorphism and the population structure of Atlantic cod (Gadus morhua) in the northwest Atlantic. Can J Fish Aquat Sci 53:2706-2721
5. Bradbury IR, Campana SE, Bentzen P (2008) Estimating contemporary early life-history dispersal in estuarine fish: integrating molecular and otolith elemental approaches. Mol Ecol 17:1438-1450
6. 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
7. Dulvy NK, Jennings S, Rogers SI, Maxwell DL (2006) Threat and decline in fishes: an indicator of marine biodiversity. Can J Fish Aquat Sci 63:1267-1275
8. Espeland SH, Gundersen AF, Olsen EM, Knutsen H, Gjøsæter J, Stenseth NC (2007) Home range and elevated egg densities within an inshore spawning ground of coastal cod. ICES J Mar Sci 64:920-928
9. Estoup A, Largiader CR, Perrot E, Chourrout D (1996) Rapid one-tube DNA extraction for reliable PCR detection of fish polymorphic markers and transgenes. Mol Mar Biol Biotechnol 5:295-298
10. Excoffier L, Smouse P, Quattro J (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479-491
11. Gibb FM, Gibb IM, Wright PJ (2007) Isolation of Atlantic cod (Gadus morhua) nursery areas. Mar Biol 151:1185-1194
12. Goudet J (1995) FSTAT (version 1.2): a computer program to calculate F-statistics. J Hered 86:485-486
13. Goudet J, Raymond M, Demeeus T, Rousset F (1996) Testing differentiation in diploid populations. Genetics 144:1933-1940
14. Hemmer-Hansen J, Nielsen EE, Frydenberg J, Loeschcke V (2007) Adaptive divergence in a high gene flow environment: Hsc70 variation in the European flounder (Platicthys flesus L.). Heredity 99:592-600
15. Hoelzel AR, Hey J, Dahlheim ME, Nicholson C, Burkanov V, Black N (2007) Evolution of population structure in a highly social top predator, the killer whale. Mol Biol Evol 24:1407-1415
16. 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
17. Hutchinson WF, Van Oosterhou C, Rogers SI, Carvalho GR (2003) Temporal analysis of archived samples indicates marked genetic changes in declining North Sea cod (Gadus morhua). Proc R Soc Lond B 270:2125-2132
18. 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
19. Knutsen H, Jorde PE, André C, Stenseth NC (2003) Fine-scaled geographical population structuring in a highly mobile marine species: the Atlantic cod. Mol Ecol 12:385-394
20. Knutsen H, Olsen EM, Ciannelli L, Espeland SH and others (2007) Egg distribution, bottom topography and small-scale cod population structure in a coastal marine system. Mar Ecol Prog Ser 333:249-255
21. Kusumo HT, Pfister CA, Wooton JT (2006) Small-scale genetic structure in the sea palm Postelsia palmaeformis Ruprecht (Phaeophyceae). Mar Biol 149:731-742
22. Manni F, Guerard 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
23. Mathews LM (2007) Evidence for restricted gene flow over small spatial scales in a marine snapping shrimp Alpheus angulosus. Mar Biol 152:645-655
24. Miller KM, Le KD, Beacham TD (2000) Development of tri-and tetranucleotide repeat microsatellite loci in Atlantic cod (Gadus morhua). Mol Ecol 9:238-239
25. Moen T, Hayes B, Nilsen F, Delghandi M and others (2008) Identification and characterisation of novel SNP markers in Atlantic cod and their application in genetic mapping and population genetics. BMC Genet 9:18
26. Nei M, Tajima F, Tatano Y (1983) Accuracy of estimated phylogenetic trees from molecular data. J Mol Evol 19:153-170
27. Nielsen EE, Hansen MM, Schmidt C, Meldrup D, Grønkjær P (2001) Determining the population of origin of individual cod in the Northeast Atlantic. Nature 413:272
28. 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
29. Nielsen EE, Bach LA, Kotlicki P (2006a) HYBRIDLAB (version 1.0): a program for generating simulated hybrids from population samples. Mol Ecol Notes 6:971-973
30. Nielsen EE, Hansen MM, Meldrup D (2006b) Evidence of microsatellite hitch-hiking selection in Atlantic cod (Gadus morhua L.): Implications for inferring population structure in non-model organisms. Mol Ecol 15:3219-3229
31. Nielsen EE, MacKenzie BR, Magnussen E, Meldrup D (2007) Historical analysis of Pan I in cod (Gadus morhua); no evidence of a recent selective sweep in populations from the southern part of the species distribution. Can J Fish Aquat Sci 64:1448-1455
32. O'Leary DB, Coughlan J, Dillane E, McCarthy TV, Cross TF (2007) Microsatellite variation in cod Gadus morhua throughout its geographic range. J Fish Biol 70:310-335
33. O'Reilly PT, Canino MF, Bailey KM, Bentzen P (2000) Isolation of twenty low stutter di- and tetra nucleotide microsatellites for population analysis of walleye pollock and other gadoids. J Fish Biol 56:1074-1086
34. Palumbi SR (2003) Population genetics, demographic connectivity and the design of marine protected areas. Ecol Appl 13:146-158
35. Pampoulie C, Gysels ES, Maes GE, Hellemans B, Leentjes V, Jones AG, Volckaert FAM (2004) Evidence for fine-scale genetic structure and estuarine colonisation in a potential high gene flow marine goby (Pomatoschistus minutus). Heredity 92:434-445
36. Pampoulie C, Steingrund P, Stefánsson MÖ, Daníelsdóttir AK (2008) 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
37. Poulsen NA, Nielsen EE, Schierup MH, Loeschcke V, Grønkjær P (2006) Long-term stability and effective population size in North Sea and Baltic Sea cod (Gadus morhua). Mol Ecol 15:321-331
38. Rice WR (1989) Analysing tables of statistical tests. Evolution 43:223-225
39. 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
40. Schneider S, Kueffer JM, Roessli D, Excoffier L (2000) Arlequin, version 2.000. Genetics and Biometry Lab, Department of Anthropology, University of Geneva, Switzerland, available at www.anthropologie.unige.ch/arlequin/
41. 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 (Pan I) locus. J Fish Biol 70:271-290
42. Wang J (2004) Sibship reconstruction from genetic data with typing errors. Genetics 166:1963-1979
43. Waples RS (1998) Separating the wheat from the chaff: patterns of genetic differentiation in high gene flow species. J Hered 89:438-450
44. Waples RS, Gaggiotti O (2006) What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity. Mol Ecol 15:1419-1439
45. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358-1370
46. 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
47. ST ≠ 1/(4Nm + 1). Heredity 82:117-125
48. Wright PJ, Galley E, Gibb IM, Neat FC (2006a) Fidelity of adult cod to spawning grounds in Scottish waters. Fish Res 77:148-158
49. Wright PJ, Neat FC, Gibb FM, Gibb IM, Thordason H (2006b) Evidence for metapopulation structuring in cod from the west of Scotland and North Sea. J Fish Biol 69:181-199
50. Young FW (1996) ViSta: the visual statistics system. Research Memorandum 94-1(b) (2nd edn). L. L. Thursone Psychometric Laboratory, University of North Carolina, Chapel Hill
51. Zbinden JA, Largiadèr CR, Leippert F, Margaritoulis D, Arlettaz R (2007) High frequency of multiple paternity in the largest rookery of Mediterranean loggerhead sea turtles. Mol Ecol 16:3703-3711