Population structure of the thornback ray (Raja clavata L.) in British waters

Journal of Sea Research

Volumn 56, Issue 4, 2006, Pages 305-316

  Chevolot, Malia ^a   Ellis, Jim R ^b   Hoarau, Galice ^a   Rijnsdorp, Adriaan D ^c   Stam, Wytze T ^a   Olsen, Jeanine L ^a  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

^b CENTRE FOR ENVIRONMENT   (United Kingdom)

^c WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

Elasmobranchs; Genetic structure; Microsatellite; Rajidae; Thornback ray

Indexed keywords

FISH; GENETIC ANALYSIS; GENETIC DIFFERENTIATION; GENETIC STRUCTURE; JUVENILE; MIGRATION; POPULATION GENETICS;

ATLANTIC OCEAN; ENGLISH CHANNEL; EURASIA; EUROPE; IRISH SEA; NORTH SEA; WESTERN EUROPE;

ELASMOBRANCHII; RAJA CLAVATA; RAJIDAE;

EID: 33751066146     PISSN: 13851101     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.seares.2006.05.005     Document Type: Article

References (66)

1. Belkhir, K., Borsa, P., Chikhi, L., Raufaste, N., Bonhomme, F., 2004. Genetix 4.05, logiciel sous windows TM pour la génétique des populations, Version 4.05. Laboratoire Génome, Populations, Interactions, CNRS UMR 5000, Université de Montpellier II, Montpellier, France.
2. Birkeland C., and Dayton P.K. The importance in fishery management of leaving the big ones. Trends Ecol. Evol. 20 (2005) 356-358
3. Black W.C., and Krafsur E.S. A Fortran program for the calculation and analysis of 2-locus linkage disequilibrium coefficients. Theor. Appl. Genet. 70 (1985) 491-496
4. Blake K. Polymorphic forms of eye lens protein in the ray Raja clavata (Linnaeus). Comp. Biochem. Physiol., part B 54B (1976) 441-442
5. Bland J.M., and Altman D.G. Multiple significance tests-the Bonferroni method. Br. Med. J. 310 (1995) 170
6. Borsa P., Blanquer A., and Berrebi P. Genetic structure of the flounders Platichthys flesus and P. stellatus at different geographic scales. Mar. Biol. 129 (1997) 233-246
7. Brander K. Disappearance of common skate Raia-Batis from Irish Sea. Nature 290 (1981) 48-49
8. Chakraborty R., and Zhong Y.X. Statistical power of an exact test of hardy-weinberg proportions of genotypic data at a multiallelic locus. Hum. Hered. 44 (1994) 1-9
9. Chevolot M., Reusch T.B.H., Boele-Bos S., Stam W.T., and Olsen J.L. Characterization and isolation of DNA microsatellite primers in Raja clavata L. (thornback ray, Rajidae). Mol. Ecol. Notes 5 (2005) 427-429
10. Cornuet J.M., Piry S., Luikart G., Estoup A., and Solignac M. New methods employing multilocus genotypes to select or exclude populations as origins of individuals. Genetics 153 (1999) 1989-2000
11. Dulvy N.K., and Reynolds J.D. Predicting extinction vulnerability in skates. Conserv. Biol. 16 (2002) 440-450
12. Dulvy N.K., Metcalfe J.D., Glanville J., Pawson M.G., and Reynolds J.D. Fishery stability, local extinctions, and shifts in community structure in skates. Conserv. Biol. 14 (2000) 283-293
13. Ellis J.R., and Shackley S.E. Observations on egg-laying in the thornback ray. J. Fish. Biol. 46 (1995) 903-904
14. Ellis J.R., Cruz-Martinez A., Rackham B.D., and Rogers S.I. The distribution of chondrichthyan fishes around the British Isles and implications for conservation. J. North. Atl. Fish. Sci. 35 (2005) 195-213
15. Elphinstone M.S., Hinten G.N., Anderson M.J., and Nock C.J. An inexpensive and high-throughput procedure to extract and purify total genomic DNA for population studies. Mol. Ecol. Notes 3 (2003) 317-320
16. Feldheim K.A., Gruber S.H., and Ashley M.V. Population genetic structure of the lemon shark (Negaprion brevirostris) in the western Atlantic: DNA microsatellite variation. Mol. Ecol. 10 (2001) 295-303
17. Gaggiotti O.E., Lange O., Rassmann K., and Gliddon C. A comparison of two indirect methods for estimating average levels of gene flow using microsatellite data. Mol. Ecol. 8 (1999) 1513-1520
18. Garcia L.V. Controlling the false discovery rate in ecological research. Trends Ecol. Evol. 18 (2003) 553-554
19. Grift R.E., Rijnsdorp A.D., Barot S., Heino M., and Dieckmann U. Fisheries-induced trends in reaction norms for maturation in North Sea plaice. Mar. Ecol. Prog. Ser. 257 (2003) 247-257
20. Hauser L., Adcock G.J., Smith P.J., Ramirez J.H., and Carvalho G.R. Loss of microsatellite diversity and low effective population size in an overexploited population of New Zealand snapper (Pagrus auratus). Proc. Natl. Acad. Sci. USA 99 (2002) 11742-11747
21. Hedrick P.W. Perspective: highly variable loci and their interpretation in evolution and conservation. Evolution 53 (1999) 313-318
22. Heino M., and Godo O.R. Fisheries-induced selection pressures in the context of sustainable fisheries. Bull. Mar. Sci. 70 (2002) 639-656
23. Heino M., Dieckmann U., and Godo O.R. Estimating reaction norms for age and size at maturation with reconstructed immature size distributions: a new technique illustrated by application to Northeast Arctic cod. ICES J. Mar. Sci. 59 (2002) 562-575
24. Heist E.J. A review of population genetics in sharks. Am. Fish. Soc. Symp. 23 (1999) 161-168
25. Heist E.J., and Gold J.R. Microsatellite DNA variation in sandbar sharks (Carcharhinus plumbeus) from the Gulf of Mexico and mid-Atlantic Bight. Copeia (1999) 182-186
26. Hewitt GM. Some genetic consequences of ice ages, and their role in divergence and speciation. Biol. J. Linn. Soc. 58 (1996) 247-276
27. Hoarau G., Rijnsdorp A.D., Van der Veer H.W., Stam W.T., and Olsen J.L. Population structure of plaice (Pleuronectes platessa L.) in northern Europe: microsatellites revealed large-scale spatial and temporal homogeneity. Mol. Ecol. 11 (2002) 1165-1176
28. Hoarau G., Boon E., Jongma D.N., Ferber S., Palsson J., Van der Veer H.W., Rijnsdorp A.D., Stam W.T., and Olsen J.L. Low effective population size and inbreeding in plaice (Pleuronectes platessa): an abundant but overexploited flatfish. Proc. R. Soc. Lond. Ser. B-Biol. Sci. 272 (2005) 497-503
29. Holden M.J. Fecundity of Raja clavata in British waters. J. Cons. Int. Exp. Mer 36 (1975) 110-118
30. Holden M.J., Rout D.W., and Humphreys C.N. The rate of egg laying by three species of ray. J. Cons. Int. Exp. Mer. 33 (1971) 335-339
31. Hunter E., Buckley A.A., Stewart C., and Metcalfe J.D. Migratory behavior of the thornback ray, Raja clavata in the southern North Sea. J. Mar. Biol. Assoc. UK 85 (2005) 1095-1105
32. Hunter E., Buckley A.A., Stewart C., and Metcalf J.D. Repeated seasonal migration by a thornback ray in the southern North Sea. J. Mar. Biol. Assoc. UK 85 (2005) 1199-1200
33. Hutchinson F.H., Van Oosterhout C., Rogers S.I., and Carvalho G.R. Temporal analysis of archived samples indicates marked genetic changes in declining North Sea cod (Gadus morhua). Proc. R. Soc. Lond. Ser. B-Biol. Sci. 270 (2003) 2125-2132
34. Keeney D.B., Heupel M.R., Hueter R.E., and Heist E.J. Microsatellite and mitochondrial DNA analyses of the genetic structure of blacktip shark (Carcharhinus limbatus) nurseries in the northwestern Atlantic, Gulf of Mexico, and Caribbean Sea. Mol. Ecol. 14 (2005) 1911-1923
35. Mantel N. Detection of disease clustering and a generalized regression approach. Cancer Res. 27 (1967) 209
36. Moran P. Current conservation genetics: building an ecological approach to the synthesis of molecular and quantitative genetic methods. Ecol. Freshw. Fish 11 (2002) 30-55
37. Nei M. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89 (1978) 583-590
38. Neigel J.E. Is F-ST obsolete?. Conserv. Gen. 3 (2002) 167-173
39. Nielsen E.E., Nielsen P.H., Meldrup D., and Hansen M.M. Genetic population structure of turbot (Scophthalmus maximus L.) supports the presence of multiple hybrid zones for marine fishes in the transition zone between the Baltic Sea and the North Sea. Mol. Ecol. 13 (2004) 585-595
40. Nottage A.S., and Perkins E.J. Growth and maturation of roker Raja clavata L. in the Solway Firth. J. Fish. Biol. 23 (1983) 43-48
41. O'Reilly P.T., Canino M.F., Bailey K.M., and Bentzen P. Inverse relationship between F-ST and microsatellite polymorphism in the marine fish, walleye pollock (Theragra chalcogramma): implications for resolving weak population structure. Mol. Ecol. 13 (2004) 1799-1814
42. Olsen E., Lilly G.R., Heino M., Morgan M.J., Brattey J., and Dieckmann U. Assessing changes in age and size at maturation in collapsing populations of Atlantic cod (Gadus morhua). Can. J. Fish. Aquat. Sci. 62 (2005) 811-823
43. Paetkau D., Slade R., Burden M., and Estoup A. Genetic assignment methods for the direct, real-time estimation of migration rate: a simulation-based exploration of accuracy and power. Mol. Ecol. 13 (2004) 55-65
44. Pardini A.T., Jones C.S., Noble L.R., Kreiser B., Malcolm H., Bruce B.D., Stevens J.D., Cliff G., Scholl M.C., Francis M., Duffy C.A., and Martin A.P. Sex-biased dispersal of great white sharks. Nature 412 (2001) 139-140
45. Perneger T.V. What's wrong with Bonferroni adjustments. Br. Med. J. 316 (1998) 1236-1238
46. Piry S., Alapetite A., Cornuet J.M., Paetkau D., Baudouin L., and Estoup A. GENECLASS 2.0: a software for genetic assignment and first-generation migrant detection. J. Hered. 95 (2004) 536-539
47. Pogson G.H., Taggart C.T., Mesa K.A., and Boutilier R.G. Isolation by distance in the Atlantic cod, Gadus morhua, at large and small geographic scales. Evolution 55 (2001) 131-146
48. Rannala B., and Mountain J.L. Detecting immigration by using multilocus genotypes. Proc. Natl. Acad. Sci. USA 94 (1997) 9197-9201
49. Rice W.R. Analyzing tables of statistical tests. Evolution 43 (1989) 223-225
50. Rocha-Olivares A., and Vetter R.D. Effects of oceanographic circulation on the gene flow, genetic structure, and phylogeography of the rosethorn rockfish (Sebastes helvomaculatus). Can. J. Fish. Aquat. Sci. 56 (1999) 803-813
51. Rousset F. Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145 (1997) 1219-1228
52. Ruzzante D.E., Taggart C.T., and Cook D. A nuclear DNA basis for shelf- and bank-scale population structure in northwest Atlantic cod (Gadus morhua): labrador to Georges Bank. Mol. Ecol. 7 (1998) 1663-1680
53. Ryland J.S., and Ajayi T.O. Growth and population-dynamics of 3 raja species (Batoidei) in Carmarthen Bay, British-Isles. J. Cons. Int. Exp. Mer 41 (1984) 111-120
54. Schrey A.W., and Heist E.J. Microsatellite analysis of population structure in the shortfin mako (Isurus oxyrinchus). Can. J. Fish. Aquat. Sci. 60 (2003) 670-675
55. Slatkin M. A Measure of population subdivision based on microsatellite allele frequencies. Genetics 139 (1995) 457-462
56. Spencer C.C., Neigel J.E., and Leberg P.L. Experimental evaluation of the usefulness of microsatellite DNA for detecting demographic bottlenecks. Mol. Ecol. 9 (2000) 1517-1528
57. Stehmann, M., 1995. Maturation guide for elasmobranchs. Report of the ICES study group on elasmobranch fishes. Report CM 1995/G:3. 85 p.
58. Stehmann M., and Bürkel D.L. Rajidae. In: Whitehead P.J.P., Bauchot M.L., Hureau J.-C., Nielsen J., and Tortonese E. (Eds). Fishes of the North-eastern Atlantic and Mediterranean vol. I (1994), UNESCO, Paris 163-196
59. Van Oosterhout C., Hutchinson W.F., Wills D.P.M., and Shipley P. MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol. Ecol. Notes 4 (2004) 535-538
60. Walker P.A., and Heessen H.J.L. Long-term changes in ray populations in the North Sea. ICES J. Mar. Sci. 53 (1996) 1085-1093
61. Walker P.A., and Hislop J.R.G. Sensitive skates or resilient rays? Spatial and temporal shifts in ray species composition in the central and north-western North Sea between 1930 and the present day. ICES J. Mar. Sci. 55 (1998) 392-402
62. Walker P.A., Howlett G., and Millner R. Distribution, movement and stock structure of three ray species in the North Sea and eastern English Channel. ICES J. Mar. Sci. 54 (1997) 797-808
63. Waples R.S. Separating the wheat from the chaff: Patterns of genetic differentiation in high gene flow species. J. Hered. 89 (1998) 438-450
64. Weir B.S., and Cockerham C.C. Estimating F-statistics for the analysis of population structure. Evolution 38 (1984) 1358-1370
65. Whittamore J.M., and McCarthy I.D. The population biology of the thornback ray, Raja clavata in Caernarfon Bay, north Wales. J. Mar. Biol. Assoc. UK 85 (2005) 1089-1094
66. Wright S. Evolution and the Genetics of Population. Vol. 2. The Theory of Gene Frequencies (1969), University of Chicago Press, Chicago