Evidence of microsatellite hitch-hiking selection in Atlantic cod (Gadus morhua L.): Implications for inferring population structure in nonmodel organisms

Molecular Ecology

Volumn 15, Issue 11, 2006, Pages 3219-3229

  Nielsen, Einar E ^a   Hansen, Michael M ^a   Meldrup, Dorte ^a  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

Author keywords

Gadus morhua; Hitch hiking selection; Marine fish; Microsatellites; Population structure

Indexed keywords

DNA; MICROSATELLITE DNA;

ALLELE; ANIMAL; ARTICLE; ATLANTIC COD; CHEMISTRY; DNA SEQUENCE; GENETIC SELECTION; GENETIC VARIABILITY; GENETICS; POPULATION GENETICS; SEA;

ALLELES; ANIMALS; DNA; GADUS MORHUA; GENETICS, POPULATION; MICROSATELLITE REPEATS; OCEANS AND SEAS; SELECTION (GENETICS); SEQUENCE ANALYSIS, DNA; VARIATION (GENETICS);

GADUS MORHUA; PISCES;

EID: 33748619762     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2006.03025.x     Document Type: Article

References (61)

1. Arnason E (2004) Mitochondrial cytochrome b DNA variation in the high-fecundity Atlantic cod: trans-Atlantic clines and shallow gene genealogy. Genetics, 166, 1871-1885.
2. ST: fish, allozymes and the Lewontin-Krakauer test revisited. Genetics, 152, 653-659.
3. Beacham TD, Brattey J, Miller KM et al. (2002) Multiple stock structure of Atlantic cod (Gadus morhua) off Newfoundland and Labrador determined from genetic variation. Ices Journal of Marine Science, 59, 650-665.
4. Beaumont MA (1999) Detecting population expansion and decline using microsatellites. Genetics, 153, 2013-2029.
5. ST tell us? Trends in Ecology & Evolution, 20, 435-440.
6. Beaumont MA, Balding DJ (2004) Identifying adaptive genetic divergence among populations from genome scans. Molecular Ecology, 13, 969-980.
7. Beaumont MA, Nichols RA (1996) Evaluating loci for use in the genetic analysis of population structure. Proceedings of the Royal Society of London. Series B, Biological Sciences, 263, 1619-1626.
8. Beerli P, Felsenstein J (2001) Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proceedings of the National Academy of Sciences, USA, 98, 4563-4568.
9. Bentzen P, Taggart CT, Ruzzante DE et al. (1996) Microsatellite polymorphism and the population structure of Atlantic cod (Gadus morhua) in the northwest Atlantic. Canadian Journal of Fisheries and Aquatic Sciences, 53, 2706-2721.
10. Berg E, Sarvas TH, Harbitz A et al. (2005) Accuracy and precision in stock separation of north-east Arctic and Norwegian coastal cod by otoliths - comparing readings, image analyses and a genetic method. Marine and Freshwater Research, 56, 753-762.
11. Brooker AL, Cook D, Bentzen P, Wright JM, Doyle RW (1994) Organization of microsatellites differs between mammals and cold-water teleost fishes. Canadian Journal of Fisheries and Aquatic Sciences, 51, 1959-1966.
12. Campbell D, Bernatchez L (2004) Genomic scan using AFLP markers as a means to assess the role of directional selection in the divergence of sympatric whitefish ecotypes. Molecular Biology and Evolution, 21, 945-956.
13. Campbell D, Duchesne P, Bernatchez L (2003) AFLP utility for population assignment studies: analytical investigation and empirical comparison with microsatellites. Molecular Ecology, 12, 1979-1991.
14. DeWoody JA, Avise JC (2000) Microsatellite variation in marine, freshwater and anadromous fishes compared with other animals. Journal of Fish Biology, 56, 461-473.
15. Endler JA (1986) Natural Selection in the Wild. Princeton University Press, Princeton, New Jersey.
16. Estoup A, Largiader CR, Perrot E, Chourrout D (1996) Rapid one-tube DNA extraction for reliable PCR detection of fish polymorphic markers and transgenes. Molecular Marine Biology and Biotechnology, 5, 295-298.
17. ST CALC: a collection of computer programs for calculating unbiased estimates of genetic differentiation and determining their significance for microsatellite data. Molecular Ecology, 6, 881-885.
18. Goudet J (1995) FSTAT (version 1.2): a computer programme to calculate F-statistics. Journal of Heredity, 86, 485-486.
19. Guinand B, Lemaire C, Bonhomme F (2004) How to detect polymorphisms undergoing selection in marine fishes? A review of methods and case studies, including flatfishes. Journal of Sea Research, 51, 167-182.
20. Hedrick PW (1999) Perspective: highly variable loci and their interpretation in evolution and conservation. Evolution, 53, 313-318.
21. Hedrick PW (2005) A standardized genetic differentiation measure. Evolution, 59, 1633-1638.
22. 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. Marine Ecology Progress Series, 223, 251-260.
23. Hutchinson WF, Oosterhout Cv, Rogers SI, Carvalho GR (2003) Temporal analysis of archived samples indicates marked genetic changes in declining North Sea cod (Gadus morhua). Proceedings of the Royal Society of London. Series B, Biological Sciences, 270, 2125-2132.
24. Jarne P, Lagoda PJL (1996) Microsatellites, from molecules to populations and back. Trends in Ecology & Evolution, 11, 424-429.
25. Jones AG, Ardren WR (2003) Methods of parentage analysis in natural populations. Molecular Ecology, 12, 2511-2523.
26. Jørgensen HBH, Hansen MM, Bekkevold D et al. (2005) Marine landscapes and population genetic structure of herring (Clupea harengus L.) in the Baltic Sea. Molecular Ecology, 14, 3219-3234.
27. Karlsson S, Mork J (2005) Deviation from Hardy-Weinberg equilibrium, and temporal instability in allele frequencies at microsatellite loci in a local population of Atlantic cod. Ices Journal of Marine Science, 62, 1588-1596.
28. Kauer M, Dieringer D, Schlotterer C (2003) Nonneutral admixture of immigrant genotypes in African Drosophila melanogaster populations from Zimbabwe. Molecular Biology and Evolution, 20, 1329-1337.
29. Knutsen H, Jorde PE, Andre C et al. (2003) Fine-scaled geographical population structuring in a highly mobile marine species: the Atlantic cod. Molecular Ecology, 12, 385-394.
30. Lewontin RC, Krakauer J (1973) Distribution of gene frequency as a test of theory of selective neutrality of polymorphisms. Genetics, 74, 175-195.
31. Lynch M, Walsh B (1998) Genetics and Analysis of Quantitative Traits. Sinauer Associates, Sunderland, Massachusetts.
32. Manel S, Gaggiotti OE, Waples RS (2005) Assignment methods: matching biological questions with appropriate techniques. Trends in Ecology & Evolution, 20, 136-142.
33. Miller KM, Le KD, Beacham TD (2000) Development of tri- and tetranucleotide repeat microsatellite loci in Atlantic cod (Gadus morhua). Molecular Ecology, 9, 238-239.
34. Morin PA, Luikart G, Wayne RK (2004) SNPs in ecology, evolution and conservation. Trends in Ecology & Evolution, 19, 208-216.
35. Mork J, Ryman N, Ståhl G, Utter F, Sundnes G (1985) Genetic variation in Atlantic cod (Gadus morhua) throughout its range. Canadian Journal of Fisheries and Aquatic Sciences, 42, 1580-1587.
36. Nei M (1973) Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences, USA, 70, 3321-3323.
37. Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics, 89, 583-590.
38. Nielsen EE, Kenchington E (2001) Prioritising marine fish and shellfish populations for conservation: a useful concept? Fish and Fisheries, 2, 328-343.
39. Nielsen EE, Hansen MM, Schmidt C, Meldrup D, Grønkjær P (2001) Population of origin of Atlantic cod. Nature, 413, 272.
40. 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. Molecular Ecology, 12, 1497-1508.
41. Nielsen EE, Nielsen PH, Meldrup D, Hansen MM (2004) 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. Molecular Ecology, 13, 585-595.
42. Nielsen EE, Gronkjaer P, Meldrup D et al. (2005) Retention of juveniles within a hybrid zone between North Sea and Baltic Sea Atlantic cod (Gadus morhua). Canadian Journal of Fisheries and Aquatic Sciences, 62, 2219-2225.
43. 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. Journal of Fish Biology, 56, 1074-1086.
44. ST and microsatellite polymorphism in the marine fish, walleye pollock (Theragra chalcogramma): implications for resolving weak population structure. Molecular Ecology, 13, 1799-1814.
45. Pogson GH, Fevolden SE (2003) Natural selection and the genetic differentiation of coastal and Arctic populations of the Atlantic cod in northern Norway: a test involving nucleotide sequence variation at the pantophysin (PanI) locus. Molecular Ecology, 12, 63-74.
46. Pogson GH, Mesa KA, Boutilier RG (1995) Genetic population structure and gene flow in the Atlantic cod Gadus morhua: a comparison of allozyme and nuclear RFLP loci. Genetics, 139, 375-385.
47. 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). Molecular Ecology, 15, 321-331.
48. Ranum LPW, Day JW (2002) Dominantly inherited, non-coding microsatellite expansion disorders. Current Opinions in Genetics and Development, 12, 266-271.
49. Ruzzante DE, Taggart CT, Cook C, Goddard S (1996) Genetic differentiation between inshore and offshore Atlantic cod (Gadus morhua) off Newfoundland: Microsatellite DNA variation and antifreeze level. Canadian Journal of Fisheries and Aquatic Sciences, 53, 634-645.
50. 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. Molecular Ecology, 7, 1663-1680.
51. 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. Fisheries Research, 43, 79-97.
52. Ruzzante DE, Wroblewski JS, Taggart CT et al. (2000) Bay-scale population structure in coastal Atlantic cod in Labrador and Newfoundland, Canada. Journal of Fish Biology, 56, 431-447.
53. Schlötterer C (2002) A microsatellite-based multilocus screen for the identification of local selective sweeps. Genetics, 160, 753-763.
54. Schlötterer C, Dieringer D (2005) A novel test statistics for the identification of local selective sweeps based on microsatellite gene diversity. In: Selective Sweep (ed. Nurminski D), pp. 55-64. Eurekah.com and Klüver Academic/Plenum Publishers, Georgetown, TX, USA.
55. Sick K (1965) Haemoglobin polymorphism of cod in the Baltic and the Danish Belt Sea. Hereditas, 54, 49-73.
56. Slate J (2005) Quantitative trait locus mapping in natural populations: progress, caveats and future directions. Molecular Ecology, 14, 363-379.
57. Thuillet AC, Bataillon T, Poirier S et al. (2005) Estimation of long-term effective population sizes through the history of durum wheat using microsatellite data. Genetics, 169, 1589-1599.
58. Van Tienderen PH, de Haan AA, van der Linden CG et al. (2002) Biodiversity assessment using markers for ecologically important traits. Trends in Ecology and Evolution, 17, 577-582.
59. Vasemagi A, Nilsson J, Primmer CR (2005) Expressed sequence tag-linked microsatellites as a source of gene-associated polymorphisms for detecting signatures of divergent selection in Atlantic salmon (Salmo salar L.). Molecular Biology and Evolution, 22, 1067-1076.
60. Vitalis R, Dawson K, Boursot P (2001) Interpretation of variation across marker loci as evidence of selection. Genetics, 158, 1811-1823.
61. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution, 38, 1358-1370.