Sixty years of anthropogenic pressure: A spatio-temporal genetic analysis of brown trout populations subject to stocking and population declines

Molecular Ecology

Volumn 18, Issue 12, 2009, Pages 2549-2562

  Hansen, Michael M ^a   Fraser, Dylan J ^b   Meier, Kristian ^a   Mensberg, Karen Lise D ^a  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^b DALHOUSIE UNIVERSITY   (Canada)

Author keywords

Admixture; Effective population size; Gene flow; Local adaptation; Microsatellite DNA; Stocking

Indexed keywords

DNA; MICROSATELLITE DNA;

ANIMAL; ARTICLE; CLUSTER ANALYSIS; CROSS BREEDING; DENMARK; DNA SEQUENCE; FOOD INDUSTRY; GENETIC VARIABILITY; GENETICS; POPULATION DENSITY; POPULATION DYNAMICS; POPULATION GENETICS; TROUT;

ANIMALS; CLUSTER ANALYSIS; CROSSES, GENETIC; DENMARK; DNA; FISHERIES; GENETIC VARIATION; GENETICS, POPULATION; MICROSATELLITE REPEATS; POPULATION DENSITY; POPULATION DYNAMICS; SEQUENCE ANALYSIS, DNA; TROUT;

SALMO TRUTTA; SALMONIDAE;

EID: 66749124265     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2009.04198.x     Document Type: Article

References (88)

1. Adkison MD (1995) Population differentiation in Pacific salmon: local adaptation, genetic drift, or the environment? Canadian Journal of Fisheries and Aquatic Sciences, 52, 2762 2777. (Pubitemid 26473286)
2. Allendorf FW, Leary RF, Spruell P, Wenburg JK (2001) The problems with hybrids: setting conservation guidelines. Trends in Ecology & Evolution, 16, 613 622. (Pubitemid 32947021)
3. Araki H, Berejikian BA, Ford MJ, Blouin MS (2008) Fitness of hatchery-reared salmonids in the wild. Evolutionary Applications, 1, 342 355.
4. Araki H, Waples RS, Ardren WR, Cooper B, Blouin MS (2007) Effective population size of steelhead trout: influence of variance in reproductive success, hatchery programs, and genetic compensation between life-history forms. Molecular Ecology, 16, 953 966. (Pubitemid 46270557)
5. e) reveals genetic compensation in steelhead trout. Molecular Ecology, 12, 35 49. (Pubitemid 36108105)
6. 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. (Pubitemid 32295016)
7. Benjamini Y, Yekutieli D (2001) The control of the false discovery rate in multiple testing under dependency. Annals of Statistics, 29, 1165 1188. (Pubitemid 33575263)
8. Bohonak AJ (2002) ibd (isolation by distance): a program for analyses of isolation by distance. Journal of Heredity, 93, 153 154. (Pubitemid 34755399)
9. Bouzat JL, Lewin HA, Paige KN (1998) The ghost of genetic diversity past: historical DNA analysis of the greater prairie chicken. American Naturalist, 152, 1 6. (Pubitemid 28301213)
10. Cairney M, Taggart JB, Hoyheim B (2000) Characterization of microsatellite and minisatellite loci in Atlantic salmon (Salmo salar L.) and cross-species amplification in other salmonids. Molecular Ecology, 9, 2175 2178. (Pubitemid 32053362)
11. Caroffino DC, Miller LM, Kapuscinski AR, Ostazeski JJ (2008) Stocking success of local-origin fry and impact of hatchery ancestry: monitoring a new steelhead (Oncorhynchus mykiss) stocking program in a Minnesota tributary to Lake Superior. Canadian Journal of Fisheries and Aquatic Sciences, 65, 309 318.
12. Dawson MN, Sen Gupta A, England MH (2005) Coupled biophysical global ocean model and molecular genetic analyses identify multiple introductions of cryptogenic species. Proceedings of the National Academy of Sciences, USA, 102, 11968 11973. (Pubitemid 41291113)
13. Dieperink C, Ejbye-Ernst M, Jensen AR et al 1997) Laksefiskene Og Fiskeriet I Vadehavsområdet. DFU Rapport 40-97. Danish Institute for Fisheries Research, Charlottenlund, Denmark.
14. Dieringer D, Schlotterer C (2003) Microsatellite Analyser (msa): a platform independent analysis tool for large microsatellite data sets. Molecular Ecology Notes, 3, 167 169. (Pubitemid 36374637)
15. Dionne M, Caron F, Dodson JJ, Bernatchez L (2008) Landscape genetics and hierarchical genetic structure in Atlantic salmon: the interaction of gene flow and local adaptation. Molecular Ecology, 17, 2382 2396.
16. Edmands S (2007) Between a rock and a hard place: evaluating the relative risks of inbreeding and outbreeding for conservation and management. Molecular Ecology, 16, 463 475. (Pubitemid 46161073)
17. El Mousadik A, Petit RJ (1996) High level of genetic differentiation for allelic richness among populations of the argan tree [Argania spinosa (L.) Skeels] endemic to Morocco. Theoretical and Applied Genetics, 92, 832 839. (Pubitemid 26270161)
18. Eldridge WH, Naish KA (2007) Long-term effects of translocation and release numbers on fine-scale population structure among coho salmon (Oncorhynchus kisutch). Molecular Ecology, 16, 2407 2421. (Pubitemid 46897133)
19. Ellstrand NC, Prentice HC, Hancock JF (1999) Gene flow and introgression from domesticated plants into their wild relatives. Annual Review of Ecology and Systematics, 30, 539 563. (Pubitemid 30065637)
20. Estoup A, Presa P, Krieg F, Vaiman D, Guyomard R (1993) (CT)n and (GT)n microsatellites - a new class of genetic markers for Salmo trutta (brown trout). Heredity, 71, 488 496. (Pubitemid 2010337)
21. Estoup A, Rousset F, Michalakis Y et al 1998) Comparative analysis of microsatellite and allozyme markers: a case study investigating microgeographic differentiation in brown trout (Salmo trutta). Molecular Ecology, 7, 339 353.
22. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software Structure: a simulation study. Molecular Ecology, 14, 2611 2620. (Pubitemid 40886055)
23. Excoffier L, Laval G, Schneider S (2005) Arlequin version 3.0: an integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online, 1, 47 50.
24. Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics, 164, 1567 1587. (Pubitemid 37102217)
25. Felsenstein J (1989) Phylogeny inference package (version 3.2). Cladistics, 5, 164 166.
26. Ferguson A, Taggart JB (1991) Genetic differentiation among the sympatric brown trout (Salmo trutta) populations of Lough Melvin, Ireland. Biological Journal of the Linnean Society, 43, 221 237.
27. Franklin IR (1980) Evolutionary change in small populations. In : Conservation Biology: An Evolutionary-Ecological Perspective (eds Soulé ME, Wilcox BA), pp. 135 150. Sinauer Associates, Sunderland, Massachusetts.
28. Fraser DJ, Cook AM, Eddington JD, Bentzen P (2008) Mixed evidence for reduced local adaptation in wild salmon resulting from interbreeding with escaped farmed salmon: complexities in hybrid fitness. Evolutionary Applications, 1, 501 512.
29. Fraser DJ, Hansen MM, Østergaard S et al 2007a) Comparative estimation of effective population sizes and temporal gene flow in two contrasting population systems. Molecular Ecology, 16, 3866 3889. (Pubitemid 47397332)
30. Fraser DJ, Jones MW, McParland TL, Hutchings JA (2007b) Loss of historical immigration and the unsuccessful rehabilitation of extirpated salmon populations. Conservation Genetics, 8, 527 546. (Pubitemid 46682952)
31. Fraser DJ, Lippe C, Bernatchez L (2004) Consequences of unequal population size, asymmetric gene flow and sex-biased dispersal on population structure in brook charr (Salvelinus fontinalis). Molecular Ecology, 13, 67 80. (Pubitemid 38106474)
32. Garant D, Fleming IA, Einum S, Bernatchez L (2003) Alternative male life-history tactics as potential vehicles for speeding introgression of farm salmon traits into wild populations. Ecology Letters, 6, 541 549. (Pubitemid 36658669)
33. Garant D, Forde SE, Hendry AP (2007) The multifarious effects of dispersal and gene flow on contemporary adaptation. Functional Ecology, 21, 434 443. (Pubitemid 46802125)
34. Gharbi K, Gautier A, Danzmann RG et al 2006) A linkage map for brown trout (Salmo trutta): chromosome homeologies and comparative genome organization with other salmonid fish. Genetics, 172, 2405 2419.
35. Goudet J (1995) fstat (version 1.2): a computer program to calculate F-statistics. Journal of Heredity, 86, 485 486.
36. Guinand B, Scribner KT, Page KS, Burnham-Curtis MK (2003) Genetic variation over space and time: analyses of extinct and remnant lake trout populations in the Upper Great Lakes. Proceedings of the Royal Society B: Biological Sciences, 270, 425 433. (Pubitemid 36250168)
37. Hansen MM (2002) Estimating the long-term effects of stocking domesticated trout into wild brown trout (Salmo trutta) populations: an approach using microsatellite DNA analysis of historical and contemporary samples. Molecular Ecology, 11, 1003 1015. (Pubitemid 34635171)
38. Hansen MM, Ruzzante DE, Nielsen EE, Bekkevold D, Mensberg KLD (2002) Long-term effective population sizes, temporal stability of genetic composition and potential for local adaptation in anadromous brown trout (Salmo trutta) populations. Molecular Ecology, 11, 2523 2535. (Pubitemid 35436674)
39. Hansen MM, Ruzzante DE, Nielsen EE, Mensberg KLD (2001) Brown trout (Salmo trutta) stocking impact assessment using microsatellite DNA markers. Ecological Applications, 11, 148 160. (Pubitemid 32113858)
40. Hansen MM, Skaala O, Jensen LF, Bekkevold D, Mensberg KLD (2007) Gene flow, effective population size and selection at major histocompatibility complex genes: brown trout in the Hardanger Fjord, Norway. Molecular Ecology, 16, 1413 1425. (Pubitemid 46474779)
41. Hutchings JA, Fraser DJ (2008) The nature of fisheries- and farming-induced evolution. Molecular Ecology, 17, 294 313. (Pubitemid 350292473)
42. Jonsson B, Jonsson N (2006) Cultured Atlantic salmon in nature: a review of their ecology and interaction with wild fish. ICES Journal of Marine Science, 63, 1162 1181. (Pubitemid 44164368)
43. Kawecki TJ, Ebert D (2004) Conceptual issues in local adaptation. Ecology Letters, 7, 1225 1241. (Pubitemid 39588356)
44. Larsen K (1993) The sea trout spawning run into Danish streams 1900-60. IV. West Jutland from the Limfjord to the German Border. Meddelelser fra Ferskvandsfiskerilaboratoriet 1/93. Silkeborg, Inland Fisheries Laboratory.
45. Legendre P, Legendre L (1998) Numerical Ecology. Elsevier, Amsterdam, The Netherlands.
46. Leonard JA (2008) Ancient DNA applications for wildlife conservation. Molecular Ecology, 17, 4186 4196.
47. Lynch M, O'Hely M (2001) Captive breeding and the genetic fitness of natural populations. Conservation Genetics, 2, 363 378. (Pubitemid 33635447)
48. Martinez-Cruz B, Godoy JA, Negro JJ (2007) Population fragmentation leads to spatial and temporal genetic structure in the endangered Spanish imperial eagle. Molecular Ecology, 16, 477 486. (Pubitemid 46161074)
49. McGinnity P, Prodohl P, Ferguson K et al 2003) Fitness reduction and potential extinction of wild populations of Atlantic salmon, Salmo salar, as a result of interactions with escaped farm salmon. Proceedings of the Royal Society B: Biological Sciences, 270, 2443 2450. (Pubitemid 37500236)
50. Mclean JE, Bentzen P, Quinn TP (2003) Differential reproductive success of sympatric, naturally spawning hatchery and wild steelhead trout (Oncorhynchus mykiss) through the adult stage. Canadian Journal of Fisheries and Aquatic Sciences, 60, 433 440. (Pubitemid 36901164)
51. Narum SR, Zendt JS, Graves D, Sharp WR (2008) Influence of landscape on resident and anadromous life history types of Oncorhynchus mykiss. Canadian Journal of Fisheries and Aquatic Sciences, 65, 1013 1023.
52. Nei M, Tajima F, Tateno Y (1983) Accuracy of estimated phylogenetic trees from molecular data. 2. Gene frequency data. Journal of Molecular Evolution, 19, 153 170.
53. Nielsen EE, Hansen MM (2008) Waking the dead: the value of population genetic analyses of historical samples. Fish and Fisheries, 9, 450 461.
54. Nielsen EE, Hansen MM, Loeschcke V (1997) Analysis of microsatellite DNA from old scale samples of Atlantic salmon Salmo salar: a comparison of genetic composition over 60 years. Molecular Ecology, 6, 487 492. (Pubitemid 27210837)
55. Nielsen EE, Hansen MM, Loeschcke V (1999a) Analysis of DNA from old scale samples: technical aspects, applications and perspectives for conservation. Hereditas, 130, 265 276. (Pubitemid 29423808)
56. Nielsen EE, Hansen MM, Loeschcke V (1999b) Genetic variation in time and space: microsatellite analysis of extinct and extant populations of Atlantic salmon. Evolution, 53, 261 268. (Pubitemid 29300677)
57. O'Reilly PT, Hamilton LC, McConnell SK, Wright JM (1996) Rapid analysis of genetic variation in Atlantic salmon (Salmo salar) by PCR multiplexing of dinucleotide and tetranucleotide microsatellites. Canadian Journal of Fisheries and Aquatic Sciences, 53, 2292 2298. (Pubitemid 126720654)
58. Paetkau D, Slade R, Burden M, Estoup A (2004) Genetic assignment methods for the direct, real-time estimation of migration rate: a simulation-based exploration of accuracy and power. Molecular Ecology, 13, 55 65. (Pubitemid 38106473)
59. Paetkau D, Waits LP, Clarkson PL, Craighead L, Strobeck C (1997) An empirical evaluation of genetic distance statistics using microsatellite data from bear (Ursidae) populations. Genetics, 147, 1943 1957. (Pubitemid 27525481)
60. Palstra FP, O'Connell MF, Ruzzante DE (2007) Population structure and gene flow reversals in Atlantic salmon (Salmo salar) over contemporary and long-term temporal scales: effects of population size and life history. Molecular Ecology, 16, 4504 4522. (Pubitemid 47620528)
61. Pertoldi C, Hansen MM, Loeschcke V et al 2001) Genetic consequences of population decline in the European otter (Lutra lutra): an assessment of microsatellite DNA variation in Danish otters from 1883 to 1993. Proceedings of the Royal Society of London Series B: Biology Sciences, 268, 1775 1781. (Pubitemid 32844024)
62. Pichler FB, Baker CS (2000) Loss of genetic diversity in the endemic Hector's dolphin due to fisheries-related mortality. Proceedings of the Royal Society B: Biological Sciences, 267, 97 102. (Pubitemid 30047625)
63. Piry S, Alapetite A, Cornuet JM et al 2004) GeneClass2: a software for genetic assignment and first-generation migrant detection. Journal of Heredity, 95, 536 539. (Pubitemid 39383165)
64. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945 959. (Pubitemid 30397141)
65. Roberge C, Normandeau E, Einum S, Guderley H, Bernatchez L (2008) Genetic consequences of interbreeding between farmed and wild Atlantic salmon: insights from the transcriptome. Molecular Ecology, 17, 314 324. (Pubitemid 350292462)
66. Rousset F (1997) Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics, 145, 1219 1228. (Pubitemid 27149123)
67. Ruzzante DE, Hansen MM, Meldrup D, Ebert KM (2004) Stocking impact and migration pattern in an anadromous brown trout (Salmo trutta) complex: where have all the stocked spawning sea trout gone? Molecular Ecology, 13, 1433 1445. (Pubitemid 38688896)
68. Saitou N, Nei M (1987) The neighbor-joining method - a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4, 406 425.
69. Schwartz MK, Luikart G, Waples RS (2007) Genetic monitoring as a promising tool for conservation and management. Trends in Ecology & Evolution, 22, 25 33. (Pubitemid 44959168)
70. Slettan A, Olsaker I, Lie O (1995) Atlantic salmon, Salmo salar, microsatellites at the Ssosl25, Ssosl85, Ssosl311, Ssosl417 loci. Animal Genetics, 26, 281 282.
71. Slettan A, Olsaker I, Lie Ø (1996) Polymorphic Atlantic salmon, Salmo salar L., microsatellites at the SSOSL438, SSOSL439 and SSOSL444 loci. Animal Genetics, 27, 57 64.
72. Slettan A, Olsaker I, Lie O (1997) Segregation studies and linkage analysis of Atlantic salmon microsatellites using haploid genetics. Heredity, 78, 620 627. (Pubitemid 27266522)
73. Smith TB, Mila B, Grether GF et al 2008) Evolutionary consequences of human disturbance in a rainforest bird species from Central Africa. Molecular Ecology, 17, 58 71. (Pubitemid 350292470)
74. Storz JF, Beaumont MA (2002) Testing for genetic evidence of population expansion and contraction: an empirical analysis of microsatellite DNA variation using a hierarchical Bayesian model. Evolution, 56, 154 166. (Pubitemid 34243807)
75. Svärdson G, Faderström Å (1982) Adaptive differences in the long-distance migration of some trout (Salmo trutta) stocks. Reports of the Institute of Freshwater Research, Drottningholm, 60, 51 80.
76. Taylor EB (1991) A review of local adaptation in Salmonidae, with particular reference to Pacific and Atlantic salmon. Aquaculture, 98, 185 207.
77. Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) Micro-Checker: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes, 4, 535 538. (Pubitemid 39147523)
78. Vasemägi A, Gross R, Paaver T, Koljonen ML, Nilsson J (2005) Extensive immigration from compensatory hatchery releases into wild Atlantic salmon population in the Baltic Sea: spatio-temporal analysis over 18 years. Heredity, 95, 76 83. (Pubitemid 40968610)
79. Verardi A, Lucchini V, Randi E (2006) Detecting introgressive hybridization between free-ranging domestic dogs and wild wolves (Canis lupus) by admixture linkage disequilibrium analysis. Molecular Ecology, 15, 2845 2855. (Pubitemid 44215458)
80. Wandeler P, Hoeck PEA, Keller LF (2007) Back to the future: museum specimens in population genetics. Trends in Ecology & Evolution, 22, 634 642. (Pubitemid 350180149)
81. Wang JL (2001) A pseudo-likelihood method for estimating effective population size from temporally spaced samples. Genetical Research, 78, 243 257.
82. Wang IA, Gilk SE, Smoker WW, Gharrett AJ (2007) Outbreeding effect on embryo development in hybrids of allopatric pink salmon (Oncorhynchus gorbuscha) populations, a potential consequence of stock translocation. Aquaculture, 272, S152 S160.
83. Wang JL, Whitlock MC (2003) Estimating effective population size and migration rates from genetic samples over space and time. Genetics, 163, 429 446. (Pubitemid 36222685)
84. Waples RS (2006) A bias correction for estimates of effective population size based on linkage disequilibrium at unlinked gene loci. Conservation Genetics, 7, 167 184. (Pubitemid 43873272)
85. Waples RS, Do C (2008) ldne: a program for estimating effective population size from data on linkage disequilibrium. Molecular Ecology Resources, 8, 753 756.
86. 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. Molecular Ecology, 15, 1419 1439.
87. Waples RS, Yokota M (2007) Temporal estimates of effective population size in species with overlapping generations. Genetics, 175, 219 233. (Pubitemid 46168567)
88. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution, 38, 1358 1370. (Pubitemid 16277759)