An examination of genetic diversity and effective population size in Atlantic salmon populations

Genetics Research

Volumn 91, Issue 6, 2009, Pages 395-412

  Nikolic, Natacha ^a   Butler, James R A ^b   Bagliènire, Jean Luc ^c   Laughton, Robert ^d   McMyn, Iain A G ^e   Chevalet, Claude ^a  

^a CEMAGREF   (France)

^b JAMES COOK UNIVERSITY   (Australia)

^c AGROCAMPUS OUEST   (France)

^d Spey Fishery Board Research Office   (United Kingdom)

^e Kyle of Sutherland District Salmon Fishery Board   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA MARKER; MICROSATELLITE DNA;

ALLELE; ARTICLE; ATLANTIC SALMON; CONTROLLED STUDY; DEMOGRAPHY; EFFECTIVE POPULATION SIZE; EUROPE; GENE FLOW; GENE FREQUENCY; GENE LOCATION; GENE LOCUS; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC VARIABILITY; GENOTYPE; INTERMETHOD COMPARISON; NONHUMAN; POPULATION GENETICS; PREDICTION; SENSITIVITY AND SPECIFICITY;

ANIMAL MIGRATION; ANIMALS; GENETIC VARIATION; GENETICS, POPULATION; POPULATION DENSITY; SALMO SALAR;

SALMO SALAR;

EID: 77949643213     PISSN: 00166723     EISSN: 14695073     Source Type: Journal    
DOI: 10.1017/S0016672309990346     Document Type: Article

References (104)

1. Anonymous (2000). Revised Guidance Updating Scottish Office Circular No. 6/1995. Nature Conservation: Implementation in Scotland of EC Directives on the Conservation of Natural Habitats and of Wild Flora and Fauna and the Conservation of Wild Birds (The Habitats and Bird Directives), p. 96. Edinburgh: Scottish Executive.
2. Anonymous (2001). Report of the Working Group on the Atlantic salmon. ICES CM2001/ACFM 15, p. 199.
3. Anonymous (2003). Report of the working group on the Atlantic salmon. ICES CM2001/ACFM, 19, p. 297.
4. Bagliniè re, J. L(976). Etude des populations de Saumon atlantique (Salmo salar L. 1766) en Bretagne-Basse-Normandie. 1 - Caractéristiques des smolts de la Rivière Ellé. Annales d'Hydrobiologie 7141-158
5. Bagliniè re, J. L. (1979). Production de juvéniles de Saumon atlantique (Salmo salar L.) sur quatre affluents du Scorff, rivière de Bretagne-Sud. Annales de Limnologie 3, 347-366.
6. Bagliniè re, J. L. & Champigneulle, A. (1986). Populations estimates of juvenile Atlantic salmon (Salmo salar) as indices of smolt production in the River Scorff, Brittany. Journal of Fish Biology 29, 467-482.
7. Bagliniè re, J. L. & Maisse, G. (1985). Precocious maturation and smoltification in wild Atlantic salmon in the armoricain Massif, France. Aquaculture 45, 249-263.
8. Bagliniè re, J. L., Maisse, G. & Nihouarn, A. (1993). Comparison of two methods of estimating Atlantic salmon, Salmo salar, wild smolt production. In Production of Juvenile Atlantic salmon, Salmo salar, in Natural Waters (ed. R. J. Gibson & R. E. Cuting). Canadian Special Publication in Fisheries and Aquatic Sciences 118, 189-201.
9. Bagliniè re, J. L., Marchand, F. & Vauclin, V. (2005). Interannual changes in recruitment of Atlantic salmon (Salmo salar) population in the River Oir (Lower Normandy, France): relationship with spawners and in-stream habitat. Journal of Marine Science 62, 695-707.
10. Barton, N. H. & Slatkin, M. (1986). A quasi-equilibrium theory of the distribution of rare alleles in a subdivided population. Heredity 56, 409-415.
11. Beaumont, M. A. (1999). Detecting population expansion and decline using microsatellites. Genetics 153, 2013-2029.
12. Belkhir, K., Borsa, P., Goudet, J., Chikhi, L. & Bonhomme, F. (1998). GENETIX, Logiciel sous WindowsTM pour la Génétique des Populations, Laboratoire Génome et Populations, CNRS UPR 9060. Montpellier, France: Université de Montpellier II.
13. Berthier, P., Beaumont, M. A., Cornuet, J. M. &Luikart, G. (2002). Likelihood-based estimate of the effective population size using temporal changes in allele frequency: a genealogical approach. Genetics 160, 741-751.
14. Butler, J. R. A. (2004). Moray Firth Seal Management Plan: A Pilot Project for Managing Interactions Between Seals and Salmon in Scotland, pp. 64. Aberlour, Morayshire : Spey Fishery Board.
15. Butler, J. R. A., Middlemas, S. J., McKelvey, S. A., McMyn, I., Leyshon, B., Walker, I., Thompson, P. M., Boyd, I. L., Duck, C., Armstrong, J. D., Graham, I. M. & Baxter, J. M. (2008). The Moray Firth Seal Management Plan: an adaptive framework for balancing the conservation of seals, salmon, fisheries and wildlife tourism in the UK. Aquatic Conservation: Marine and Freshwater Ecosystems 18, 1025-1038.
16. Butler, J. R. A., Radford, A., Riddington, G. & Laughton, R. (2009). Evaluating an ecosystem service provided by Atlantic salmon and other fish species in the River Spey, Scotland: the economic impact of recreational rod fisheries. Fisheries Research 96, 259-266.
17. Caron, F. & Fontaine, P. M. (2003). L'é tat des stocks de Saumon atlantique au Québec en 2002. Société de la faune et des parcs du Québec. Direction sur la Faune, pp. 48.
18. Chakraborty, R. & Kimmel, M. (1999). Statistics of microsatellite loci : estimation of mutation rate and pattern of population expansion. In Microsatellites: Evolution and Applications (ed. D. B. Goldstein & C. Schlötterer), pp. 139-150. Oxford, UK: Oxford University Press.
19. Chevalet, C. & Nikolic, N. (2010). Distribution of coalescence times and distances between microsatellite alleles with changing effective population size. Theoretical Population Biology, in press.
20. Consuegra, S., Verspoor, E., Knox, D. & De Leaniz, C. G. (2005). Asymmetric gene flow and the evolutionary maintenance of genetic diversity in small, peripheral Atlantic salmon populations. Conservation Genetics 6, 823-842.
21. Cornuet, J.-M., Santos, F., Beaumont, M. A., Robert, C. P., Marin, J.-M., Balding, D. J., Guillemaud, T. & Estoup, A. (2008). Inferring population history with DIYABC: a user-friendly approach to approximate Bayesian computation. Bioinformatics 24, 2713-2719.
22. Deonier, R. C., Waterman, M. S. & Tavaré , S. (2005). Computational Genome Analysis: An Introduction, pp. 403-404. New York: Springer.
23. Dodson, J. J., Gibson, R. J., Cunjak, R. A., Friedland, K. D., Garcia de Leaniz, C., Gross, M. R., Newbury, R., Nielsen, J. L., Power, M. E. & Roy, S. (1998). Elements in the development of conservation plans for Atlantic salmon (Salmo salar). Canadian Journal of Fisheries and Aquatic Sciences 55, 312-323.
24. Drummond, A. J., Rambaut, A., Shapiro, B. & Pybus, O. G. (2005). Bayesian coalescent inference of past population dynamics from molecular sequences. Molecular Biology and Evolution 22, 1185-1192.
25. Estoup, A., Largiadè r, C.-R., Perrot, E. & Chourrout, D. (1996). One-tube rapid DNA extraction for reliable PCR detection of fish polymorphic markers and transgenes. Molecular Marine Biology and Biotechnology 5, 295-298.
26. Feldman, M. W., Kumm, J. & Pritchard, J. (1999). Mutation and migration in models of microsatellite evolution. In Microsatellites : Evolution and Applications (ed. D. B. Goldstein & C. Schlötterer), pp. 98-115. Oxford, UK: Oxford University Press.
27. Felsenstein, J. (1992). Estimating effective population size from samples of sequences: inefficiency of pairwise and segregating sites as compared to phylogenetic estimates. Genetical Research 59, 139-147.
28. Finnegan, A. K. & Stevens, J. R. (2008). Assessing the long-term genetic impact of historical stocking events on contemporary populations of Atlantic salmon, Salmo salar. Fisheries Management and Ecology 15, 315-326.
29. Fleming, I. A. (1996). Reproductive strategies of Atlantic salmon: Ecology and evolution. Reviews of Fish Biology and Fisheries 6, 379-416.
30. Frankham, R. (1995). Conservation genetics. Annual Review of Genetics 29, 305-327.
31. Frankham, R., Ballou, J. D. & Briscoe, D. A. (2002). Introduction to Conservation Genetics. Cambridge, UK: Cambridge University Press.
32. Franklin, I. R. (1980). Evolutionary change in small populations. In Conservation Biology: An Evolutionary- Ecological Perspective (ed. M. E. Soule & B. A. Wilcox), pp. 135-149. Sunderland, MA: Sinauer Associates.
33. Franklin, I. R. & Frankham, R. (1998). How large must populations be to retain evolutionary potential? Animal Conservation 1, 69-73.
34. Garant, D., Dodson, J. J. & Bernatchez, L. (2000). Ecological determinants and temporal stability of the within-river population structure in Atlantic salmon (Salmo salar L.). Molecular Ecology 9, 615-628.
35. Garcia-Vazquez, E., Moran, P., Martinez, J. L., Perez, J., de Gaudemar, B. & Beall, E. (2001). Alternative mating strategies in Atlantic salmon and brown trout. Journal of Heredity 92, 146-149.
36. Goudet, J. (1995). Fstat version 1.2: a computer program to calculate F-statistics. Journal of Heredity 86, 485-486.
37. Guyomard, R. (1994). La diversité génétique des populations de saumon atlantique. In Le saumon atlantique: Biologie et gestion de la ressource (ed. J. C. Gueguen et P. Prouzet), pp. 141-151. Brest, France: IFREMER.
38. Gross, M. R. (1998). One species with two biologies : Atlantic salmon (Salmo salar) in the wild and in aquaculture. Canadian Journal of Fisheries and Aquatic Sciences 55, 131-144.
39. Hansen, L. P. & Jonsson, B. (1994). Homing of Atlantic salmon: effects of juvenile learning on transplanted postspawners. Animal Behavior 47, 220-222.
40. Hawkins, A. D. (2000). Problems facing salmon in the sea - summing up. In The Ocean Life of Atlantic salmon: Environmental and Biological Factors Influencing Survival (ed. D. H. Mills), pp. 211-222. Oxford: Fishing News Books.
41. Heled, J. & Drummond, A. J. (2008). Bayesian inference of population size history from multiple loci. BMC Evolutionary Biology 8, 289.
42. Hey, J. & Nielsen, R. (2004). Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 167, 747-760.
43. IUCN (International Union for Conservation of Nature) (1994). IUCN Red List Categories. Gland, Switzerland: IUCN, Species Survival Commission.
44. Jones, M. W. & Hutchings, J. A. (2001). The influence of male parr body size and mate competition on fertilization success and effective population size in Atlantic salmon. Heredity 86, 675-684.
45. Jones, M. W. & Hutchings, J. A. (2002). Individual variation in Atlantic salmon fertilization success: implications for effective population size. Ecological Applications 12, 184-193.
46. Jonsson, B. & Jonsson, N. (2004). Factors affecting marine production of Atlantic salmon (Salmo salar). Canadian Journal of Fisheries and Aquatic Sciences 61, 2369-2383.
47. Jordan, W. C., Cross, T. F., Crozier, W. W., Ferguson, A., Galvin, P., Hurrell, R. H., McGinnity, P., Martin, S. A. M., Moffett, I. J. J., Price, D. J., Youngson, A. F. & Verspoor, E. (2005). Allozyme variation in Atlantic salmon from the British Isles : associations with geography and the environment. Journal of Zoology 65(Suppl. A), 146-168.
48. Jorde, P. & Ryman, N. (1996). Demographic genetics of brown trout (Salmo trutta) and estimation of effective population size from temporal change in allele frequencies. Genetics 143, 1369-1381.
49. King, J. P., Kimmel, M. & Chakraborty, R. (2000). A power analysis of microsatellite-based statistics for inferring past population growth. Molecular Biology and Evolution 17, 1859-1868.
50. King, T. L., Kalinowski, S. T., Schill, W. B., Spidle, A. P. & Lubinski, B. A. (2001). Population structure of Atlantic salmon (Salmo salar L.): a range-wide perspective from microsatellite DNA variation. Molecular Ecology 10, 807-821.
51. Klemetsen, A., Amundsen, P. A., Dempson, J. B., Jonsson, B., Jonsson, N., O'Connell, M. F. & Mortensen, E. (2003). Atlantic salmon Salmo salar L., brown trout Salmo trutta L. and Arctic charr Salvelinus alpinus (L.): a review of aspects of their life histories. Ecology of Freshwater Fish 12, 1-59.
52. Knockaert, C. (2006). Salmonidé s d'aquaculture. De la Production à la Consommation, pp. 327. Versailles, France: Quae Editions.
53. Kuhner, M. K. (2006). LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters. Bioinformatics Applications Notes 22, 768-770.
54. Kuhner, M. K., Yamato, J. & Felsenstein, J. (1995). Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling. Genetics 140, 1421-1430.
55. Lande, R. (1988). Genetics and demography in biological conservation. Science 241, 1455-1460.
56. Laughton, R. (1991). The movements of adult Atlantic salmon (Salmo salar L.) in the River Spey, as determined by radio telemetry during 1988-1989. Scottish Fisheries Research Report 50.
57. Leberg, P. (2005). Genetic approaches for estimating the effective size of populations. Journal of Wildlife Management 69, 1385-1399.
58. Ligoxygakis, P. (2001). Genetic diversity and conservation efforts. Trends in Genetics 17, 442.
59. Luikart, G. H., Cornuet, J. M. & Allendorf, F. W. (1999). Temporal changes in alleles frequencies provide estimators of population bottleneck size. Conservation Biology 13, 523-530.
60. Lynch, M. & Lande, R. (1998). The critical effective size for a genetically secure population. Animal Conservation 1, 70-72.
61. Mace, G. M. & Lande, R. (1991). Assessing extinction threats - toward a reevaluation of IUCN threatened species categories. Conservation Biology 5, 148-157.
62. McGinnity, P., Prodohl, P., Ferguson, A., Hynes, R., O'Maoileidigh, N., Baker, N., Cotter, C., O'Hea, B., Cooke, D., Rogan, G., Taggart, J. B. & Cross, T. (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 of London B 270, 2443-2450.
63. Nei, M. (1978). Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89, 583-590.
64. Nei, M. & Tajima, F. (1981). Genetic drift and estimation of effective population size. Genetics 98, 625-640.
65. Nielsen, E. E., Hansen, M. M. & Loeschcke, V. (1999). Genetic variation in time and space: microsatellite analysis of extinct and extant populations of Atlantic salmon. Evolution 53, 261-268.
66. Nielsen, R. & Wakeley, J. (2001). Distinguishing migration from isolation. A Markov Chain Monte Carlo approach. Genetics 158, 885-896
67. Nikolic, N., Fève, K., Chevalet, C., Høyheim, B. & Riquet, J. (2009). A set of 37 microsatellite DNA markers for genetic diversity and structure analysis of Atlantic salmon Salmo salar populations. Journal of Fish Biology 74, 458-466.
68. Norris, A. T., Bradley, D. G. & Cunningham, E. P. (1999). Microsatellite genetic variation between and within farmed Atlanctic salmon (Salmo salar) populations. Aquaculture 180, 247-264.
69. O'Reilly, P. T., Herbinger, C. & Wright, J. M. (1998). Analysis of parentage determination in Atlantic salmon (Salmo salar) using microsatellites. Animal Genetics 29, 363-370.
70. Ovenden, J. R., Peel, D., Street, R., Courtney, A. J., Hoyle, S. D., Peel, S. L. & Podlich, H. (2007). The genetic effective and adult census size of an Australian population of tiger prawns (Penaeus esculentus). Molecular Ecology 16, 127-138.
71. Palstra, F. P. & Ruzzante, D. E. (2008). Genetic estimates of contemporary effective population size : what can they tell us about the importance of genetic stochasticity for wild population persistence? Molecular Ecology 17, 3428-3447.
72. Parrish, D. L., Behnke, J., Gephard, S. R., McCormick, S. D. & Reeves, G. H. (1998). Why aren't there more Atlantic salmon (Salmo salar)? Canadian Journal of Fisheries and Aquatic Sciences 55(Suppl. 1), 281-287.
73. Peakall, R. & Smouse, P. E. (2006). GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6, 288-295.
74. Porcher, J. P. & Bagliniè re, J. L. (2001). Le Saumon atlantique. In Atlas des poisons d'eau douce de France (ed. P. Keith et J. Allardi (coords)). Patrimoines Naturels 47, 240-243.
75. Peel, D., Ovenden, J. R. & Peel, S. L. (2004). NeEstimator: software for estimating effective population size, Version 1.3. Queensland Government, Department of Primary Industries and Fisheries.
76. Piry, S., Alapetite, A., Cornuet, J.-M., Paetkau, D., Baudouin, L. & Estoup, A. (2004). GeneClass2: a software for genetic assignment and first-generation migrant detection. Journal of Heredity 95, 536-539.
77. Piry, S., Luikart, G. & Cornuet, J.-M. (1999). Bottleneck: a program for detecting recent effective population size reductions from allele data frequencies. Journal of Heredity 90, 502-503.
78. Primmer, C. R., Veselov, A. J., Zubchenko, A., Poututkin, A., Bakhmet, I. & Koskinen, M. T. (2006). Isolation by distance within a river system: genetic population structuring of Atlantic salmon, Salmo salar, in tributaries of the Varzuga River in northwest Russia. Molecular Ecology 15, 653-666
79. Pritchard, J. K., Stephens, M. & Donnelly, P. J. (2000). Inference of population structure using multilocus genotype data. Genetics 155, 945-959.
80. Rannala, B. & Mountain, J. L. (1997). Detecting immigration by using multilocus genotypes. Proceedings of the National Academy of Sciences of the USA 94, 9197-9221.
81. Raymond, M. & Rousset, F. (1995). GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. Journal of Heredity 86, 248-249.
82. Saglio, P. (1994). Le retour aux sites de frai ou "homing" : les mécanismes chimiosensoriels. In Le saumon atlantique (ed. J. C. Gueguen and P. Prouzet), pp. 101-122. Brest, France: IFREMER.
83. Schuelke, M. (2000). An economic method for the fluorescent labeling of PCR fragments. Nature Biotechnology 18, 233-234.
84. Shriver, M. D., Jin, L., Ferrell, R. E. & Deka, R. (1997). Microsatellite data support an early population expansion in Africa. Genome Research 7, 586-591.
85. Slatkin, M. (1995). A measure of population subdivision based on microsatellite allele frequencies. Genetics 139, 1463.
86. Stabell, O. B. (1984). Homing and olfaction in Salmonids - a critical review with special reference to the Atlantic salmon. Biological Reviews of the Cambridge Philosophical Society 59, 333-388.
87. Sta? hl, G. (1987). Genetic population structure of Atlantic salmon. In Population Genetics and Fisheries Management (ed. N. Ryman and F. M. Utter), pp. 121-140. Seattle, WA: University of Washington Press.
88. Stewart, D. C., Smith, G. W. & Youngson, A. F. (2002). Tributary-specific variation in timing of return of adult Atlantic salmon (Salmo salar) to freshwater has a genetic component. Canadian Journal of Fisheries and Aquatic Science 59, 276-281.
89. Storz, J. F. & Beaumont, M. A. (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.
90. Tallmon, D. A., Luikart, G. & Beaumont, M. A. (2004). Comparative evaluation of a new effective population size estimator based on approximate Bayesian computation. Genetics 167, 977-988.
91. Taylor, E. B. (1991). A review of local adaptation in Salmonidae, with particular reference to Pacific and Atlantic salmon. Aquaculture 98, 185-207.
92. Vaha, J. P., Erkinaro, J., Niemela, E. & Primmer, C. R. (2007). Life-history and habitat features influence the within-river genetic structure of Atlantic salmon. Molecular Ecology 16, 2638-2654.
93. Vaha, J. P., Erkinaro, J., Niemela, E. & Primmer, C. R. (2008). Temporally stable genetic structure and low migration in an Atlantic salmon population complex: implications for conservation and management. Evolutionary Applications 1, 137-154.
94. Wang, J. & Whitlock, M. C. (2003). Estimating effective population size and migration rates from genetic samples over space and time. Genetics 163, 429-446.
95. Wang, J. L. (2001). A pseudo-likelihood method for estimating effective population size from temporally spaced samples. Genetical Research 78, 243-257.
96. Wang, J. L. (2005). Estimation of effective population sizes from data on genetic markers. Philosophical Transactions of the Royal Society of London, Series B, Biological Sciences 360, 1395-1409.
97. Waples, R. S. (1989). A generalized approach for estimating effective population size from temporal changes in allele frequency. Genetics 121, 379-391.
98. Waples, R. S. (1990). Conservation genetics of Pacific salmon. III. Estimating effective population size. Journal of Heredity 81, 277-289.
99. Waples, R. S. (2002). Effective size of fluctuating salmon populations. Genetics 161, 783-791.
100. Weir, B. S. & Cockerham, C. C. (1984). Estimating F-statistics for the analysis of population structure. Evolution 38, 1358-1370.
101. Whitlock, M. C. & McCauley, D. E. (1999). Indirect measures of gene flow and migration: Fst=1/(4Nm+1). Heredity 82, 117-125.
102. Wilson, I. J. & Balding, D. J. (1998). Genealogical inference from microsatellite data. Genetics 150, 499-510.
103. Wright, S. (1931). Evolution in Mendelian populations. Genetics 16, 97-159.
104. Wright, S. (1938). Size of population and breeding structure in relation to evolution. Science 87, 430-431.