Loss of historical immigration and the unsuccessful rehabilitation of extirpated salmon populations

Conservation Genetics

Volumn 8, Issue 3, 2007, Pages 527-546

  Fraser, Dylan J ^a   Jones, Matthew W ^a   McParland, Tara L ^a   Hutchings, Jeffrey A ^a  

^a DALHOUSIE UNIVERSITY   (Canada)

Author keywords

Asymmetric gene flow; Atlantic salmon; Effective population size; Effective census size ratio; Genetic compensation; Metapopulation; Recolonization; Rehabilitation; Reintroduction; Temporal stability

Indexed keywords

CENSUS; CONSERVATION GENETICS; CONSERVATION PLANNING; DNA; EFFECTIVE POPULATION SIZE; FUTURE PROSPECT; GENE FLOW; GENETIC STRUCTURE; GENETIC VARIATION; HYPOTHESIS TESTING; IMMIGRATION; METAPOPULATION; RECOLONIZATION; REINTRODUCTION; RIVER SYSTEM; SALMONID;

ATLANTIC OCEAN; BAY OF FUNDY;

SALMO SALAR;

EID: 34247598261     PISSN: 15660621     EISSN: 15729737     Source Type: Journal    
DOI: 10.1007/s10592-006-9188-8     Document Type: Article

References (82)

1. Adkison MD (1995) Population differentiation in Pacific salmon: local adaptation, genetic drift, or the environment? Can J Fish Aquat Sci 52:2762-2777
2. Alexander DR, Galbraith P (1982) A plan to re-establish a natural population of Atlantic salmon in the Point Wolfe River, Fundy National Park. Can Man Rep Fish Aquat Sci 1667:1-8
3. Amiro PG (2003) Population status of Inner Bay of Fundy Atlantic salmon (Salmo salar), to 1999. Can Tech Rep Fish Aquat Sci 2488:44
4. Angers B, Bernatchez L (1998) Combined use of SMM and non-SMM methods to infer fine structure and evolutionary history of closely related brook charr (Salvelinus fontinalis, Salmonidae) populations from microsatellites. Mol Biol Evol 15:143-159
5. Ardlie KG, Kruglyak L, Seielstadt M (2002) Patterns of linkage disequilibrium in the human genome. Nature Rev Genet 3:299-309
6. e) reveals genetic compensation in steelhead trout. Mol Ecol 12:35-49
7. Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F (2000) GENETIX 4.02, Logiciel Sous Windows Pour la Genetique des Populations. Laboratoire Genome, Populations, Interactions, Université de Montpellier II, Montpellier, France
8. Chebanov NA (1991) The effect of spawner density on spawning success, egg survival, and size structure of the progeny of the sockeye salmon (Oncorhynchus nerka). J Ichthyo 31:101-106
9. COSEWIC (2006) COSEWIC assessment and update status report on Atlantic salmon (Salmo salar) Inner Bay of Fundy populations. Committee of the Status of Endangered Wildlife in Canada, Ottawa
10. Consuegra S, Verspoor E, Knox D, García de Leániz C. (2005) Asymmetric gene flow and the evolutionary maintenance of genetic diversity in small, peripheral Atlantic salmon populations. Conserv Genet 6:823-842
11. Cooper AB, Mangel M (1999) The dangers of ignoring metapopulation structure for the conservation of salmonids. Fish Bull 97:213-226
12. Cornuet J-M, Luikart G (1996) Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144:2001-2014
13. Cornuet J-M, Piry S, Luikart G, Estoup A, Solignac M (1999) New methods employing multilocus genotypes to select or exclude populations as origins of individuals. Genetics 153:1989-2000
14. Crow JF, Kimura M (1970) An introduction to population genetics theory. Burgess Publication Co
15. Dadswell M (1968) Atlantic salmon (Salmo salar) investigations in the Point Wolfe and Upper Salmon Rivers in Fundy National Park. Manuscript Report, Limnology Section, Canadian Wildlife Service
16. Department of Fisheries and Oceans (DFO) (2002) Atlantic salmon Maritimes Provinces Overview for 2002. Stock Status Report 2002/026, Department of Fisheries and Oceans
17. Di Rienzo A, Peterson AC, Garza JC, Values AM, Slatkin M, Freimer NB (1994) Mutational processes of simple sequence repeat loci in human populations. Proc Natl Acad Sci USA 91:3166-3170
18. Ellegren H (2000) Heterogeneous mutation processes in human microsatellite DNA sequences. Nature Gen 24:400-402
19. Ford MJ, Teel D, Van Doornik DM, Kuligowski D, Lawson PW (2004) Genetic population structure of central Oregon coast coho salmon (Oncorhynchus kisutch). Conserv Genet 5:797-812
20. Frankham R, Ballou JD, Briscoe DA (2002) Introduction to conservation genetics. Cambridge University Press, UK
21. Franklin IR (1980) Evolutionary changes in small populations. In: Soule ME, Wilcox BA (eds) Conservation biology. An evolutionary-ecological perspective. Sinauer Assoc, Sunderland, Massachusetts, pp 135-149
22. Fraser DJ, Lippe C, Bernatchez L (2004) Consequences of unequal effective population size, asymmetric gene flow, and sex-biased dispersal on population structure in brook charr (Salvelinus fontinalis). Mol Ecol 13:67-80
23. Fraser DJ, Bernatchez L (2005) Adaptive migratory divergence among sympatric brook charr populations. Evolution 59:611-624
24. Fundy National Park (FNP) (2002) Juvenile Atlantic salmon densities, 1983-2002, Fundy National Park. Monitoring project data summary
25. Gibson AJF, Amiro PG (2003) Abundance of Atlantic salmon (Salmo salar) in the Stewiacke River, Nova Scotia, from 1965-2002. Research document 2002/108, Canadian Science Advisory Secretariat, Department of Fisheries and Oceans, Dartmouth, Nova Scotia
26. Gibson AJF, Bryan J, Amiro PG (2003) Release of hatchery-reared Atlantic salmon into inner Bay of Fundy rivers from 1900-2002. Canadian Data Report of Fisheries and Aquatic Sciences 1123, Department of Fisheries and Oceans, Dartmouth, Nova Scotia
27. Goudet J (2001) FSTAT, a program to estimate and test gene diversities and fixation indices, Version 2.9.3. Institut d'Écologie, Université de Lausanne, Lausanne
28. 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. Mol Ecol 11:2523-2535
29. Hanski I, Gaggiotti O (2004) Ecology, evolution and genetics of metapopulations. Academic Press, San Diego, California USA
30. Heath DD, Busch C, Kelly J, Atagi DY (2002) Temporal change in genetic structure and effective population size in steelhead trout (Oncorhynchus mykiss). Mol Ecol 11:197-214
31. Hedrick PW, Gilpin ME (1997) Genetic effective size of a metapopulation. In: Hanski I, Gilpin ME (eds) Metapopulation biology: ecology, genetics and evolution. Academic Press, San Diego, CA, pp 165-181
32. Hoffman EA, Scheuler FW, Blouin MS (2004) Effective population sizes and temporal stability of genetic structure in Rana pipiens, the northern leopard frog. Evolution 58:2536-2545
33. Hutchings JA (2003) Development of a population recovery strategy for inner Bay of Fundy Atlantic salmon populations in Fundy National park. Dalhousie University, Halifax Nova, Scotia
34. Jessop BM (1976) Distribution and timing of tag recoveries from native and nonnative Atlantic salmon (Salmo salar) released into the Big Salmon River, New Brunswick. J Fish Res Board Can 33:829-833
35. Jessop BM (1986) Atlantic salmon (Salmo salar) of the Big Salmon River, New Brunswick. Canadian Technical Report in Fisheries and Aquatic Sciences #1415
36. Jones MW, Clay D (1995) Components of Atlantic salmon database in Fundy National Park: 1957-1994.Unpublished manuscript of Parks Canada 93-15, Alma, New Brunswick, Canada
37. Jones MW, Hutchings JA (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
38. Jones MW, Hutchings JA (2002) Individual variation in Atlantic salmon fertilization success: implications for effective population size. Ecol Appl 12:184-193
39. Kalinowski ST (2002) Evolutionary and statistical properties of three genetic distances. Mol Ecol 11:1263-1273
40. Keller LF, Waller DM (2002) Inbreeding effects in wild populations. Trends Ecol Evol 17:230-241
41. King TL, Kalinowski ST, Schill WB, Spidle AP, Lubinski BA (2001) Population structure of Atlantic salmon (Salmo salar L.): a range-wide perspective from microsatellite DNA variation. Mol Ecol 10:807-821
42. Korman J, Ahrens RMN, Higgins PS, Walters CJ (2002). Effects of observer efficiency, arrival timing, and survey life on estimates of escapement for steelhead trout (Oncorhynchus mykiss) derived from repeat mark-recapture experiments. Can J Fish Aquat Sci 59:1116-1131
43. Koskinen M, Haugen T, Primmer C (2002) Contemporary fisherian life-history evolution in small salmonid populations. Nature 419:826-830
44. Lande R (1988) Genetics and demography in biological conservation. Science 241:1455-1460
45. Langella O (2001) Centre National de la Recherche Scientifique, Laboratoire Populations, Génétique et Evolution, Gif sur Yvettev; http://www.cnrsgif.fr/page/bioinfo/populations
46. Latch EK, Rhodes Jr. OE (2005) The effects of gene flow and population isolation on the genetic structure of reintroduced wild turkey populations: are genetic signatures of source populations maintained?. Conserv Genet 6:981-997
47. Leberg PL (2002) Estimating allelic richness: effects of sample size and bottlenecks. Mol Ecol 11:2445-2449
48. McVean GAT (2002) A genealogical interpretation of linkage disequilibrium. Genetics 162:987-991
49. Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583-590
50. Nunney L (1999) The effective size of a hierarchically-structured population. Evolution 53:1-10
51. Ohta T (1982) Linkage disequilibrium with the island model. Genetics 101:139-155
52. O'Connell MF, Dempson JB, Mullins CC, Reddin DG, Bourgeois CE, Porter TR, Cochrane NM, Caines D (2002) Status of Atlantic salmon (Salmo salar L.) stocks of insular Newfoundland (SFAs 3-14A), 2001. Canadian Science Advisory Secretariat Research Document 2002/028, Department of Fisheries and Oceans, Ottawa
53. O'Reilly PT (1997) Development of molecular genetic markers in Atlantic salmon (Salmo salar) and an illustration of their application to aquaculture and fisheries. PhD Dissertation, Dalhousie University, Halifax, Nova Scotia
54. 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. Can J Fish Aquat Sci 53:2292-2298
55. Ostergaard S, Hansen MM, Loeschcke V, Nielsen EE (2003) Long-term temporal changes of genetic composition in brown trout (Salmo trutta L.) populations inhabiting an unstable environment. Mol Ecol 12:3123-3135
56. Page RDM (1996) TREEVIEW: an application to display phylogenetic trees on personal computers. Comp Appl Biosci 12:357-358
57. Perley MH (1851) Report upon the fisheries of the Bay of Fundy. Her Majesty's Emigration officer. J House Assembly. Saint John, New Brunswick. Microfilm, Provincial Archives of New Brunswick
58. Piry S, Luikart G, Cornuet J (1999) BOTTLENECK: a computer program for detecting recent reductions in the effective size using allele frequency data. J Hered 90:502-503
59. Policansky D, Magnuson JJ (1998) Genetics, metapopulations, and ecosystem management of fisheries. Ecol Appl 8:S119-S123
60. Raymond M, Rousset F (1995) GENEPOP (3.3): population genetics software for exact tests and ecumenicism. J Hered 86:248-249
61. Reznick DN, Bryga H, Endler JA (1990) Experimentally-induced life history variation in a natural population. Nature 346:357-359
62. Rice WR (1989) Analyzing tables of statistical tests. Evolution 43:223-225
63. Rieman BE, Dunham JB (2000) Metapopulations and salmonids: a synthesis of life history patterns and empirical observations. Ecol Fresh Fish 9:51-64
64. Ruzzante DE (1998)Acomparison of several measures of genetic distance and population structure with microsatellite data: bias and sampling variance. Can J Fish Aquat Sci 55:1-14
65. Ryman N, Jorde PE (2001) Statistical power when testing for genetic differentiation. Mol Ecol 10:2361-2373
66. Shrimpton JM, Heath DD (2003) Census vs. effective population size in chinook salmon: large and small-scale environmental perturbation effects. Mol Ecol 12:2571-2583
67. Shriver MD, Jin L, Chakraborty R, Boerwinkle E (1993) VNTR allele frequency distributions under the stepwise mutation approach: a computer simulation approach. Genetics 134:983-993
68. Tero N, Aspi J, Siikimaki P, Jakalaniemi A, Tuomi J (2003) Genetic structure and gene flow in a metapopulation of an endangered plant species, Silene tatarica. Mol Ecol 12:2073-2085
69. Thurow RF, Peterson JB, Guzevich JW (2006) Utility and validation of day and night snorkel counts for estimating bull trout abundance in first and third order streams. North Am J Fish Manage 26:217-232
70. Wang J (2001) A pseudo-likelihood method for estimating effective population size from temporally placed samples. Genet Res 78:243-257
71. Wang J, Whitlock MC (2003) Estimating effective population size and migration rates from genetic samples over space and time. Genetics 163:429-446
72. Waples RS (1989) A generalized approach for estimating effective population size from temporal changes in allele frequency. Genetics 121:379-391
73. Waples RS (1990a) Conservation genetics of Pacific salmon III. Estimating effective population size. J Hered 81:277-289
74. Waples RS (1990b) Conservation genetics of Pacific Salmon. II. Effective population size and the rate of loss of genetic variability. J Hered 81:267-276
75. Waples RS (2002a) Definition and estimation of effective population size in the conservation of endangered species. In: Beissinger SR, McCullough DR (eds) Population viability analysis. Univ. Chicago Press, pp 147-168
76. Waples RS (2002b) The effective size of fluctuating salmon populations. Genetics 161:783-791
77. Waples RS (2005) Genetic estimates of contemporary effective population size: to what time periods do the estimates apply?. Mol Ecol 14:3335-3352
78. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358-1370
79. Whitlock MC, Barton NH (1997) The effective size of a subdivided population. Genetics 146:427-441
80. Williamson-Natesan EG (2005) Comparison of methods for detecting bottlenecks from microsatellite loci. Conserv Genet 6:551-562
81. Wilson G, Rannala B (2003) Bayesian inference of recent migration rates using multilocus genotypes. Genetics 168:1177-1191
82. Wright S (1943) Isolation by distance. Genetics 28:114-138