Genetic and otolith isotopic markers identify salmon populations in the Columbia River at broad and fine geographic scales

Environmental Biology of Fishes

Volumn 89, Issue 3, 2010, Pages 533-546

  Barnett Johnson, Rachel ^a,c   Teel, David J ^b   Casillas, Edmundo ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b NORTHWEST FISHERIES SCIENCE CENTER   (United States)

^c U S BUREAU OF RECLAMATION   (United States)

Author keywords

Conservation; Ecology; Freshwater; Habitat; Management; Marine

Indexed keywords

ABUNDANCE; ECOSYSTEM MODELING; FISHERY MANAGEMENT; GENETIC MARKER; GEOGRAPHICAL VARIATION; GROWTH RATE; HATCHERY; ISOTOPIC ANALYSIS; OTOLITH; REPRODUCTIVE SUCCESS; SALMONID; SURVIVAL;

COLUMBIA RIVER;

ONCORHYNCHUS TSHAWYTSCHA; SALMONIDAE;

EID: 78149413942     PISSN: 03781909     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10641-010-9662-5     Document Type: Article

References (68)

1. Abaunza P, Murta AG, Campbell N, Cimmaruta R, Comesana AS, Dahle G, Garcia Santamaria MT, Gordo LS, Iversen SA, MacKenzie K, Magoulas A, Mattiucci S, Molloy J, Nascetti G, Pinto AL, Quinta R, Ramos P, Sanjuan A, Santos AT, Stransky C, Zimmermann C (2008) Stock identity of horse mackerel (Trachurus trachurus) in the Northeast Atlantic and Mediterranean Sea: Integrating the results from different stock identification approaches. Fish Res 89: 196-209.
2. Bacon CR, Weber PK, Larson KA, Reisenbichler R, Fitzpatrick JA, Wooden JL (2004) Migration and rearing histories of Chinook salmon (Oncorhynchus tshawytscha) determined by ion microprobe Sr isotope and Sr: Ca transects of otoliths. Can J Fish Aquat Sci 61: 2425-2439.
3. Bailey RE, Margolis L (1987) Comparison of the parasite fauna of juvenile sockeye salmon (Oncorhynchus nerka) from southern British Columbia and Washington State lakes. Can J Zool 65: 420-431.
4. Barnett-Johnson R (2007) Spatial scales of mixing and natal source contributions of salmon populations in the coastal ocean detected by otolith and genetic signatures of origin. University of California, Dissertation.
5. Barnett-Johnson R, Ramos FC, Grimes CB, MacFarlane RB (2005) Validation of Sr isotopes in otoliths by laser ablation multicollector inductively coupled plasma mass spectrometry (LA-MC-ICPMS): opening avenues in fisheries science applications. Can J Fish Aquat Sci 62: 2425-2430.
6. Barnett-Johnson R, Pearson TE, Ramos FC, Grimes CB, MacFarlane RB (2008) Tracking natal origins of salmon using isotopes, otoliths, and landscape geology. Limnol Oceanogr 53: 1633-1642.
7. Beacham TD, Candy JR, Jonsen KL, Supernault J, Wetklo M, Deng L, Miller KM, Withler RE, Varnavskaya N (2006) Estimation of stock composition and individual identification of Chinook salmon across the Pacific Rim using microsatellite variation. Trans Am Fish Soc 135: 861-888.
8. Botsford LW, Brumbaugh DR, Grimes C, Kellner JB, Largier J, O'Farrell MR, Ralston S, Soulanille E, Wespestad V (2009) Connectivity, sustainability, and yield: bridging the gap between conventional fisheries management and marine protected areas. Rev Fish Biol Fish 19: 69-95.
9. Bradbury IR, Campana SE, Bentzen P (2008) Estimating contemporary early life-history dispersal in an estuarine fish: integrating molecular and otolith elemental approaches. Mol Ecol 17: 1438-1450.
10. Cadrin SX, Friedland KD, Waldman JR (2005) Stock identification methods: applications in fisheries science. Elsevier Academic Press, San Francisco.
11. Camp VE, Ross ME, Hanson WE (2004) Genesis of flood basalts and Basin and Rang volcanic rocks from the Stenns Mountain to the Malheur River Gorge, Oregon. Geol Soc Am Bull 115: 105-128.
12. Campana SE, Thorrold SR (2001) Otoliths, increments, and elements: keys to a comprehensive understanding of fish populations? Can J Fish Aquat Sci 58: 30-38.
13. Carlson SM, Seamons TR (2008) A review of quantitative genetic components of fitness in salmonids: implications for adaptation to future change. Evol Appl 1: 222-238.
14. Carlson SM, Quinn TP (2007) Ten years of varying lake level and selection in size-at-maturity in sockeye salmon. Ecology 88: 2620-2629.
15. Carlson SM, Rich HB, Quinn TP (2009) Does variation in selection imposed by bears drive divergence among populations in the size and shape of sockeye salmon? Evolution 63: 1244-1261.
16. Chapman DW (1986) Salmon and steelhead abundance in the Columbia River in the nineteenth century. Trans Am Fish Soc 115: 662-670.
17. Cowen RK, Sponaugle S (2009) Larval dispersal and marine population connectivity. Annu Rev Mar Sci 1: 443-66.
18. Feyrer F, Hobbs J, Baerwald M, Sommer T, Yin Q, Clark K, May B, Bennett W (2007) Otolith microchemistry provides information complementary to microsatellite DNA for a migratory fish. Trans Am Fish Soc 136: 469-476.
19. Fukuhara FM, Murai S, LaLanne JJ, Sribhibhadh A (1962) Continental origin of red salmon as determined from morphological characters. Int North Pacific Fish Comm Bull 8: 15-109.
20. Gillanders BM (2002) Temporal and spatial variability in elemental composition of otoliths: implications for determining stock identity and connectivity of populations. Can J Fish Aquat Sci 59: 669-679.
21. Henry K (1961) Radical identification of Fraser River sockeye salmon (Oncorhynchus nerka) by means of scales and its application to salmon management. Int North Pacific Fish Comm Bull 12.
22. Hansen MM, Kenchington E, Nielsen EE (2001) Assigning individual fish to populations using microsatellite DNA markers. Fish Fish 2: 93-112.
23. 15 N enrichment in agricultural catchments: field patterns and applications to tracking Atlantic salmon (Salmo salar). Chem Geol 147: 281-294.
24. Hauser L, Seamons R, Dauer M, Naish KA, Quinn TP (2006) An empirical verification of population assignment methods by marking and parentage data: hatchery and wild steelhead. Mol Ecol 15: 3157.
25. Hobbs JA, Yin Q, Burton J, Bennett WA (2005) Retrospective determination of natal habitats for an estuarine fish with otolith strontium isotope ratios. Mar Freshwat Res 56: 655-660.
26. Hobson K, Barnett-Johnson R, Cerling T (2009) Using isoscapes to track animal migration. In: West J, Bowen G, Dawson T, Tu K (eds.) Isoscapes: Understanding movement patterns and processes on earth through isotope mapping. Springer Press, Berlin, Germany, pp 273-298.
27. Hooper PR (1997) The Columbia River flood basalt province: Current status. In: Mahoney JJ, Coffin MF (eds.) Large igneous provinces: Continental, oceanic, and planetary flood volcanism: Am Geophys Union Geophys Monogr 100: 1-27.
28. Ingram BL, Weber PK (1999) Salmon origin in California's Sacramento-San Joaquin river system as determined by otolith strontium isotopic composition. Geology 27: 851-854.
29. Kalinowski ST, Manlove KR, Taper ML (2007) ONCOR A computer program for genetic stock identification. Department of Ecology, Montana State University, Bozeman, MT. Available at http://www. montana. edu/kalinowski/kalinowski_software. htm.
30. Kennedy BP, Folt CL, Blum JD, Chamberlain CP (1997) Natural isotope markers in salmon. Nature 387: 766-767.
31. Lasmanis R (1991) Geology Wash Rocks Miner 66: 262-277.
32. MacKenzie K (2009) The use and abuse of parasites as stock markers for fish. Fish Res 97: 1-2.
33. MacCrimmon HR, Claytor RR (1985) Meristic and morphometric identify of Baltic stocks of Atlantic salmon (Salmo salar). Can J Zool 63: 2032-2037.
34. Margolis L (1963) Parasites as indicators of the geographic origin of sockeye salmon, Oncorhynchus nerka (Walbaum) occurring in the North Pacific Ocean and adjacent seas. Int North Pacific Fish Comm Bull 11: 101-156.
35. Marques JF, Teixeria CM, Cabral HN (2006) Differentiation of commercially important flatfish populations along the Portuguese coast: Evidence from morphology and parasitology. Fish Res 81: 293-305.
36. Marshall S, Bernard D, Conrad R, Cross B, McBride D, McGregor A, McPherson S, Oliver G, Sharr S, Ban Allen B (1987) Application of scale pattern analysis to the management of Alaska's sockeye salmon (Oncorhynchus nerka) fisheries. In: Smith HD, Margolis L, Wood CC (ed) Sockeye salmon (Oncorhynchus nerka) population biology and future management. Can Spec Publ Fish Aquat Sci 96: 307-326.
37. Miller JA (2007) Scales of variation in otolith elemental chemistry of juvenile staghorn sculpin (Leptocottus armatus) in three Pacific Northwest estuaries. Mar Biol 151: 483-494.
38. 86Sr within otolith cores. Fish Res 95: 373-378.
39. Miller JA, Banks MA, Gomez-Uchida D, Shanks AL (2005) A comparison of population structure in black rockfish (Sebastes melanops) as determined with otolith microchemistry and microsatellite DNA. Can J Fish Aquat Sci 62: 2189-2198.
40. Milton DA, Chenery SP (2001) Can otolith chemistry detect the population structure of the shad hilsa Tenualosa ilisha? Comparison with the results of genetic and morphometric studies. Mar Ecol Prog Ser 222: 239-251.
41. Moran P, Teel DJ, LaHood ES, Drake J, Kalinowski S (2006) Standardizing multi-laboratory microsatellite data in Pacific salmon: an historical view of the future. Ecol Freshw Fish 15: 597-605.
42. Myers JM, Kope RG, Bryant GJ, Teel D, Lierheimer LJ, Wainwright TC, Grant WS, Waknitz FW, Neely K, Lindley ST, Waples RS (1998) Status review of Chinook salmon from Washington, Idaho, Oregon, and California. U. S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-35, 443 p.
43. Narum SR, Banks M, Beacham TD, Bellinger MR, Campbell MR, Dekoning SJ, Eliz A, Guthrie CM III, Kozfkay C, Miller KM, Moran P, Phillips R, Seeb LW, Smith CT, Warheit K, Young SF, Garza JC (2008) Differentiating salmon populations at broad and fine geographic scales with microsatellite and single nucleotide polymorphisms. Mol Ecol 17: 3464-3477.
44. O' Connell M, Wright JM (1997) Microsatellite DNA in fishes. Rev Fish Biol Fisher 7: 331-363.
45. Palumbi SR (2004) Marine reserves and ocean neighborhoods: the spatial scale of marine populations and their management. Annu Rev Env Resour 29: 31-68.
46. Planes S, Jones GP, Thorrold SR (2009) Larval dispersal connects fish populations in a network of marine protected areas. P Natl Acad Sci USA 106: 5693-5697.
47. 86Sr variations in minerals and groundmass from basalts using LA-MC-ICPMS. Chem Geol 211: 135-158.
48. Ramos FC, Wolff JA, Tollstrup DL (2006) Sr isotope disequilibrium in Columbia River flood basalts: Evidence for rapid shallow-level open-system processes. Geology 33: 457-460.
49. Rannala B, Mountain JL (1997) Detecting immigration by using multilocus genotypes. P Natl Acad Sci USA 94: 9197-9201.
50. Ruttenberg BI, Warner RR (2006) Spatial variation in the chemical composition of natal otoliths from a reef fish in the Galapagos Islands. Mar Ecol Prog Ser 328: 225-236.
51. Seeb LW, Antonovich A, Banks MA, Beacham TD, Bellinger MR, Blankenship SM, Campbell MR, Decovich NA, Garza JC, Guthrie CM III, Lundrigan TA, Moran P, Narum SR, Stephenson JJ, Supernault KJ, Teel DJ, Templin WD, Wenburg JK, Young SF, Smith CT (2007) Development of a standardized DNA database for Chinook Salmon. Fisheries 32: 540-552.
52. Secor DH (1999) Specifying divergent migrations in the concept of stock: the contingent hypothesis. Fish Res 43: 13-34.
53. Selkoe KA, Henzler CM, Gaines SD (2008) Seascape genetics and the spatial ecology of marine populations. Fish Fish 9: 363-377.
54. Singleton MJ, Maher K, DePaulo DJ, Conrad ME, Dresel PE (2006) Dissolution rates and vadose zone drainage from strontium isotope measurements of groundwater in Pasco Basin, WA unconfined aquifer. J Hydrol 321: 39-58.
55. Standish JD, Sheehy M, Warner RR (2008) Use of otolith natal elemental signatures as natural tags to evaluate connectivity among open-coast fish populations. Mar Ecol Prog Ser 356: 259-268.
56. Taylor EB (1991) A review of local adaptation in salmonidae, with particular reference to Pacific and Atlantic salmon. Aquaculture 98: 185-207.
57. Thresher RE (1999) Elemental composition of otoliths as a stock delineator in fishes. Fish Res 43: 165-204.
58. Utter F, Teel D, Milner G, Isaac D (1987) Genetic estimates of stock compositions of 1983 Chinook salmon harvests off the Washington Coast and the Columbia River. Fish Bull 85: 13-23.
59. Utter FM, Chapman DW, Marshall AR (1995) Genetic population structure and history of Chinook salmon of the Upper Columbia River. Am Fish Soc Symp 17: 149-165.
60. Waknitz, FW, Mathews GM, Wainwright T, Winans GA (1995) Status review for Mid-Columbia River summer Chinook salmon. NOAA Tech. Mem. NMFS-NWFSC-22, 80 p. (Available from Natl. Mar. Fish. Serv., Northwest Fisheries Science Center, Coastal Zone and Estuarine Studies Division, 2725 Montlake Blvd. E., Seattle, WA 98112-2097).
61. Walther BD, Thorrold SR (2008) Geochemical signatures in otoliths record natal origins in American shad. Trans Amer Fish Soc 137: 57-69.
62. Waples RS, Gustafson RG, Weitkamp LA, Myers JM, Johnson OW, Busby PJ, Hard JJ, Bryant GJ, Waknitz FW, Neely K, Teel D, Grant WS, Winans GA, Phelps S, Marshall A, Baker B (2001) Characterizing diversity in salmon from the Pacific Northwest Journal of Fish Biology 59 (Suppl. A): 1-41.
63. Waples RS, Teel DJ, Myers JM, Marshall AM (2004) Life history variation in Chinook salmon: historic contingency and parallel evolution. Evolution 58: 386-403.
64. Weitkamp LA (2010) Marine distributions of Chinook salmon (Oncorhynchus tshawytscha) from the West Coast of North America determined by coded wire tag recoveries. Trans Am Fish Soc 139: 147-170.
65. Weissenborn AE (1969) Geologic map of Washington: U. S. Geological Survey, Miscellaneous Geologic Investigations Map I-583, scale 1: 2000000.
66. Winans GA (1984) Multivariate morphometric variability in Pacific salmon: technical demonstration. Can J Fish Aquat Sci 41: 1150-1159.
67. Winans GA, Viele D, Grover A, Palmer-Zwahlen M, Teel D, van Doornik D (2001) Update of genetic stock identification of Chinook salmon in the Pacific Northwest: Test fisheries in California. Rev Fish Sci 9: 213-237.
68. Wood CC, Rutherford DT, McKinnell S (1989) Identification of sockeye salmon (Oncorhynchus nerka) stocks in mixed-stock fisheries in British Columbia and southeast Alaska using biological markers. Can J Fish Aquat Sci 46: 2108-2120.