Comparative landscape genetic analysis of three Pacific salmon species from subarctic North America

Conservation Genetics

Volumn 12, Issue 1, 2011, Pages 223-241

  Olsen, Jeffrey B ^a   Crane, Penelope A ^a   Flannery, Blair G ^a   Dunmall, Karen ^b   Templin, William D ^c   Wenburg, John K ^a  

^a U S FISH AND WILDLIFE SERVICE   (United States)

^b Kawerak Inc   (United States)

^c ALASKA DEPARTMENT OF FISH AND GAME   (United States)

Author keywords

Landscape genetics; Pacific salmon; Population structure; Subarctic

Indexed keywords

CLIMATE CHANGE; COMPARATIVE STUDY; CONSERVATION GENETICS; DATA SET; DIVERGENCE; FISHERY MANAGEMENT; GENETIC ANALYSIS; GENETIC VARIATION; HETEROGENEITY; LANDSCAPE ECOLOGY; POPULATION STRUCTURE; PRECIPITATION (CLIMATOLOGY); SALMONID; SPATIAL ANALYSIS; SUBARCTIC REGION; WATERSHED;

NORTH AMERICA;

ONCORHYNCHUS; ONCORHYNCHUS TSHAWYTSCHA;

EID: 78650991482     PISSN: 15660621     EISSN: 15729737     Source Type: Journal    
DOI: 10.1007/s10592-010-0135-3     Document Type: Article

References (57)

1. Anderson MJ (2003) DISTLM forward: a FORTRAN computer program to calculate a distance-based multivariate analysis for a linear model using forward selection. Department of Statistics, University of Auckland, New Zealand. http://www. stat. auckland. ac. nz/~mja/Programs. htm.
2. Balkenhol N, Waits LP, Dezzani RJ (2009) Statistical approaches in landscape genetics: an evaluation of methods for linking landscape and genetic data. Ecography 32: 818-830.
3. Beacham TD, Jonsen KL, Supernault J, Wetklo M, Deng L, Varnavskaya N (2006) Pacific Rim population structure of Chinook salmon as determined from microsatellite analysis. Trans Am Fish Soc 135: 1604-1621.
4. Bohonak AJ (2002) IBD (isolation by distance); a program for analysis of isolation by distance. J Hered 93: 153-154.
5. Brannian LK, Evenson MJ, Hilsinger JR (2006) Escapement goal recommendations for select Arctic-Yukon-Kuskokwim region salmon stocks, 2007. Alaska Department of Fish and Game, Fishery Manuscript No. 06-07, Anchorage. http://www. sf. adfg. state. ak. us/FedAidPDFs/fm06-07. pdf.
6. Carmichael LE, Krizan J, Nagy JA, Fuglei E, Dumond M, Johnson D, Veitch A, Berteaux D, Strobeck C (2007) Historical and ecological determinants of genetic structure in arctic canids. Mol Ecol 16: 3466-3483.
7. Crane P, Molyneaux D, Lewis C, Wenburg J (2007) Genetic variation among coho salmon populations from the Kuskokwim Region and application to stock-specific harvest estimation. Alaska Fisheries Technical Report No. 96, U. S. Fish and Wildlife Service, Anchorage. http://alaska. fws. gov/fisheries/genetics/reports. htm.
8. Dillane E, McGinnity P, Coughlan JP, Cross MC, Eyto ED, Kenchington E, Prodöhl P, Cross TF (2008) Demographics and landscape features determine intrariver population structure in Atlantic salmon (Salmo salar L.): the case of the River Moy in Ireland. Mol Ecol 17: 4786-4800.
9. 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. Mol Ecol 17: 2382-2396.
10. Dupanloup I, Schneider S, Excoffier L (2002) A simulated annealing approach to define the genetic structure of populations. Mol Ecol 11: 2571-2581.
11. Ecological Stratification Working Group (1996) A National Ecological Framework for Canada. Agriculture and Agri-Food Canada, Research Branch, Centre for Land and Biological Resources Research and Environment Canada, State of Environment Directorate, Ottawa/Hull, 125 pp. http://sis. agr. gc. ca/cansis/publications/ecostrat/intro. html.
12. Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3. 0: an integrated software program for population genetic data analysis. Evol Bioinform Online 1: 47-50.
13. Flannery B, Beacham T, Wetklo M, Smith C, Templin B, Antonovich A, Seeb L, Miller S, Schlei O, Wenburg JK (2006) Run timing, migratory patterns, and harvest information of Chinook salmon stocks within the Yukon River. Alaska Fisheries Technical Report No. 92, U. S. Fish and Wildlife Service. http://alaska. fws. gov/fisheries/genetics/reports. htm.
14. Foll M, Gaggiotti O (2006) Identifying the environmental factors that determine the genetic structure of populations. Genetics 174: 875-891.
15. Gagnon M, Angers B (2006) The determinant role of temporary proglacial drainages on the genetic structure of fishes. Mol Ecol 15: 1051-1065.
16. Gallant AL, Binnian EF, Omernik JM, Shasby MB (1995) Ecoregions of Alaska US Geological Survey Professional Paper 1567, 73 pp. http://pubs. er. usgs. gov/usgspubs/pp/pp1567.
17. Gharrett AJ, Shirley SM, Tromble GR (1987) Genetic relationships among populations of Alaskan chinook salmon (Oncorhynchus tshawytscha). Can J Fish Aquat Sci 44: 765-774.
18. Goudet J (2001) FSTAT, a program to estimate and test gene diversities and fixation indices (version 2. 9. 3). http://www. unil. ch/izea/softwares/fstat. html.
19. Groot C, Margolis L (1991) Pacific salmon life histories. University of British Columbia Press, Vancouver, BC.
20. Gustafson RG, Winans GA (1999) Distribution and population genetic structure of river- and sea-type sockeye salmon in western North America. Ecol Freshw Fish 8: 181-193.
21. Hassol SJ, Berner J, Callaghan TV, Fox S, Furgal C, Hoel AH et al (2005) Arctic climate impact assessment. Cambridge University Press, Cambridge. http://www. acia. uaf. edu/.
22. Heginbottom JA, Brown J, Melnikov ES, Ferrians OJ Jr (1993) Circum-arctic map of permafrost and ground ice conditions. In: Proceedings of the sixth international conference on Permafrost, Wushan, vol 2. South China University Press, Guangzhou, China, pp 1132-1136. http://nsidc. org/data/docs/fgdc/ggd318_map_circumarctic/brown. html.
23. Hendry AP, Castric V, Kinnison MT, Quinn TP (2004) The evolution of philopatry and dispersal: homing versus straying in salmonids. In: Hendry AP, Stearns S (eds) Evolution illuminated: Salmon and their relatives. Oxford University Press, Oxford, pp 52-91.
24. Holderegger R, Wagner HH (2008) Landscape genetics. Bioscience 58: 199-207.
25. Jones SH, Fahl CB (1994) Magnitude and frequency of floods in Alaska and conterminous basins of Canada. US Geological Survey Water-Resources Investigations Report, 93-4197, 122 pp. http://pubs. er. usgs. gov/usgspubs/wri/wri934179.
26. Jørgensen HBH, Hansen MM, Bekkevold D, Ruzzante DE, Loeschcke V (2005) Marine landscapes and population genetic structure of herring (Clupea harengus L.) in the Baltic Sea. Mol Ecol 14: 3219-3234.
27. Kalinowski ST (2005) HP-RARE 1. 0: a computer program for performing rarefaction on measures of allelic richness. Mol Ecol Notes 5: 187-189.
28. Kaufman DS, Manley WF (2004) Pleistocene maximum and late Wisconsin glacier extents across Alaska, U. S. A. In: Ehlers J, Gibbard PL (eds) Quarternary glaciations extent and chronology, part II: North America. Elsevier, Amsterdam, 440 pp.
29. Kittlein MJ, Gaggiotti OE (2008) Interactions between environmental factors can hide isolation by distance patterns: a case study of Ctenomys rionegrensis in Uruguay. Proc R Soc Lond B 275: 2633-2638.
30. L'Abáe-Lund JH, Vøllestad LA (1985) Homing precision of roach Rutilus rutilus in Lake Arungen, Norway. Environ Biol Fish 13: 235-239.
31. Lapointe M, Eaton B, Driscol S, Latulippe C (2000) Modeling the probability of salmonid egg pocket scour due to floods. Can J Fish Aquat Sci 57: 1120-1130.
32. Le Corre V, Kremer A (2003) Genetic variability at neutral markers, quantitative trait loci and trait in a subdivided population under selection. Genetics 164: 1205-1219.
33. Lindsey CC, McPhail JD (1986) Zoogeography of fishes of the Yukon and Mackenzie basins. In: Hocutt CH, Wiley EO (eds) The zoogeography of North American freshwater fishes. Wiley, New York, pp 639-674.
34. MacLean R, Oswood MW, Irons JG, McDowell WH (1999) The effect of permafrost on stream biogeochemistry: a case study of two streams in the Alaskan (U. S. A.) taiga. Biogeochemistry 47: 239-267.
35. Manel S, Schwartz MK, Luikart G, Taberlet P (2003) Landscape genetics: combining landscape ecology and population genetics. TREE 18: 189-197.
36. Manier MK, Arnold SJ (2006) Ecological correlates of population genetic structure: a comparative approach using a vertebrate metacommunity. Proc R Soc Lond B 273: 3001-3009.
37. Manni F, Guerard E, Heyer E (2004) Geographic patterns of (genetic, morphologic, linguistic) variation: how barriers can be detected by using Monmonier's algorithm. Hum Biol 76: 173-190.
38. Marten A, Brändle M, Brandl R (2006) Habitat type predicts genetic population differentiation in freshwater invertebrates. Mol Ecol 15: 2643-2651.
39. Olsen JB, Flannery BG, Beacham TD, Bromaghin JF, Crane PA, Lean CF, Dunmall KM, Wenburg JK (2008) The influence of hydrographic structure and seasonal run timing on genetic diversity and isolation-by-distance in chum salmon (Oncorhynchus keta). Can J Fish Aquat Sci 65: 2026-2042.
40. Petren K, Grant PR, Grant BR, Keller L (2005) Comparative landscape genetics and the adaptive radiation of Darwin's finches: the role of peripheral isolation. Mol Ecol 14: 2943-2957.
41. Primmer CR, Veselov AJ, Zubchenko A, Poututkin A, Bakhmet I, Koskinen MT (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. Mol Ecol 15: 653-666.
42. Quinn TP (2005) The behavior and ecology of Pacific salmon and trout. University of Washington Press, Seattle, WA.
43. Quinn T, Tallman R (1987) Seasonal environmental predictability and homing in riverine fishes. Environ Biol Fish 18: 155-159.
44. Rice WR (1989) Analyzing tables of statistical tests. Evolution 43: 223-225.
45. Rousset F (2008) Genepop'007: a complete re-implementation of the genepop software for Windows and Linux. Mol Ecol Res 8: 103-106.
46. Sandercock FK (1991) Life history of coho salmon. In: Groot C, Margolis L (eds) Pacific salmon life histories. University of British Columbia Press, Vancouver, BC, pp 392-446.
47. Seeb LW, Crane PA (1999) High genetic heterogeneity in chum salmon in western Alaska, the contact zone between northern and southern lineages. Trans Am Fish Soc 128: 58-87.
48. Seeb LW, Antonovich A, Banks MA, Beacham TD, Bellinger MR, Blankenship SM et al (2007) Development of a standardized DNA database for Chinook salmon. Fisheries 32: 540-552.
49. Short AEZ, Caterino MS (2009) On the validity of habitat as a predictor of genetic structure in aquatic systems: a comparative study using California water beetles. Mol Ecol 18: 403-414.
50. Smith CT, Nelson RJ, Wood CC, Koop BF (2001) Glacial biogeography of North American coho salmon (Oncorhynchus kisutch). Mol Ecol 10: 2775-2785.
51. Smouse PE, Long JC, Sokal RR (1986) Multiple regression and correlation extensions of the Mantel test matrix correspondence. Syst Zool 35: 627-632.
52. Storfer A, Murphy MA, Evans JS et al (2006) Putting the 'landscape' in landscape genetics. Heredity 98: 128-142.
53. Utter FM, McPhee MV, Allendorf FW (2009) Population genetics and the management of Arctic-Yukon-Kuskokwim salmon populations. In: Krueger CC, Zimmerman CE (eds) Pacific salmon: ecology and management of western Alaska's populations. American Fisheries Society, Symposium 70, Bethesda, MD, pp 97-123.
54. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38: 1358-1370.
55. Whiteley AR, Spruell P, Allendorf F (2004) Ecological and life history characteristics predict population genetic divergence of two salmonids in the same landscape. Mol Ecol 13: 3675-3688.
56. Wilmot RL, Everett RJ, Spearman WJ, Baccus R, Varnavskaya NV, Putivkin SV (1994) Genetic stock structure of Western Alaska chum salmon and a comparison with Russian far east stocks. Can J Fish Aquat Sci 51: 84-94.
57. Wright S (1943) Isolation by distance. Genetics 28: 114-138.