Abstract
The lower Columbia River drainage once supported a run of over a million chum salmon. By the late 1950s, the run had decreased to often a few hundred fish. With the exception of Grays River near the coast and an aggregation of chum salmon spawning in creeks and the main stem near Bonneville Dam in the Columbia Gorge, most populations were thought to be extinct. However, chum salmon consistently return in low numbers to tributaries originating in the Cascade Range: the Cowlitz, Lewis, and Washougal rivers. To assess whether Cascade spawners were strays or remnants of former populations, chum salmon from the Coastal, Cascade and Gorge ecoregional zones were characterized at 17 microsatellite loci. Significant heterogeneity in genotype distributions was detected between zones and collections formed regional groups in a neighbor-joining tree. Cascade collections had higher allelic richness and private alleles, and the Cowlitz River supported genetically divergent fall and summer runs, the only summer chum salmon run extant in the Columbia River drainage. We propose that chum salmon in the Cascade zone are remnants of original populations. We attribute the divergence between zonal groups to diverse ecological conditions in each zone, which promoted regional genetic adaptation, and to genetic drift experienced in small populations.
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References
MA Banks MS Blouin BA Baldwin VK Rashbrook HA Fitzgerald SM Blankenship D Hedgecock (1999) ArticleTitleIsolation and inheritance of novel microsatellites in chinook salmon (Oncorhynchus tshawytscha) J. Hered. 90 281–288 Occurrence Handle10.1093/jhered/90.2.281 Occurrence Handle1:CAS:528:DyaK1MXhs1yktL4%3D
TD Beacham L Margolis RJ Nelson (1998) ArticleTitleA comparison of methods of stock identification for sockeye salmon (Oncorhynchus nerka) in Barkley Sound, British Columbia N. Pac. Anad. Fish Comm. Bull 1 227–239
WG Bucholz SJ Miller WJ Spearman (2001) ArticleTitleIsolation and characterization of chum salmon microsatellite loci and use across species Anim. Gen. 32 IssueID5 317
M Cainey JB Taggart B Høyheim (2000) ArticleTitleCharacterization of microsatellite and minisatellite loci in Atlantic salmon (Salmo salar L.) and cross-species amplification in other salmonids Mol. Ecol. 9 2175–2178
LL Cavalli-Sforza AWF Edwards (1967) ArticleTitlePhylogenetic analysis: models and estimation procedures Am. J. Human Genet. 19 233–257
D Dieringer C Schlötterer (2003) ArticleTitleMicrosatellite analyzer (MSA)- a platform independent analysis tool for large microsatellite data sets Mol. Ecol. Notes 3 IssueID1 167–169 Occurrence Handle10.1046/j.1471-8286.2003.00351.x Occurrence Handle1:CAS:528:DC%2BD3sXivVyitbw%3D
J Felsenstein (1993) Phylogeny inference package (PHYLIP) Version 3..5c University of Washington Seattle
Fulton LA (1970) Spawning areas and abundance of steelhead trout and coho, sockeye, and chum salmon in the Columbia river basin – past and present. NOAA Tech. Report NMFS-SSRF 618, 37 p.
JC Garza EG Williamson (2001) ArticleTitleDetection of reduction in population size using data from microsatellite loci Mol. Ecol. 10 305–318 Occurrence Handle10.1046/j.1365-294x.2001.01190.x Occurrence Handle1:STN:280:DC%2BD3MvgvFSntg%3D%3D Occurrence Handle11298947
J Glaubitz (2004) ArticleTitleCONVERT: A user-friendly program to reformat diploid genotypic data for commonly used population genetic software packages Mol. Ecol. Notes 4 IssueID2 309–310 Occurrence Handle10.1111/j.1471-8286.2004.00597.x Occurrence Handle1:CAS:528:DC%2BD2cXlt1ChtL4%3D
Goudet J (2001) FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3). Updated from Goudet (1995) Available from http://www.unilch/izea/softwares/fstat.html.
LP Hansen B Johnson (1991) ArticleTitleEvidence of a genetic component in the seasonal return pattern of Atlantic salmon, Salmo salar L. J. Fish. Bio. 38 251–258
WR Heard (1991) Life history of pink salmon (Oncorhynchus gorbuscha) C Groot L Margolis (Eds) Pacific Salmon Life Histories UBC Press Vancouver, BC 119–230
Johnson OW, Grant WS, Kope RG, Neely K, Waknitz FW, Waples RS (1997) Status review of chum salmon from Washington, Oregon, and California. NOAA technical memorandum NMFS-NWFSC-32. US Department of Commerce.
Kalinowski, ST (2005) HP-RARE 1.0: a computer program for performing rarefaction on measures of allelic richness. Mol. Ecol. Notes, In press.
Keller K (2001) 1999 Columbia River chum return. Columbia River Progress Report 2000–6. Washington Department of Fish and Wildlife, 12 p.
MT Kinnison P Bentzen MJ Unwins TP Quinn (2002) ArticleTitleReconstructing recent divergence: evaluating nonequilibrium population structure in New Zealand Chinook salmon Mol. Ecol. 11 739–754 Occurrence Handle10.1046/j.1365-294X.2002.01477.x Occurrence Handle1:CAS:528:DC%2BD38XktFahsrs%3D Occurrence Handle11972761
McElhany P, Backman T, Busack C, Heppell S, Kolmes S, Maule A, Myers J, Rawding D, Shively D, Steel, A., Steward C., Whitesel T. (2003) Interim report on viability criteria for Willamette and lower Columbia basin Pacific salmonids. Interim report from the Willamette/Lower Columbia Technical Recovery Team. March 2003.
SKJ McConnell DE Ruzzante PT O’Reilly L Hamilton JM Wright (1997) ArticleTitleMicrosatellite loci reveal highly significant genetic differentiation among Atlantic salmon (Salmo salar L.) stocks from the east coast of Canada Mol. Ecol. 6 1075–1089 Occurrence Handle10.1046/j.1365-294X.1997.00282.x
Myers J, Busack C, Rawding D, Marshall A (2002) Identifying historical populations of Chinook and chum salmon and steelhead within the lower Columbia River and upper Willamette River evolutionarily significant units. Draft report to the co-managers from the Willamette/Lower Columbia River Technical Recovery Team.
M Nei (1987) Molecular Evolutionary Genetics Columbia University Press New York
EE Nielsen MM Hansen V Loeschke (1997) ArticleTitleAnalysis of microsatellite DNA from old scale samples of Atlantic salmon (Salmo salar): a comparison of genetic composition over 60 years Mol. Ecol. 6 487–492 Occurrence Handle10.1046/j.1365-294X.1997.00204.x Occurrence Handle1:CAS:528:DyaK2sXjsFOhs7c%3D
EE Nielsen MM Hansen V Loeschke (1999) ArticleTitleGenetic variation in time and space: microsatellite analysis of extinct and extant populations of Atlantic salmon Evolution 53 IssueID1 261–268
EE Nielsen MM Hansen LA Bach (2001) ArticleTitleLooking for a needle in a haystack: discovery of indigenous Atlantic salmon (Salmo salar L.) in stocked populations Cons. Gen. 2 219–232
NMFS (National Marine Fisheries Service) (1999) Endangered and threatened species: Threatened status for two ESU’s of chum salmon in Washington and Oregon. [Docket 980219042-9069-02, No. 011498B. 25 March 1999] 64(57), 14508–14517. NMFS 1999.
NOAA (2004 in preparation) Updated status review of listed ESU’s of West Coast Salmon Preliminary conclusions regarding the updated status of listed ESU’s of West Coast salmon and steelhead. Co-manager review draft. Available at http://www.nwfsc.noaa.gov/trt/brt/Chum.pdf.
JB Olsen SL Wilson EJ Kretschmer KC Jones JE Seeb (2000) ArticleTitleCharacterization of 14 tetranucleotide microsatellite loci derived from sockeye salmon Mol. Ecol. 9 2185–2187 Occurrence Handle1:CAS:528:DC%2BD3MXot1OqtQ%3D%3D Occurrence Handle11123645
Page R (2001) Treeview: Tree drawing software for Apple MacIntosh and Windows. Available at http://taxonomy/zoology/gla.ac.uk/rod/rod.html.
SR Phelps LL LeClair S Young HL Blankenship (1994) ArticleTitleGenetic diversity patterns of chum salmon in the Pacific Northwest Can. J. Fish. Aquat. Sci. 51 IssueID(Supplement 1) 65–83
JK Pritchard M Stephens P Donnelly (2000) ArticleTitleInference of population structure using multilocus genotype data Genetics 155 945–959 Occurrence Handle1:STN:280:DC%2BD3cvislKrtA%3D%3D Occurrence Handle10835412
TP Quinn MJ Unwin MT Kinnison (2000) ArticleTitleEvolution of temporal isolation in the wild: genetic divergence in timing of migration and breeding in introduced populations of Chinook salmon Evolution 54 1372–1385 Occurrence Handle1:STN:280:DC%2BD3cvltVeiuw%3D%3D Occurrence Handle11005303
KM Ramstad CA Woody GK Sage FW Allendorf (2004) ArticleTitleFounding events influence genetic population structure of sockeye salmon (Oncorhynchus nerka) in Lake Clark, Alaska Mol. Ecol. 13 277–290 Occurrence Handle10.1046/j.1365-294X.2003.2062.x Occurrence Handle1:STN:280:DC%2BD2c%2FitFCrsA%3D%3D Occurrence Handle14717887
M Raymond F Rousset (1995) ArticleTitleGENEPOP (Version 3.3): Population genetics software for exact tests and ecumenicism J. Hered. 86 248–249
CE Rexroad SuffixIII RL Coleman AM Martin WK Hershberger J Killefer (2001) ArticleTitleThirty-five polymorphic microsatellite markers for rainbow trout (Oncorhynchus mykiss) Animal Genetics 32 IssueID5 317 Occurrence Handle10.1046/j.1365-2052.2001.0730b.x Occurrence Handle1:CAS:528:DC%2BD3MXot1Srtb8%3D Occurrence Handle11683722
EO Salo (1991) Life history of chum salmon, Oncorhynchus keta C. Groot L. Margolis (Eds) Pacific Salmon Life Histories UBC Press Vancouver, BC, Canada 231–309
S Schneider D Roessli L Excoffier (2000) Arlequin version (2.001): a software for population genetic data analysis Genetics and Biometry Laboratory, University of Geneva Switzerland
KT Scribner JR Gust RL Fields (1996) ArticleTitleIsolation and characterization of novel salmon microsatellite loci: cross-species amplification and populations genetic applications Can. J. Fish. Aquat. Sci. 53 833–841 Occurrence Handle10.1139/cjfas-53-4-833 Occurrence Handle1:CAS:528:DyaK28Xlslyls7c%3D
CR Sherwood DA Jay RB Harvey P Hamilton CA Simenstad (1990) Historical changes in the Columbia River Estuary F. Small (Eds) Prog. Oceanogr. NumberInSeries25 Estuarine System Columbia River 299–352
MP Small T Beacham R Withler RJ Nelson (1998) ArticleTitleDiscriminating coho salmon (Oncorhynchus kisutch) populations within the Fraser River, British Columbia using microsatellite DNA markers Mol. Ecol. 7 141–155 Occurrence Handle10.1046/j.1365-294x.1998.00324.x Occurrence Handle1:CAS:528:DyaK1cXitlegt7Y%3D
WW Smoker AJ Gharrett MS Stekoll (1998) ArticleTitleGenetic variation of return date in a population of pink salmon: a consequence of fluctuating environment and dispersive selection? AK Fish. Res. Bull 5 46–54
CT Smith BF Koop RJ Nelson (1998) ArticleTitleIsolation and characterization of coho salmon (Oncorhynchus kisutch) microsatellites and their use in other salmonids Mol. Ecol. 7 1614–1616 Occurrence Handle1:CAS:528:DyaK1cXnsFSgtb0%3D Occurrence Handle9819912
AP Spidle WB Schill BA Lubinski TL King (2001) ArticleTitleFine-scale population structure in Atlantic salmon from Maine’s Penobscot River drainage Cons. Genet. 2 11–24 Occurrence Handle1:CAS:528:DC%2BD3MXmsl2gu7s%3D
EB Taylor (1991) ArticleTitleA review of local adaptation in Salmonidae, with particular reference to Pacific and Atlantic salmon Aquaculture 98 185–207 Occurrence Handle10.1016/0044-8486(91)90383-I
C Oosterhout ParticleVan WF Hutchinson DPM Wills P Shipley (2004) ArticleTitleMicro-Checker: software for identifying and correcting genotyping errors in microsatellite data Mol. Ecol. Notes 4 535–538
RS Waples (1990) ArticleTitleConservation genetics of Pacific salmon. II. Effective population size and the rate of loss of genetic variability J. Hered. 81 267–276
Washington Department of Fish and Wildlife (WDFW) 2000. Columbia River chum salmon. In WDFW web site: Chum salmon 2000 available at http://www.wa.gov/wdfw/fish/chum.
KS Williamson JF Cordes BP May (2002) ArticleTitleCharacterization of microsatellite loci in Chinook salmon (Oncorhynchus tshawytscha) and cross-species amplification in other salmonids Mol Ecol Notes 2 IssueID1 17 Occurrence Handle10.1046/j.1471-8286.2002.00129.x Occurrence Handle1:CAS:528:DC%2BD38XislOgur0%3D
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Small, M.P., Frye, A.E., Von Bargen, J.F. et al. Genetic Structure of Chum Salmon (Oncorhynchus keta) Populations in the Lower Columbia River: Are Chum Salmon in Cascade Tributaries Remnant Populations?. Conserv Genet 7, 65–78 (2006). https://doi.org/10.1007/s10592-005-7967-2
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DOI: https://doi.org/10.1007/s10592-005-7967-2