Conservation Genetics

, Volume 8, Issue 2, pp 437–454 | Cite as

Population structure and genetic diversity of trout (Oncorhynchus mykiss) above and below natural and man-made barriers in the Russian River, California

  • Kristy Deiner
  • John Carlos Garza
  • Robert Coey
  • Derek J. Girman
Original Paper


The effects of landscape features on gene flow in threatened and endangered species play an important role in influencing the genetic structure of populations. We examined genetic variation of trout in the species Oncorhynchus mykiss at 22 microsatellite loci from 20 sites in the Russian River basin in central California. We assessed relative patterns of genetic structure and variation in fish from above and below both natural (waterfalls) and man-made (dams) barriers. Additionally, we compared sites sampled in the Russian River with sites from 16 other coastal watersheds in California. Genetic variation among the 20 sites sampled within the Russian River was significantly partitioned into six groups above natural barriers and one group consisting of all below barrier and above dam sites. Although the below-barrier sites showed moderate gene flow, we found some support for sub-population differentiation of individual tributaries in the watershed. Genetic variation at all below-barrier sites was high compared to above-barrier sites. Fish above dams were similar to those from below-barrier sites and had similar levels of genetic diversity, indicating they have not been isolated very long from below-barrier populations. Population samples from above natural barriers were highly divergent, with large F st values, and had significantly lower genetic diversity, indicating relatively small population sizes. The origins of populations above natural barriers could not be ascertained by comparing microsatellite diversity to other California rivers. Finally, below-barrier sites farther inland were more genetically differentiated from other watersheds than below-barrier sites nearer the river’s mouth.


Trout Microsatellite Landscape features Genetic differentiation Life history types 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.



We thank B. Freel for the initial inspiration for this project. We also thank K. Adams, L. Gilbert-Horvath, M. Hachmyer, A. Martinez, S. McNeil, J. Neilsen, J. Philips, S. Thibault, and T. Weiseth for their valuable contribution to this study in the field and in the lab. Additionally, we thank reviewers at the California Academy of Sciences, D. Pearse, R. Waples, and two anonymous reviewers for comments and suggestions that greatly improved the manuscript. This research was funded in part by a grant from the California Department of Fish and Game (Agreement No. P0030495) and in part by Sonoma State University and NOAA Fisheries.


  1. Bagley MJ, Gall GAE (1998) Mitochondrial and nuclear DNA sequence variability of rainbow trout (Oncorhynchus mykiss). Mol Ecol 7:945–961PubMedCrossRefGoogle Scholar
  2. Banks M, Blouin M, Baldwin B et al. (1999) Isolation and inheritance of novel microsatellites in Chinook salmon (Oncorhynchus tshawytscha). J Hered 90:281–288CrossRefGoogle Scholar
  3. Behnke RJ (1972) The systematics of salmonid fishes of recently glaciated lakes. J Fish Res Board Can 29:639–671Google Scholar
  4. Benhke RJ (2002) Comment: first documented case of anadromy in a population of introduced rainbow trout in Patagonia, Argentina. Trans Am Fish Soc 131:582–585CrossRefGoogle Scholar
  5. Busby PJ, Wainwright TC, Bryant GJ, Lierheimer LJ, Waples RS, Waknitz FW, Lagomarsino IV (1996) Status review of West Coast steelhead from Washington, Idaho, Oregon, and California. National Marine Fisheries Service, Northwest Fisheries Science Center, Technical Memorandum 27, SeattleGoogle Scholar
  6. Carlsson J, Nilsson J (2001) Effects of geomorphological structures on genetic differentiation among brown trout populations in a northern boreal river drainage. Trans Am Fish Soc 130:36–45CrossRefGoogle Scholar
  7. Castric V, Bonney F, Bernatchez L (2001) Landscape structure and hierarchical genetic diversity in the Brook Charr, Salvelinus fontinalis. Evolution 55:1016–1028PubMedCrossRefGoogle Scholar
  8. Castric V, Bernatchez L, Belkhir K, Bonhomme F (2002) Heterozygote deficiencies in small lacustrine populations of brook charr Salvelinus fontinalis Mitchill (Pisces, Salmonidae): a test of alternative hypotheses. Heredity 89:27–35PubMedCrossRefGoogle Scholar
  9. Cavalli-Sforza L, Edwards A (1967) Phylogenetic analysis: models and estimation procedures. Evolution 32:550–570CrossRefGoogle Scholar
  10. CDFG (2002) Draft Russian River Restoration Plan (ed. Coey R). California Department of Fish and Game, Yountville, CaliforniaGoogle Scholar
  11. Condrey MJ, Bentzen P (1998) Characterization of coastal cutthroat trout (Oncorhynchus clarki) microsatellites and their conservation in other salmonids. Mol Ecol 7:783–792Google Scholar
  12. Cornuet JM, Piry S, Luikart G, Estoup A, Solignac M (1999) New methods employing multilocus genotypes to select or exclude populations as origins of individuals. Genetics 153:1989–2000PubMedGoogle Scholar
  13. Crispo E, Bentson P, Reznick DR, Kinnison MT, Hendry AP (2006) The relative influence of natural selection and geography on gene flow in guppies. Mol Ecol 15:49–62PubMedCrossRefGoogle Scholar
  14. Currens KP, Schreck CB, Li HW (1990) Allozyme and morphological divergence of rainbow trout (Oncorhynchus mykiss) above and below waterfalls in the Deschutes River, Oregon. Copeia 1990: 730–746Google Scholar
  15. Deiner KL (2004) The effect of landscape features on the genetic structure and diversity of steelhead and rainbow trout (Oncorhynchus mykiss) in the Russian River watershed. MS Thesis, Sonoma State University, California, USAGoogle Scholar
  16. Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479–494PubMedGoogle Scholar
  17. Federal Register (1997) Vol. 62, No. 159, 43937–43954Google Scholar
  18. Felsenstein J (1995) PHYLIP (Phylogeny Inference Package). University of Washington, Box 357360, Seattle, WA 98105, USAGoogle Scholar
  19. Fleming IA, Jonsson B, Gross MR, Lamberg A (1996) An experimental study of the reproductive behavior and success of farmed and wild Atlantic salmon. J Appl Ecol 33:893–905CrossRefGoogle Scholar
  20. Garza JC, Gilbert-Horvath L, Anderson J, Williams T, Spence B, Fish H (2004) Population structure and history of steelhead trout in California. In: Irvine J (ed) Workshop on application of stock identification in defining marine distribution and migration of salmon. North Pacific Anadromous Fish Commission, Honolulu, Hawaii, USA, Nov.1–2, 2003, 5, pp 129–131Google Scholar
  21. Girman DJ, Vilà C, Geffen E, Creel S, Mills MGL, McNutt JW, Ginsberg J, Kat P, Mamiya KH, Wayne RK (2001) Patterns of population subdivision, gene flow and genetic variability in the African wild dog (Lycaon pictus). Mol Ecol 10:1703–1723.Google Scholar
  22. Goodnight KF, Queller DC (2001) Relatedness v5.0.8. Goodnight Software, HustonGoogle Scholar
  23. Goudet J (2001) FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3). Available from
  24. Healey MC (1991) Life history of Chinook salmon (Oncorhynchus tshawytscha). In: Groot C, Margolis L (eds) Pacific salmon life histories. UBC Press, Vancouver, pp 311–394Google Scholar
  25. Heard WR (1991) Life history of pink salmon (Oncorhynchus gorbuscha). In: Groot C, Margolis L (eds) Pacific salmon life histories. UBC Press, Vancouver, pp 119–230Google Scholar
  26. Hedrick PW, Gilpin ME (1997) Genetic effective size of a metapopulation. In: Hanski IA, Gilpin ME (eds) Metapopulation biology: ecology, genetics, and evolution. Academic Press, California, pp 165–181Google Scholar
  27. Hilderbrand RH, Kershner JL (2000) Conserving inland cutthroat trout in small streams: how much stream is enough? N Am J Fish Manage 20:513–520CrossRefGoogle Scholar
  28. Hill WG (1981) Estimation of effective population size from data on linkage disequilibrium. Gene Res 38:229–239Google Scholar
  29. 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 10:807–821PubMedCrossRefGoogle Scholar
  30. LeClair LL, Phelps SR, Tynan TJ (1999) Little gene flow from a hatchery strain of chum salmon to local wild populations. N Am J Fish Manage 19:530–535CrossRefGoogle Scholar
  31. Lewis PO, Zaykin D (2001) Genetic data analysis: computer program for the analysis of allelic data, v1.1 (d16c). Program distributed by authors over the internet from
  32. Manel S, Schwartz MK, Luikart G, Taberlet P (2003) Landscape genetics: combining landscape ecology and population genetics. Trends Ecol Evol 18:189–197CrossRefGoogle Scholar
  33. McConnell SK, Hamilton L, Morris D et al (1995) Isolation of salmonid microsatellite loci and their application to population genetics of Canadian east coast stocks of Atlantic salmon. Aquaculture 137:19–30CrossRefGoogle Scholar
  34. Moran P, Pendas AM, Garcia-Vazquez E, Izquierdo JT, Rutherford DT (1994) Electrophoresis assessment of the contribution of transplanted Scottish Atlantic salmon (Salmo salar) to the Esva River (Northern Spain). Can J Fish Aquat Sci 51:248–252CrossRefGoogle Scholar
  35. Morris DB, Richard KR, Wright JM (1996) Microsatellites from rainbow trout (Oncorhynchus mykiss) and their use for genetic studies of salmonids. Can J Fish Aquat Sci 53:120– 126CrossRefGoogle Scholar
  36. Moyle PB (2002) Inland fishes of California. University of California Press, LondonGoogle Scholar
  37. Nei M, Maruyama T, Charkraborty R (1975) The bottleneck effect and genetic variability in populations. Evolution 29:1–10CrossRefGoogle Scholar
  38. Neraas LP, Spruell P (2001) Fragmentation of riverine systems: the genetic effects of dams on bull trout (Salvelinus confluentus) in the Clark Fork River system. Mol Ecol 10:1153–1164PubMedCrossRefGoogle Scholar
  39. Nielsen JL, Fountain MC, Wright JM (1997) Biogeographic analysis of Pacific trout (Oncorhynchus mykiss) in California and Mexico based on mitochondrial DNA and nuclear microsatellites. In: Kocher TD, Stepien CA (eds) Molecular systematics of fishes. Academic Press, London, pp 53–73Google Scholar
  40. Northcote TG (1969) Patterns and mechanisms in lake-ward migratory behavior of juvenile trout. In: Northcote TG (ed) Symposium on salmon and trout streams. Institute of Fisheries, The University of British Columbia, Vancouver, pp 183–203Google Scholar
  41. Olsen JB, Miller SJ, Spearman WJ, Wenburg JK (2003) Patterns of intra- and inter-population genetic diversity in Alaskan coho salmon: implications for conservation. Conserv Genet 4:557–569CrossRefGoogle Scholar
  42. O’Reilly PT, Hamilton LC, McConnell SK, Wright JM (1996) Rapid detection of genetic variation in Atlantic salmon (Salmo salar) by PCR multiplexing of dinucleotide and tetranucleotide microsatellites. Can J Fish Aquat Sci 53:2292–2298CrossRefGoogle Scholar
  43. Page RDM (1996) TREEVIEW: an application to display phylogenetic trees on personal computers. Comp Appl Biosci 12:357–358PubMedGoogle Scholar
  44. Palti Y, Fincham MR, Rexroad CE (2002) Characterization of 38 polymorphic microsatellite markers for rainbow trout (Oncorhynchus mykiss). Mol Ecol Notes 2:449–452CrossRefGoogle Scholar
  45. Poissant J, Knight TW, Ferguson MM (2005) Nonequilibrium conditions following landscape rearrangement: the relative contribution of past and current hydrological landscapes on the genetic structure of a stream-dwelling fish. Mol Ecol 14:1321–1331CrossRefGoogle Scholar
  46. Pudovkin AI, Zaykin DV, Hedgecock D (1996) On the potential for estimating the effective number of breeders from heterozygote-excess in progeny. Genetics 144:383–387PubMedGoogle Scholar
  47. Quinn TP (1993) A review of homing and straying of wild and hatchery-produced salmon. Fish Res 18:29–44CrossRefGoogle Scholar
  48. Rannala B, Mountain JL (1997) Detecting immigration by using multilocus genotypes. Proc Natl Acad Sci USA 94:9197–9221PubMedCrossRefGoogle Scholar
  49. Raymond M, Rousset F (1995) An exact test for population differentiation. Evolution 49:1280–1283CrossRefGoogle Scholar
  50. Raymond M, Rousset F (1997) GENEPOP version 3.4, August 1997. University of Montpellier II, MontpellierGoogle Scholar
  51. Reisner M (1993) Cadillac Desert: The American west and its disappearing water. Revised and updated edition. Penguin Books, New YorkGoogle Scholar
  52. Rice WR (1989) Analyzing tables of statistical tests. Evolution 43:223–225CrossRefGoogle Scholar
  53. Schneider S, Kueffer J, Roessli D, Excoffier L (2000) Arlequin: a software for population genetic data analysis. Version 2.0. Genetic and Biometry Laboratory, University of Geneva, SwitzerlandGoogle Scholar
  54. Scribner KT, Gust JR, Fields RL (1996) Isolation and characterization of novel microsatellite loci: cross-species amplification and population genetic applications. Can J Fish Aquat Sci 53:685–693CrossRefGoogle Scholar
  55. Sherwin WB, Moritz C (2000) Managing and monitoring genetic erosion. In: Young AG, Clarke GM (eds) Genetics, demography and viability of fragmented populations. Cambridge University Press, New York, pp 9–34Google Scholar
  56. Small MP, Beacham TD, Withler RE, Nelson RJ (1998) Discriminating coho salmon (Oncorhynchus kisutch) populations within the Fraser River, British Columbia using microsatellite DNA markers. Mol Ecol 7:141–155CrossRefGoogle Scholar
  57. Smith CT, Koop BF, Nelson RJ (1998) Isolation and characterization of coho salmon (Oncorhynchus kisutch) microsatellites and their use in other salmonids. Mol Ecol 7:1614–1616PubMedGoogle Scholar
  58. Spidle AP, Schill WB, Lubinski BA, King TL (2001) Fine-scale population structure in Atlantic salmon from Maine’s Penobscot River drainage. Conserv Genet 2:11–24CrossRefGoogle Scholar
  59. Srikwian S, Woodruff DS (2000) Genetic erosion in isolated small-mammal populations following rainforest fragmentation. In: Young AG, Clarke GM (eds) Genetics, demography and viability of fragmented populations. Cambridge University Press, New York, pp 149–172Google Scholar
  60. Steiner Environmental Consulting (1996) A history of the salmonid decline in the Russian River. Potter Valley, CA pp 1–86Google Scholar
  61. Taberlet P, Bouvet J (1991) A single plucked feather as a source of DNA for bird genetic studies. Auk 108:959–960Google Scholar
  62. Takezaki N, Nei M (1996) Genetic distances and reconstruction of phylogenetic trees from microsatellite DNA. Genetics 144:389–399PubMedGoogle Scholar
  63. Waples RS (1991) Genetic interactions between hatchery and wild salmonids: lessons from the Pacific Northwest. Can J Fish Aquat Sci 48:124–133Google Scholar
  64. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 138:1358–1370CrossRefGoogle Scholar
  65. Weir BS, Cockerham CC (1996) Genetic data analysis II: methods for descrete population genetic data. Sinauer Assoc., Inc., Sunderland, MA, USAGoogle Scholar
  66. Wenburg JK, Bentzen, P (2001) Genetic and behavioral evidence for restricted gene flow among coastal cutthroat trout populations. Trans Am Fish Soc 130:1049–1069CrossRefGoogle Scholar
  67. Williams RN, Leary RF, Currens KP (1997) Localized genetic effect of a long-term hatchery stocking program on resident rainbow trout in the Metolius River. N Am J Fish Manage 17:1079–1093CrossRefGoogle Scholar
  68. Williamson KS, Cordes JF, May BP (2002) Characterization of microsatellite loci in Chinook salmon (Oncorhynchus tshawytscha) and cross-species amplification in other salmonids. Mol Ecol Notes 2:17–19CrossRefGoogle Scholar
  69. Wishard LN, Seeb JE, Utter FM, Stefan D (1984) A genetic investigation of suspected redband trout populations. Copeia 1984:120–132Google Scholar

Copyright information

© Springer Science+Business Media B.V. 2006

Authors and Affiliations

  • Kristy Deiner
    • 1
  • John Carlos Garza
    • 2
  • Robert Coey
    • 3
  • Derek J. Girman
    • 1
  1. 1.Department of BiologySonoma State UniversityRohnert ParkUSA
  2. 2.NOAA Southwest Fisheries Science CenterSanta CruzUSA
  3. 3.California Department of Fish and GameYountvilleUSA

Personalised recommendations