iBet uBet web content aggregator. Adding the entire web to your favor.
iBet uBet web content aggregator. Adding the entire web to your favor.



Link to original content: https://doi.org/10.1007/s10592-006-9183-0
Population structure and genetic diversity of trout (Oncorhynchus mykiss) above and below natural and man-made barriers in the Russian River, California | Conservation Genetics Skip to main content

Advertisement

Springer Nature Link
Log in

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

  • Original Paper
  • Published:
Conservation Genetics Aims and scope Submit manuscript

Abstract

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Bagley MJ, Gall GAE (1998) Mitochondrial and nuclear DNA sequence variability of rainbow trout (Oncorhynchus mykiss). Mol Ecol 7:945–961

    Article  PubMed  CAS  Google Scholar 

  • Banks M, Blouin M, Baldwin B et al. (1999) Isolation and inheritance of novel microsatellites in Chinook salmon (Oncorhynchus tshawytscha). J Hered 90:281–288

    Article  CAS  Google Scholar 

  • Behnke RJ (1972) The systematics of salmonid fishes of recently glaciated lakes. J Fish Res Board Can 29:639–671

    Google Scholar 

  • Benhke RJ (2002) Comment: first documented case of anadromy in a population of introduced rainbow trout in Patagonia, Argentina. Trans Am Fish Soc 131:582–585

    Article  Google Scholar 

  • 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, Seattle

  • 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 130:36–45

    Article  Google Scholar 

  • Castric V, Bonney F, Bernatchez L (2001) Landscape structure and hierarchical genetic diversity in the Brook Charr, Salvelinus fontinalis. Evolution 55:1016–1028

    Article  PubMed  CAS  Google Scholar 

  • 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 89:27–35

    Article  PubMed  CAS  Google Scholar 

  • Cavalli-Sforza L, Edwards A (1967) Phylogenetic analysis: models and estimation procedures. Evolution 32:550–570

    Article  Google Scholar 

  • CDFG (2002) Draft Russian River Restoration Plan (ed. Coey R). California Department of Fish and Game, Yountville, California

  • Condrey MJ, Bentzen P (1998) Characterization of coastal cutthroat trout (Oncorhynchus clarki) microsatellites and their conservation in other salmonids. Mol Ecol 7:783–792

    Google Scholar 

  • 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 153:1989–2000

    PubMed  CAS  Google Scholar 

  • 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 15:49–62

    Article  PubMed  CAS  Google Scholar 

  • 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: 730–746

  • 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, USA

  • 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 131:479–494

    PubMed  CAS  Google Scholar 

  • Federal Register (1997) Vol. 62, No. 159, 43937–43954

  • Felsenstein J (1995) PHYLIP (Phylogeny Inference Package). University of Washington, Box 357360, Seattle, WA 98105, USA

  • 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 33:893–905

    Article  Google Scholar 

  • 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 129–131

  • 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 

  • Goodnight KF, Queller DC (2001) Relatedness v5.0.8. Goodnight Software, Huston

  • Goudet J (2001) FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3). Available from http://www.unil.ch/izea/softwares/fstat.html

  • Healey MC (1991) Life history of Chinook salmon (Oncorhynchus tshawytscha). In: Groot C, Margolis L (eds) Pacific salmon life histories. UBC Press, Vancouver, pp 311–394

    Google Scholar 

  • Heard WR (1991) Life history of pink salmon (Oncorhynchus gorbuscha). In: Groot C, Margolis L (eds) Pacific salmon life histories. UBC Press, Vancouver, pp 119–230

    Google Scholar 

  • 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 165–181

    Google Scholar 

  • Hilderbrand RH, Kershner JL (2000) Conserving inland cutthroat trout in small streams: how much stream is enough? N Am J Fish Manage 20:513–520

    Article  Google Scholar 

  • Hill WG (1981) Estimation of effective population size from data on linkage disequilibrium. Gene Res 38:229–239

    Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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 19:530–535

    Article  Google Scholar 

  • 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 http://www.lewis.eeb.uconn.edu/lewishome/software.html

  • Manel S, Schwartz MK, Luikart G, Taberlet P (2003) Landscape genetics: combining landscape ecology and population genetics. Trends Ecol Evol 18:189–197

    Article  Google Scholar 

  • 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 137:19–30

    Article  Google Scholar 

  • 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 51:248–252

    Article  Google Scholar 

  • 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– 126

    Article  CAS  Google Scholar 

  • Moyle PB (2002) Inland fishes of California. University of California Press, London

    Google Scholar 

  • Nei M, Maruyama T, Charkraborty R (1975) The bottleneck effect and genetic variability in populations. Evolution 29:1–10

    Article  Google Scholar 

  • 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 10:1153–1164

    Article  PubMed  CAS  Google Scholar 

  • 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 53–73

    Google Scholar 

  • 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 183–203

    Google Scholar 

  • 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 4:557–569

    Article  CAS  Google Scholar 

  • 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 53:2292–2298

    Article  CAS  Google Scholar 

  • Page RDM (1996) TREEVIEW: an application to display phylogenetic trees on personal computers. Comp Appl Biosci 12:357–358

    PubMed  CAS  Google Scholar 

  • Palti Y, Fincham MR, Rexroad CE (2002) Characterization of 38 polymorphic microsatellite markers for rainbow trout (Oncorhynchus mykiss). Mol Ecol Notes 2:449–452

    Article  CAS  Google Scholar 

  • 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 14:1321–1331

    Article  Google Scholar 

  • Pudovkin AI, Zaykin DV, Hedgecock D (1996) On the potential for estimating the effective number of breeders from heterozygote-excess in progeny. Genetics 144:383–387

    PubMed  CAS  Google Scholar 

  • Quinn TP (1993) A review of homing and straying of wild and hatchery-produced salmon. Fish Res 18:29–44

    Article  Google Scholar 

  • Rannala B, Mountain JL (1997) Detecting immigration by using multilocus genotypes. Proc Natl Acad Sci USA 94:9197–9221

    Article  PubMed  CAS  Google Scholar 

  • Raymond M, Rousset F (1995) An exact test for population differentiation. Evolution 49:1280–1283

    Article  Google Scholar 

  • Raymond M, Rousset F (1997) GENEPOP version 3.4, August 1997. University of Montpellier II, Montpellier

  • Reisner M (1993) Cadillac Desert: The American west and its disappearing water. Revised and updated edition. Penguin Books, New York

    Google Scholar 

  • Rice WR (1989) Analyzing tables of statistical tests. Evolution 43:223–225

    Article  Google Scholar 

  • 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, Switzerland

  • 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 53:685–693

    Article  Google Scholar 

  • 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 9–34

    Google Scholar 

  • 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 7:141–155

    Article  CAS  Google Scholar 

  • Smith CT, Koop BF, Nelson RJ (1998) Isolation and characterization of coho salmon (Oncorhynchus kisutch) microsatellites and their use in other salmonids. Mol Ecol 7:1614–1616

    PubMed  CAS  Google Scholar 

  • Spidle AP, Schill WB, Lubinski BA, King TL (2001) Fine-scale population structure in Atlantic salmon from Maine’s Penobscot River drainage. Conserv Genet 2:11–24

    Article  CAS  Google Scholar 

  • 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 149–172

    Google Scholar 

  • Steiner Environmental Consulting (1996) A history of the salmonid decline in the Russian River. Potter Valley, CA pp 1–86

    Google Scholar 

  • Taberlet P, Bouvet J (1991) A single plucked feather as a source of DNA for bird genetic studies. Auk 108:959–960

    Google Scholar 

  • Takezaki N, Nei M (1996) Genetic distances and reconstruction of phylogenetic trees from microsatellite DNA. Genetics 144:389–399

    PubMed  CAS  Google Scholar 

  • Waples RS (1991) Genetic interactions between hatchery and wild salmonids: lessons from the Pacific Northwest. Can J Fish Aquat Sci 48:124–133

    Google Scholar 

  • Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 138:1358–1370

    Article  Google Scholar 

  • Weir BS, Cockerham CC (1996) Genetic data analysis II: methods for descrete population genetic data. Sinauer Assoc., Inc., Sunderland, MA, USA

    Google Scholar 

  • Wenburg JK, Bentzen, P (2001) Genetic and behavioral evidence for restricted gene flow among coastal cutthroat trout populations. Trans Am Fish Soc 130:1049–1069

    Article  CAS  Google Scholar 

  • 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 17:1079–1093

    Article  Google Scholar 

  • 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 2:17–19

    Article  CAS  Google Scholar 

  • Wishard LN, Seeb JE, Utter FM, Stefan D (1984) A genetic investigation of suspected redband trout populations. Copeia 1984:120–132

Download references

Acknowledgements

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.

Author information

Authors and Affiliations

  1. Department of Biology, Sonoma State University, 1801 E. Cotati Ave., Rohnert Park, CA, 94928, USA

    Kristy Deiner & Derek J. Girman

  2. NOAA Southwest Fisheries Science Center, Santa Cruz, CA, 95060, USA

    John Carlos Garza

  3. California Department of Fish and Game, Yountville, CA, 94599, USA

    Robert Coey

Authors
  1. Kristy Deiner
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. John Carlos Garza
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Robert Coey
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Derek J. Girman
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Derek J. Girman.

Appendix

Appendix

Appendix I Sample sizes (N), number of alleles (A) and observed and expected heterozygosities (Ho and He) at 22 microsatellite loci with all individuals for the twenty sites sampled on the Russian River watershed. Abbreviations listed in Table 1 and loci described in Table 3
Full size table

Rights and permissions

Reprints and permissions

About this article

Cite this article

Deiner, K., Garza, J.C., Coey, R. et al. Population structure and genetic diversity of trout (Oncorhynchus mykiss) above and below natural and man-made barriers in the Russian River, California. Conserv Genet 8, 437–454 (2007). https://doi.org/10.1007/s10592-006-9183-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10592-006-9183-0

Keywords

Search

Navigation