Skip to main content
Log in

Population genetic structure and ancestry of Oncorhynchus mykiss populations above and below dams in south-central California

  • Research Article
  • Published:
Conservation Genetics Aims and scope Submit manuscript

Abstract

Genetic analyses of coastal Oncorhynchus mykiss, commonly known as steelhead/rainbow trout, at the southern extreme of their geographic range in California are used to evaluate ancestry and genetic relationships of populations both above and below large dams. Juvenile fish from 20 locations and strains of rainbow trout commonly planted in reservoirs in the five study basins were evaluated at 24 microsatellite loci. Phylogeographic trees and analysis of molecular variance demonstrated that populations within a basin, both above and below dams, were generally each other’s closest relatives. Absence of hatchery fish or their progeny in the tributaries above dams indicates that they are not commonly spawning and that above-barrier fish are descended from coastal steelhead trapped at dam construction. Finally, no genetic basis was found for the division of populations from this region into two distinct biological groups, contrary to current classification under the US and California Endangered Species Acts.

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

Access this article

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

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Aguilar A, Garza JC (2006) A comparison of variability and population structure for major histocompatibility complex and microsatellite loci in California coastal steelhead (Oncorhynchus mykiss Walbaum). Mol Ecol 15:923–937

    Article  CAS  PubMed  Google Scholar 

  • Banks MA, Blouin MS, Baldwin BA, Rashbrook VK, Fitzgerald HA, Blankenship SM, Hedgecock D (1999) Isolation and inheritance of novel microsatellites in Chinook salmon (Oncorhynchus tshawytscha). J Hered 90:281–288. doi:10.1093/jhered/90.2.281

    Article  CAS  Google Scholar 

  • Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F (1996–2004) GENETIX 4.05, logiciel sous Windows TM pour la génétique des populations. Laboratoire Génome, populations, interactions, CNRS UMR 5000, Université de Montpellier II, Montpellier, France

  • Berg WJ, Gall GAE (1988) Gene flow and genetic differentiation among California coastal rainbow trout populations. Can J Fish Aquat Sci 45:122–131

    Google Scholar 

  • Busby PJ, Wainwright TC, Bryant GJ et al (1996) Status review of west coast steelhead from Washington, Idaho, Oregon, and California. National Oceanographic and Atmospheric Administration Tech. Memo. NMFS-NWFSC-27. http://www.nwfsc.noaa.gov/publications/techmemos/tm27/tm27.htm

  • 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. doi:10.1577/1548-8659(2001)130<0036:EOGSOG>2.0.CO;2

    Article  Google Scholar 

  • Castric V, Bonney F, Bernatchez L (2001) Landscape structure and hierarchical genetic diversity in the Brook Charr, Salvelinus fontinalis. Evol Int J Org Evol 55:1016–1028. doi:10.1554/0014-3820(2001)055[1016:LSAHGD]2.0.CO;2

    CAS  Google Scholar 

  • Cavalli-Sforza LL, Edwards AWF (1967) Phylogenetic analysis: models and estimation procedures. Evol Int J Org Evol 32:550–570. doi:10.2307/2406616

    Google Scholar 

  • Chan KMA, Levin SA (2005) Leaky prezygotic isolation and porous genomes: rapid introgression of maternally inherited DNA. Evol Int J Org Evol 59:720–729

    CAS  Google Scholar 

  • Crispo E, Bentzen 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. doi:10.1111/j.1365-294X.2005.02764.x

    Article  CAS  PubMed  Google Scholar 

  • Deiner K, Garza JC, Coey R, Girman DJ (2007) Population structure and genetic diversity of trout (Oncorhynchus mykiss) above and below natural and manmade-barriers in the Russian River, California. Conserv Genet 8:437–454. doi:10.1007/s10592-006-9183-0

    Article  Google Scholar 

  • Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction sites. Genetics 131:479–491

    CAS  PubMed  Google Scholar 

  • Excoffier L, Laval G, Schneider S (2005) ARLEQUIN, version 3.0: an integrated software package for population genetics data analysis. Evol Bioinform Online 1:47–50

    CAS  PubMed  Google Scholar 

  • Felsenstein J (1993) PHYLIP (Phylogeny Inference Package), version 3.57c. Department of Genetics, University of Washington, Box 357360, Seattle, WA 98105, USA

  • Felsenstein J (2004) Inferring phylogenies. Sinauer Associates, Sunderland, MA

    Google Scholar 

  • Garza JC, Williamson E (2001) Detection of reduction in population size using data from microsatellite loci. Mol Ecol 10:305–318. doi:10.1046/j.1365-294x.2001.01190.x

    Article  CAS  PubMed  Google Scholar 

  • Garza JC, Gilbert-Horvath E, Anderson J, Williams T, Spence B, Fish H (2004) Population structure and history of steelhead trout in California. In: Irvine J et al (eds) Workshop on application of stock identification in defining marine distribution and migration of salmon (Honolulu, HI, USA, November 1–2, 2003). North Pacific Anadromous Fish Commission, Technical Report 5:129–131

  • Goudet J (1995) FSTAT (Version 1.2): a computer program to calculate F-statistics. J Hered 86:485–486

    Google Scholar 

  • Greenwald GM, Campton DE (2005) Genetic influence of hatchery-origin fish to natural populations of rainbow trout in the Santa Ynez River, California. A synopsis and supplemental evaluation of: Nielsen JL, Zimmerman CE, Olson JB, Wiacek TC, Kretschmer EJ, Greenwald GM, Wenburg JK (2003) Population genetic structure of Santa Ynez River rainbow trout 2001 based on microsatellite and mtDNA analyses. Final report submitted to U.S. Fish and Wildlife Service under intra-agency Agreement No. 11440-1-4000 between the U.S. Fish and Wildlife Service (Ventura, CA) and the U.S. Geological Survey (Anchorage, AK)

  • Hedrick PW (1999) Perspective: highly variable loci and their interpretation in evolution and conservation. Evolution 53:313–318

    Google Scholar 

  • Jackson TR, Ferguson MM, Danzmann RG, Fishback AG, Ihssen PE, O’Connell M, Crease TJ (1998) Identification of two QTL influencing upper temperature tolerance in three rainbow trout (Oncorhynchus mykiss) half-sib families. Heredity 80:143–151. doi:10.1046/j.1365-2540.1998.00289.x

    Article  Google Scholar 

  • McConnell SK, O’Reilly P, Hamilton L, Wright JM, Bentzen P (1995) Polymorphic microsatellite loci from Atlantic salmon (Salmo salar): genetic differentiation of North American and European populations. Can J Fish Aquat Sci 52:1863–1872. doi:10.1139/f95-779

    Article  CAS  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. doi:10.1139/cjfas-53-1-120

    Article  CAS  Google Scholar 

  • National Oceanic and Atmospheric Administration (1997) Endangered and threatened species: listing of several evolutionarily significant units (ESUs) of west coast steelhead. US Fed Regist 62:43937–43954

    Google Scholar 

  • National Oceanic and Atmospheric Administration (2002) Endangered and threatened species: range extension for endangered steelhead in southern California. US Fed Regist 67:21586–21598

    Google Scholar 

  • Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York

    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

    Chapter  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. doi:10.1023/A:1025684104113

    Article  CAS  Google Scholar 

  • O’Malley KG, Sakamoto T, Danzmann RG, Ferguson MM (2002) Quantitative trait loci for spawning date and body weight in rainbow trout: testing for conserved effects across ancestrally duplicated chromosomes. J Hered 94:273–284. doi:10.1093/jhered/esg067

    Article  Google Scholar 

  • O’Reilly PT, Hamilton LC, McConnell SK, Wright JM (1996) Rapid analysis of genetic variation in Atlantic salmon (Salmo salar) by PCR multiplexing of dinucleotide and tetranucleotide microsatellites. Can J Fish Aquat Sci 53:2292–2298. doi:10.1139/cjfas-53-10-2292

    Article  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Pearse DP, Donohoe C, Garza JC (2007) Population genetics of steelhead (Oncorhynchus mykiss) in the Klamath River. Environ Biol Fishes 80:377–387. doi:10.1007/s10641-006-9135-z

    Article  Google Scholar 

  • Perry GM, Danzmann RG, Fergusson MM, Gibson JP (2001) Quantitative trait loci for upper thermal tolerance in outbred strains of rainbow trout (Oncorhynchus mykiss). Heredity 86:333–341. doi:10.1046/j.1365-2540.2001.00838.x

    Article  CAS  PubMed  Google Scholar 

  • Piry S, Alapetite A, Cornuet J-M, Paetkau D, Baudouin L, Estoup A (2004) GeneClass2: a software for genetic assignment and first-generation migrant detection. J Hered 95:536–539. doi:10.1093/jhered/esh074

    Article  CAS  PubMed  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. doi:10.1111/j.1365-294X.2005.02500.x

    Article  Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    CAS  PubMed  Google Scholar 

  • Rannala B, Mountain JL (1997) Detecting immigration by using multilocus genotypes. Proc Natl Acad Sci USA 94:9197–9201. doi:10.1073/pnas.94.17.9197

    Article  CAS  PubMed  Google Scholar 

  • Raymond M, Rousset F (1995) Genepop version 1.2: population genetics software for exact tests and ecumenicism. J Hered 86:248–249

    Google Scholar 

  • Ryman N, Laikre L (1991) Effects of supportive breeding on the genetically effective population size. Conserv Biol 5:325–329. doi:10.1111/j.1523-1739.1991.tb00144.x

    Article  Google Scholar 

  • Scribner KT, Gust JR, Fields RL (1996) Isolation and characterization of novel salmon microsatellite loci: cross-species amplification and population genetic applications. Can J Fish Aquat Sci 53:833–841. doi:10.1139/cjfas-53-4-833

    Article  CAS  Google Scholar 

  • Small MP, Beacham TD, Withler RE, Nelson RJ (1998) Discrimination of coho salmon (Oncorhynchus kisutch) populations within the Fraser River, British Columbia using microsatellite DNA markers. Mol Ecol 7:141–155. doi:10.1046/j.1365-294x.1998.00324.x

    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 7:1613–1621. doi:10.1046/j.1365-294X.1998.00474.x

    Article  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. doi:10.1023/A:1011580217381

    Article  CAS  Google Scholar 

  • Wang J (2004) Sibship reconstruction from genetic data with typing errors. Genetics 166:1963–1979. doi:10.1534/genetics.166.4.1963

    Article  PubMed  Google Scholar 

  • Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evol Int J Org Evol 38:1358–1370. doi:10.2307/2408641

    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. doi:10.1577/1548-8659(2001)130<1049:GABEFR>2.0.CO;2

    Article  CAS  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. doi:10.1046/j.1471-8286.2002.00129.x

    Article  CAS  Google Scholar 

Download references

Acknowledgments

Many other people contributed substantially to this work. Primary among them are K. Adams, A. Aguilar, H. Fish, A. Martinez and D. Pearse. Many land owners and agency staff assisted in sampling design and collection, including J. O’Brien and M. Larson, California Department of Fish and Game. K. Perry, M. Lacy, R. Bloom and M. Paul provided useful comments on an early draft.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to John Carlos Garza.

Appendix

Appendix

Appendix 1 Pairwise genetic differentiation (F ST) between 20 population samples and four hatchery strains from Southern California

Rights and permissions

Reprints and permissions

About this article

Cite this article

Clemento, A.J., Anderson, E.C., Boughton, D. et al. Population genetic structure and ancestry of Oncorhynchus mykiss populations above and below dams in south-central California. Conserv Genet 10, 1321 (2009). https://doi.org/10.1007/s10592-008-9712-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s10592-008-9712-0

Keywords

Navigation