Conservation Genetics

, Volume 15, Issue 3, pp 729–742 | Cite as

Impact of dams on distribution, population structure, and hybridization of two species of California freshwater sculpin (Cottus)

  • Jason Baumsteiger
  • Andres Aguilar
Research Article


Dams represent a beneficial way to maximize riverine potential, though the benefits often come with costs. Modified conditions to rivers downstream of dams (release temperature, flow, barriers to migration) can lead to changes in species compositions. In California, these effects are amplified, as limited water resources lead to extensive anthropogenic changes. Our study examined the role of seven western Sierra Nevada river dams on localized distribution and population structure of native riffle sculpin (Cottus gulosus) and their role in potential hybridization with native prickly sculpin (C. asper). Individuals were collected above and below dams, genotyped with 10 microsatellite loci, and analyzed for possible hybridization. Three downstream locations (American, Tuolumne, and Kings River) support populations of both species whereas the remaining downstream sites supported only prickly sculpin. River specific genetic population structure was found for both species but was more extensive in riffle sculpin. Hybridization was limited to the Kings River, and represented less than 3 % of individuals sampled. Comparisons between dams including elevation above sea level, type of dam, distance from dam to sampling location, and average released water temperature showed no correlation with riffle sculpin presence below a dam. Expanded sampling within the Kings River found no association with distance and riffle sculpin or hybrid presence, although both were limited to recent trout restoration areas. Therefore, despite initial inclinations, dams show no direct correlation with sculpin distributions or hybridization in the Great Central Valley of California.


Anthropogenic Microsatellites Species ranges Riverine 



The authors wish to thank L. Long and H. Isner of the Kings River Conservation District for their assistance, information, and expertise. Additionally, we wish to thank E. Guzman and K. Gibson of the California Department of Fish and Game, E. Rible and the East Bay Municipal Utility District, members of the CDFG Nimbus Dam Fish Hatchery for their help with sampling, and Dr. P. Moyle of UC Davis for lending us a backpack electroshocker. D. Jacobs and an anonymous reviewer further improved the manuscript. Funding was provided by a Sigma Xi Grants-in-Aide of Research award to J. Baumsteiger.

Supplementary material

10592_2014_574_MOESM1_ESM.docx (120 kb)
Supplementary material 1 (DOCX 120 kb)


  1. Adams W (2000) Downstream impacts of dams. In WCD Thematic Review I.1: The social impact of large dams: equity and distribution issues, prepared for the World Commission on Dams: Cape Town. Accessed Dec 2012
  2. Aguado E, Cayan D, Riddle L, Roos M (1992) Climatic fluctuations and the timing of West Coast streamflow. J Clim 5(12):1468–1483CrossRefGoogle Scholar
  3. Allendorf FW, Leary RF, Spruell P, Wenburg JK (2001) The problems with hybrids: setting conservation guidelines. Trends Ecol Evol 16(11):613–622CrossRefGoogle Scholar
  4. Anderson EC, Thompson EA (2002) A model-based method for identifying species hybrids using multilocus genetic data. Genetics 160(3):1217–1229PubMedCentralPubMedGoogle Scholar
  5. Anselmetti FS, Bühler R, Finger D, Girardclos S, Lancini A, Rellstab C, Sturm M (2007) Effects of Alpine hydropower dams on particle transport and lacustrine sedimentation. Aquat Sci Res Bound 69(2):179–198CrossRefGoogle Scholar
  6. Baltz DM, Moyle PB, Knight NJ (1982) Competitive interactions between benthic stream fishes, riffle sculpin, Cottus gulosus, and speckled dace, Rhinichthys osculus. Can J Fish Aquat Sci 39(11):1502–1511CrossRefGoogle Scholar
  7. Baumsteiger J, Aguilar A (2012) Nine original microsatellite loci in prickly sculpin (Cottus asper) and their applicability to other closely related Cottus species. Con Genet Res 5(1):1–4Google Scholar
  8. Baumsteiger J, Kinziger AP, Aguilar A (2012) Life history and biogeographic diversification of an endemic Western North American freshwater fish clade using a comparative species tree approach. Mol Phylogen Evol 65(2012):940–952CrossRefGoogle Scholar
  9. Bednarek AT (2001) Undamming rivers: a review of the ecological impacts of dam removal. Environ Manag 27(6):803–814Google Scholar
  10. Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F (2004) GENETIX 4.05, Population genetics software for Windows TM. Université de Montpellier II. MontpellierGoogle Scholar
  11. Bernasconi G, Ashman TL, Birkhead TR, Bishop JDD, Grossniklaus U, Kubli E, Marshall DL, Schmid B, Skogsmyr I, Snook RR, Taylor D, Till-Bottraud I, Ward PI, Zeh DW, Helliregel B (2004) Evolutionary ecology of the prezygotic stage. Science 303(5660):971–975Google Scholar
  12. Bond CE (1963) Distribution and ecology of freshwater sculpins, genus Cottus, in Oregon. Unpublished Ph.D. dissertation. Oregon State University, CorvallisGoogle Scholar
  13. Brown LR (2000) Fish communities and their associations with environmental variables, lower San Joaquin River drainage, California. Environ Biol Fish 57(3):251–269CrossRefGoogle Scholar
  14. California Department of Water Resources (2013). Accessed 1 June 2013
  15. Cayan DR (1996) Interannual climate variability and snowpack in the western United States. J Clim 9(5):928–948CrossRefGoogle Scholar
  16. Cech TV (2009) Principles of water resources: history, development, management, and policy. Wiley, SomersetGoogle Scholar
  17. Cech JJ Jr, Mitchell SJ, Castleberry DT, McEnroe M (1990) Distribution of California stream fishes: influence of environmental temperature and hypoxia. Environ Biol Fish 29(2):95–105CrossRefGoogle Scholar
  18. Chan K, Levin SA (2005) Leaky prezygotic isolation and porous genomes: rapid introgression of maternally inherited DNA. Evolution 59(4):720–729PubMedCrossRefGoogle Scholar
  19. Clark DH, Gillespie AR (1997) Timing and significance of late-glacial and Holocene cirque glaciation in the Sierra Nevada, California. Quat Int 38:21–38CrossRefGoogle Scholar
  20. Clarkson RW, Childs MR, Schaefer SA (2000) Temperature effects of hypolimnial-release dams on early life stages of Colorado River Basin big-river fishes. Copeia 2:402–412CrossRefGoogle Scholar
  21. Coyle KJ (1993) The new advocacy for aquatic species conservation. J North Am Benth Soc 12:185–188CrossRefGoogle Scholar
  22. Earl DA, von Holdt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Res 4(2):359–361CrossRefGoogle Scholar
  23. Englebrecht CC, Largiader CR, Hanfling B, Tautz D (1999) Isolation and characterization of polymorphic microsatellite loci in the European bullhead Cottus gobio L. (Osteichthyes) and their applicability to related taxa. Mol Ecol 8:1957–1969CrossRefGoogle Scholar
  24. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14(8):2611–2620PubMedCrossRefGoogle Scholar
  25. Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol Bioinform Online 1:47–50PubMedCentralGoogle Scholar
  26. Foote CJ, Brown GS (1998) Ecological relationship between freshwater sculpins (genus Cottus) and beach-spawning sockeye salmon (Oncorhynchus nerka) in Illiamna Lake, Alaska. Can J Fish Aqua Sci 55(6):1524–1533CrossRefGoogle Scholar
  27. Glaubitz JC (2004) convert: a user-friendly program to reformat diploid genotypic data for commonly used population genetic software packages. 4: 309-310. Mol Ecol Notes 4(309):310–486Google Scholar
  28. Goudet J (1995) FSTAT (Version 1.2): a computer program to calculate f-statistics. J Hered 86(6):485–486Google Scholar
  29. Hart DD, Poff NL (2002) A special section on dam removal and river restoration. Bioscience 52(8):653–655CrossRefGoogle Scholar
  30. Jakobsson M, Rosenberg NA (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23(14):1801–1806PubMedCrossRefGoogle Scholar
  31. Jeffres CA, Klimley AP, Merz JE, Cech JJ (2006) Movement of Sacramento sucker, Catostomus occidentalis, and hitch, Lavinia exilicauda, during a spring release of water from Camanche Dam in the Mokelumne River, California. Environ Biol Fish 75(4):365–373CrossRefGoogle Scholar
  32. Kalinowski ST (2005) HP-Rare: a computer program for performing rarefaction on measures of allelic diversity. Mol Ecol Notes 5:187–189CrossRefGoogle Scholar
  33. Karr JR (2001) Defining and measuring river health. Freshw Biol 41(2):221–234CrossRefGoogle Scholar
  34. Katz J, Moyle PB, Quiñones RM, Israel J, Purdy S (2012) Impending extinction of salmon, steelhead, and trout (Salmonidae) in California. Environ Biol Fish 2012:1–18Google Scholar
  35. Kiernan JD, Moyle PB, Crain PK (2012) Restoring native fish assemblages to a regulated California stream using the natural flow regime concept. Ecol Appl 22(5):1472–1482PubMedCrossRefGoogle Scholar
  36. Kondolf GM, Anderson S, Lave R, Pagano L, Merenlender A, Bernhardt ES (2007) Two decades of river restoration in California: what can we learn? Restor Ecol 15(3):516–523CrossRefGoogle Scholar
  37. Kontula T, Kirilchik SV, Väinölä R (2003) Endemic diversification of the monophyletic cottoid fish species flock in Lake Baikal explored with mtDNA sequencing. Mol Phylogenet Evol 27(1):143–155PubMedCrossRefGoogle Scholar
  38. Kratzer CR, Shelton JL (1998) Water quality assessment of the San Joaquin–Tulare basins, California: analysis of available data on nutrients and suspended sediment in surface water, 1972-1990 (No. 1587). US Dept. of the Interior, US Geological SurveyGoogle Scholar
  39. Krejsa RJ (1965) The systematics of the prickly sculpin, Cottus asper: an investigation of genetic and non-genetic variation within a polytypic species. Ph.D. dissertation, University of British Columbia, VancouverGoogle Scholar
  40. Krejsa RJ (1967) The Systematics of the Prickly Sculpin, Cottus asper Richardson, a polytypic species. Part I. Synonymy, nomenclatural history, and distribution. Pac Sci 21:241–251Google Scholar
  41. Lessard JL, Hayes DB (2003) Effects of elevated water temperature on fish and macroinvertebrate communities below small dams. River Res Appl 19(7):721–732CrossRefGoogle Scholar
  42. Lewis PO, Zaykin D (2001) Genetic Data Analysis: Computer program for the analysis of allelic data. Version 1.0 (d16c). Free program distributed by the authors over the internet from Accessed 15 Dec 2012
  43. Ligon FK, Dietrich WE, Trush WJ (1995) Downstream ecological effects of dams. Bioscience 1995:183–192CrossRefGoogle Scholar
  44. Marchetti MP, Moyle PB (2001) Effects of flow regime on fish assemblages in a regulated California stream. Ecol Apps 11(2):530–539CrossRefGoogle Scholar
  45. Marchetti MP, Moyle PB, Levine R (2004) Invasive species profiling? Exploring the characteristics of non-native fishes across invasion stages in California. Freshw Biol 49(5):646–661CrossRefGoogle Scholar
  46. Marmulla G (2001) Dams, fish and fisheries: opportunities, challenges and conflict resolution, vol 419. Food and Agriculture Organization, RomeGoogle Scholar
  47. Marschall EA, Mather ME, Parrish DL, Allison GW, McMenemy JR (2011) Migration delays caused by anthropogenic barriers: modeling dams, temperature, and success of migrating salmon smolts. Ecol Apps 21(8):3014–3031CrossRefGoogle Scholar
  48. McCully P (1996) Silenced rivers: the ecology and politics of large dams. Zed Books, New YorkGoogle Scholar
  49. Merz JE (2002) Comparison of diets of prickly sculpin and juvenile fall-run Chinook salmon in the lower Mokelumne River, California. Southwest Nat 2002:195–204CrossRefGoogle Scholar
  50. Mills TJ, McEwan DR, Jennings MR (1997) California salmon and steelhead: beyond the crossroads. In: Pacific salmon & their ecosystems. Springer, US, pp 91–111Google Scholar
  51. Moyle PB (1977) In defense of sculpins. Fisheries 2:20–23CrossRefGoogle Scholar
  52. Moyle PB (2002) Inland fishes of California. University of California Press, BerkeleyGoogle Scholar
  53. Moyle PB, Li HW (1979) Community ecology and predator-prey relationships of warm water streams. In: Clepper HW (ed) Predatory-prey systems in fisheries management. Sport Fishing Institute, Washington DC, pp 171–180Google Scholar
  54. Moyle PB, Nichols RD (1974) Decline of native fish fauna of the Sierra-Nevada foothills, central California. Am Midl Nat 92:72–83CrossRefGoogle Scholar
  55. Moyle PB, Williams JE (1990) Biodiversity loss in the temperate zone: decline of the native fish fauna of California. Cons Bio 4(3):275–284CrossRefGoogle Scholar
  56. Moyle PB, Yoshiyama RM, Williams JE, Wikramanayake E (1996) Fish species of special concern in California. California Department of Fish and Game, SacramentoGoogle Scholar
  57. Naiman RJ, Décamps H (1997) The ecology of interfaces: the riparian zone. Annu Rev Ecol Sys 28:621–658CrossRefGoogle Scholar
  58. Nielsen EE, Bach LA, Kotlicki P (2006) HYBRIDLAB (version 1.0): a program for generating simulated hybrids from population samples. Mol Ecol Notes 6(4):971–973CrossRefGoogle Scholar
  59. Nolte AW, Freyhof J, Stemshorn KC, Tautz D (2005a) An Invasive lineage of sculpins, Cottus sp. (Pisces, Teleostei) in the Rhine with new habitat adaptations has originated from hybridization between old phylogeographic groups. P Roy Soc B Biol Sci 272:2379–2387CrossRefGoogle Scholar
  60. Nolte AW, Stemshorn KC, Tautz D (2005b) Direct cloning of microsatellite loci from Cottus gobio through a simplified enrichment procedure. Mol Ecol Notes 5:628–636CrossRefGoogle Scholar
  61. Olden JD, Naiman RJ (2009) Incorporating thermal regimes into environmental flows assessments: modifying dam operations to restore freshwater ecosystem integrity. Freshw Biol 55(1):86–107CrossRefGoogle Scholar
  62. Page LM, Burr BM (2011) A field guide to freshwater fishes: North America north of Mexico. Houghton Mifflin Harcourt, BostonGoogle Scholar
  63. Pereira WE, Domagalski JL, Hostettler FD, Brown LR, Rapp JB (1996) Occurrence and accumulation of pesticides and organic contaminants in river sediment, water and clam tissues from the San Joaquin River and tributaries, California. Environ Tox Chem 15(2):172–180CrossRefGoogle Scholar
  64. Pitchford RJ, Visser PS (1975) The effect of large dams on river water temperature below the dams, with special reference to bilharzia and the Verwoerd Dam. S Afr J Sci 71(7):212–213Google Scholar
  65. Poff NL, Olden JD, Merritt DM, Pepin DM (2007) Homogenization of regional river dynamics by dams and global biodiversity implications. Proc Natl Acad Sci USA 104(14):5732–5737PubMedCentralPubMedCrossRefGoogle Scholar
  66. Preston WL (1981) Vanishing landscapes: land and life in the Tulare Lake Basin. University of California Press, BerkeleyGoogle Scholar
  67. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155(2):945–959PubMedCentralPubMedGoogle Scholar
  68. R Core Team (2012) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL
  69. Randolph B, Troy P (2008) Attitudes to conservation and water consumption. Environ Sci Policy 11(5):441–455CrossRefGoogle Scholar
  70. Rice WR (1989) Analyzing tables of statistical tests. Evololution 43:223–225CrossRefGoogle Scholar
  71. Robins R, Miller RR (1957) Classification, variation, and distribution of the sculpins, genus Cottus, inhabiting Pacific slope waters in California and southern Oregon with a key to the species. Calif Fish Game 43(3):213–233Google Scholar
  72. Rosenberg NA (2003) DISTRUCT: a program for the graphical display of population structure. Mol Ecol Notes 4(1):137–138CrossRefGoogle Scholar
  73. Schick RS, Lindley ST (2007) Directed connectivity among fish populations in a riverine network. J Appl Ecol 44(6):1116–1126CrossRefGoogle Scholar
  74. Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol 18:233–234PubMedCrossRefGoogle Scholar
  75. Stanley EH, Doyle MW (2003) Trading off: the ecological effects of dam removal. Front Ecol Environ 1(1):15–22CrossRefGoogle Scholar
  76. Swanson PWR, Chomycia JC (2011) Resolving complex issues with large scale river restoration; a case study: the San Joaquin River in California. Water Prac Tech 6(4). doi:  10.2166/wpt.2011.0074
  77. Tabor RA, Footen BA, Fresh KL, Celedonia MT, Mejia F, Low DL, Park L (2007) Smallmouth bass and largemouth bass predation on juvenile Chinook salmon and other Salmonids in the Lake Washington basin. N Am J Fish Man 27:1174–1188CrossRefGoogle Scholar
  78. Utzinger J, Roth C, Peter A (1998) Effects of environmental parameters on the distribution of bullhead Cottus gobio with particular consideration of the effects of obstructions. J App Ecol 35:882–892CrossRefGoogle Scholar
  79. Vicuna S, Dracup JA (2007) The evolution of climate change impact studies on hydrology and water resources in California. Clim Change 82(3):327–350CrossRefGoogle Scholar
  80. Wang J (2004) Sibship reconstruction from genetic data with typing errors. Genetics 166:1963–1979PubMedCentralPubMedCrossRefGoogle Scholar
  81. Wang J (2013) A simulation module in the computer program colony for sibship and parentage analysis. Mol Ecol Res 13:734–739CrossRefGoogle Scholar
  82. Ward JV (1997) An expansive perspective of riverine landscapes: pattern and process across scales. GAIA 6:52–60Google Scholar
  83. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370CrossRefGoogle Scholar
  84. Yoshiyama RM, Gerstung ER, Fisher FW, Moyle PB (2001) Historical and present distribution of Chinook salmon in the Central Valley drainage of California. Contrib Biol Cent Val Salmon Fish Bull 179:71–176Google Scholar
  85. Young RG, Collier KJ (2009) Contrasting responses to catchment modification among a range of functional and structural indicators of river ecosystem health. Freshw Biol 54(10):2155–2170CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  1. 1.School of Natural Sciences & Sierra Nevada Research InstituteUniversity of California MercedMercedUSA
  2. 2.Department of Biological SciencesCalifornia State University, Los AngelesLos AngelesUSA

Personalised recommendations