Conservation Genetics

, Volume 19, Issue 1, pp 111–127 | Cite as

Riverscape genetics identifies speckled dace (Rhinichthys osculus) cryptic diversity in the Klamath–Trinity Basin

  • Jesse C. WiesenfeldEmail author
  • Damon H. Goodman
  • Andrew P. Kinziger
Research Article


Cataloging biodiversity is of great importance given that habitat destruction has dramatically increased extinction rates. While the presence of cryptic species poses challenges for biodiversity assessment, molecular analysis has proven useful in uncovering this hidden diversity. Using nuclear microsatellite markers and mitochondrial DNA we investigated the genetic structure of Klamath speckled dace (Rhinichthys osculus klamathensis), a subspecies endemic to the Klamath–Trinity basin. Analysis of 25 sample sites within the basin uncovered cryptic diversity including three distinct genetic groups: (1) a group that is widely distributed throughout the Klamath River mainstem and its tributaries, (2) a group distributed in the Trinity River, the largest tributary to the Klamath River, and (3) a group identified above a 10 m waterfall in Jenny Creek, a small tributary to the Klamath River. All groups were resolved as divergent in nuclear microsatellite analysis and exhibited levels of divergence in mitochondrial DNA that were comparable to those observed among recognized Rhinichthys species. No physical barriers currently separate the Klamath and Trinity groups and the precise mechanism that generated and maintains the groups as distinct despite contact and hybridization is unknown. The present study highlights the importance of incorporating molecular analysis into biodiversity research to uncover cryptic diversity. We recommend that future biodiversity inventories recognize three genetically distinct groups of speckled dace in the Klamath–Trinity Basin.


Riverscape genetics Cryptic species Speckled dace Rhinichthys osculus 



The authors would like to thank the following for help with field collections: Conrad Newell, Sam Rizza, and Robbie Mueller (Humboldt State University (HSU)), Bret Harvey (US Forest Service), Rodney Nakamoto (US Forest Service), Bill Tinniswood (Oregon Department of Fish and Wildlife). Thanks to Tom Huteson for help drafting Fig. 6, Chloe Joesten (HSU) for her help in the laboratory and to Dana Herman (HSU) for providing assistance with GIS analysis. Thanks to Stewart Reid (Western Fishes Inc.) for his assistance and collection of Rogue River speckled dace and to Thomas Dowling (Wayne State University) for supplying the Rogue River mtDNA sequences. Additionally, we would like to thank the three anonymous reviewers for their comments on previous versions of this manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

10592_2017_1027_MOESM1_ESM.docx (1.4 mb)
Supplementary material 1 (DOCX 1458 KB)


  1. Aalto KR (2006) The Klamath peneplain: a review of JS Diller’s classic erosion surface. Geolog Soc Am Special Papers 410:451–463Google Scholar
  2. Abell RM, Thieme ML, Revenga C, Bryer M, Kottelat M, Bogutskaya N, Coad B, Mandrak K, Contreras Balderas S, Bussing W, Stiassny M, Skelton P, Allen R, Unmack P, Naseka A, Ng R, Sindorf N, Robertson J, Armijo E, Higgins J, Heibel J, Wikramanake E, Olson D, Lopez H, Reis R, Lundberg J, Sabaj Perze M, Petry P (2008) Freshwater ecoregions of the world: a new map of biogeographic units for freshwater biodiversity conservation. Bioscience 58:403–414. CrossRefGoogle Scholar
  3. Anderson TK (2008) Inferring bedrock uplift in the Klamath Mountains Province from river profile analysis and digital topography. Master’s thesis, Texas Tech UniversityGoogle Scholar
  4. Ardren WR, Baumsteiger J, Allen CS (2010) Genetic analysis and uncertain taxonomic status of threatened Foskett Spring speckled dace. Conserv Genet 11:1299–1315. CrossRefGoogle Scholar
  5. Avise JC (2004) Molecular markers, natural history and evolution. Springer Science & Business Media, ChicagoGoogle Scholar
  6. Baerwald MR, May B (2004) Characterization of microsatellite loci for five members of the minnow family Cyprinidae found in the Sacramento–San Joaquin Delta and its tributaries. Mol Ecol Notes 4:385–390. CrossRefGoogle Scholar
  7. Baldwin EM (1981) Geology of Oregon. Kendall/Hunt Publishing, IowaGoogle Scholar
  8. Ballard JWO, Whitlock MC (2004) The incomplete natural history of mitochondria. Mol Ecol 13:729–744. CrossRefPubMedGoogle Scholar
  9. 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 39:1502–1511. CrossRefGoogle Scholar
  10. Bernardo J (2011) A critical appraisal of the meaning and diagnosability of cryptic evolutionary diversity, and its implications for conservation in the face of climate change: the systematics association, Cambridge University Press, CambridgeCrossRefGoogle Scholar
  11. Bickford D, Lohman DJ, Sodhi NS, Ng P, Meier R, Winker K, Ingram K, Das I (2007) Cryptic species as a window on diversity and conservation. Trends Ecol Evol 22:148–155. CrossRefPubMedGoogle Scholar
  12. Billman EJ, Lee JB, Young DO, McKelll M, Evans R, Shiozawa D (2010) Phylogenetic divergence in a desert fish: differentiation of speckled dace within the bonneville, lahontan, and upper snake river basins. Western North Am Nat 70:39–47CrossRefGoogle Scholar
  13. Bond CE (1994) Keys to Oregon freshwater fishes. OSU Book Stores, CorvallisGoogle Scholar
  14. Brown LR, Moyle PB (1997) Invading species in the Eel River, California: successes, failures, and relationships with resident species. Environ Biol Fishes 49:271–291. CrossRefGoogle Scholar
  15. Buggs RJA (2007) Empirical study of hybrid zone movement. Heredity 99:301–312CrossRefPubMedGoogle Scholar
  16. Burnham KP, Anderson DR (2002) Model selection and multimodel inference: a practical information-theoretic approach. Springer, BerlinGoogle Scholar
  17. Carstens BC, Knowles LL (2007) Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers. Syst Biol 56:400–411. CrossRefPubMedGoogle Scholar
  18. Castric V, Bonney F, Bernatchez L (2001) Landscape Structure and Hierarchical Genetic diversity in the brook charr Salvelinus Fontinalis. Evolution 55:1016–1028. CrossRefPubMedGoogle Scholar
  19. Chapin FS III, Zavaleta ES, Eviner VT et al (2000) Consequences of changing biodiversity. Nature 405:234–242. CrossRefPubMedGoogle Scholar
  20. Clement M, Posada D, Crandall KA (2000) TCS: a computer program to estimate gene genealogies. Mol Ecol 9:1657–1659CrossRefPubMedGoogle Scholar
  21. Dowling TE, Naylor GJ (1997) Evolutionary relationships of minnows in the genus Luxilus (Teleostei: Cyprinidae) as determined from cytochrome b sequences. Copeia 1997(4)758–765CrossRefGoogle Scholar
  22. Dowling TE, Tibbets CA, Minckley WL, Smith GR, McEachran JD (2002) Evolutionary relationships of the plagopterins (Teleostei: Cyprinidae) from cytochrome b sequences. Copeia 2002:665–678CrossRefGoogle Scholar
  23. Dudgeon D, Arthington AH, Gessner MO et al (2006) Freshwater biodiversity: importance, threats, status and conservation challenges. Biol Rev 81:163–182. CrossRefPubMedGoogle Scholar
  24. Earl DA, vonHoldt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4:359–361. CrossRefGoogle Scholar
  25. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797. CrossRefPubMedPubMedCentralGoogle Scholar
  26. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software structure: a simulation study. Mol Ecol 14:2611–2620. CrossRefPubMedGoogle Scholar
  27. Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol Bioinformatics 1:47–50CrossRefGoogle Scholar
  28. Felsenstein J (2005) Phylip (phylogeny inference package) version 3.6 (2004) distributed by the author. Department of Genome Sciences, University of Washington, SeattleGoogle Scholar
  29. Girard P, Angers B (2006) Characterization of microsatellite loci in longnose dace (Rhinichthys cataractae) and interspecific amplification in five other Leuciscinae species. Mol Ecol Notes 6:69–71. CrossRefGoogle Scholar
  30. Goudet J (1995) FSTAT (version 1.2): a computer program to calculate F-statistics. J Hered 86(6):485–486CrossRefGoogle Scholar
  31. Harrison RG (1990) Hybrid zones: Windows on evolutionary process, vol 7. In: Futuyma D, Antonovics J (ed) Oxford surveys in evolutionary biology. Oxford University Press, Oxford, pp 69–128Google Scholar
  32. Harvey BC, White JL, Nakamoto RJ (2004) An emergent multiple predator effect may enhance biotic resistance in a stream fish assemblage. Ecology 85:127–133. CrossRefGoogle Scholar
  33. Heled J, Drummond AJ (2010) Bayesian inference of species trees from multilocus data. Mol Biol Evol 27:570–580CrossRefPubMedGoogle Scholar
  34. Hershey OH (1900) Ancient alpine glaciers of the Sierra Costa Mountains in California. J Geol 8:42–57CrossRefGoogle Scholar
  35. Hoekzema K, Sidlauskas BL (2014) Molecular phylogenetics and microsatellite analysis reveal cryptic species of speckled dace (Cyprinidae: Rhinichthys osculus) in Oregon’s Great Basin. Mol Phylogenet Evol 77:238–250. CrossRefPubMedGoogle Scholar
  36. Hohler DB (1981) A dwarfed population of Catostomus rimiculus (Catostomidae: Pisces) in Jenny Creek, Jackson, County, Oregon. MS Thesis, Oregon State UniversityGoogle Scholar
  37. Houston DD, Evans RP, Shiozawa DK (2012) Evaluating the genetic status of a Great Basin endemic minnow: the relict dace (Relictus solitarius). Conserv Genet 13:727–742. CrossRefGoogle Scholar
  38. Jenkins M (2003) Prospects for biodiversity. Science 302:1175–1177. CrossRefPubMedGoogle Scholar
  39. Jensen JL, Bohonak AJ, Kelley ST (2005) Isolation by distance, web service. BioMed Central Genet 6:13. Google Scholar
  40. Jombart T (2008) Adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24:1403–1405. CrossRefPubMedGoogle Scholar
  41. Jombart T, Devillard S, Balloux F (2010) Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BioMed Central Genetics 11:94. PubMedPubMedCentralGoogle Scholar
  42. Kalinowski ST (2005) hp-rare 1.0: a computer program for performing rarefaction on measures of allelic richness. Mol Ecol Notes 5:187–189. CrossRefGoogle Scholar
  43. Kinziger AP, Nakamoto RJ, Anderson EC, Harvey BC (2011) Small founding number and low genetic diversity in an introduced species exhibiting limited invasion success (speckled dace, Rhinichthys osculus). Ecol Evol 1:73–84. CrossRefPubMedPubMedCentralGoogle Scholar
  44. Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452. CrossRefPubMedGoogle Scholar
  45. Maddison WP, Knowles LL (2006) Inferring Phylogeny despite dncomplete lineage sorting. Syst Biol 55:21–30. CrossRefPubMedGoogle Scholar
  46. McNeely JA, Miller KR, Reid WV, Mittermeier RA, Werner TB (1990) Conserving the world’s biodiversity. World Conservation Union (IUCN) & World Wide Fund for Nature (WWF), Gland, Suiça & World Resources Institute (WRI), Conservation International (CI) & World Bank. EUA, Washington, DCGoogle Scholar
  47. McPhail JD, Taylor EB (2009) Phylogeography of the longnose dace (Rhinichthys cataractae) species group in northwestern North America: the origin and evolution of the Umpqua and Millicoma dace. Can J Zool 87:491–497. CrossRefGoogle Scholar
  48. Meirmans PG, Van Tienderen PH (2004) genotype and genodive: two programs for the analysis of genetic diversity of asexual organisms. Mol Ecol Notes 4:792–794. CrossRefGoogle Scholar
  49. Minckley WL, Hendrickson DA, Bond CE (1986) Geography of western North American freshwater fishes: description and relationships to intracontinental tectonism. In: Hocutt CH, Wiley EO (eds) The zoogeography of North American freshwater fishes. Wiley, New York, pp 519–613Google Scholar
  50. Moyle PB (2002) Inland fishes of California. Univ of California PressGoogle Scholar
  51. Moyle PB, Katz JVE, Quiñones RM (2011) Rapid decline of California’s native inland fishes: a status assessment. Biol Conserv 144:2414–2423. CrossRefGoogle Scholar
  52. Moyle PB, Quiñones RM, Katz JV, Weaver J (2015) Fish species of special concern in California. California Department of Fish and Wildlife, SacramentoGoogle Scholar
  53. Murphy NP, King RA, Delean S (2015) Species, ESUs or populations? Delimiting and describing morphologically cryptic diversity in Australian desert spring amphipods. Invertebrate Syst 29:457–467. CrossRefGoogle Scholar
  54. Myers N, Mittermeier RA, Mittermeier CG, Da Fonseca GA, Kent J (2000) Biodiversity hotspots for conservation priorities. Nature 403:853–858. CrossRefPubMedGoogle Scholar
  55. Narum SR (2006) Beyond Bonferroni: Less conservative analyses for conservation genetics. Conserv Genet 7:783–787. CrossRefGoogle Scholar
  56. Niemiller ML, Graening GO, Fenolio DB et al (2013) Doomed before they are described? The need for conservation assessments of cryptic species complexes using an amblyopsid cavefish (Amblyopsidae: Typhlichthys) as a case study. Biodivers Conserv 22:1799–1820. CrossRefGoogle Scholar
  57. Noss RF (1990) Indicators for monitoring biodiversity: a hierarchical approach. Conserv Biol 4:355–364CrossRefGoogle Scholar
  58. Oakey DD, Douglas ME, Douglas MR (2004) Small fish in a large landscape: diversification of Rhinichthys osculus (Cyprinidae) in Western North America. Copeia. Google Scholar
  59. Pearsons TN, Li HW, Lamberti GA (1992) Influence of habitat complexity on resistance to flooding and resilience of stream fish assemblages. Trans Am Fish Soc 121:427–436CrossRefGoogle Scholar
  60. Peden AE, Hughes GW (1981) Life history notes relevant to the Canadian status of the speckled dace (Rhinichthys osculus). Syesis 14:21–31Google Scholar
  61. Pfenninger M, Schwenk K (2007) Cryptic animal species are homogeneously distributed among taxa and biogeographical regions. BioMed Central Evol Biol 7:121. Google Scholar
  62. Pfrender ME, Hicks J, Lynch M (2004) Biogeographic patterns and current distribution of molecular-genetic variation among populations of speckled dace, Rhinichthys osculus (Girard). Mol Phylogenet Evol 30:490–502. CrossRefPubMedGoogle Scholar
  63. Piggott MP, Chao NL, Beheregaray LB (2011) Three fishes in one: cryptic species in an Amazonian floodplain forest specialist. Biol J Linn Soc 102:391–403CrossRefGoogle Scholar
  64. Posada D (2008) jModelTest: phylogenetic model averaging. Mol Biol Evol 25:1253–1256. CrossRefPubMedGoogle Scholar
  65. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedPubMedCentralGoogle Scholar
  66. R Core Team (2016). R: A language and environment for statistical computing. R Foundation for Statistical Computing, ViennaGoogle Scholar
  67. Raymond M, Rousset F (1995) GENEPOP (Version 1.2): population genetics software for exact tests and ecumenicism. J Hered 86:248–249CrossRefGoogle Scholar
  68. Ricciardi A, Rasmussen JB (1999) Extinction rates of north american freshwater fauna. Conserv Biol 13:1220–1222. CrossRefGoogle Scholar
  69. Rice WR (1989) Analyzing tables of statistical tests. Evol Int J Org Evol 43:223–225CrossRefGoogle Scholar
  70. Rosenberg NA (2004) DISTRUCT: a program for the graphical display of population structure. Mol Ecol Notes 4:137–138. CrossRefGoogle Scholar
  71. Sharp RP (1960) Pleistocene glaciation in the Trinity Alps of northern California. Am J Sci 258:305–340. CrossRefGoogle Scholar
  72. Smith GR (1973) Analysis of several hybrid Cyprinid fishes from Western North America. Copeia 1973:395–410. CrossRefGoogle Scholar
  73. Smith GR, Dowling TE (2008) Correlating hydrographic events and divergence times of speckled dace (Rhinichthys, Teleostei, Cyprinidae) in the Colorado River drainage. In: Reheis M, Hershler R, Miller D (eds) Late cenozoic drainage history of the southwestern Great Basin and lower Colorado River region: Geologic and biotic perspectives. Special paper 439. Geological Society of America, Boulder, pp 301–317CrossRefGoogle Scholar
  74. Tamura K, Stecher G, Peterson D, Flipski A, Kumar S (2013) MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729. CrossRefPubMedPubMedCentralGoogle Scholar
  75. Turner TF, Dowling TE, Broughton RE, Gold JR (2004) Variable microsatellite markers amplify across divergent lineages of cyprinid fishes (subfamily Leusicinae). Conserv Genet 5:279–281. CrossRefGoogle Scholar
  76. Van Oosterhout C, Hutchinson WF, Wills DP, Shipley P (2004) MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538CrossRefGoogle Scholar
  77. Walsh PS, Metzger DA, Higuchi R (1991) Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques 10:506–513PubMedGoogle Scholar
  78. Waters JM, Rowe DL, Burridge CP, Wallis GP (2010) Gene trees versus species trees: reassessing life-history evolution in a freshwater fish radiation. Syst Biol 59:504–517. CrossRefPubMedGoogle Scholar

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© Springer Science+Business Media B.V., part of Springer Nature 2017

Authors and Affiliations

  1. 1.Department of Fisheries BiologyHumboldt State UniversityArcataUSA
  2. 2.Cramer Fish SciencesSacramentoUSA
  3. 3.US Fish and Wildlife ServiceArcataUSA

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