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

Abstract

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.

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Acknowledgements

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.

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Correspondence to Jesse C. Wiesenfeld.

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Wiesenfeld, J.C., Goodman, D.H. & Kinziger, A.P. Riverscape genetics identifies speckled dace (Rhinichthys osculus) cryptic diversity in the Klamath–Trinity Basin. Conserv Genet 19, 111–127 (2018). https://doi.org/10.1007/s10592-017-1027-6

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  • DOI: https://doi.org/10.1007/s10592-017-1027-6

Keywords

  • Riverscape genetics
  • Cryptic species
  • Speckled dace
  • Rhinichthys osculus