National Park Service U.S. Department of the Interior Natural Resource Program Center Inventory of Fish Species in the Snake River Watershed Within Yellowstone National Park Natural Resource Technical Report NPS/GRYN/NRTR–2008/119 ON THE COVER Upper main stem of the Snake River, Yellowstone National Park. NPS photo. Inventory of Fish Species in the Snake River Watershed Within Yellowstone National Park Natural Resource Technical Report NPS/GRYN/NRTR–2008/119 Authors Daniel L. Mahony Fisheries and Aquatic Sciences Program Yellowstone National Park P.O. Box 168 Yellowstone National Park, Wyoming 82190 Mark A. Novak Bridger-Teton National Forest P.O. Box 1888 Jackson, Wyoming 83001 Todd M. Koel Fisheries and Aquatic Sciences Program Yellowstone National Park P.O. Box 168 Yellowstone National Park, Wyoming 82190 Editing and Design Alice Wondrak Biel Inventory & Monitoring Program National Park Service–Intermountain Region 12795 West Alameda Parkway Denver, Colorado 80225 August 2008 U.S. Department of the Interior National Park Service Natural Resource Program Center Fort Collins, Colorado The Natural Resource Publication series addresses natural resource topics that are of inter- est and applicability to a broad readership in the National Park Service and to others in the management of natural resources, including the scientifi c community, the public, and the NPS conservation and environmental constituencies. Manuscripts are peer-reviewed to en- sure that the information is scientifi cally credible, technically accurate, appropriately writ- ten for the intended audience, and is designed and published in a professional manner. The Natural Resource Technical Report series is used to disseminate the peer-reviewed results of scientifi c studies in the physical, biological, and social sciences for both the advancement of science and the achievement of the National Park Service’s mission. The reports provide contributors with a forum for displaying comprehensive data that are often deleted from journals because of page limitations. Current examples of such reports include the results of research that addresses natural resource management issues; natural resource inventory and monitoring activities; resource assessment reports; scientifi c literature reviews; and peer-reviewed proceedings of technical workshops, conferences, or symposia. Views, statements, fi ndings, conclusions, recommendations, and data in this report are solely those of the author(s) and do not necessarily refl ect views and policies of the U.S. Department of the Interior, National Park Service. Mention of trade names or commercial products does not constitute endorsement or recommendation for use by the National Park Service. Printed copies of reports in this series may be produced in limited quantity, and are only available as long as the supply lasts. You may send a request to: Greater Yellowstone Network 229 AJM Johnson Hall Montana State University Bozeman, Montana 59717 This report is also available electronically from the Greater Yellowstone Network website, http://science.nature.nps.gov/im/units/GRYN/index.cfm, or at http://www.nature.nps.gov/publications/NRPM/index.cfm. When original printed copies are exhausted, copies can be obtained from: Technical Information Center (TIC) Denver Service Center National Park Service P.O. Box 25287 Denver, CO 80225-0287 Please cite this publication as: Mahony, D., M. A. Novak, and T. Koel. 2008. Inventory of fi sh species in the Snake River Watershed within Yellowstone National Park. Natural Resource Technical Report NPS/GRYN/NRTR–2008/119. National Park Service, Fort Collins, Colorado. NPS D-65, August 2008 Contents Figures ...................................................................................................................... iii Tables ..........................................................................................................................v Photos .......................................................................................................................vii Acronyms ...................................................................................................................ix Executive Summary ...................................................................................................xi Acknowledgements ...............................................................................................xiii Chapter 1: Introduction ............................................................................................ 1 1.1 Background and objectives ...................................................................................................... 1 1.2 Study Area ................................................................................................................................. 2 Chapter 2: Methods .................................................................................................. 5 2.1 Fish distribution ........................................................................................................................ 5 2.2 Population characteristics ........................................................................................................ 5 2.3 Classifi cation by spotting pattern ........................................................................................... 5 2.4 Genetic analyses ....................................................................................................................... 6 Chapter 3: Results ..................................................................................................... 7 3.1 Snake River main stem ............................................................................................................. 7 3.2 Forest Creek ............................................................................................................................ 10 3.3 Coulter Creek .......................................................................................................................... 12 3.4 Heart River .............................................................................................................................. 12 3.5 Sickle Creek ............................................................................................................................. 14 3.6 Crooked Creek ........................................................................................................................ 14 3.7 Big Game Creek ...................................................................................................................... 15 3.8 Plateau Creek .......................................................................................................................... 16 3.9 Fox Creek ................................................................................................................................. 16 3.10 Genetic analyses ................................................................................................................... 16 Chapter 4: Discussion .............................................................................................. 19 Chapter 5: Literature Cited ..................................................................................... 21 Appendix A: Photo Sets .......................................................................................... 23 Appendix B: Fish Species Named in This Report ................................................... 33 ii Inventory of Fish Species in the Snake River Watershed within Yellowstone National Park Contents iii Figures Figure 1.2. Snake River basin with main stem river and primary tributaries. .................................... 3 Figure 2.3. Spotting patterns typical of Yellowstone cutthroat trout, Snake River fi ne-spotted cutthroat trout, and indeterminate cutthroat trout............................................................ 6 Figure 3.1-1. Locations where all cutthroat trout were found, and where those classifi ed as the fi ne-spotted form based on spotting patterns were identifi ed in the fi eld. ..................... 7 Figure 3.1-2. Length-frequency distribution of cutthroat trout captured from the main stem of the Snake River in 2004. ....................................................................................................9 Figure 3.1-3. Individual total lengths (mm) of cutthroat trout caught in the Snake River main stem in 2004, grouped by sample reach. .............................................................................. 9 Figure 3.2. Length-frequency distribution of cutthroat trout from Forest Creek. .......................... 10 Figure 3.3-1. Length-frequency distribution of cutthroat trout from Coulter Creek. ..................... 13 Figure 3.3-2. Length-frequency distribution of cutthroat trout from Coulter Creek tributaries. .. 13 Figure 3.4. Length-frequency distribution of cutthroat trout from the Heart River. ...................... 14 Figure 3.5. Length-frequency distribution of cutthroat trout from Sickle Creek. ........................... 15 Figure 3.6. Length-frequency distribution of cutthroat trout from Crooked Creek. ...................... 15 Figure 3.8. Length-frequency distribution of cutthroat trout from Plateau Creek. ........................ 16 Figure 3.9. Length-frequency distribution of cutthroat trout from Fox Creek. ...............................17 Figure 3.10. Location and proportion of cutthroat haplotypes observed in the Snake River watershed, 2004–2005. .......................................................................................................