Monitoring Demographic and Genetic Responses of a Threatened Inland Trout to Habitat Reconnection

References

• Anderson, E. C., and K. K. Dunham. 2008. The influence of family groups on inferences made with the program Structure. Molecular Ecology Resources 8:1219–1229.
   PubMed Web of Science ®Google Scholar
• Antao, T., A. Perez-Figueroa, and G. Luikart. 2010. Early detection of population declines: high power of genetic monitoring using effective population size estimators. Evolutionary Applications 4:144–154.
   PubMed Web of Science ®Google Scholar
• Behnke, R. J. 1992. Native trout of western North America. American Fisheries Society, Bethesda, Maryland.
   Google Scholar
• Bernhardt, E. S., M. A. Palmer, J. D. Allan, G. Alexander, K. Barnas, S. Brooks, J. Carr, S. Clayton, C. Dahm, J. Follstad-Shah, D. Galat, S. Gloss, P. Goodwin, D. Hart, B. Hassett, R. Jenkinson, S.Katz, G. M. Kondolf, P. S. Lake, R. Lave, J. L.Meyer, T. K. O’Donnell, L. Pagano, B. Powell, E. Sudduth. 2005. Synthesizing U.S. river restoration efforts. Science 308:636–637.
   Google Scholar
• Chelgren, N. D., and J. B. Dunham. 2015. Connectivity and conditional models of access and abundance of species in stream networks. Ecological Applications 25:1357–1372.
   PubMed Web of Science ®Google Scholar
• Clarkin, K., A. Connor, M. J. Furniss, B. Gubernick, M. Love, K. Moynan, and S. WilsonMusser. 2005. National inventory and assessment procedure—for identifying barriers to aquatic organism passage at road-stream crossings. U.S. Forest Service, San Dimas Technology and Development Center, National Technology and Development Program, San Dimas, California.
   Google Scholar
• Coffin, P. D., and W. F. Cowan. 1995. Lahontan Cutthroat Trout (Oncorhynchus clarki henshawi) recovery plan. U.S. Fish and Wildlife Service, Region 1, Portland, Oregon.
   Google Scholar
• Dauwalter, D. C., F. J. Rahel, and K. G. Gerow. 2009. Temporal variation in trout populations: implications for monitoring and trend detection. Transactions of the American Fisheries Society 138:38–51.
   Web of Science ®Google Scholar
• Dauwalter, D. C., F. J. Rahel, and K. G. Gerow. 2010. Power of revisit monitoring designs to detect forestwide declines in trout populations. North American Journal of Fisheries Management 30:1462–1468.
   Web of Science ®Google Scholar
• Development Core Team. 2009. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna.
   Google Scholar
• Dunham, J. B., M. Peacock, C. R. Tracy, J. Nielsen, and G. L. Vinyard. 1999. Assessing extinction risk: integrating genetic information. Conservation Ecology [online serial] 3(1):2.
   Google Scholar
• Dunham, J. B., B. E. Rieman, and J. T. Peterson. 2002. Patch-based models of species occurrence: lessons from salmonid fishes in streams. Pages 327–334 in J. M. Scott, P. J. Heglund, M. L. Morrison, J. B. Haufler, M. G. Raphael, W. A. Wall, and F. B. Samson, editors. Predicting species occurrences: issues of scale and accuracy. Island Press, Covelo, California.
   Google Scholar
• Dunham, J. B., G. L. Vinyard, and B. E. Rieman. 1997. Habitat fragmentation and extinction risk of Lahontan Cutthroat Trout. North American Journal of Fisheries Management 17:1126–1133.
   Google Scholar
• Dunham, J. B., K. A. Young, R. E. Gresswell, and B. E. Rieman. 2003. Effects of fire on fish populations: landscape perspectives on persistence of native fishes and nonnative fish invasions. Forest Ecology and Management 178:183–196.
   Web of Science ®Google Scholar
• Dunning, J. B., B. J. Danielson, and H. R. Pulliam. 1992. Ecological processes that affect populations in complex landscapes. Oikos 65:169–175.
   Web of Science ®Google Scholar
• Earl, D. A., B. M. VonHoldt, and M. Bridget. 2012. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources 4:359–361.
   Web of Science ®Google Scholar
• Ebersole, J. L., P. J. Wigington, S. G. Leibowitz, R. L. Comeleo, and J. Van Sickle. 2015. Predicting the occurrence of cold-water patches at intermittent and ephemeral tributary confluences with warm rivers. Freshwater Science 34:111–124.
   Web of Science ®Google Scholar
• El Mousadik, A., and E. Petit. 1996. High levels of genetic differentiation for allelic richness among populations of the argan tree (Argania spinosa (L.) Skeels) endemic of Morocco. Theoretical and Applied Genetics 92:832–839.
   PubMed Web of Science ®Google Scholar
• Elliott, J., R. L. Haskins, and G. Weller. 1997. Lahontan Cutthroat Trout species management plan for the upper Humboldt River drainage basin. Nevada Division of Wildlife, Carson City.
   Google Scholar
• Evans, C., and D. Snyder. 2012. Maggie Creek watershed restoration project, 1993 south operations area project mitigation plan, 2011 monitoring summary and evaluation of biological standards. Elko District Bureau of Land Management, Elko, Nevada.
   Google Scholar
• Fagan, W. F. 2002. Connectivity, fragmentation, and extinction risk in dendritic metapopulations. Ecology 83:3243–3249.
   Web of Science ®Google Scholar
• Fausch, K. D., B. E. Rieman, J. B. Dunham, M. K. Young, and D. P. Peterson. 2009. Invasion versus isolation: trade-offs in managing native salmonids with barriers to upstream movement. Conservation Biology 23:859–870.
   PubMed Web of Science ®Google Scholar
• Fausch, K. D., C. E. Torgersen, C. V. Baxter, and H. W. Li. 2002. Landscapes to riverscapes: bridging the gap between research and conservation of stream fishes. Bioscience 52:483–498.
   Web of Science ®Google Scholar
• Goudet, J. 2001. FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3). Available: http://www.unil.ch/izea/softwares/fstat.html. (March 2016).
   Google Scholar
• Gresswell, R. E. 1999. Fire and aquatic ecosystems in forested biomes of North America. Transactions of the American Fisheries Society 128:193–221.
   Web of Science ®Google Scholar
• Haak, A. L., and J. E. Williams. 2012. Spreading the risk: native trout management in a warmer and less certain future. North American Journal of Fisheries Management 32:387–401.
   Web of Science ®Google Scholar
• Haak, A. L., and J. E. Williams. 2013. Using native trout restoration to jumpstart freshwater conservation planning in the Interior West. Journal of Conservation Planning 9:38–52.
   Google Scholar
• Hansen, M. M., E. E. Nielsen, and K.-L. D. Mensberg. 1997. The problem of sampling families rather than populations: relatedness among individuals in samples of juvenile Brown Trout Salmo trutta L. Molecular Ecology 6:469–474.
   Web of Science ®Google Scholar
• Hassett, B., M. Palmer, E. Bernhardt, S. Smith, J. Carr, and D. Hart. 2005. Restoring watersheds project by project: trends in Chesapeake Bay tributary restoration. Frontiers in Ecology and the Environment 3:259–267.
   Web of Science ®Google Scholar
• Heller, N. E., and E. S. Zavaleta. 2009. Biodiversity management in the face of climate change: a review of 22 years of recommendations Biological Conservation 142:14–32.
   Google Scholar
• Hilderbrand, R. H. 2003. The roles of carrying capacity, immigration, and population synchrony on persistence of stream-resident Cutthroat Trout. Biological Conservation 110:257–266.
   Web of Science ®Google Scholar
• Hill, W. G. 1981. Estimation of effective population size from data on linkage disequilibrium. Genetical Research 38:209–216.
   Web of Science ®Google Scholar
• Hoban, S., J. A. Arntzen, M. W. Bruford, J. A. Godoy, A. R. Hoelzel, G. Segelbacher, C. Vilà, and G. Bertorelle. 2014. Comparative evaluation of potential indicators and temporal sampling protocols for monitoring genetic erosion. Evolutionary Applications 7:984–998.
   PubMed Web of Science ®Google Scholar
• Horton, G. A. 2000. Humboldt River chronology, part I. Nevada Division of Water Planning, Carson City.
   Google Scholar
• Hudy, M., J. A. Coombs, K. H. Nislow, and B. H. Letcher. 2010. Dispersal and within-stream spatial population structure of Brook Trout revealed by pedigree reconstruction analysis. Transactions of the American Fisheries Society 139:1276–1287.
   Web of Science ®Google Scholar
• Isaak, D. J., and R. F. Thurow. 2006. Network-scale spatial and temporal variation in Chinook Salmon (Oncorhynchus tshawytscha) redd distributions: patterns inferred from spatially continuous replicate surveys. Canadian Journal of Fisheries and Aquatic Sciences 63:285–296.
   Web of Science ®Google Scholar
• Isaak, D. J., M. K. Young, D. E. Nagel, D. L. Horan, and M. C. Groce. 2015. The cold-water climate shield: delineating refugia for preserving salmonid fishes through the 21st century. Global Change Biology 21:2540–2553.
   PubMed Web of Science ®Google Scholar
• Jackobsson, M., and N. A. Rosenberg. 2007. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23:1801–1806.
   PubMed Web of Science ®Google Scholar
• Jones, O. R., and I. J. Wang. 2010. COLONY: a program for parentage and sibship inference from multilocus genotype data. Molecular Ecology Resources 10:551–555.
   PubMed Web of Science ®Google Scholar
• Lake, P. S., N. Bond, and P. Reich. 2007. Linking ecological theory with stream restoration. Freshwater Biology 52:597–615.
   Web of Science ®Google Scholar
• Langduth, E. L., S. A. Cushman, M. K. Schwartz, K. S. McKelvey, M. Murphy, and G. Luikart. 2010. Quantifying the lag time to detect barriers in landscape genetics. Molecular Ecology 19:4179–4191.
   PubMed Web of Science ®Google Scholar
• Lawler, J. J. 2009. Climate change adaptation strategies for resource management and conservation planning. Annals of the New York Academy of Sciences 1162:79–98.
   PubMed Web of Science ®Google Scholar
• Letcher, B. H., K. H. Nislow, J. A. Coombs, M. J. O’Donnell, and T. L. Dubreuil. 2007. Population response to habitat fragmentation in a stream-dwelling Brook Trout population. PLoS (Public Library of Science) ONE [online serial] 2(11):e1139.
   PubMed Web of Science ®Google Scholar
• Luikart, G., N. Ryman, D. Tallmon, M. K. Schwartz, and F. W. Allendorf. 2010. Estimation of census and effective population sizes: the increasing usefulness of DNA-based approaches. Conservation Genetics 11:355–373.
   Web of Science ®Google Scholar
• Maceina, M. J., and D. L. Pereira. 2007. Recruitment. Pages 121–186 in C. S. Guy and M. L. Brown, editors. Analysis and interpretation of freshwater fisheries data. American Fisheries Society, Bethesda, Maryland.
   Google Scholar
• Manel, S., O. E. Gaggiotti, and R. S. Waples. 2005. Assignment methods: matching biological questions with appropriate techniques. Trends in Ecology and Evolution 20:136–142.
   PubMed Web of Science ®Google Scholar
• Manel, S., M. K. Schwartz, G. Luikart, and P. Taberlet. 2003. Landscape genetics: combining landscape ecology and population genetics. Trends in Ecology and Evolution 18:189–197.
   Web of Science ®Google Scholar
• McCullough, D. A., J. M. Bartholow, H. I. Jager, R. L. Beschta, E. F. Cheslak, M. L. Deas, J. L. Ebersole, J. S. Foott, S. L. Johnson, K. R. Marine, M. G. Mesa, J. H. Petersen, Y. Souchon, K. F. Tiffan, and W. A. Wurtsbaugh. 2009. Research in thermal biology: burning questions for coldwater stream fishes. Reviews in Fisheries Science 17:90–115.
   Web of Science ®Google Scholar
• Miller, S. A. 2011. Population assessment of Lahontan Cutthroat Trout, 2011. Oregon Department of Fish and Wildlife, Salem.
   Google Scholar
• Mills, L. S., and F. W. Allendorf. 1996. The one-migrant-per-generation rule in conservation management. Conservation Biology 10:1509–1518.
   Web of Science ®Google Scholar
• Nakagawa, S., and H. Schielzeth. 2013. A general and simple method for obtaining R2 from generalized linear mixed-effects models. Methods in Ecology and Evolution 4:133–142.
   Web of Science ®Google Scholar
• Neel, M. C., K. McKelvey, N. Ryman, M. W. Lloyd, R. Short Bull, F. W. Allendorf, M. K. Schwartz, and R. S. Waples. 2013. Estimation of effective population size in continuously distributed populations: there goes the neighborhood. Heredity 111:189–199.
   PubMed Web of Science ®Google Scholar
• Neumann, R. M., C. S. Guy, and D. W. Willis. 2012. Length, weight, and associated incides. Pages 637–670 in A. V. Zale, D. L. Parrish, and T. M. Sutton, editors. Fisheries techniques, 3rd edition. American Fisheries Society, Bethesda, Maryland.
   Google Scholar
• Neville, H., J. Dunham, and M. Peacock. 2006a. Assessing connectivity in salmonid fishes with DNA microsatellite markers. Pages 318–342 in K. Crooks and M. A. Sanjayan, editors. Connectivity conservation. Cambridge University Press, Cambridge, UK.
   Google Scholar
• Neville, H., J. Dunham, A. Rosenberger, J. Umek, and B. Nelson. 2009. Influences of wildfire, habitat size, and connectivity on trout in headwater streams revealed by patterns of genetic diversity. Transactions of the American Fisheries Society 138:1314–1327.
   Web of Science ®Google Scholar
• Neville, H. M., J. B. Dunham, and M. M. Peacock. 2006b. Landscape attributes and life history variability shape genetic structure of trout populations in a stream network. Landscape Ecology 21:901–916.
   Web of Science ®Google Scholar
• Neville, H. M., and D. P. Peterson. 2014. Genetic monitoring of trout movement after culvert remediation: family matters. Canadian Journal of Fisheries and Aquatic Sciences 71:1680–1694.
   Web of Science ®Google Scholar
• Novinger, D. C., and F. J. Rahel. 2003. Isolation management with artificial barriers as a conservation strategy for Cutthroat Trout in headwater streams. Conservation Biology 17:772–781.
   Web of Science ®Google Scholar
• Osborne, M. J., E. W. Carson, and T. F. Turner. 2012. Genetic monitoring and complex population dynamics: insights from a 12-year study of the Rio Grande Silvery Minnow. Evolutionary Applications 5:553–574.
   PubMed Web of Science ®Google Scholar
• Paetkau, D., R. Slade, M. Burden, M. Burden, and A. Estoup. 2004. Genetic assignment methods for the direct, real-time estimation of migration rate: a simulation-based exploration of accuracy and power. Molecular Ecology 13:55–65.
   PubMed Web of Science ®Google Scholar
• Peacock, M. M., H. Neville, and V. Kirchoff. 2004. Ten species specific microsatellite loci for Lahontan Cutthroat Trout, Oncorhynchus clarki henshawi. Molecular Ecology Notes 4:557–559.
   Web of Science ®Google Scholar
• Peterson, D. P., S. J. Wenger, B. E. Rieman, and D. J. Isaak. 2013. Linking climate change and fish conservation efforts using spatially explicit decision support tools. Fisheries 38:112–127.
   Web of Science ®Google Scholar
• Petit, R. J., A. El Mousadik, and O. Pons. 1998. Identifying populations for conservation on the basis of genetic markers. Conservation Biology 12:844–855.
   Web of Science ®Google Scholar
• Pickett, S. T. A., and J. N. Thompson. 1978. Patch dynamics and the design of nature reserves. Biological Conservation 13:27–37.
   Web of Science ®Google Scholar
• Pierce, R., C. Podner, and K. Carim. 2013. Response of wild trout to stream restoration over two decades in the Blackfoot River basin, Montana. Transactions of the American Fisheries Society 142:68–81.
   Web of Science ®Google Scholar
• Platts, W. S., and R. L. Nelson. 1988. Fluctuations in trout populations and their implications for land-use evaluation. North American Journal of Fisheries Management 8:333–345.
   Google Scholar
• Pritchard, J. K., M. Stephens, and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945–959.
   PubMed Web of Science ®Google Scholar
• Raeymaekers, J. A. M., D. Raeymaekers, I. Koizumi, S. Geldof, and F. A. M. Volckaert. 2009. Guidelines for restoring connectivity around water mills: a population genetic approach to the management of riverine fish. Journal of Applied Ecology 46:562–571.
   Web of Science ®Google Scholar
• Rahel, F. J. 2013. Intentional fragmentation as a management strategy in aquatic systems. Bioscience 63:362–372.
   Web of Science ®Google Scholar
• Ray, C., M. M. Peacock, and J. B. Dunham. 2007. Demography and population dynamics of Lahontan Cutthroat Trout (Oncorhynchus clarkii henshawi) stream populations in eastern Nevada. U.S. Fish and Wildlife Service, Reno, Nevada.
   Google Scholar
• Rieman, B. E., and J. B. Dunham. 2000. Metapopulations of salmonids: a synthesis of life history patterns and empirical observations. Ecology of Freshwater Fishes 9:51–64.
   Web of Science ®Google Scholar
• Robinson, M. L., V. S. Kirchoff, and M. M. Peacock. 2009. Characterization of 13 microsatellites for Lahontan Cutthroat Trout (Oncorhynchus clarki henshawi) and cross-amplification in six other salmonids. Molecular Ecology Resources 9:134–136.
   PubMed Web of Science ®Google Scholar
• Rolls, R. J., T. Ellison, S. Faggotter, and D. T. Robers. 2013. Consequences of connectivity alteration on riverine fish assemblages: potential opportunities to overcome constraints in applying conventional monitoring designs. Aquatic Conservation: Marine and Freshwater Ecosystems 23:624–640.
   Web of Science ®Google Scholar
• Roni, P., K. Hanson, and T. Beechie. 2008. Global review of the physical and biological effectiveness of stream habitat rehabilitation techniques. North American Journal of Fisheries Management 28:856–890.
   Web of Science ®Google Scholar
• Roni, P., G. Pess, T. Beechie, and S. Morley. 2010. Estimating changes in Coho Salmon and steelhead abundance from watershed restoration: how much restoration is needed to measurably increase smolt production? North American Journal of Fisheries Management 30:1469–1484.
   Google Scholar
• Rosenberger, A. E., J. B. Dunham, J. R. Neuswanger, and S. F. Railsback. 2015. Legacy effects of wildfire on stream thermal regimes and Rainbow Trout ecology: an integrated analysis of observation and individual-based models. Freshwater Science 34:1571–1584.
   Web of Science ®Google Scholar
• Saura, M., and R. Faria. 2011. Genetic tools for restoration of fish populations. Applied Ichthyology 27(Supplement 3):5–15.
   Web of Science ®Google Scholar
• Scheuerell, M. D., E. R. Buhle, B. X. Semmens, M. J. Ford, T. Cooney, and R. W. Carmichael. 2015. Analyzing large-scale conservation interventions with Bayesian hierarchical models: a case study of supplementing threatened Pacific salmon. Ecology and Evolution 5:2115–2125.
   PubMed Web of Science ®Google Scholar
• Schlosser, I. J. 1995. Critical landscape attributes that influence fish population dynamics in headwater streams. Hydrobiologia 303:71–81.
   Web of Science ®Google Scholar
• Schlosser, I. J., and P. L. Angermeier. 1995. Spatial variation in demographic processes of lotic fishes: conceptual models, empirical evidence, and implications for conservation. Pages 392–401 in J. L. Nielsen and D. A. Powers, editors. Evolution and the aquatic ecosystem: defining unique units in population conservation. American Fisheries Society, Symposium 17, Bethesda, Maryland.
   Google Scholar
• Schwartz, M. K., G. Luikart, and R. S. Waples. 2006. Genetic monitoring as a promising tool for conservation and management. Trends in Ecology and Evolution 22:25–33.
   PubMed Web of Science ®Google Scholar
• Sedell, J. R., G. H. Reeves, F. R. Hauer, J. A. Stanford, and C. P. Hawkins. 1990. Role of refugia in recovery from disturbances – modern fragmented and disconnected river systems. Environmental Management 14:711–724.
   Web of Science ®Google Scholar
• Simonds, G., M. Ritchie, and E. Sant. 2009. Evaluation of factors affecting Lahontan Cutthroat Trout recovery in three large watersheds. Open Range Consulting, Park City, Utah.
   Google Scholar
• Taylor, E. B., M. D. Stamford, and J. S. Baxter. 2003. Population subdivision in Westslope Cutthroat Trout (Oncorhynchus clarki lewisi) at the northern periphery of its range: evolutionary inferences and conservation implications. Molecular Ecology 12:2609–2622.
   PubMed Web of Science ®Google Scholar
• USFWS (U.S. Fish and Wildlife Service). 2009. Lahontan Cutthroat Trout (Oncorhynchus clarkii henshawi) 5-year review: summary and evaluation. USFWS, Reno, Nevada.
   Google Scholar
• Vaha, J.-P., J. Erkinaro, E. Niemela, and C. R. Primmer. 2007. Life-history and habitat features influence the within-river genetic structure of Atlantic Salmon. Molecular Ecology 16:2638–2654.
   PubMed Web of Science ®Google Scholar
• Van Deventer, J. S. 1989. Microcomputer software system for generating population statistics from electrofishing data–user’s guide for MicroFish 3.0. Available: http://microfish.org/MicroFish3DemoVersionUsersGuide.htm. (March 2016).
   Google Scholar
• Van Deventer, J. S., and W. S. Platts. 1985. A computer software system for entering, managing, and analyzing fish capture data from streams. U.S. Forest Service Research Note INT‑352.
   Google Scholar
• Wang, J., and A. W. Santure. 2009. Parentage and sibship inference from multilocus genotype data under polygamy. Genetics 181:1579–1594.
   PubMed Web of Science ®Google Scholar
• Waples, R. S., and P. R. England. 2011. Estimating contemporary effective population size on the basis of linkage disequilibrium in the face of migration. Genetics 189: 633–644.
   PubMed Web of Science ®Google Scholar
• Wenger, S. J., D. J. Isaak, C. H. Luce, H. M. Neville, K. D. Fausch, J. B. Dunham, D. C. Dauwalter, M. K. Young, M. M. Elsner, B. E. Rieman, A. F. Hamlet, and J. E. Williams. 2011. Flow regime, temperature and biotic interactions drive differential declines of trout species under climate change. Proceedings of the National Academy of Sciences of the USA 108:14175–14180.
   PubMed Web of Science ®Google Scholar
• White Horse Associates. 2011. Maggie Creek watershed restoration project remote sensing monitoring, Elko, NV. White Horse Associates, Smithfield, Utah.
   Google Scholar
• Whiteley, A. R., J. A. Coombs, M. Hudy, Z. Robinson, A. R. Colton, K. H. Nislow, and B. H. Letcher. 2013. Fragmentation and patch size shape genetic structure of Brook Trout populations. Canadian Journal of Fisheries and Aquatic Sciences 70:678–688.
   Web of Science ®Google Scholar
• Whiteley, A. R., J. A. Coombs, B. H. Letcher, and K. H. Nislow. 2014. Simulation and empirical analysis of novel sibship-based genetic determination of fish passage. Canadian Journal of Fisheries and Aquatic Sciences 71:1667–1679.
   Web of Science ®Google Scholar
• Whitlock, M. C., and D. E. McCauley. 1999. Indirect measures of gene flow and migration: Fst/ = 1/(4Nm+1). Heredity 82:117–125.
   PubMed Web of Science ®Google Scholar
• Wofford, J. E. B., R. E. Gresswell, and M. A. Banks. 2005. Influence of barriers to movement on within-watershed genetic variation of Coastal Cutthroat Trout. Ecological Applications 15:628–637.
   Web of Science ®Google Scholar
• Wright, S. 1969. Evolution and the genetics of populations, the theory of gene frequencies, volume 2. University of Chicago Press, Chicago.
   Google Scholar