Aquatic systems are complex and our understanding of how they function continues to evolve. Our research activities help inform our planning and restoration work to make sure that our efforts are consistent with the most current scientific knowledge of coldwater fisheries and their habitats. 2014 Neville, H.M. and D.P. Peterson. Genetic monitoring of trout movement after culvert remediation: family matters. 2014. Canadian Journal of Fisheries and Aquatic Sciences, 71: 1–15. We can learn a lot about movement and population dynamics by looking at how different families, and siblings within families, are distributed throughout stream networks 2013 Al-Chokhachy, R., S.J. Wenger, D.J. Isaak and J.L. Kershner. 2013. Characterizing the thermal suitability of instream salmonids: a cautionary example from the Rocky Mountains. Transactions of the American Fisheries Society 142: 793-801. Not all methods of estimating trout temperature preferences yield the same results. Dauwalter, D.C. 2013. Fish assemblage associations and thresholds with existing and projected oil and gas development. Fisheries Management and Ecology, 20:289-301. This study explores how past and future oil and gas development in the upper Green River basin may impact riverine fish communities. Goode, J.R., J.M. Buffington, D.J. Isaak, D. Tonina, R.F. Thurow, S.J. Wenger, D.E. Nagel, C.H. Luce, D. Tetzlaff and C. Soulsby. 2013. Understanding potential effects of climate change on streambed scour and risks to salmonid survival in mountain basins. Hydrologic Processes 27:750-765. This study explores how a changing climate could increase the frequency of high flows, mobilizing rocks and sand that could crush salmon and trout eggs. Neville, H. M. and L. Bernatchez. 2013. Coding Gene Single Nucleotide Polymorphism Population Genetics of Nonnative Brook Trout: The Ghost of Introductions Past. Transactions of the American Fisheries Society 142:5, 1215-1231. This paper evaluates genetic diversity in different strains of brook trout introduced to Idaho over 100 years ago, and characterizes how this diversity translates to, and may have bolstered, patterns of genetic variation observed today in naturalized populations of non-native brook trout. Peterson, E.E., J.M. Ver Hoef, D.J. Isaak, J. A. Falke, M.-J. Fortin, C.E. Jordan, K. McNyset, P. Monestiez, A.S. Ruesch, A. Sengupta, N. Som, E.A. Steel, D.M. Chokhachy, C.E. Torgersen, S.J. Wenger. 2013. Modelling dendritic ecological networks in space: an integrated network perspective. Ecology Letters 16: 707-719. We present more realistic approaches for modeling fish, temperature, and other stuff in stream networks. Praggastis, A. and J.E. Williams. 2013. Salmon's Presence in Nevada's Past. Nevada Historical Society Quarterly. 56:14-32. While salmon once spawned in abundance in the headwater streams of northern Nevada, they are all but absent there today. We examine the causes of decline as well as strategies for recovery. Wenger, S.J., N.A. Som, D.C. Dauwalter, D.J. Isaak, H.M. Neville, C.H. Luce, J.B. Dunham, M.K. Young, K.D. Fausch and B.E. Rieman. 2013. Probabilistic accounting of uncertainty in forecasts of species distributions under climate change. Global Change Biology, DOI: 10.1111/gcb.12294. We show how to incorporate uncertainty into predicting how species distributions may change in the future, using bull trout as an example. 2012 Wenger, S.J., and J.D. Olden. 2012. Assessing transferability of ecological models: an underappreciated aspect of statistical validation. Methods in Ecology and Evolution. doi: 10.1111/j.2041-210X.2011.00170.x. Sometimes, ecological predictions aren’t as good as we think they are; we demonstrate an way to get more honest estimates of predictive ability. 2011 Dauwalter, D. C., S. J. Wenger, K. R. Gelwicks, and K. A. Fesenmyer. 2011. Land use associations with declining native fishes in the Upper Colorado River Basin. Transactions of the American Fisheries Society 140:646-658. Colorado River Basin fishes have declined, and this study explores how land uses may have played a role in the decline of some extant native fishes. Neville, H.M., and J.B. Dunham. Patterns of Hybridization of Nonnative Cutthroat Trout and Hatchery Rainbow Trout with Native Redband Trout in the Boise River, Idaho. North American Journal of Fisheries Management 31:1163–1176. Hybridization with non-native species, including with hatchery rainbow trout originating from the Pacific coast, is one of the biggest threats to native redband trout; we found many populations in this high-visibility watershed were hybridized, but also uncovered a suite of unaltered populations that could be prioritized for conservation. Wenger S.J., D.J. Isaak, J.B. Dunham, K.D. Fausch, C.H. Luce, H.M. Neville, B.E. Rieman, M.K. Young, D.E. Nagel, D.L. Horan, and G.L. Chandler. 2011. Role of climate and invasive species in structuring trout distributions in the interior Columbia River Basin, USA. Canadian Journal of Fisheries and Aquatic Sciences 68:988-1008. We study how native trout are affected by stream flows, stream temperature, and competition with introduced species. 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, 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 108(34):14175–14180. In this large study, we assess how and why distributions of different trout species may change in the future. 2010 Dauwalter, D.C., W.L. Fisher, F.J. Rahel. 2010. Warmwater streams. Pages 657 – 697 in Hubert, W.A. and M.C. Quist, editors. Inland Fisheries Management in North America, third edition. American Fisheries Society, Bethesda, Maryland. This book chapter, written by top scientists that have experience working in warmwater streams, describes how warmwater streams function and the types of approaches used to manage stream habitat and resident fish communities. Wenger, S.J., C.H. Luce, A.F. Hamlet, D.J. Isaak and H.M. Neville. 2010. Macroscale hydrologic modeling of ecologically relevant flow metrics. Water Resources Research 46 (W09513): 10pp. doi:10.1029/2009WR008839. We estimate stream flows across the Northwestern US and examine how good these predictions are compared to real measurement. 2009 Neville H, Dunham J, Rosenberger A, Umek J, Nelson B. 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. Using genetic variability as a metric of population size and stability, we found that isolation by road culverts may pose greater threats to populations of native trout than wildfire and related disturbances. Wenger, S.J., A.H. Roy, C.R. Jackson, E.S. Bernhardt, T.L. Carter, S. Filoso, C.A. Gibson, N.B. Grimm, W.C. Hession, S.S. Kaushal, E. Martí, J.L. Meyer, M.A. Palmer, M.J. Paul, A.H. Purcell, A. Ramirez, A.D. Rosemond, K.A. Schofield, T.R. Schueler, E. Sudduth, C.J. Walsh. 2009. Twenty-six key research questions in urban stream ecology: an assessment of the state of the science. Journal of the North American Benthological Society 28: 1080-1098. A large team of scientists identify the major future challenges in understanding urban streams. Williams, J.E., A.L. Haak, H.M. Neville, and W.T. Colyer. 2009. Potential consequences of climate change to persistence of cutthroat trout populations. North American Journal of Fisheries Management 29:533-548. This report assesses broad-scale impacts of climate change to western trout populations and examines the increasing vulnerability to disturbances from wildfires, flooding, and drought. Williams, J.E., and J. Meka Carter. 2009. Managing native trout past peak water. Southwest Hydrology 8(2):26-27, 34. This report takes a close look at increasing drought in the Desert Southwest and impacts on Apache trout with potential management solutions. 2008 Wenger, S.J. 2008. The use of surrogates to predict the stressor response of imperiled species. Conservation Biology 22:1564-15. It can be difficult to know how rare species will respond to stressors, such as urbanization and climate change; we show how to make a best guess based on the response of other species. Wenger, S.J., T.L. Carter, R. A. Vick and L.A. Fowler. 2008. Runoff limits: an ecologically-based stormwater management program. Stormwater 9(2): 45-58. We propose a new program for managing stormwater to protect aquatic species. Wenger, S.J. and M.C. Freeman. 2008. Estimating species occurrence, abundance and detection probability using zero-inflated distributions. Ecology 89: 2953-2959. We show a way to simultaneously estimate the probability of a species occurring and its abundance, even when species detection is uncertain. Wenger, S.J., J.T. Peterson, M.C. Freeman, B.J. Freeman and D.D.Homans. 2008. Stream fish occurrence in response to impervious cover, historic land use and hydrogeomorphic factors. Canadian Journal of Fisheries and Aquatic Sciences 65:1250-1264. We examine how fish are affected by urban development after accounting for historical legacies and natural variables. 2007 Deacon, J.E., A.E. Williams, C.D. Williams, and J.E. Williams. 2007. Fueling population growth in Las Vegas: how large-scale groundwater withdrawal could burn regional biodiversity. BioScience 57:688-698. Research into the impacts of proposed groundwater withdrawals by the Southern Nevada Water Authority across northern and central Nevada on the native fishes and spring-dependent species as a result of their efforts to maintain growth in the Las Vegas Metropolitan Region. Neville H., Isaak D. J., Thurow R., Dunham J., Rieman B. 2007. Microsatellite variation reveals weak genetic structure and retention of genetic variability in threatened Chinook salmon (Oncorhynchus tshawytscha) within a Snake River watershed. Conservation Genetics 8(1):133-147. Despite dramatic declines in recent history, this uniquely wild, threatened population of Chinook salmon was found to have retained surprising levels of genetic diversity and population structure, providing a better understanding of recent population dynamics and management needs. 2006 Neville H., Dunham J., Peacock M. 2006. Assessing connectivity in salmonid fishes with DNA microsatellite markers. In: Crooks K., Sanjayan M.A., editors. Connectivity Conservation. Cambridge, UK: Cambridge University Press. p 318-342. This book chapter used examples from well-studied salmon systems to showcase how genetic tools can be used to identify movement within and among populations, and help managers make informed conservation decisions. Neville H.M., Dunham J.B., Peacock M.M. 2006. Landscape attributes and life history variability shape genetic structure of trout populations in a stream network. Landscape Ecology 21:901-916. This was one of the first characterizations of “metapopulation” dynamics in trout, where we found expected associations between genetic patterns and migratory life histories, habitat size, connectivity and stability. Neville H.M., Isaak D.J., Dunham J.B., Thurow R.F., Rieman B.E. 2006. Fine-scale natal homing and localized movement as shaped by sex and spawning habitat in Chinook salmon: insights from spatial autocorrelation analysis of individual genotypes. Molecular Ecology 15:4589–4602. In a first application of genetic tools to characterize local homing patterns in salmon, our results suggested that females (but not males) returned within several kilometers of natal areas to spawn but also that this behavior was influenced by within-watershed habitat structure. Williams, J.E., and E.P. Pister. 2006. Lifestyles and ethical values to sustain salmon and ourselves. Pages 577-596 in, R.T. Lackey, D.H. Lach, and S.L. Duncan, eds. Salmon 2100: the future of wild Pacific salmon. American Fisheries Society, Bethesda, Maryland. Two top scientists become philosophers to describe how people will have to change their lifestyles if we want to keep wild salmon around through the next century.