Seasonal Distribution and Habitat Associations of Salmonids with Extended Juvenile Freshwater Rearing in Different Precipitation Zones of the Skagit River, WA January, 2020 Erin D. Lowery1*, Jamie N. Thompson1, Ed Connor2, Dave Pflug2, Bryan Donahue1, Jon- Paul Shannahan3 Introduction a freshwater rearing period lasting more than one Anadromous salmonids (Salmonidae spp.) year (Quinn 2005, SRSC and WDFW 2005). experience a variety of freshwater and marine As climate change progresses, the timing and habitats through the completion of their life cycle. magnitude of hydrologic cycles are expected to shift Certain life stages and habitats have been associated significantly, and these changes could dramatically with critical periods of growth or survival, wherein affect the overall capacity of watersheds to support the growth performance achieved within the critical anadromous salmonids as well as the spatial- period is highly and positively correlated to survival temporal distribution of habitats that support the through subsequent life stages. Alternatively, positive growth trajectories that improve the survival disproportionately high or variable mortality might of these fishes (Battin et al. 2007; Schindler et al. be associated with these periods, but the variability 2008). Pacific salmonids, Oncorhynchus and in mortality is strongly mediated by growth or Salvelinus spp., that rely on extended freshwater environmental conditions (Beamish and Mahnken rearing like steelhead O. mykiss, spring, summer, and 2001). The timing and location of these critical fall Chinook salmon O. tshawytscha, Coho salmon O. periods can vary considerably among species, kisutch, Sockeye salmon O. nerka, and Bull Trout S. populations, among years within populations, and confluentus are likely to be more vulnerable to could operate on the growth performance achieved climatic shifts in hydrology and thermal regime than in either freshwater (e.g., Steelhead, Ward et al. 1989; species that exhibit ocean-type freshwater rearing Ward 2000; spring Chinook, Zabel and Williams strategies like Pink O. gorbuscha, Chum O. keta, and 2002) or marine habitats (Coho, Beamish et al. 2004; most fall Chinook salmon. pink salmon Moss et al. 2005 and Cross et al. 2009; The Puget Sound/Salish sea region contains many ocean-type Chinook, Duffy and Beauchamp 2011; populations of Pacific salmon and trout yearling spring Chinook Tomaro et al. 2012). Life (Oncorhynchus spp.), and char (Salvelinus spp.). The history diversity and migrations can stabilize the primary freshwater life-history for salmon in this magnitude of inter-annual population variability by region, besides Coho salmon and steelhead, is an buffering the impact of catastrophic events that ocean-type migrant. Some Puget Sound rivers also negatively affect some life history types, while other have stream-type Chinook salmon, but little is life history types might benefit from anomalous known about habitat associations of these southern conditions (portfolio effect; Hilborn et al. 2003; latitude populations in the warmer, wetter Schindler et al. 2010). Two common life-histories are watersheds on the west side of the Cascade expressed in stream-rearing salmonid populations: Mountain Range. The Skagit River in northwest 1) ocean-type characterized by a sub-yearling ocean Washington State is the largest tributary to Puget migration within 0-6 months of becoming a free Sound and contains one of the largest populations swimming juvenile; and 2) stream-type characterized of Bull Trout Salvelinus confluentus and Chinook 1 *Corresponding Author: [email protected] 1. U.S. Geological Survey, Washington Cooperative Fish and Wildlife Research Unit, School of Aquatic and Fishery Sciences, University of Washington, Box 355020, Seattle, Washington 98195-5020, USA 2. Seattle City Light, Environment, Lands, and Licensing Business Unit, 700 5th Ave, Suite 3200, Seattle, WA 98104 3. Upper Skagit Indian Tribe 25944 Community Plaza Way, Sedro-Woolley, WA 98284 1 salmon Oncorhynchus tshawytscha in the Puget (SRSC and WDFW 2005). Stream type life history Sound region and a regionally large population of expression in Chinook stocks has been observed at steelhead; all three species are listed as threatened the WDFW Skagit Mainstem juvenile trap and has under the Endangered Species Act (ESA). The Skagit been observed in otolith and scale samples from River also contains among the largest populations of returning adults (Beamer et a. 2005b). Currently Pink and Chum salmon in the lower 48 states information on outmigration estimates confound (Connor and Pflug 2004). recovery actions for this life history strategy in all six All stocks of Chinook and Coho salmon, steelhead, Skagit populations due to bias in trapping efficiency and Bull Trout in the Skagit River basin express a for these individuals (Seiler et al. 1998, Kinsel et al. stream-type life history. Steelhead and Bull Trout are 2008). more plastic in their life history strategies but exhibit The long-term goal of Chinook salmon recovery is to ontogenetic trajectories similar to the stream-type achieve self- sustaining populations of Skagit and life history observed in Pacific salmon. Of the data Puget Sound Chinook salmon in terms of gaps identified in individual recovery plans; habitat abundance, productivity, spatial distribution, and use, production estimates, and identification of diversity conceptually recognized as viable salmonid limiting factors for all three listed species have been populations (McElhany et al. 2000). The stream type highlighted as a priority for recovery and require life history strategy is an example of life history comprehensive investigations to meet recovery diversity expressed by Puget Sound Chinook salmon. objectives. Currently fishery managers are at The timing and spatial diversity of adult spawning different stages of recovery planning based on their was also used to measure uniqueness of populations scientific understanding of both the biological and across Puget Sound. McElhany et al. (2000) ecological requirements of these species. Currently recommended the use of the viable salmonid little is known about habitat use by stream-type population approach across Puget Sound to identify juveniles of all three listed species within the Puget de-listing criteria. The occurrence of the stream type Sound/Salish Sea basin. Habitat occupation and life history is an example of a diversity indicator, seasonal distribution by fishes will vary due to highlighting the importance of this strategy as a rare behavioral, environmental, and ecological factors. and diminishing component of Puget Sound By linking our understanding of these species to the Chinook populations. location of habitat types, we gain a spatial and This project will help managers and researchers temporal perspective of the freshwater rearing identify ontogenetically mediated behaviors such as period of each of the listed species in the Skagit River habitat selection, distribution, and rearing location basin. from the basin to the stream or habitat reach scale. The Skagit Chinook Recovery Plan (SRSC and WDFW Most research on stream-type Chinook salmon, Bull 2005) identified habitat use by the stream type life Trout, and steelhead in Washington State has been history as a data gap and research priority. SRSC and conducted in the Columbia River basin, rather than WDFW (2005) called for a detailed investigation of Puget Sound, where all three species, but not the seasonal habitat use and distribution of this life- same life histories, are commonly found in sympatry. history across the Skagit watershed. Information on Currently no research focuses on the interaction of habitat use could then inform additional modelling these species/life history types since they are efforts to predict productivity and survival for future uniquely sympatric in the Puget Sound/Salish Sea recovery actions, adaptive management plan region. The Skagit River is an opportune location to updates, and design criteria for habitat restoration. study these fishes in this manner since this is the only In the Skagit River, stream type life history smolts river system where population levels are large have consistently contributed to the spawning enough to provide sufficient opportunities for escapement of the six independent Chinook detailed observations. populations, with spring stocks having a higher proportion than the other summer and fall stocks 2 Goals and Objectives Study Area This investigation was designed to describe the The Skagit River is the largest tributary to Puget spatial-temporal distribution of the stream-type life Sound draining an approximate 8,100 km2, from the history expressed by anadromous salmonids in the mountainous regions of the Western Cascades in Skagit River, WA. The results of this investigation are Washington state and Southern British Columbia, intended to fill data gaps necessary for effective and the northern Puget Sound lowlands (Figure 1). recovery planning of Chinook salmon, steelhead, Flow regimes and upland precipitation are and Bull Trout in the Skagit River basin, and to inform characterized by three major hydrological regions similar efforts in other watersheds in the Puget within the basin, which include snowmelt, mixed Sound region. The specific objectives of this snow and rain, and rain (Beechie 1992, Beechie et al. investigation are to; 1) describe the spatial 2006). In general, stream flows and upland distribution of stream-type juvenile Chinook and precipitation in