https://cpw.cvlcollections.org/files/original/ad6ceb327ae912b213ed563776ca3513.pdf d9288426177bb5f3a0642d1655e85d89 PDF Text Text The research in this publication was partially or fully funded by Colorado Parks and Wildlife. Dan Prenzlow, Director, Colorado Parks and Wildlife • Parks and Wildlife Commission: Marvin McDaniel, Chair • Carrie Besnette Hauser, Vice-Chair Marie Haskett, Secretary • Taishya Adams • Betsy Blecha • Charles Garcia • Dallas May • Duke Phillips, IV • Luke B. Schafer • James Jay Tutchton • Eden Vardy �Received: 23 March 2021 Accepted: 28 September 2021 DOI: 10.1111/jfb.14918 FISH REGULAR PAPER Habitat associations of rainbow trout Oncorhynchus mykiss and brown trout Salmo trutta fry Eric R. Fetherman1 | 1 Colorado Parks and Wildlife, Fort Collins, Colorado, USA 2 Department of Fish, Wildlife and Conservation Biology, Colorado State University, Fort Collins, Colorado, USA Brian W. Avila2 Abstract Habitat restoration activities continue to increase in large rivers, but many of these projects focus on improving juvenile or adult habitats. Incorporating the habitat associations of fry into restoration designs will allow for broader successes from restora- Correspondence Eric R. Fetherman, Colorado Parks and Wildlife, 317 West Prospect Road, Fort Collins, CO 80526, USA. Email: eric.fetherman@state.co.us tion for all life stages and may be useful for either multispecies or specific-species management. This study investigated the habitat associations of rainbow trout Oncorhynchus mykiss and brown trout Salmo trutta fry in the upper Colorado River, focusing on the mean substrate size (D50), velocity (m s 1 ), depth (m) and presence of wood in near-shore habitats. S. trutta and O. mykiss were found in higher numbers in fry sites with a D50 of 151 mm (ranging from 96 to 206 mm), velocities ranging from 0.20 to 0.23 m s 1 and depths ranging from 0.17 to 0.18 m. Although there was con- siderable overlap in habitat associations between the two species, there may be opportunities for single-species management, if this is a goal of such restoration activities, by adjusting design criteria based on differing habitat associations. In addition, the results suggest that including larger particle sizes in near-shore habitats and upstream of fry sites could decrease Tubifex tubifex habitat and thereby fry infection severity by reducing exposure to Myxobolus cerebralis. Stocking, interspecific competition and/or the presence of pathogens can affect fry habitat associations and cause deviations from demonstrated suitability indices. As such, evaluating system-specific differences in habitat associations may allow future habitat restoration activities to be more effective. KEYWORDS brown trout, Colorado River, habitat associations, Oncorhynchus mykiss, rainbow trout, Salmo trutta 1 | I N T RO DU CT I O N levels, shoreline development and loss of marshes in the Great Lakes have been related to the decline of northern pike Esox lucius Alteration of aquatic systems due to biotic factors, such as the imple- L. populations (Casselman & Lewis, 1996). Salmon populations on the mentation of dams, water and land use for agricultural development West Coast of the United States have been listed as threatened or and physical manipulation of lotic systems (e.g., whitewater parks), endangered as a result of loss of habitat due to barriers to migration and abiotic factors, such as fires, floods and warming of stream tem- (Nehlsen et al., 1991; Northwest Power Planning Council, 1987; peratures (Fox et al., 2016; Gido et al., 2010; Kustu et al., 2010), has Sheer & Steel, 2006). Habitat degradation in the form of sediment led to habitat degradation and resulted in changes to flow regimes, accumulation in Windy Gap Reservoir, Colorado, has contributed to habitat connectivity, increased severity and spread of disease and, the establishment and perpetuation of Myxobolus cerebralis, the para- ultimately, fish population declines. For example, changing water site that causes whirling disease, in the upper Colorado River, J Fish Biol. 2021;1–11. wileyonlinelibrary.com/journal/jfb © 2021 Fisheries Society of the British Isles. 1 �2 FISH FETHERMAN AND AVILA resulting in rainbow trout Oncorhynchus mykiss (Walbaum 1792) pop- O. mykiss fry from desired habitats (Gatz et al., 1987), and fry stocking ulation decline (Nehring, 2006). Tubifex tubifex worms, the secondary success may be affected by predation from larger S. trutta (Avila host for M. cerebralis (Markiw & Wolf, 1983; Wolf & Markiw, 1984), et al., 2018). Although mechanical removals may be an option for prefer sand/silt habitats with high organic matter (Granath Jr. & reducing competition and predation between stocked O. mykiss and Gilbert, 2002), and accumulation of fine particles in near-shore salmo- S. trutta, removals can be both time intensive and expensive nid fry habitats due to decreased or regulated flows contributes to (Fetherman et al., 2015). Restoration activities could present an alter- T. tubifex proliferation (Thompson, 2011) and increased infection rates native to mechanical removals if habitat associations differed between in susceptible individuals. Habitat is clearly a driving factor in fish pop- the two species, especially in locations where these management ulation dynamics, and a broader understanding of how species inter- actions are already planned or taking place. act with their habitat throughout their life cycle, and how habitat The aim of this study was to first assess the physical habitat vari- degradation affects those interactions, is needed for effective popula- ables that affect fry abundance and distribution in the upper Colorado tion management. River, Colorado, and determine if fry habitat preferences differ As an organism grows and matures, its use of habitat changes between S. trutta and O. mykiss fry such that habitat restoration activ- over time (Hayes et al., 1996; Shutter, 1990). Salmonids use a suite of ities could target specific habitats to reduce competition between the habitats throughout their life cycle. Within streams, fry, as compared two species during early life stages. Based on previous research to older life stages, prefer the shallower and slower velocities typically (Fetherman et al., 2014) and observations from continued long-term found along the margins (Horner & Bjornn, 1976; Miller, 1957; Raleigh monitoring, it was expected that mean substrate size, velocity and et al., 1984), with cover types that commonly consist of vegetation depth in near-shore habitats would differ between the two species and interstitial spaces between rocks, allowing for easier escape from and potentially between stocked and wild O. mykiss fry due to differ- predators (Griffith, 1972; Raleigh et al., 1984). Overwinter fry habitat ences in their genetic background. In addition, the authors expected consists of shallow water with low velocity (Bustard & Narver, 1975; that habitat associations of both S. trutta and O. mykiss fry would dif- Huusko et al., 2007), with cobble-boulder substrate providing the fer from published suitability indices (SI) (Raleigh et al., 1984; Raleigh main cover (Griffith & Smith, 1995). As fry grow, habitat preferences et al., 1986) due to interspecific competition, O. mykiss fry stocking or change (Cramer & Ackerman, 2009), and fish move into deeper and the presence of M. cerebralis (established). Second, the authors faster water that is shared with adults (Raleigh et al., 1984). The expected variations in habitat across sites to differentially affect expo- deeper and faster water provides larger prey (aquatic insects and fish) sure to M. cerebralis and thereby the presence and abundance of sal- and cover consisting of larger substrate types (boulders), logs, debris, monid fry. Restoration activities could target favourable T. tubifex overhanging banks and riffles (Bustard & Narver, 1975). Juvenile and habitats that perpetuate M. cerebralis exposure, thereby increasing the adult overwinter habitat tends to differ from summer habitat (Raleigh survival and establishment success of O. mykiss. et al., 1984), where instream substrate, log jams, undercut banks and overhanging vegetation are often used if present (Wesche, 1980), as are deeper pools where depth is assumed to provide the requisite 2 M A T E R I A L S A N D M ET H O D S | cover requirements (Cunjak, 1996). Stocking is a key management strategy for reestablishing, 2.1 | Site description maintaining or enhancing stream and river salmonid populations, and specific habitat variables likely play an important role in the retention, The fry habitat associations study was conducted in a 6.3 km survival and growth of stocked fish. For example, stream temperature section of the upper Colorado River (Grand County, Colorado; affects the survival of O. mykiss in their first winter (Meyer and Grif- Figure 1). Flows through this section of the Colorado River are par- fith, 1997), and temperature and water velocities have been shown to tially regulated by Windy Gap dam, with discharge over the course of affect the growth of age-0 O. mykiss (Korman & Campana, 2009). the study (July through October 2018) averaging 3.8 m3 s 3 1 1 , ranging Increasing the success of stocking events may require an understand- from 1.8 to 7.7 m ing of habitat associations of both wild and stocked fish and stocking section range from 3.4� C in the winter to 16.2� C in the summer, with fish into the correct habitats to increase survival and recruitment. In a mean annual temperature of 10.7� C (Fetherman et al., 2014). s (USGS, 2019). Temperatures in this addition, different strains of fish may be stocked for a myriad of rea- The whirling disease parasite M. cerebralis was established in the sons, e.g., varied angling opportunities or disease-resistance character- upper Colorado River in the early 1990s (Nehring, 2006). The result istics. Disease may be an especially important consideration in was the elimination of O. mykiss age-0 recruitment, leading to the col- conjunction with habitat in systems where specific pathogens are lapse of the O. mykiss population, leaving S. trutta as the dominant sal- established. Avila et al. (2018) showed that the stream characteristics monid in the system (Nehring & Walker, 1996). S. trutta are more in systems in which M. cerebralis was present or absent affected the resistant to M. cerebralis than O. mykiss, having evolved with survival of two M. cerebralis–resistant strains of O. mykiss, stocked as M. cerebralis in their native, European home ranges (Hedrick fry, 2 months after stocking. The presence of other species may also et al., 1999; Hedrick et al., 2003; Hoffman, 1970), and reproduce nat- affect stocking success. Previous work has shown that brown trout urally and are self-sustaining within the study section. O. mykiss Salmo trutta L. competition with O. mykiss results in the exclusion of populations in the river are primarily maintained through stocking of �FISH FETHERMAN AND AVILA 3 F I G U R E 1 Fry site locations used to obtain abundance estimates or single-pass counts for Salmo trutta and Oncorhynchus mykiss in the upper Colorado River study section in Grand County, Colorado, downstream of Windy Gap Reservoir. The 20 15.2 m sites, sampled five times from July through October 2018, included one abundance estimation and four single-pass sites at the Sheriff Ranch, four single-pass sites at Kinney Creek, two abundance estimation and five single-pass sites in the Red Barn area and one abundance estimation and three single-pass sites at Hitching Post M. cerebralis–resistant O. mykiss, previously subcatchable fish by running the quick set-up function on the LR-24 units. Three passes [172–238 mm total length (TL); Fetherman et al., 2014] and more were completed through each site, and fry were removed on each recently fry (<50 mm TL), although some natural reproduction does pass. The number of O. mykiss and S. trutta fry captured was recorded, occur. per pass, and all fry encountered were measured and returned to Fry stocking, which was considered to increase survival by reduc- the site. ing hatchery-related behavioural conditioning (Jackson & Brown, An additional 16 sites were included to increase sample size and 2011; Olla et al., 1998), became the primary management option for inference regarding fry habitat associations: 4 sites at Sheriff Ranch, this section of the Colorado River after low recruitment and survival 4 sites at Kinney Creek, 5 sites in the Red Barn area and 3 sites at rates were observed using subcatchable O. mykiss (Fetherman Hitching Post (Figure 1). Due to limited sampling time, only one et al., 2014). Stocked O. mykiss fry have shown increased survival and removal pass was conducted through each of these 16 sites to obtain recruitment compared to stocking larger fish in the Colorado and counts per site, by species, using the same electrofishing methods Gunnison rivers (Fetherman & Schisler, 2016). On 16 July 2018, described earlier for fry abundance estimation. All 20 sites were sam- O. mykiss fry (62,000; 37.7 ± 0.3 mm TL) were stocked from a raft in pled five times, twice in July, before and after O. mykiss fry stocking, the margins on both sides of the river between Hitching Post and the and once a month near the end of August, September and October. lowermost Red Barn fry sampling site (Figure 1). 2.3 2.2 | | Ethical statement Fry sampling Sampling was approved by Colorado Parks and Wildlife (CPW), and Fry were sampled at 20 15.2 m long sites, 4 in which abundance was care and use of experimental animals complied with the guidelines estimated and 16 from which single-pass counts were obtained and policies of CPW, as approved by the CPW scientific collection (Figure 1). Fry abundance was estimated at one site at the Sheriff permit DOW087. Ranch, two sites in the Red Barn area and one site at Hitching Post. These four sites were historically sampled on an annual basis to monitor natural reproduction (Fetherman et al., 2014) and stocked fry sur- 2.4 | Habitat data collection vival. Fry estimates were accomplished using two Smith-Root LR-24 backpack electrofishing units running side-by-side to cover available Habitat covariate data considered to explain fry habitat associations fry habitat. Backpack settings for voltage were recorded from each and distribution were collected from each of the 20 sites on all five site to determine their effect on fry detection probabilities, obtained sampling occasions. Covariates included mean substrate size (D50) �FISH 4 FETHERMAN AND AVILA obtained through pebble counts, temperature (� C), dissolved oxygen concentration (percentage saturation and mg l October only), velocity (m s 1 and including five encounter occasions, with each occasion containing ; August through a “1” if the species was detected and “0” if it was not detected. 1 ), depth (m), fry site width (m) and pres- Encounter histories also included site-specific individual covariates for ence of wood in the site (binomial; present or absent). Pebble counts D50, backpack voltage settings, velocity, depth, temperature and pres- were obtained, and D50 was calculated using the methods presented ence of wood, and the O. mykiss encounter histories included an addi- in Rosgen (1996). Because river discharge was low and relatively con- tional individual covariate representing whether the site had been sistent across the 5 months of the study, pebble counts were col- stocked in July. Model sets included intercept models for detection lected once from each site in July and did not change between the probability, P, and occupancy probability, ψ. Additional models were July and October sampling occasions. Temperature and dissolved oxy- constructed in which P varied by the individual or additive combina- gen were obtained from the lower, middle and upper thirds of each tions of D50, backpack voltage and/or velocity, and ψ varied by D50, fry site, using a YSI Pro 1020 dissolved oxygen and temperature velocity, depth, temperature, presence of wood and/or stocking status meter. The sensor was placed at an average depth at half the fry site (O. mykiss only). Models were ranked using AIC corrected for small width, and values were recorded once consistency in the readings was sample sizes (AICc), compared using AICc differences (ΔAICc) and achieved. Depth measurements and depth-average velocity, measured ranked using model weights (wi; Burnham & Anderson, 2002). Model- by setting a flow sensor to 0.6 of the measured depth from the water averaged parameter estimates and associated unconditional standard surface, were recorded at the same three locations using a Marsh- errors were reported from each model set (wi > 0; Anderson, 2008). McBirney flowmeter attached to a wading rod that measured depth in Fry abundance estimates, N, were obtained from three pass 0.03 m increments (Avila, 2016; Richer et al., 2020). Fry site width removal data using a Huggins closed capture–recapture estimator in was measured based on the farthest distance from shore a fry of programme MARK. As a removal estimate, only P was estimated from either species was captured within the site and changed with each the likelihood, whereas the recapture probability, c, was set to zero visit. Finally, wood, in the form of downed trees or woody growth since fish could not be recaptured on subsequent passes. Fry length from the bank, was recorded as present or absent in each site. Similar was included as an individual covariate in the encounter histories. The to pebble counts, the presence of wood in a site did not change model set included an intercept model for P, as well as models in between the July and October sampling occasions. which P differed individually or additively by pass, fish length, velocity, D50, backpack voltage settings and stocking status, and N was estimated as a derived parameter (Huggins, 1989). S. trutta and O. mykiss 2.5 | M. cerebralis sample collection abundances were estimated separately. Fry abundance estimates and counts were used to explore habitat Although stocking of M. cerebralis–resistant O. mykiss fry has resulted in associations of S. trutta and O. mykiss fry. Initially, Proc Corr (SAS increased survival and recruitment (Fetherman & Schisler, 2016), the institute, 2019) was used to obtain Pearson correlation coefficients pathogen continues to persist in the upper Colorado River and remains and determine if habitat variables were correlated. Width was highly an obstacle for reestablishing O. mykiss in the system. In October, up to correlated with fry TL, likely because fry move towards the centre of five S. trutta fry and five O. mykiss fry, dependent upon availability, were the river as they get larger (Chapman & Bjornn, 1969; Mitro & collected from each of the four abundance estimation sites at Sheriff Zale, 2002; Northcote, 1992). Other habitat variables (e.g., D50) were Ranch, Red Barn and Hitching Post as part of a long-term monitoring collected based on site width and considered to be more explanatory, study of M. cerebralis infection and prevalence in wild fish populations. so width was removed from further analyses. Within the count data, In addition, one to two fry per species per site were collected from the presence of wood was correlated with velocity, D50, and stocking sta- 16 single-pass count sites in the Sheriff Ranch, Kinney Creek, Red Barn tus, and velocity, depth and temperature were correlated with each and Hitching Post areas. Collecting fry in October ensured full develop- other. For the abundance data, presence of wood was correlated with ment of myxospores following previous natural exposure to the velocity, temperature and depth. Although these habitat variables triactinomyxon, the infectious waterborne stage of the parasite were later retained in the habitat association model sets, correlated (Hedrick & El-Matbouli, 2002) released by T. tubifex. Myxospores were variables were never included in the same model. enumerated (O'Grodnick, 1975) from whole fish using the pepsin– The authors used a general linear model (GLM) as implemented in trypsin digest method (Markiw and Markiw & Wolf, 1974) by the CPW SAS Proc GLM to evaluate fry habitat associations. Model sets were Aquatic Animal Health Laboratory (Brush, Colorado). constructed separately using abundance or count data for S. trutta and O. mykiss and included an intercept model, and individual and additive combinations of D50, presence of wood, temperature, depth, 2.6 | Statistical analyses velocity and stocking status, within the confines of the previously described correlation analyses. In addition, a quadratic relationship Occupancy rates were estimated for each species using the occupancy was included for D50, temperature, depth and velocity to determine if estimation with detection <1 estimator in programme MARK (White & instead of a linear relationship a minimum or maximum value for these Burnham, 1999). Model sets were structured separately for S. trutta covariates existed within the range of measurements recorded. To and O. mykiss fry using encounter histories constructed for each site balance parameter number and sample size, only one quadratic �FISH FETHERMAN AND AVILA 5 relationship was included in any given model; nonetheless, other vari- fairly narrow across sites, ranging from 12.8 to 15.8� C, although tem- ables were considered additively with the quadratic relationship. peratures in July reached 22.7� C and in October were as low as Model weights and ΔAICc ranking were used to determine support for 3.3� C. Dissolved oxygen saturation was generally greater than 100%, each of the models in the set, and parameter estimates were reported and concentration was greater than 8 mg l from the candidate model with the lowest AICc value (Burnham & gen was not included as an explanatory variable for fry abundance or Anderson, 2002). distribution because it never decreased below levels considered opti- Two AIC analyses were conducted using a GLM to determine 1 . As such, dissolved oxy- mal for trout (Piper et al., 1982). Average velocity ranged from 0.03 to 1 how M. cerebralis exposure affected salmonid fry distribution across 0.50 m s the sites and if certain habitat variables were associated with fry 0.6 to 3.8 m. Depth and velocity were higher during periods of higher myxospore count. The first analysis included two models, an intercept discharge in July, whereas fry site width was widest in October when model and a model in which the change in fry numbers between July fry started moving towards the centre of the river as they grew. and October was explained by myxospore count, as a measure of Wood, either downed trees or woody growth from the shore, was infection severity, obtained from fry collected in October. The second present in 50% of the sites (Table 1). , depth ranged from 0.09 to 0.22 m and width varied from analysis included individual and additive combinations of the habitat variables measured in the fry sites as explanatory variables for fry myxospore counts obtained from the various sites. The results are 3.2 | Fry occupancy presented as described earlier for the fry habitat association analyses. S. trutta fry were detected in all sites during all sampling occasions, with the exception of one site in the Kinney Creek area in October. 3 RESULTS | Occupancy for S. trutta was estimated to be one, with depth and D50 being the best predictors of ψ, although regression coefficients for 3.1 | Habitat characteristics of fry sites both overlapped zero. S. trutta P (±unconditional S.E.) within any given sampling occasion was ≥0.98 (±0.01). O. mykiss fry were not detected D50 varied widely among fry sites, averaging 72 (S.E., 13) mm and rang- in all fry sites, with two sites in the Kinney Creek area in which ing from 0 to 220 mm (Table 1). The average temperature range was O. mykiss fry were never observed. Despite less-frequent detection, T A B L E 1 Absolute (D50 and presence of wood) and average (±S.E.) values for temperature, dissolved oxygen (DO) concentration, velocity, depth and width for the 20 sites (Sheriff Ranch = SR, Kinney Creek = KC, Red Barn = RB and Hitching Post = HP) from which Salmo trutta and Oncorhynchus mykiss fry abundance estimates or single-pass counts were obtained in July through October 2018 Site D50 (mm) Temperature (� C) DO (% sat.) DO (mg l 1 ) Velocity (m s 1 ) Depth (m) Width (m) Wood SR1 96 14.1 ± 3.3 105 ± 6 9.2 ± 0.4 0.19 ± 0.04 0.20 ± 0.01 2.7 ± 0.5 SR2 53 12.8 ± 2.8 103 ± 5 9.2 ± 0.5 0.32 ± 0.05 0.31 ± 0.02 1.8 ± 0.4 SR3 31 13.7 ± 3.0 107 ± 5 9.3 ± 0.5 0.13 ± 0.04 0.15 ± 0.01 2.4 ± 0.3 SR4 177 13.8 ± 3.0 107 ± 5 9.3 ± 0.4 0.28 ± 0.07 0.17 ± 0.01 2.6 ± 0.3 SR5 6 14.2 ± 3.0 105 ± 6 9.1 ± 0.5 0.11 ± 0.05 0.15 ± 0.03 0.7 ± 0.1 KC1 115 14.0 ± 2.6 106 ± 2 8.7 ± 0.5 0.08 ± 0.03 0.14 ± 0.01 2.2 ± 0.3 + KC2 26 14.6 ± 2.5 103 ± 3 8.5 ± 0.6 0.03 ± 0.02 0.17 ± 0.02 1.5 ± 0.3 + KC3 0 14.5 ± 2.4 116 ± 3 9.6 ± 0.6 0.26 ± 0.07 0.15 ± 0.01 0.6 ± 0.1 KC4 81 15.3 ± 2.2 113 ± 3 9.0 ± 0.5 0.07 ± 0.04 0.18 ± 0.02 1.5 ± 0.2 RB1 82 15.4 ± 1.8 118 ± 1 9.4 ± 0.5 0.22 ± 0.04 0.16 ± 0.01 3.4 ± 0.7 RB2 112 15.8 ± 1.8 115 ± 3 9.1 ± 0.5 0.35 ± 0.06 0.15 ± 0.02 1.9 ± 0.4 RB3 30 15.6 ± 1.6 118 ± 3 9.2 ± 0.5 0.17 ± 0.04 0.09 ± 0.01 1.8 ± 0.2 RB4 19 15.5 ± 1.6 119 ± 3 9.3 ± 0.5 0.50 ± 0.08 0.22 ± 0.01 1.4 ± 0.3 + RB5 44 15.0 ± 1.7 110 ± 3 8.8 ± 0.5 0.25 ± 0.08 0.14 ± 0.01 1.8 ± 0.2 + RB6 10 14.7 ± 1.7 102 ± 4 8.2 ± 0.6 0.07 ± 0.03 0.22 ± 0.01 1.2 ± 0.3 + RB7 220 14.5 ± 1.7 100 ± 3 8.1 ± 0.6 0.04 ± 0.01 0.14 ± 0.02 3.0 ± 0.4 + HP1 120 14.4 ± 2.1 105 ± 4 8.7 ± 0.2 0.18 ± 0.04 0.19 ± 0.01 3.5 ± 0.7 HP2 39 13.7 ± 1.8 109 ± 2 9.0 ± 0.4 0.11 ± 0.05 0.14 ± 0.01 1.7 ± 0.2 + HP3 66 14.3 ± 1.8 111 ± 5 9.0 ± 0.3 0.15 ± 0.04 0.19 ± 0.01 2.7 ± 0.5 + HP4 121 14.4 ± 2.1 103 ± 5 8.4 ± 0.3 0.12 ± 0.03 0.13 ± 0.01 3.8 ± 0.7 + + �FISH 6 FETHERMAN AND AVILA O. mykiss fry ψ was estimated to be 0.99 (±0.01), with D50 being the S. trutta abundance was similarly predicted by a quadratic rela- best predictor of ψ, although the regression coefficient overlapped tionship for D50, which appeared in all but the second model of the zero. Nonetheless, P was lower than that for S. trutta fry at 0.65 set, and had a cumulative AICc weight of 0.90. Abundance was highest (±0.06). D50 had a positive effect on P, suggesting that O. mykiss were in the site with a D50 of 120 mm, within the optimum range obtained more likely to be detected in sites with a larger D50. from the S. trutta fry count data. Presence of wood (cumulative AICc weight = 0.99) was the only other variable to have an effect, appearing in the first two models. S. trutta abundance was lowest in one of 3.3 | S. trutta fry habitat associations the four sites that contained wood (Figure 3). A quadratic relationship for D50 appeared in the top four models of the S. trutta single pass count analysis and had the highest cumulative 3.4 | O. mykiss fry habitat associations weight of any variable in the model set (cumulative AICc weight = 0.81). The number of S. trutta fry per site was maximized at a D50 of Stocking had the largest effect on O. mykiss fry single-pass counts 151 mm and was ≥10 per site (658 fry per km) between a D50 of (cumulative AICc weight = 0.95), appearing in all models with ΔAICc 96 and 206 mm (Figure 2). Temperature (cumulative AICc weight = ≤ 5.58. The top model also contained the effects of D50 (cumulative 0.35) appeared in the top model, but the next highest model in which AICc weight = 0.5) and temperature (cumulative AICc weight = 0.33), it was included had a ΔAICc of 4.85. Depth and velocity (cumulative although the effect of temperature was expected given a similar effect AICc weights of 0.11), linear relationships of which were included in in S. trutta fry counts. Velocity (cumulative AICc weight = 0.20) models with ΔAICc of 2.29 and 2.39, respectively, appeared to have appeared in the third model of the set (ΔAICc = 0.94). Because stock- lesser effects on S. trutta fry counts (Figure 2). Upon further examina- ing had a large effect on fry count, D50 and velocity were compared tion of fry sites with a D50 between 96 and 206 mm containing ≥10 between sites where stocking did or did not (i.e., natural reproduction) S. trutta fry per site (n = 13), counts were highest when depth aver- occur. There was no observable relationship between counts and D50 aged 0.18 (±0.03) m and velocity averaged 0.20 (±0.09) m s 1 . Sites or velocity in sites in which only natural reproduction occurred, likely meeting these average depth and velocity criteria contained 2.2 and due to the lower counts obtained from those sites. O. mykiss fry num- 1.5 times more S. trutta fry than stocked O. mykiss fry, respectively. bers in stocked sites increased with an increase in D50 (Figure 4), although S. trutta and O. mykiss fry counts were similar at the maxi- 25 in increased counts of O. mykiss fry in stocked sites (Figure 4). In sites y = -0.01x2 + 0.10x + 3.68 R² = 0.21 20 15 0 50 100 150 200 250 S. tru�a Fry Count D50 (mm) 60 y = -4.18x + 8.72 R² < 0.01 20 15 50 10 5 0 S. tru�a Fry Count dance (cumulative AICc weight = 0.62), appearing in the top three models of the set. A quadratic effect for velocity appeared in the top 0 (c) , 13% higher than the average Stocking also had the largest effect on O. mykiss trout fry abun- 0 25 1 velocity for S. trutta fry. 5 30 118 (±71) mm, 22% lower than the average D50 for S. trutta fry, and velocity averaged 0.23 (±0.13) m s 10 (b) containing more than five O. mykiss fry (328 fry per km), D50 averaged 0.05 0.1 0.15 0.2 0.25 Depth (m) 0.3 0.35 0.4 30 25 S. tru�a Fry Abundance 30 S. tru�a Fry Count mum measured D50 of 220 mm. Similarly, increased velocities resulted (a) y = 0.48x - 22.45 R² = 0.55 40 30 20 10 20 y = -0.49x + 8.10 R² < 0.01 15 0 0 10 20 40 60 80 100 120 140 D50 (mm) 5 0 0 0.1 0.2 0.3 0.4 0.5 0.6 Velocity (m/s) F I G U R E 2 Salmo trutta fry single-pass counts and associations with (a) D50, (b) depth and (c) velocity 0.7 F I G U R E 3 Salmo trutta fry abundances from the four sites in which three pass removals were conducted in July through October 2018 and associations with D50 and presence of wood. The trendline shows the relationship between S. trutta fry abundance and D50 in the three sites in which wood was absent ( ) Wood ( ) No Wood �FISH FETHERMAN AND AVILA (a) 30 30 O. mykiss Fry Abundance (a) O. mykiss Fry Count 25 20 15 10 y = 0.02x + 1.36 R² = 0.08 5 25 y = 446.40x2 - 200.36x + 26.43 R² = 0.56 20 15 10 y = 54.90x2 - 36.84x + 6.41 R² = 0.40 5 0 0.00 y = 0.01x + 0.22 R² = 0.08 0.10 50 100 150 200 30 O. mykiss Fry Count 25 20 15 y = 7.84x + 1.58 R² = 0.05 10 5 (b) 30 25 0.10 0.20 0.30 0.40 0.50 0.40 0.50 0.60 20 15 y = -88.52x + 22.43 R² = 0.12 10 y = 8.04x + 0.13 R² = 0.03 5 0 0.00 y = 1.66x + 0.18 R² = 0.10 0 0.00 0.30 250 D50 (mm) O. mykiss Fry Abundance 0 0.20 Velocity (m s-1) 0 (b) 7 0.05 0.10 0.15 0.20 0.25 Depth (m) 0.70 Velocity (m s-1) F I G U R E 4 Oncorhynchus mykiss fry counts from sites in which O. mykiss were or were not (i.e., natural reproduction) stocked and associations with (a) D50 and (b) velocity. A trendline shows the relationship between each habitat variable and the fry count data for both the sites that were stocked (dotted line) and not stocked (solid line) ( ) Not Stocked ( ) Stocked F I G U R E 5 Oncorhynchus mykiss fry abundances from the four sites in which three pass removals were conducted in July through October 2018 and associations with (a) velocity and (b) depth. A trendline shows the relationship between each habitat variable and the fry abundance data for both the sites that were stocked (dotted line) and not stocked (solid line) ( ) Not Stocked ( ) Stocked the intercept model as the top model (wintercept = 0.72, wchange = 0.28). In addition, the measured habitat variables appeared to have lit- model, and when compared across sites that were or were not tle effect on myxospore count, with the intercept model being the top stocked, a similar positive relationship was observed between velocity model of the set. Nonetheless, models containing individual habitat and abundance as for the count data (Figure 5). The average velocity in the stocked sites was 0.24 (±0.09) m s 1 , but the highest abun1 covariates appeared in models with a ΔAICc ≤ 2.24. D50 (cumulative AICc weight = 0.40) had a negative effect on myxospore count, . Despite suggesting that myxospore counts decreased with an increase in D50. lower O. mykiss fry abundance overall, 1.5 times more stocked Although depth, velocity and temperature appeared in weighted dance was obtained from sites with a velocity of 0.45 m s O. mykiss fry were present than S. trutta fry in sites with a velocity of 0.45 m s 1 . Depth had the second-highest cumulative AICc weight (0.35) relative to stocking. The average depth in stocked fry sites was models within the set (cumulative AICc weights = 0.26, 0.24 and 0.24, respectively), no effect on myxospore count was observed for these three variables. 0.17 (±0.03) m, and overall, depth had a negative effect on O. mykiss fry abundance in stocked sites (Figure 5). The highest abundances were obtained in sites with a depth of 0.13 m, which contained 1.7 4 | DI SCU SSION times more stocked O. mykiss fry than S. trutta fry. Unlike O. mykiss fry counts, no effect of D50 on O. mykiss fry abundance was observed. The results show that S. trutta and O. mykiss fry exhibit varying but overlapping habitat associations in the upper Colorado River, especially with respect to mean substrate size, velocity and depth. Occu- 3.5 | M. cerebralis habitat correlations pancy results suggest that there were no fry sites that contained only S. trutta or O. mykiss fry, which resulted in weak statistical relation- Myxospore counts (±S.E.) for O. mykiss averaged 12,268 (±9333) ships between occupancy and measured habitat variables, such as D50 myxospores per fish, ranging from 0 to 109,233 myxospores per fish , because all sites contained both species. Had there been more sites across the sites, whereas S. trutta averaged 11,123 (±4744) in which one or the other species was absent, the relationship myxospores per fish, ranging from 0 to 134,678 myxospores per fish. between occupancy and D50 would likely have been more apparent. Myxospore count did not appear to have an effect on the change in Nonetheless, detection probability results suggest that O. mykiss were salmonid fry numbers within a site between July and October, with more likely to occupy sites with a higher D50, and this was supported �8 FISH FETHERMAN AND AVILA by the fry count results showing that O. mykiss numbers in stocked O. mykiss fry counts exhibited a linear increase with D50 up to sites increased with an increase in D50. Given the overlap in site occu- 220 mm, which is consistent with habitat SI, suggesting highest suit- pancy and average habitat associations of S. trutta and O. mykiss fry, ability (SI = 1) in cobble/rubble and boulder (particle size 250– differences in expected (Raleigh et al., 1984) and observed suitabilities 4000 mm) substrates and SI ≤ 0.13 in substrates classified as gravel or for O. mykiss may be a result of competitive exclusion from more suit- smaller (Raleigh et al., 1984). A similar effect was not observed with able habitat by S. trutta fry (Gatz et al., 1987), which are more abun- O. mykiss abundance, likely due to the smaller number of abundance dant. S. trutta densities increased in many of Colorado's rivers after estimation sites which contained a wide range of D50 values, depths the loss of O. mykiss populations to whirling disease (Nehring & and velocities that may have affected their suitability for O. mykiss fry. Thompson, 2001), with similar declines observed in several drainages Suitability for O. mykiss fry typically decreases in both sites that are in Montana (Baldwin et al., 1998; Granath Jr. et al., 2007). Mechanical shallower and have higher velocities (Raleigh et al., 1984), but the removal of S. trutta populations has been studied as a management authors found the opposite associations with depth and velocity in option for reintroducing or increasing O. mykiss populations in Colo- their study. Nonetheless, it is important to note that values for veloc- rado waters, with some locations showing greater success than others ity and depth were obtained independently (i.e., no interaction), so it (Fetherman et al., 2015; Fetherman et al., 2018). S. trutta population is unknown whether a combination of higher velocities and shallower manipulation has not been attempted in the upper Colorado River, depths would be beneficial for O. mykiss fry. Interactions were not and current management, O. mykiss fry stocking, has resulted in included in the model sets to prevent over-parameterization. Statisti- increased fry survival and recruitment (Fetherman & Schisler, 2017). cal relationships and habitat association inferences may have been Despite overlapping associations, the results suggest that there may stronger if the data set had been large enough to include interactions, be an opportunity to further increase O. mykiss fry survival through and the authors suggest incorporating interactions between habitat exclusion of S. trutta fry, which could be accomplished by incorporat- variables into future studies, if possible. ing higher velocities (>0.23 m s 1 ) and shallower depths (<0.17 m) O. mykiss fry habitat associations were especially apparent in sites into near-shore habitats during restoration. This is supported by the in which O. mykiss had been stocked, primarily because natural repro- higher O. mykiss vs. S. trutta abundances observed in shallower and duction in the upper Colorado River remains low (Fetherman et al., higher-velocity sites even though O. mykiss fry were less abundant 2014) and wild fry were more difficult to detect. It is probable, given overall throughout the study section. their genetics and history of domestication (Hedrick et al., 2003; Schisler Habitat associations for both S. trutta and O. mykiss fry were simi- et al., 2006), that stocked M. cerebralis–resistant fry act differently from lar to published SI for some habitat variables but differed for others. more wild-type fish and may exhibit different habitat associations than Habitat SI for S. trutta fry are highest (SI = 1.0) in gravel (particle size those previously described (Raleigh et al., 1984). O. mykiss fry stocking 2–64 mm) and lower (SI = 0.35) in cobble/rubble (particle size 64– shows promise for restoring O. mykiss populations reduced by whirling 250 mm) substrate types (Raleigh et al., 1986). Nonetheless, the disease (Avila et al., 2018; Fetherman et al., 2018) and will likely con- results suggest that S. trutta fry are more often associated with cob- tinue to be the primary management option for reestablishing or ble/rubble in the Colorado River and less so with gravel, although high enhancing O. mykiss populations in systems where M. cerebralis is counts were obtained from some gravel-dominated sites. The depth established. As such, understanding the habitat associations of stocked at which S. trutta numbers were highest is well shallower than that O. mykiss fry increases the knowledge of how these fish will interact considered optimal for S. trutta fry (0.40 m; Raleigh et al., 1986), with a novel lotic environment. The lack of clear habitat associations for although all of the sites were shallower than 0.40 m (SI < 0.19 for wild O. mykiss fry may also suggest that habitat restoration activities ini- depth across all sites). Velocity was within the optimal range (SI = 1) tially designed to increase the survival of stocked O. mykiss fry will not previously reported for S. trutta fry (Raleigh et al., 1986). Cover is also have detrimental effects on wild fry survival when these systems even- an important component in S. trutta fry habitat suitability (Raleigh tually become wild fry dominated and rely on stocking declines, espe- et al., 1986), with a maximum suitability when cover is greater cially because wild populations established using M. cerebralis–resistant than 10%. The presence of wood did not increase fry counts or abun- O. mykiss will have similar genetic backgrounds. dances for either species, although the percentage of the site occu- Overall, infection severity, as measured by myxospore count, did pied by wood was not quantified and could have been lower than not have an effect on the change in fry number between July and 10%, or wood may not have functioned as cover. S. trutta abundances October. Nonetheless, only those individuals more resistant to were lowest in one of the four sites that contained wood, but this site M. cerebralis are expected to be present in October (Fetherman et al., was also shallower with higher velocities that likely made the site less 2014), which may have resulted in the lack of an effect. Myxospore suitable for S. trutta fry. Temperature was within the optimal range count decreased with an increase in D50. T. tubifex worms prefer for both S. trutta and O. mykiss fry (Raleigh et al., 1984; Raleigh et al., sand/silt habitats with high organic matter (Granath Jr. & Gilbert, 1986); nonetheless, an effect of temperature was observed for both 2002), and releases of the waterborne infectious stage of the parasite, species. Overall, fry numbers were reduced in later sampling months triactinomyxons, from the worms likely drive salmonid infection sever- when temperatures were cooler, which has been observed previously ity (Hedrick & El-Matbouli, 2002; Kerans & Zale, 2002). As such, the (Fetherman et al., 2014) and is likely a result of life history (Chapman results suggest that including larger particle sizes in near-shore habi- & Bjornn, 1969; Mitro & Zale, 2002; Northcote, 1992). tats could decrease T. tubifex habitat and thereby infection severity, �FISH FETHERMAN AND AVILA 9 especially in O. mykiss fry. It is important to note, however, that habi- RE FE RE NCE S tat variables were collected within the fry sites only. Triactinomyxons Anderson, D. R. (2008). Model based inference in the life sciences: A primer on evidence. New York, NY: Springer. Avila, B. W. (2016). Survival of rainbow trout fry in the wild: a comparison of two whirling disease resistant strains (Masters thesis). Colorado State University library. Retrieved from http://hdl.handle.net/10217/ 178916. Avila, B. W., Winkelman, D. L., & Fetherman, E. R. (2018). Survival of whirling-disease-resistant rainbow trout fry in the wild: a comparison of two strains. Journal of Aquatic Animal Health, 30, 280–290. Baldwin, T. J., Peterson, J. E., McGhee, G. C., Staigmiller, K. D., Motteram, E. S., Downs, C. C., & Stanek, D. R. (1998). Distribution of Myxobolus cerebralis in salmonid fishes in Montana. Journal of Aquatic Animal Health, 10, 361–371. Burnham, K. P., & Anderson, D. R. (2002). Model selection and multimodel inference: A practical information-theoretic approach (2nd ed.). New York, NY: Springer-Verlag. Bustard, D. R., & Narver, D. W. (1975). Aspects of the winter ecology of juvenile Coho salmon (Oncorhynchus kisutch) and steelhead trout (Salmo gairdneri). Journal of the Fisheries Research Board of Canada, 32, 667–687. Casselman, J. M., & Lewis, C. A. (1996). Habitat requirements of northern pike (Esox lucius). Canadian Journal of Fisheries and Aquatic Sciences, 53(Suppl. 1), 161–174. Chapman, D. W., & Bjornn, T. C. (1969). Distribution of salmonids in streams with special references to food and feeding. In T. G. Northcote (Ed.), Symposium on Salmon and Trout in streams. H. R. MacMillan Lectures in Fisheries (pp. 153–176). University of British Columbia: Vancouver, British Columbia, Canada. Cramer, S. P., & Ackerman, N. K. (2009). Linking stream carrying capacity for salmonids to habitat features. American Fisheries Society Symposium, 71, 225–254. Cunjak, R. A. (1996). Winter habitat of selected stream fishes and potential impacts from land-use activity. Canadian Journal of Fisheries and Aquatic Sciences, 53(Suppl. 1), 267–282. Fetherman, E. R., & Schisler, G. J. (2016). Sport Fish Research Studies. Federal Aid Project F-394-R15. Federal Aid in Fish and Wildlife Restoration, Job Progress Report. Fort Collins, CO: Colorado Parks and Wildlife, Aquatic Wildlife Research Section. Fetherman, E. R., & Schisler, G. J. (2017). Sport Fish Research Studies. Federal Aid Project F-394-R16. Federal Aid in Fish and Wildlife Restoration, Job Progress Report. Fort Collins, CO: Colorado Parks and Wildlife, Aquatic Wildlife Research Section. Fetherman, E. R., Schisler, G. J., & Avila, B. W. (2018). Sport Fish Research Studies. Federal Aid Project F-394-R17. Federal Aid in Fish and Wildlife Restoration, Job Progress Report. Fort Collins, CO: Colorado Parks and Wildlife, Aquatic Wildlife Research Section. Fetherman, E. R., Winkelman, D. L., Baerwald, M. R., & Schisler, G. J. (2014). Survival and reproduction of Myxobolus cerebralis resistant rainbow trout in the Colorado River and increased survival of age-0 progeny. PLoS One, 9(5), e96954. Fetherman, E. R., Winkelman, D. L., Bailey, L. L., Schisler, G. J., & Davies, K. (2015). Brown trout removal effects on short-term survival and movement of Myxobolus cerebralis-resistant rainbow trout. Transactions of the American Fisheries Society, 144, 610–626. Fox, B. D., Bledsoe, B. P., Kolden, E., Kondratieff, M. C., & Myrick, C. A. (2016). Eco-hydraulic evaluation of a whitewater park as a fish passage barrier. Journal of the American Water Resources Association, 52(2), 420–442. Gatz, A. J., Sale, M. J., & Loar, J. M. (1987). Habitat shifts in rainbow trout: competitive influences of brown trout. Oecologia, 74, 7–19. Gido, K. B., Dodds, W. K., & Eberle, M. E. (2010). Retrospective analysis of fish community change during a half-century of landuse and streamflow changes. Journal of North American Benthological Society, 29(3), 970–987. are buoyant and distributed throughout the water column (Kerans & Zale, 2002). Therefore, additional upstream habitat manipulations, specifically increased particle sizes to reduce T. tubifex habitat and increased velocities to prevent sediment deposition, may be required to reduce the production of and contact with triactinomyxons in nearshore fry habitats. Habitat restoration activities continue to increase in large rivers (Roni et al., 2008; Vigmostad et al., 2005), including the upper Colorado River. Although many of these projects focus on improving juvenile and adult fish habitat (Roni, 2019; Roni et al., 2008), it is important to consider fry habitat and other ecosystem disturbances that may affect early life-stage survival during these activities as part of a broader biomic restoration approach (Johnson et al., 2020). In addition, restoration activities could be useful for either specific species or multispecies management, depending on the goals of the project. Current management in the Colorado River is focused on reestablishing O. mykiss, and the results suggest that there are opportunities for exclusion of S. trutta fry by adjusting design criteria based on differing habitat associations. Nonetheless, once O. mykiss are established, the goal will be to manage for both S. trutta and O. mykiss fry to provide diverse angling opportunities for Colorado anglers. The results suggest that a D50 of 151 mm (96–206 mm) will maximize fry number and abundance for both species, as will velocities ranging from 0.20 to 0.23 m s 1 and depths ranging from 0.17 to 0.18 m. Management strategies being used to (re)establish, maintain or enhance populations, e.g., stocking, should be considered as they may affect how salmonid fry associate with, distribute across and, ultimately, survive in near-shore habitats. In systems where pathogens, e.g., M. cerebralis, are established, the effects of habitat on the persistence of the pathogen life cycle should be considered for all primary-host susceptible life stages and species and incorporated into habitat restoration designs. Finally, the results show that factors such as interspecific competition, stocking and presence of pathogens can cause deviations in habitat associations from demonstrated SI and that evaluating system-specific differences may allow future habitat restoration activities to be more effective. ACKNOWLEDGEMEN TS The authors thank J. Ewert and C. Prince for help with data collection in the field; L. Gerk, A. Kraft and V. Vincent for their help with myxospore enumeration; and G. Wilcox for preparing the map of the upper Colorado River study reach. AUTHOR CONTRIBUTIONS E.R.F. assisted with data generation, data analysis and manuscript preparation. B.W.A. helped with concepts, data generation and manuscript preparation. 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How to cite this article: Fetherman, E. R., & Avila, B. W. (2021). Habitat associations of rainbow trout Oncorhynchus mykiss and brown trout Salmo trutta fry. Journal of Fish Biology, 1–11. https://doi.org/10.1111/jfb.14918 � Dublin Core The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/. Title A name given to the resource Journal Articles Description An account of the resource CPW peer-reviewed journal publications Text A resource consisting primarily of words for reading. Examples include books, letters, dissertations, poems, newspapers, articles, archives of mailing lists. Note that facsimiles or images of texts are still of the genre Text. Dublin Core The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/. Title A name given to the resource Habitat associations of rainbow trout Oncorhynchus mykiss and brown trout Salmo trutta fry Description An account of the resource <span>Habitat restoration activities continue to increase in large rivers, but many of these projects focus on improving juvenile or adult habitats. Incorporating the habitat associations of fry into restoration designs will allow for broader successes from restoration for all life stages and may be useful for either multispecies or specific-species management. This study investigated the habitat associations of rainbow trout </span><i>Oncorhynchus mykiss</i><span> and brown trout </span><i>Salmo trutta</i><span> fry in the upper Colorado River, focusing on the mean substrate size (</span><i>D</i>₅₀<span>), velocity (m s</span>⁻¹<span>), depth (m) and presence of wood in near-shore habitats. </span><i>S. trutta</i><span> and </span><i>O. mykiss</i><span> were found in higher numbers in fry sites with a </span><i>D</i>₅₀<span> of 151 mm (ranging from 96 to 206 mm), velocities ranging from 0.20 to 0.23 m s</span>⁻¹<span> and depths ranging from 0.17 to 0.18 m. Although there was considerable overlap in habitat associations between the two species, there may be opportunities for single-species management, if this is a goal of such restoration activities, by adjusting design criteria based on differing habitat associations. In addition, the results suggest that including larger particle sizes in near-shore habitats and upstream of fry sites could decrease </span><i>Tubifex tubifex</i><span> habitat and thereby fry infection severity by reducing exposure to </span><i>Myxobolus cerebralis</i><span>. Stocking, interspecific competition and/or the presence of pathogens can affect fry habitat associations and cause deviations from demonstrated suitability indices. As such, evaluating system-specific differences in habitat associations may allow future habitat restoration activities to be more effective.</span> Bibliographic Citation A bibliographic reference for the resource. Recommended practice is to include sufficient bibliographic detail to identify the resource as unambiguously as possible. <a href="https://doi.org/10.1111/jfb.14918" target="_blank" rel="noreferrer noopener">https://doi.org/10.1111/jfb.14918</a> Creator An entity primarily responsible for making the resource Fetherman, Eric R. Avila, Brian W. Subject The topic of the resource Brown trout Colorado River Habitat associations <em>Oncorhynchus mykiss</em> Rainbow trout <em>Salmo trutta</em> Extent The size or duration of the resource. 11 pages Date Created Date of creation of the resource. 2021-10-04 Rights Information about rights held in and over the resource <a href="http://rightsstatements.org/vocab/InC-NC/1.0/" target="_blank" rel="noreferrer noopener">In Copyright - Non-Commercial Use Permitted</a> Format The file format, physical medium, or dimensions of the resource application/pdf Language A language of the resource English Is Part Of A related resource in which the described resource is physically or logically included. Journal of Fish Biology Type The nature or genre of the resource Article