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2011-2016 Salmonid Redd Abundance and Juvenile Salmonid Spatial Structure in the Smith River Basin, California and Oregon
Abstract and Figures
We investigated two essential population viability metrics of salmonids over five consecutive years in the Smith River basin (Oregon and California), with ESA listed coho salmon as the focal species. First, we monitored adult salmonid escapement and distribution from 2011 to 2016 using live fish, carcass, and redd counts as defined in California's Coastal Salmonid Monitoring Plan. Second, we estimated the summer spatial structure of juvenile salmonids and adult coastal cutthroat trout annually from 2012 to 2016 using multiple-pass snorkel surveys in an occupancy modeling framework. We constructed separate sample frames for each monitoring component using a reproducible approach that relied on empirical and modeled stream habitat information. Each sample frame was divided into survey reaches resulting in 161.8 kilometers of stream habitat (68 reaches, 30 sub-reaches) for the adult sample frame and 298.1 kilometers (126 reaches, 40 sub-reaches) for the juvenile spatial structure sample frame. We estimate the adult sampling frame covered 78% of potential coho salmon spawning habitat and the juvenile sampling frame covered essentially all likely summer juvenile coho salmon rearing habitats. This report provides detailed results from the 2015-2016 survey effort not reported previously as well as five-year summaries spanning the length of this monitoring effort. This document is also supported by previously published reports offering greater detail on annual results (i.e. Garwood and Larson [2014], Garwood et al. [2014] and Walkley and Garwood [2015]). We completed 1896 spawning ground surveys across 87 survey reaches over the five years representing a sum total of 3346 kilometers surveyed. We made 1380 live adult coho salmon observations over the five years with annual observations ranging from 125 in 2015-2016 to 494 in 2013-2014. All but nine live coho salmon observations occurred in Mill Creek; eight observations were recorded in Rowdy Creek over three winters and one observation occurred in Hurdygurdy Creek during the 2013-2014 season. We recovered 196 coho salmon carcasses over the five years ranging from 15 in 2014-2015 to 82 in 2011-2012. All but five coho salmon carcasses were observed in Mill Creek; one carcass was found in Morrison Creek during the 2012-2013 season and four were found in Rowdy Creek during the 2013-2014 season. We were able to verify 293 individual coho salmon redds over the five seasons. All verified redds were found in the upper Mill Creek subbasin. Since our coho salmon observations were almost exclusively clustered in the Mill Creek, we determined that our redd population estimates for the whole sample frame were biased high and unreliable based largely on excessive between-reach error estimates. However, Chinook salmon and steelhead estimates were determined for the sample frame since these species were more evenly distributed throughout the basin. We estimated total coho salmon redd abundance annually in the Mill Creek subbasin which ranged from 149 (95% CI: 139-159) redds in 2014-2015 to 482 (95% CI: 464-501) redds in 2011-2012. Chinook salmon were far more abundant, with estimated redd abundances ranging from 516 in 2013-2014 to 3819 in 2011-2012. Our sampling did not cover the entire steelhead spawning season. However, we estimated steelhead redd abundance during our sampling period to range from 356 in 2013-2014 to 1120 in 2015-2016. Last, hatchery origin Chinook salmon and steelhead were observed spawning throughout much of the sampling frame over the five years, especially in Rowdy Creek and Mill Creek. The mean hatchery proportion of Chinook salmon carcasses ranged from 8.8% in tributaries below the Smith River forks to 32.9% in Rowdy Creek. No carcasses were observed above the forks. The mean hatchery proportion of live steelhead ranged from 5.3% below the forks to 28.6% in Rowdy Creek. No live hatchery steelhead were observed above the Smith River forks though sample sizes were small. We used multi-scaled occupancy models to estimate the probability of salmonid occupancy at the sample reach and at the sample unit (within reach) simultaneously while accounting for species detection probabilities. From 2012 to 2016 we completed a 323 reach surveys totaling 608 cumulative stream kilometers within the Smith River. We sampled 7254 pools over the five years with annual totals ranging from 1115 pools to 1837 pools. Only ten of the 167 reaches (6%) did not get surveyed at least once over the five-year period due a lack of access to a few private lands. We documented juvenile coho salmon occurring in 64 of the 157 (41%) individual reaches surveyed at least once over the five years. Annual reach-level occupancy estimates were numerically similar between years but declined annually from 0.42 in 2012 to 0.30 in 2016. Annual pool-level occupancy estimates ranged from 0.47 to 0.68. The annual estimated proportion of area occupied declined each year of the study from 0.29 in 2012 to 0.14 in 2016. The difference in PAO was most apparent between 2012 and 2016 with 2016 representing less than half of the estimated PAO in 2012. Coho salmon maintained patchy distributions relative to the sampling frame over the five years. Based on the summer distribution data collected throughout the basin, we describe five extant juvenile coho salmon patches. Four of the five patches are maintained by independent spawning sub-populations and we consider the lower mainstem Smith River and tributaries to be the only significant non-natal coho salmon rearing patch. Coho salmon juveniles used a variety of non-natal rearing habitats highlighting diversity in life-history and complementary resource needs. Last, in addition to coho salmon, we describe spatial structure estimates and detailed distributions of stream-type juvenile Chinook salmon, age zero and 1+ trout, and adult coastal cutthroat trout. Chinook salmon carcass observed on a spawner survey in Craigs Creek, South Fork Smith River. Photo: Zach Wenderott
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... Coho Salmon inhabiting the Smith River are part of the Southern Oregon/ Northern California Coast evolutionarily significant unit and are currently listed as threatened under the U.S. Endangered Species Act. The California Department of Fish and Wildlife (CDFW) uses UVC methods (i.e., snorkeling) to determine the spatial distribution of juvenile Coho Salmon in the Smith River each summer (Walkley and Garwood 2017), and we integrated eDNA collections into CDFW's preexisting survey protocols over two survey seasons (2020-2021). The detection capabilities estimated using the CDFW snorkeling surveys are very high (>0.9; ...
... Nearly all of the basin (98%) is within the Klamath and Siskiyou mountains. The Smith River is the largest freeflowing coastal river in California; there are no dams, and anadromous fishes have access to the entire basin (Garwood and Larson 2014;Walkley and Garwood 2017). ...
... During July and August of 2020 and 2021, eDNA sampling was conducted in conjunction with the annual UVC survey of the Smith River basin executed as part of the CDFW Coastal Salmonid Monitoring Program (Adams et al. 2011;Garwood and Ricker 2016;Walkley and Garwood 2017). For the UVC survey, sampling units of approximately 1-3 km in length (hereafter, "reaches") were selected using a generalized random tessellation stratified algorithm out of 166 total sampling units that represent all juvenile salmonid rearing habitat in the Smith River basin during summer base flow conditions ( Figure 1; Stevens and Olsen 2004;Garwood and Larson 2014). ...
Objective
This study compares the probability of detecting juvenile Coho Salmon Oncorhynchus kisutch using both environmental DNA (eDNA) techniques and underwater visual count (UVC) surveys in northern California rivers. Here, UVC surveys commonly have detection probabilities ( p ) surpassing 0.90, providing an ideal setting to examine the performance of newer eDNA methods. We also evaluate the potential for using eDNA concentrations to predict the count of Coho Salmon within pool habitats.
Methods
We conducted paired eDNA and UVC surveys in 96 pools across 25 stream reaches within the Smith River basin, California. Method‐specific p and the effect of environmental covariates were estimated using multiscale occupancy modeling. We used generalized linear models to evaluate the relationship of fish counts to eDNA concentrations and habitat covariates.
Result
The eDNA and UVC methods showed a high degree of agreement in detecting the presence of Coho Salmon within a pool (93% agreement) and survey reach (80% agreement). Detection probabilities for eDNA ( p eDNA ) and for UVC ( p UVC ) were similar and high at median levels of pool residual depth and contributing basin area ( p eDNA = 91%, p UVC = 89%). Contributing basin area (a proxy for discharge) had a strong, negative effect that was more pronounced for p eDNA than for p UVC (e.g., in the largest basins, p eDNA = 34% whereas p UVC = 77%). We did not find eDNA concentrations to be a good predictor of Coho Salmon counts in small pools.
Conclusion
This study demonstrates that eDNA methods yielded nearly identical results to UVC surveys in catchments <36 km ² and can provide a highly effective approach for determining the distribution of Coho Salmon. However, additional investigation is required before eDNA could be used to estimate relative abundance in small pools.
... The goal of this study was to compare eDNA and UVC surveys for monitoring the spatial distribution of naturally spawned juvenile coho salmon (Oncorhynchus (CDFW) uses UVC to determine the spatial distribution of juvenile coho salmon in the Smith River each summer (Walkley and Garwood 2017). I integrated eDNA collections into CDFW's pre-existing survey protocols over two survey seasons (2020-2021) for a robust comparison of eDNA and UVC methods. ...
... The Smith River basin encompasses 1,862 km 2 ranging from sea level to 1,954 m. Nearly all of the basin (98%) is within the Klamath-Siskiyou mountain ranges and has a rugged, complex topography with only 2% of the basin within the coastal plain (Walkley and Garwood 2017). The Smith River is the largest free-flowing coastal river in California providing unrestricted access for anadromous and resident salmonids (Garwood and Larson 2014). ...
... The number of pools to sample in a reach is also an important sampling consideration. Pool-level occupancy by juvenile coho salmon in this system has previously been estimated to be 0.47 (SE 0.02; Walkley and Garwood 2017); at this pool occupancy rate, surveying five pools within a reach for eDNA would yield a >95% cumulative probability of detecting coho salmon at the reach scale. However, additional work is still needed to develop an optimal eDNA sampling protocol for the Smith River survey that balances pool-level occupancy estimates and the downstream transportation of eDNA particles. ...
Environmental DNA (eDNA) has developed into a useful tool for determining the distribution of rare aquatic species, but relatively few studies have directly compared the detection probabilities of this method with other conventional survey techniques. These comparisons can inform which method may be better suited to address study objectives. In this study, the overall goal was to compare the ability of eDNA and underwater visual count (UVC) surveys to detect juvenile coho salmon (Oncorhynchus kisutch), a species of conservation concern at the southern extent of its geographic range. Specifically, I address two objectives: (1) compare the ability of eDNA and UVC surveys to detect coho salmon and the influence of environmental covariates on detectability and (2) evaluate the utility of eDNA concentrations and habitat covariates to predict the count of coho salmon within small pools. Water samples for eDNA analysis and snorkel surveys were conducted at 96 pools across 25 stream reaches in the Smith River basin, California. I used multi-scale occupancy models to estimate method-specific detection probabilities (p) and the effect of habitat covariates, including basin area (as a proxy for discharge), residual pool depth, and large woody debris. Results showed that eDNA and UVC surveys had a high degree of agreement in detecting the presence of coho salmon at both iii the pool scale (93% agreement) and reach scale (80% agreement), however there were several occasions where only one method detected coho salmon. The top occupancy model, identified using Akaike's information criterion, indicated that the detection probabilities were best predicted by method, basin area, residual pool depth, and an interaction between method and basin area. Under median habitat conditions, detection probabilities were similar and high for both methods (peDNA=91%, pUVC=89%). Residual pool depth had a slight positive effect on peDNA and pUVC. Detection probabilities for both methods were affected negatively by increasing basin size, but p declined more substantially for eDNA; at the highest basin areas, peDNA =40% compared to pUVC=78%. Finally, eDNA concentrations were a poor predictor of coho salmon count in small pools. The absence of a relationship between eDNA concentrations and fish counts is contrary to other studies and may have resulted as a consequence of the relatively small differences in counts observed between pools, which ranged from 0 to 210 individuals. Overall, this study illustrates that eDNA methods were as sensitive as UVC surveys for detecting coho presence under most conditions but could not be used to produce reliable estimates of the average observed count of the target species in this system. Therefore, these findings support the use of eDNA methods for monitoring the distributions of a rare species but indicate that implementation should be guided by study objectives and local environmental conditions. iv ACKNOWLEDGEMENTS
The downstream movement of coho salmon nomads (age 0), conventionally considered surplus fry, has been an accepted characteristic of juvenile coho salmon for the past 40 to 50 yr. The fate of these nomads, however, was not known and they were assumed to perish in the ocean. Several studies and observations have recently provided new insights into the fate of nomads and the role of the stream-estuary ecotone and estuary in developing this life history strategy that promotes coho resilience. Chinook and sockeye salmon have developed the ocean-type life-history strategy to exploit the higher productivity of the estuarine environment and migrate to the ocean at age 0. Nomad coho can acclimate to brackish water, and survive and grow well in the stream-estuary ecotone and estuary, but instead of migrating to the ocean they return upstream into freshwater to overwinter before migrating to the ocean as smolts. Nomads may enter the estuarine environment from natal or non-natal streams, rear there throughout the summer, and then emigrate to a non-natal stream for overwintering and smolting in the spring. These estuarine and overwintering habitats have enabled coho to develop this unique nomad life history strategy that may help to ensure their resilience. Restoring estuarine habitats may be essential to the recovery of depressed populations of coho.
State and federal agencies are tasked to recover Coho Salmon populations to a level where the risk of extinction is negligible. Thus, bold recovery actions and robust population monitoring programs are needed. This updated list of 542 Coho Salmon streams provides the best available synthesis of known historic and current Coho Salmon
distribution in the California portion of the SONCC ESU. These results have practical applications in designing monitoring, restoration, and recovery programs. Furthermore, these results can be used to compare future Coho Salmon stream distributions to the historic record. This is one of two companion reports covering the historic distribution of Coho Salmon and other aquatic species in found in Northern California coastal streams.
Pacific lampreys Entosphenus tridentatus (formerly Lampetra triden-tata) and western brook lampreys L. richardsoni are observed in many coastal Oregon basins; however, few data are available to adequately describe their distribution and spawning habitat associations. To document landscape-scale distribution and habitat use of spawning adult lampreys, we conducted biweekly redd surveys at 62 random-ly selected sites in Smith River (Umpqua basin, Oregon). Characteristics of lamprey habitat were measured at the redd, habitat unit, and reach scales to quantify available and occupied habitat. Pacific lampreys were found primarily in wider, low-elevation streams, whereas western brook lampreys were more widespread but concentrated in headwater and low-order streams. At the unit scale, unit type and dominant substrate were weakly correlated to presence of spawning lampreys. Both species spawned in gravel rich habitats, predominantly pool tail-outs and low gradient riffles. This study infers habitat associations and broad-scale distribution within a coastal basin to assist in the design of monitoring strategies and population assessments at a regional scale.
Patterns of salmon distribution throughout a riverscape may be expected to change over time in response to environmental conditions and population sizes. Changing patterns of use, including identification of consistently occupied locations, are informative for conservation and recovery planning. We explored interannual patterns of distribution by juvenile Coho Salmon Oncorhynchus kisutch, in 11 subbasins on the mid-coast of Oregon, USA. We found that juvenile Coho Salmon distribution expanded and contracted around stream sections that were continuously occupied (core areas). Timing of expansion or contraction was synchronous among subbasins and appeared to be related to the size of the parental spawning run. Juvenile distribution expanded from core areas when adults were abundant and contracted into core areas at lower adult abundances. The “intrinsic potential” of stream sections to support high quality habitat for Coho Salmon also appeared to inform distribution patterns. In most subbasins, when populations expanded, they moved into areas of high intrinsic potential. We identified areas that were consistently used by juvenile Coho Salmon which may be important target locations for conservation and restoration. Our study contributes to the body of work that seeks to explain the processes behind spatial and temporal patterns of freshwater habitat use by salmonids in the Pacific Northwest, thereby enhancing understanding of the complexity of biological and environmental interactions over broad scales.
Traditional approaches to the study of fragmented landscapes invoke an island‐ocean model and assume that the nonhabitat matrix surrounding remnant patches is uniform. Patch isolation, a crucial parameter to the predictions of island biogeography and metapopulation theories, is measured by distance alone. To test whether the type of interpatch matrix can contribute significantly to patch isolation, I conducted a mark‐recapture study on a butterfly community inhabiting meadows in a naturally patchy landscape. I used maximum likelihood to estimate the relative resistances of the two major matrix types (willow thicket and conifer forest) to butterfly movement between meadow patches. For four of the six butterfly taxa (subfamilies or tribes) studied, conifer was 3–12 times more resistant than willow. For the two remaining taxa (the most vagile and least vagile in the community), resistance estimates for willow and conifer were not significantly different, indicating that responses to matrix differ even among closely related species. These results suggest that the surrounding matrix can significantly influence the “effective isolation” of habitat patches, rendering them more or less isolated than simple distance or classic models would indicate. Modification of the matrix may provide opportunities for reducing patch isolation and thus the extinction risk of populations in fragmented landscapes.
Consideration of fundamental channel processes, together with map-based and field investigations, indicates that stream channel type influences salmonid spawning distributions across entire channel networks and salmonid abundance within channel reaches. Our analysis suggests that salmonid spawning patterns in mountain drainage basins of the Pacific Northwest are adapted to, among other things, the timing and depth of channel bed mobility. We hypothesize that because the bed of pool-riffle and plane-bed reaches scours to a variable fraction of the thickness of alluvium, survival to emergence is favored by either burying eggs below the annual scour depth or avoiding egg burial during times of likely bed mobility. Conversely, annual mobility of all available spawning gravel in steeper step-pool and cascade channels favors either adaptations that avoid egg burial during times of likely bed mobility or selection of protected microhabitats. Consistent with these expectations, we find that salmonid spawning distributions track channel slope distributions in several west-slope Pacific Northwest watersheds, implying that spatial differences in channel processes influence community structure in these rainfall-dominated drainage basins. More detailed field surveys confirm that different channel types host differential use by spawning salmonids and reveal finer-scale influences of pool spacing on salmonid abundance.