Shaun Clements

Optimization of an Acoustic Telemetry Array for Detecting Transmitter-Implanted Fish

Abstract The development of miniature acoustic transmitters and economical, robust automated receivers has enabled researchers to study the movement patterns and survival of teleosts in estuarine and ocean environments, including many species and age-classes that were previously considered too small for implantation. During 2001–2003, we optimized a receiver mooring system to minimize gear and data loss in areas where current action or wave action and acoustic noise are high. In addition, we conducted extensive tests to determine (1) the performance of a transmitter and receiver (Vemco, Ltd.) that are widely used, particularly in North America and Europe and (2) the optimal placement of receivers for recording the passage of fish past a point in a linear-flow environment. Our results suggest that in most locations the mooring system performs well with little loss of data; however, boat traffic remains a concern due to entanglement with the mooring system. We also found that the reception efficiency of the...

Survival of migrating salmon smolts in large rivers with and without dams.

The mortality of salmon smolts during their migration out of freshwater and into the ocean has been difficult to measure. In the Columbia River, which has an extensive network of hydroelectric dams, the decline in abundance of adult salmon returning from the ocean since the late 1970s has been ascribed in large measure to the presence of the dams, although the completion of the hydropower system occurred at the same time as large-scale shifts in ocean climate, as measured by climate indices such as the Pacific Decadal Oscillation. We measured the survival of salmon smolts during their migration to sea using elements of the large-scale acoustic telemetry system, the Pacific Ocean Shelf Tracking (POST) array. Survival measurements using acoustic tags were comparable to those obtained independently using the Passive Integrated Transponder (PIT) tag system, which is operational at Columbia and Snake River dams. Because the technology underlying the POST array works in both freshwater and the ocean, it is therefore possible to extend the measurement of survival to large rivers lacking dams, such as the Fraser, and to also extend the measurement of survival to the lower Columbia River and estuary, where there are no dams. Of particular note, survival during the downstream migration of at least some endangered Columbia and Snake River Chinook and steelhead stocks appears to be as high or higher than that of the same species migrating out of the Fraser River in Canada, which lacks dams. Equally surprising, smolt survival during migration through the hydrosystem, when scaled by either the time or distance migrated, is higher than in the lower Columbia River and estuary where dams are absent. Our results raise important questions regarding the factors that are preventing the recovery of salmon stocks in the Columbia and the future health of stocks in the Fraser River.

Effects of Transportation and Other Factors on Survival Estimates of Juvenile Salmonids in the Unimpounded Lower Columbia River

Abstract We estimated the survival of juvenile salmonids out-migrating through the lower Columbia River to the Pacific Ocean. We tested the null hypotheses that no association exists between survival and transportation type (including barge transportation and in-river migration with no transportation), release date, river flow, mean body weight, and tag type. During 2002-2004, spring-summer (SS) and fall Chinook salmon Oncorhynchus tshawytscha and steelhead O. mykiss were implanted with uniquely coded radio or acoustic transmitter tags and released during the early, middle, and late out-migration periods. A series of receiver lines were used to detect these fish and estimate survival. Estimated survival varied considerably with transportation type and release date for fall Chinook salmon and steelhead, but the results were dependent upon year. Estimated survival between the lowermost dam (Bonneville Dam) and the upper estuary (river kilometer 46) was relatively high for SS Chinook salmon and steelhead, wh...

Characterization of the Physiological Stress Response in Lingcod

Abstract The goal of this study was to describe the duration and magnitude of the physiological stress response in lingcod Ophiodon elongatus after exposure to brief handling and sublethal air stressors. The response to these stressors was determined during a 24-h recovery period by measuring concentrations of plasma cortisol, lactate, glucose, sodium, and potassium. Lingcod were subjected to brief handling followed by either a 15-min or a 45-min air stressor in the laboratory. After the 15-min stressor, an increase in cortisol or glucose could not be detected until after 5 min of recovery. Peak concentrations were measured after 30 min for cortisol and after 60 min for glucose and lactate. Glucose and lactate had returned to basal levels after 12 h, whereas cortisol did not return to basal levels until after 24 h of recovery. Immediately following a 45-min air stressor, all measured parameters were significantly elevated over levels in prestressor control fish. Cortisol concentrations tended to increase ...

Comparison of three methods for marking a small floodplain minnow

BackgroundEvaluation of the movement patterns of small-bodied fish is often hindered by the lack of a suitable long-term mark. We evaluated several techniques for long-term group and individual identification of adult (40–70 mm total length [TL]) Oregon chub (Oregonichthys crameri). We marked Oregon chub with one of two different sized passive integrated transponder (PIT) tags (a 9 × 2.12 mm, 0.067 g PIT tag [PIT-tag] or a 8.4 × 1.4 mm, 0.033 g PIT tag [PICO-tag]), a red visible implant elastomer (VIE) tag, or a freeze brand. We monitored survival, tag retention, and mark quality over 150 days. In addition, we assessed the minimum length and weight thresholds to achieve 80% and 90% survival of PIT-tagged fish.ResultsMarking with a freeze brand, PICO-tag, or VIE tag had no effect on survival (P >0.05). In contrast, marking with a PIT-tag was associated with significantly lower (P <0.05) survival than in the control group. Survival was significantly higher (P = 0.002) for fish implanted with a PICO-tag than with the larger PIT-tag.The initial minimum TL for 80% and 90% survival was 54 mm and 64 mm TL, respectively, for the PIT-tag treatment. The 90% survival threshold for PICO-tagged fish was 44 mm TL. The 80% survival threshold was outside the range of sizes used in our experiment (<40 mm TL). Similarly, the 80% and 90% survival weight thresholds for the PIT-tag treatment were 1.5 g and 2.4 g, respectively, and the 90% survival threshold for PICO-tagged fish was 0.9 g.Tag retention was 94% and 95% in the PIT-tag and PICO-tag treatments, respectively; 80% of the freeze branded fish had easily recognizable tags after 150 days and 88% of the fish marked with VIE had easily recognizable tags after 150 days.ConclusionsPICO-tags, VIE marks, and freeze brands are all feasible long-term marking techniques for Oregon chub with negligible effects on survival through 150 days. The selection of a particular technique should be based on the study design and objectives (e.g., individual versus group identification), cost, ease, speed of tagging, and survival.

An Evaluation of the Efficiency of Minnow Traps for Estimating the Abundance of Minnows in Desert Spring Systems

AbstractDesert springs are sensitive aquatic ecosystems that pose unique challenges to natural resource managers and researchers. Among the most important of these is the need to accurately quantify population parameters for resident fish, particularly when the species are of special conservation concern. We evaluated the efficiency of baited minnow traps for estimating the abundance of two at-risk species, Foskett Speckled Dace Rhinichthys osculus ssp. and Borax Lake Chub Gila boraxobius, in desert spring systems in southeastern Oregon. We evaluated alternative sample designs using simulation and found that capture–recapture designs with four capture occasions would maximize the accuracy of estimates and minimize fish handling. We implemented the design and estimated capture and recapture probabilities using the Huggins closed-capture estimator. Trap capture probabilities averaged 23% and 26% for Foskett Speckled Dace and Borax Lake Chub, respectively, but differed substantially among sample locations, t...

Effect of Commercially Available Egg Cures on the Survival of Juvenile Salmonids

There is some concern that incidental consumption of eggs cured with commercially available cures for the purpose of sport fishing causes mortality in juvenile salmon. We evaluated this by feeding juvenile spring Chinook (Oncorhynchus tshawytscha) and steelhead (O. mykiss) with eggs cured with one of five commercially available cures. We observed significant levels of mortality in both pre-smolts and smolts. Depending on the experiment, 2, 3, or 4 of the cures were associated with mortality. Mortality tended to be higher in the smolts than in the parr, but there was no clear species effect. The majority of mortality occurred within the first 10 d of feeding. Removal of sodium sulfite from the cure significantly reduced the level of mortality. Soaking the eggs prior to feeding did not reduce mortality. We observed a clear relationship between the amount of cured egg consumed each day and the survival time. We conclude that consumption of eggs cured with sodium sulfite has the potential to cause mortality in juvenile steelhead and Chinook salmon in the wild.

Distribution and Abundance of Millicoma Dace In the Coos River Basin, Oregon

Abstract The Millicoma Dace Rhinichthys cataractae is a form of Longnose Dace endemic to the Coos River drainage in southwestern Oregon. Sparse species records in the Oregon State University Ichthyology Collection and database and infrequent recent encounters prompted surveys to assess the current status and distribution of the species. In 2014, we surveyed locations that had historically supported Millicoma Dace using backpack electrofishing to describe their current distribution and abundance at these locations. In 2015, we extended these surveys further upstream in the South Coos River basin, outside of the documented historical range. We used an N-mixture model to estimate abundance and capture probability for Millicoma Dace at each sampling location. We evaluated the effects of habitat covariates on both capture probability and abundance at each sample site. We found Millicoma Dace were widespread throughout their historical range and in the South Coos River sites outside of their documented historical range. We only found Millicoma Dace associated with native fishes; we did not collect any nonnative fish during our surveys. We collected Millicoma Dace exclusively from swift-water habitats, which were relatively uncommon in the basin, and found them typically associated with cobble or boulder substrates. Millicoma Dace were most abundant in the South Fork Coos and West Fork Millicoma River subbasins. We estimated capture probabilities for Millicoma Dace ranging from 9% when substrate was dominated by bedrock to 28% when substrate was dominated by cobble or gravel. Abundance estimates ranged from 1 to 560 dace per sampling location with a total estimated abundance (sum of site estimates) of over 3200 dace for the sites we sampled.

Status, Distribution, and Movement of the Warner Sucker in the Desert of Southeastern Oregon

Abstract Warner Sucker (Catostomus warnerensis), endemic to the lakes and tributaries of the Warner basin, southeastern Oregon, USA, was listed as threatened by the US Fish and Wildlife Service in 1985 because of habitat fragmentation and threats from introduced nonnative fish. To determine progress towards recovery and document factors that may prevent recovery, we evaluated the distribution, abundance, and movements of this species between 2006 and 2013. The species exhibits 2 distinct life-history types, a lake morph and a stream morph. The abundance of suckers in the Warner Valley lakes has decreased since the mid-1990s, and the lake fish assemblages were dominated by nonnative predatory fishes. The basin experienced drought conditions from 2007 through 2010, and the lakes partially dried which affected both sucker distribution and movement. During the drought, when lake levels were low and receding, we found little evidence of sucker recruitment in the lake populations. In 2011, stream discharge was high and the lakes refilled, and in 2012 we documented successful sucker recruitment. Warner Suckers in the tributaries were widely distributed and relatively abundant, and the stream habitat was in good condition. We did not document substantial downstream movement of suckers during the spring and summer months and found little evidence of mixing between the stream and lake populations. We documented the upstream movement of large numbers of suckers in 2 tributary streams during the spawning season. We also described associations between sucker distribution and habitat characteristics in the tributaries. Our analysis indicated support for the threatened listing and suggests that recovery efforts would be most effective by focusing on improvements to both upstream and downstream passage at irrigation diversion dams and on irrigation efficiencies.

Designing a Monitoring Program to Estimate Estuarine Survival of Anadromous Salmon Smolts: Simulating the Effect of Sample Design on Inference

A number of researchers have attempted to estimate salmonid smolt survival during outmigration through an estuary. However, it is currently unclear how the design of such studies influences the accuracy and precision of survival estimates. In this simulation study we consider four patterns of smolt survival probability in the estuary, and test the performance of several different sampling strategies for estimating estuarine survival assuming perfect detection. The four survival probability patterns each incorporate a systematic component (constant, linearly increasing, increasing and then decreasing, and two pulses) and a random component to reflect daily fluctuations in survival probability. Generally, spreading sampling effort (tagging) across the season resulted in more accurate estimates of survival. All sampling designs in this simulation tended to under-estimate the variation in the survival estimates because seasonal and daily variation in survival probability are not incorporated in the estimation procedure. This under-estimation results in poorer performance of estimates from larger samples. Thus, tagging more fish may not result in better estimates of survival if important components of variation are not accounted for. The results of our simulation incorporate survival probabilities and run distribution data from previous studies to help illustrate the tradeoffs among sampling strategies in terms of the number of tags needed and distribution of tagging effort. This information will assist researchers in developing improved monitoring programs and encourage discussion regarding issues that should be addressed prior to implementation of any telemetry-based monitoring plan. We believe implementation of an effective estuary survival monitoring program will strengthen the robustness of life cycle models used in recovery plans by providing missing data on where and how much mortality occurs in the riverine and estuarine portions of smolt migration. These data could result in better informed management decisions and assist in guidance for more effective estuarine restoration projects.