2017
Permanent URI for this collectionhttps://hdl.handle.net/1807/75486
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Item Fishery collapse, recovery, and the cryptic decline of wild salmon on a major California river.(Canadian Science Publishing, 2017-11-20) Willmes, Malte; Hobbs, James A.; Sturrock, Anna M.; Bess, Zachary; Lewis, Levi S; Glessner, Justin J.G.; Johnson, Rachel C; Kurth, Ryon; Kindopp, JasonFall-run Chinook salmon (Oncorhynchus tshawytscha) from the Sacramento-San Joaquin River system form the backbone of Californiaâ s salmon fishery and are heavily subsidized through hatchery production. Identifying temporal trends in the relative contribution of hatchery- versus wild-spawned salmon is vital for assessing the status and resiliency of wild salmon populations. Here, we reconstructed the proportion of hatchery fish on natural spawning grounds in the Feather River, a major tributary to the Sacramento River, using strontium isotope (87Sr/86Sr) ratios of otoliths collected during carcass surveys from 2002-2010. Our results show that prior to the 2007-2008 salmon stock collapse 55-67% of in-river spawners were of hatchery origin; however, hatchery contributions increased drastically (89%) in 2010 following the collapse. Data from a recent hatchery marking program corroborate our results, showing that hatchery fish continued to dominate (~90%) in 2011-2012. Though the rebound in abundance of salmon in the Feather River suggests recovery of the stock post-collapse, our otolith chemistry data document a persistent decline of wild spawners, likely leading to the erosion of locally-adapted Feather River salmon populations.Item Models to predict total phosphorus concentrations in coastal embayments of eastern Georgian Bay, Lake Huron(Canadian Science Publishing, 2017-12-09) Campbell, Stuart D; Chow-Fraser, PatriciaSeveral coastal embayments of eastern Georgian Bay show signs of water-quality impairment thought to be caused by human activities. Here, we evaluate the ability of the Lakeshore Capacity Model (LCM), developed for Precambrian Shield lakes, to assess the impact of cottage development on the trophic status of ten Georgian Bay embayments. The LCM could only be applied to eight embayments due to the large size and complexity of two watersheds, and produced unacceptably high estimates of mean seasonal total phosphorus ([TP]) concentrations (exceeded 20% of measured values for five of eight embayments); accuracy of [TP] estimates could not be improved by accounting for internal phosphorus loading. We developed an additional model, the Anthro-Geomorphic Model (AGM), which uses building density and basin morphometry as variables. Estimates of [TP] for the AGM were within 20% of measured values for all sites. Compared with other aquatic systems, coastal embayments of Georgian Bay have significantly higher chlorophyll-a concentrations per unit [TP]; we suggest that the TP-CHL relationship presented in this study be used to estimate productivity in these systems.Item Fishing on floating objects (FOBs): How French tropical tuna purse seiners split fishing effort between GPS-monitored and unmonitored FOBs(Canadian Science Publishing, 2017-12-31) Snouck-Hurgronje, Julia Eleanor; Kaplan, David M.; Chassot, Emmanuel; Maufroy, Alexandra; Gaertner, DanielFishing on floating objects (FOBs) dominates catch in tropical tuna purse seine fisheries. One frequently cited advantage of deploying GPS-monitored FOBs is that the position information can be used for directed fishing to reduce search time for tuna. However, purse seiners also fish on foreign objects for which position information is not available. It is critical to quantify the prevalence of fishing on GPS-monitored versus unmonitored FOBS in order to understand how they impact fishing effort and catch per unit effort (CPUE). We analyzed French commercial, observer, and FOB trajectory data in the Atlantic and Indian oceans to determine how often purse seine vessels fish on GPS-monitored FOBs. Only 2.7-20.4% of French FOB fishing sets over 2007-2013 in both oceans were made on GPS-monitored FOBs. Though increasing over time, the low percentage suggests that French vessels do not primarily use GPS-monitored FOBs to reduce search time for tuna. We hypothesize that fishery-wide FOB deployments have important collective consequences for overall fishing effort, and recommend that future effort metrics should be based on fishery-wide FOB activities.Item Habitat suitability modeling based on a spatio-temporal model: an example for Cusk in the Gulf of Maine(Canadian Science Publishing, 2017-11-20) Runnebaum, Jocelyn; Guan, Lisha; Cao, Jie; O'Brien, Loretta; Chen, YongHabitat use and distribution is a critical aspect in the management and conservation of a species, particularly for those in decline. Habitat suitability indices (HSI) are a common method of habitat mapping dependent on empirical data that can easily lead to misunderstanding the spatio-temporal dynamics of marine species experiencing population decline and density-dependent catchability within surveys. This is especially true when only a single monitoring program with limited spatio-temporal coverage is used. A delta-GLMM was used to combine trawl and longline surveys to predict density estimates for Cusk (Brosme brosme) in un-sampled locations for use in HSIs. Catchability was estimated for longline and trawl gear without having an estimate of area fished for the longline survey. HSIs performed better using model-based density estimates from multiple surveys compared to sample-based abundance indices from a single survey. The increased spatial resolution can better inform the HSIs by providing information where the survey programs did not sample. This study provides a novel approach for integrating data from different monitoring programs for habitat modeling.Item Acoustic Telemetry Observation Systems: challenges encountered and overcome in the Laurentian Great Lakes(Canadian Science Publishing, 2017-12-17) Krueger, Charles C.; Holbrook, Christopher M.; Binder, Thomas R.; Vandergoot, Christopher S; Hayden, Todd A; Hondorp, Darryl W; Nate, Nancy; Paige, Kelli; Riley, Stephen C.; Fisk, Aaron T; Cooke, Steven JThe Great Lakes Acoustic Telemetry Observation System (GLATOS), organized in 2012, aims to advance and improve conservation and management of Great Lakes fishes by providing information on behavior, habitat use, and population dynamics. GLATOS faced challenges during establishment, including a funding agency-imposed urgency to initiate projects, a lack of telemetry expertise, and managing a flood of data. GLATOS now connects 190+ investigators, provides project consultation, maintains a web-based data portal, contributes data to Ocean Tracking Networkâ s global database, loans equipment, and promotes science transfer to managers. The GLATOS database currently has 50+ projects, 39 species tagged, 8,000+ fish released, and 150+ million tag detections. Lessons learned include: 1) seek advice from others experienced in telemetry; 2) organize networks prior to when urgent needs to share data exist; 3) establish a data management system so that all receivers can contribute to every project; 4) hold annual meetings to foster relationships, 5) involve fish managers to ensure relevancy, and 6) staff require full-time commitment to lead and coordinate projects, and to analyze data and publish results.Item Nutritional correlates of spatio-temporal variations in the marine habitat use of brown trout, Salmo trutta, veteran migrants(Canadian Science Publishing, 2017-12-17) Bordeleau, Xavier; Davidsen, Jan Grimsrud; Eldøy, Sindre Håvarstein; Sjursen, Aslak Darre; Whoriskey, Frederick G.; Crossin, Glenn T.The brown trout (Salmo trutta) is an iteroparous, anadromous salmonid that exhibits a complex continuum of feeding migration tactics, ranging from freshwater residency, to potamodromy, to estuarine migration, as well as short-to-long distance coastal migrations. While anadromous migrants are believed to play an important role in the speciesâ population dynamics, little is known about the factors driving differences in the extent of individual marine habitat use. In this study, 32 brown trout veteran migrants were acoustically tagged prior to their seaward migration and sampled for indices of their nutritional state. Our findings suggest that: i. body condition factor differed amongst fish adopting different migratory tactics, with outer-fjord migrant being in poorer condition; and ii. within migratory groups, plasma triglyceride concentration was negatively correlated with the duration of marine residency. Results support the idea of condition-dependent migration in veteran migrants, with individual variation in nutritional state influencing the spatio-temporal aspects of marine habitat use. Furthermore, overall marine minimum survival during the summer feeding migration was 86%, the highest reported estimate for this life-stage.Item Investigating trade-offs in alternative catch-share systems: an individual-based bio-economic model applied to the Bay of Biscay sole fishery(Canadian Science Publishing, 2017-12-16) Bellanger, Manuel; Macher, Claire; Merzéréaud, Mathieu; Guyader, Olivier; Le Grand, ChristelleAn individual-based bio-economic model (IAM) is presented and applied to the Bay of Biscay sole fishery to investigate alternative quota management systems from a multi-criteria perspective. For this study, the model integrates several institutional arrangements related to catch share management. The current French co-management system with non-transferability of quota is compared to an alternative ITQ system in a context of transition to maximum sustainable yield (MSY). Trade-offs between ecological and socio-economic impacts are highlighted and the effectiveness of governance scenarios is discussed in regard to the challenge of capacity adjustment. Results emphasize that the introduction of ITQ is expected to reduce by 40% the number of vessels in the fishery. While effectively mitigating the economic impacts of the transition phase to MSY, ITQs are also expected to significantly increase the fishing effort by trawlers, which may cause ecological concerns. The scenarios tested also include the simulation of a decommissioning scheme where subsequent decommissioned vessels are significantly different from the vessels that would lease out their quotas in an ITQ system, resulting in differentiated ecological and socio-economic impacts between scenarios.Item Early back-calculated size-at-age of Atlantic yellow eels sampled along ecological gradients in the Gironde and St. Lawrence hydrographical systems(Canadian Science Publishing, 2017-08-09) Patey, Géraldine; Couillard, Catherine M.; Drouineau, Hilaire; Verreault, Guy; Pierron, Fabien; Lambert, Patrick; Baudrimont, Magalie; Couture, PatriceAn international sampling program investigating the causes of the decline of American eels (Anguilla rostrata) and European eels (Anguilla anguilla) in the St. Lawrence (Canada) and Gironde (France) rivers systems provided the opportunity to compare early growth of eels of each species among habitats using back-calculated sizeâ at-age from 1 to 5 years old. Our study supports previous studies showing that the early back-calculated lengths of A. anguilla were higher in downstream and more saline Gironde system habitats than in the upstream fluvial section, and provides a new indication that length at 1-year-old is twice higher than that reported 10 years earlier. However, our data contradict the current paradigm for A. rostrata by providing evidence that early size-at-age of eels from the upstream St. Lawrence system, most distant from the spawning area, exceeds those of eels sampled downstream, at less distant sites in the estuarine section. Overall these observations are consistent with the hypothesis that the observed spatial variations in early growth rate of yellow eels sampled in the St. Lawrence and Gironde systems are the consequence of processes occurring in the first year of age such as genetic selection and/or genetically-dependent habitat choice.Item Seabird diets as bioindicators of Atlantic herring recruitment and stock size: a new tool for ecosystem-based fisheries management(Canadian Science Publishing, 2017-09-10) Scopel, Lauren C.; Diamond, Antony W.; Kress, Stephen W; Hards, Adrian R.; Shannon, PaulaEcosystem-based fishery management requires understanding of relationships between exploited fish and their predators, such as seabirds. We used exploratory regression analyses to model relationships between Atlantic herring (Clupea harengus) in the diet of seabird chicks at nine nesting colonies in the Gulf of Maine, and four types of fishery- and survey-derived herring data. We found several strong relationships, which suggests spatial structuring in herring stocks and likely patterns of herring movements before they recruit into the fishery. Some types of herring data seldom used in stock assessments â notably acoustic surveys, fixed-gear landings, and weight-at-age â correlated as strongly with seabird data as more commonly used series, such as mobile-gear landings and modeled spawning stock biomass. Seabird chick diets collected at specific locations thus offer a promising means to assess the size, distribution, and abundance of juvenile herring across a broad area prior to recruitment, which is a major source of uncertainty in fisheries. Common terns showed the most potential as a bioindicator, correlating well and showing consistent spatial patterns with 11 of 13 fishery data series.Item Genome-wide divergence patterns support fine-scaled genetic structuring associated with migration tendency in brown trout(Canadian Science Publishing, 2017-12-17) Lemopoulos, Alexandre; Uusi-Heikkilä, Silva; Vasemägi, Anti; Huusko, Ari; Kokko, Harri; Vainikka, AnssiBrown trout Salmo trutta exhibit highly diverse life histories varying from resident, slow-growing and early maturing to migratory, fast-growing and late maturing even within single watersheds. We sampled eleven locations within the transboundary Finnish-Russian River Koutajoki watershed to evaluate genomic differences among main stem and headwater sites of which some are isolated by migration barriers. Restriction site associated sequencing (RADSeq) revealed that the most headwater localities supported unique, isolated populations with generally lower heterozygosity compared to the main stem populations. The sampled migratory adults in the three main stems showed signals of admixture despite small but statistically significant genetic divergence while the headwater populations, except for two, showed high level of divergence and a lack of admixture. These results suggest that most of the headwater populations consist of resident brown trout, and that the population genetic structuring is often maintained even in the absence of migration barriers. Our results have clear implications for fisheries management and conservation: each brown trout subpopulation represents an evolutionarily important unit with unique genetic make-up and life history variation.Item Fish egg predation by Baltic sprat and herring: do species characteristics and development stage matter?(Canadian Science Publishing, 2017-12-01) Neumann, Viola; Köster, Friedrich W.; Eero, MargitPredation of eggs by clupeids has been identified as a major factor contributing to early life stage mortality of Baltic cod. We used data from ichthyoplankton sampling and clupeid stomach analyses to investigate whether eggs of other fish species are to a similar extent subject to predation, and how predation pressure differs between egg development stages. Cod, sprat and rockling eggs dominated in the ichthyoplankton fraction in herring and sprat diet, whereas flounder and dab eggs occurred only occasionally. In spring, cod eggs at advanced development stages were positively and sprat eggs generally negatively selected by both predators, while fish eggs were non-selectively consumed in summer. Predation is suggested to account for a large fraction of mortality of cod eggs at older stages, i.e. those eggs, which have survived the often detrimentally low oxygen concentration in and below the permanent halocline. The consumption rates of sprat eggs at all development stages relative to production rates were considerably lower compared to cod, suggesting that egg predation is of lesser importance for sprat recruitment.Item Sampling the stream landscape: improving the applicability of an ecoregion-level capture probability model for stream fishes(Canadian Science Publishing, 2017-11-30) Mollenhauer, Robert; Mouser, Joshua; Brewer, Shannon KThe dynamic nature of the stream landscape can result in considerably variable stream-fish capture probability (i.e., the proportion of individuals identified) across space and time. We modeled tow-barge electrofishing capture probability at multiple spatial scales for nine Ozark Highland stream fishes. In addition to fish size, we identified seven reach-scale environmental characteristics associated with variable capture probability: stream discharge, water depth, conductivity, water clarity, emergent vegetation, wetted width-depth ratio, and proportion of riffle habitat. The magnitude of the relationship between capture probability and both discharge and depth varied among stream fishes. We also identified lithological characteristics among stream segments as a coarse-scale source of variable capture probability. The resulting capture probability model can be used to adjust catch data and derive reach-scale absolute abundance estimates across a wide range of sampling conditions with similar effort as used in more traditional fisheries surveys (i.e., catch-per-unit effort). Adjusting catch data based on variable capture probability improves the comparability of datasets, thus promoting both well-informed conservation and management decisions and advances in stream-fish ecology.Item Structural uncertainty in qualitative models for ecosystem-based management of Georges Bank(Canadian Science Publishing, 2017-12-01) Wildermuth, Robert P; Fay, Gavin; Gaichas, SarahQuantitative models for marine ecosystem-based management are often constrained by availability of observations. Uncertainty about the underlying system structure can affect model estimates and conclusions about the consequences of management actions. Qualitative models can augment model development for decision-making and may provide an alternative to quantitative assessments. We apply qualitative loop analysis to assess the sensitivity of management outcomes to structural uncertainty within the Georges Bank social-ecological system. Loop analysis uses defined positive or negative relationships between system components to provide inference about cascading effects of pressures on components of management interest. We compare the sensitivity of outcomes from two management strategies in four model structures of the Georges Bank system that investigate trophic and socioeconomic model uncertainty. We summarize system responses to perturbation and compare these responses to a set of management objectives. Models with complex socioeconomic structure estimated positive outcomes more often but with less reliability than simpler models. Our analyses demonstrated tradeoffs among habitat objectives for two management strategies, as well as uncertainty about the reliability of outcomes, contingent on model structure.Item Identification of a single genomic region associated with seasonal river return timing in adult Scottish Atlantic salmon (Salmo salar L.) identified using a genome-wide association study.(Canadian Science Publishing, 2017-10-29) Cauwelier, Eef; Gilbey, John; Sampayo, James; Stradmeyer, Lee; Middlemas, Stuart JExamination of the genetic basis of the timing of the return migration of Atlantic salmon (Salmo salar L.) to freshwater from the sea, a trait of economic and conservation interest, was carried out using a genome-wide association study. Genotype data from 52,731 single nucleotide polymorphic (SNP) markers from 73 early and 49 late running two sea-winter salmon from five rivers in eastern Scotland was examined. A single region of the Atlantic salmon chromosome Ssa09 was identified, containing nine SNP markers significantly associated with run timing, a region previously linked to variation in sea age at maturity. Validation of the markers in a group of 233 one and two sea-winter fish, including adults from a novel river, again showed significant associations between the trait and the Ssa09 region, explaining ~24% of the trait variance. The SNP loci identified provide the ability to examine trait variation in populations of Atlantic salmon and so help facilitate conservation management of the differing run timing phenotypes.Item Decay processes in woody debris influence the taxonomic and functional composition of littoral macroinvertebrates(Canadian Science Publishing, 2017-11-30) Magdalena, Czarnecka; Miler, OliverWe examined the effects of woody debris decay state of on the densities, taxonomic and functional composition, and diversity of macroinvertebrates in littoral zones of undeveloped lakes. Our study revealed that the interacting effects of increasing roughness and softness of the wood, as well as changes in the quality of food resources with progressing decomposition of woody debris exerted the strongest impacts on macroinvertebrate communities. Structurally complex, decomposed wood supported higher densities and species richness of macroinvertebrates than undecayed wood. We also found several taxa which were typical for decayed wood, including macroinvertebrates considered as xylophages. Decaying wood underpinned greater functional richness than undecayed wood, with high densities of collector-gatherers and shredders which could benefit from organic matter originating from decomposing wooden tissue, as well as predators attracted by numerous potential prey inhabiting this complex habitat. As decaying wood enhanced abundant and diverse macroinvertebrate communities, which in turn could subsidize upper trophic levels, it provides a valuable habitat in littoral zones, particularly in lakes with already sparse macrophyte cover.Item Applying a knowledge-action framework for navigating barriers to incorporating telemetry science into fisheries management and conservation: a qualitative study(Canadian Science Publishing, 2017-10-13) Nguyen, Vivian M.; Young, Nathan; Cooke, Steven J.Telemetry studies have produced fundamental knowledge on animal biology and ecology that has the potential to improve management of aquatic resources such as fisheries. However, the use and integration of telemetry-derived knowledge into practice remain tenuous, so we surveyed 212 fish telemetry experts to understand existing barriers for incorporating telemetry-derived knowledge into fisheries management practices. We apply a sociological knowledge-action framework to structure the findings, which revealed four primary challenges to integrating telemetry findings into management: (1) the perceived uncertainties and unclear relevance of telemetry findings; (2) the underlying motivations and constrained rationalities of actors that can lead to inaction or suboptimal decisions; (3) the constraints of institutions, governance structures and lack of organizational support, and; (4) time and mismatches in scale, culture and worldviews. On a more positive note, the relational dimension (collaboration, trust, and relationship building) appears to be important for overcoming and avoiding barriers. We further provide recommendations to navigate these perceived barriers, and argue that these lessons also apply to other fields of applied ecology, conservation and resource management.Item Dusky sharks (Carcharhinus obscurus) undertake large-scale migrations between tropical and temperate ecosystems(Canadian Science Publishing, 2017-12-04) Braccini, Matias; de Lestang, Simon; McAuley, RoryForaging success can be mediated by parasites, but this is poorly understood for marine fish whose aggregations and patchy prey fields create conditions for intense intraspecific competition. We evaluated whether sea louse infection is associated with decreased stomach fullness of wild juvenile sockeye salmon (Oncorhynchus nerka) in Johnstone Strait, BC during their marine migration from the Fraser River. Caligus clemensi comprised 98.6% of the pre-adult and adult lice and 86.5% of the copepodites (freshly attached juvenile lice); the rest were Lepeophtheirus salmonis. We found that infection status was an important predictor of relative stomach fullness for juvenile sockeye (wet stomach content weight divided by body weight), as indicated by mixed-effects model selection, and that highly infected fish had 17% Âą 8% lower relative stomach fullness than did lightly infected fish. This louse-associated reduction in relative stomach fullness occurs as the juvenile sockeye migrate through a food-limited environment, and presumably elevated competition. Given that early marine growth for juvenile salmon is often a predictor of survival, our results highlight the importance of understanding sub-lethal effects of parasites on salmonids and possibly other fish species.Item Heavy sea louse infection is associated with decreased stomach fullness in wild juvenile sockeye salmon(Canadian Science Publishing, 2017-11-30) Godwin, Sean C.; Krkošek, Martin; Reynolds, John D.; Rogers, Luke A.; Dill, Lawrence MForaging success can be mediated by parasites, but this is poorly understood for marine fish whose aggregations and patchy prey fields create conditions for intense intraspecific competition. We evaluated whether sea louse infection is associated with decreased stomach fullness of wild juvenile sockeye salmon (Oncorhynchus nerka) in Johnstone Strait, BC during their marine migration from the Fraser River. Caligus clemensi comprised 98.6% of the pre-adult and adult lice and 86.5% of the copepodites (freshly attached juvenile lice); the rest were Lepeophtheirus salmonis. We found that infection status was an important predictor of relative stomach fullness for juvenile sockeye (wet stomach content weight divided by body weight), as indicated by mixed-effects model selection, and that highly infected fish had 17% Âą 8% lower relative stomach fullness than did lightly infected fish. This louse-associated reduction in relative stomach fullness occurs as the juvenile sockeye migrate through a food-limited environment, and presumably elevated competition. Given that early marine growth for juvenile salmon is often a predictor of survival, our results highlight the importance of understanding sub-lethal effects of parasites on salmonids and possibly other fish species.Item Temperature regimes, growth, and food consumption for female and male adult walleye in Lake Huron and Lake Erie: a bioenergetics analysis(Canadian Science Publishing, 2017-11-30) Madenjian, Charles P; Hayden, Todd A; Peat, Tyler B.; Vandergoot, Christopher S; Fielder, David G.; Gorman, Ann Marie; Pothoven, Steven A; Dettmers, John M; Cooke, Steven J; Zhao, Yingming; Krueger, Charles C.Bioenergetics modeling was used to assess the relative importance of food availability and water temperature in determining walleye (Sander vitreus) growth. Temperature regimes experienced by both female and male adult walleye in three basins of Lake Huron and in Lake Erie were determined by use of surgically implanted temperature loggers and acoustic telemetry. Temperatures experienced by walleye were higher in Lake Erie than in Lake Huron. Walleye from Lake Erie grew at nearly double the rate of walleye from Lake Huron, and weight at age for adult females averaged about 50% greater than that for adult males in both lakes. Food consumption rate for an average adult walleye in Lake Erie was nearly twice as high as that in Lake Huron. Interbasin and interlake variability in temperature regimes accounted for a moderate degree of variability in walleye growth. We concluded that the driver for faster growth in Lake Erie compared with Lake Huron was higher food availability in Lake Erie compared with Lake Huron. The sex difference in temperature regimes explained 15% of the sex difference in Lake Erie walleye growth.Item Effects of hatchery supplementation on abundance and productivity of natural-origin Chinook salmon: two decades of evaluation and implications for conservation programs(Canadian Science Publishing, 2017-11-20) Venditti, David A; Kinzer, Ryan N; Apperson, Kimberly A; Barnett, Bruce; Belnap, Matthew; Copeland, Timothy; Corsi, Matthew P; Tardy, KurtHatchery supplementation has been developed to conserve salmonid populations and provide fisheries. We evaluated supplemented and reference Chinook salmon (Oncorhynchus tshawytscha) populations prior to, during, and after supplementation ceased for 22 years in two major drainages in Idaho, USA. Basin-level analyses showed supplementation increased abundance at some life stages, but effects did not persist into the post-supplementation phase and had no apparent influence on productivity. Natural-origin juvenile abundance increased during supplementation but results for adults were ambiguous. After supplementation ceased, abundance and productivity in supplemented and reference populations returned to their pre-supplementation relationships. Intensive analyses of supplemented populations with weirs showed abundance increased at some life stages with the addition of female spawners. However, the rate of increase varied with female origin (natural > supplementation â Ľ non-treatment hatchery) and effects diminished through the life cycle. Based on these findings, we provide guidance for conservation programs. Supplementation alone is not a panacea because it does not correct limiting factors, which must be addressed to achieve population levels capable of sustaining ecological function and harvest.