Management Of Salmon Fisheries Research Articles

Wild salmon enumeration and monitoring using deep learning empowered detection and tracking

Pacific salmon have experienced declining abundance and unpredictable returns, yet remain vital to livelihoods, food security, and cultures of coastal communities around the Pacific Rim, creating a need for reliable and timely monitoring to inform sustainable fishery management. Currently, spawning salmon abundance is often monitored with in-river video or sonar cameras. However, reviewing video for estimates of salmon abundance from these programs requires thousands of hours of staff time, and data are typically not available until after the fishing season is completed. Computer vision deep learning can enable rapid and reliable processing of data, with potentially transformative applications in salmon population assessment and fishery management. Working with two First Nations fishery programs in British Columbia, Canada, we developed, trained, and tested deep learning models to perform object detection and multi-object tracking for automated video enumeration of salmon passing two First Nation-run weirs. We gathered and annotated more than 500,000 frames of video data encompassing 12 species, including seven species of anadromous salmonids, and trained models for multi-object tracking and species detection. Our top performing model achieved a mean average precision (mAP) of 67.6%, and species-specific mAP scores > 90% for coho and > 80% for sockeye salmon when trained with a combined dataset of Kitwanga and Bear Rivers’ salmon annotations. We also tested and deployed a prototype for a real-time monitoring system that can perform computer vision deep learning analyses on site. Computer vision models and off-grid monitoring systems show promise for automated counting and species identification. A key future priority will be working with stewardship practitioners and fishery managers to apply salmon computer vision, testing and applying edge-capable computing solutions for in-situ analysis at remote sites, and developing tools for independent user-led computer vision analysis by non-computer scientists. These efforts can advance in-season monitoring and decision making to support adaptive management of sustainable wild salmon fisheries.

On the Improvement of Pink Salmon Fishery Management (on the Sakhalin- Kuril Region as an example)

Purpose: Assess the current state of the pink salmon fishery management and determine ways to improve the scientific support of the pink salmon fishing to ensure the rational usage of its stocks. Methods used: Analysis of historical data and methods used to assess the state of pink salmon stocks and develop recommendations for their usage. Results: Over the past decade, discrepancies between expected and actual returns of pink salmon, to the eastern coast of Sakhalin in particular, have averaged more than double. Those inconsistencies are associated both with many uncertainties in the development of forecasts and with the representativeness of the data used. Wrong estimates form the basis of the submitted fishing strategies, which negatively affects operational fishing management. Using the returns of pink salmon in 2021–2022 as an example, it is shown that the accuracy of forecasting could be higher when using standardized primary data, for which it is necessary to restore the corresponding database, the support of which was interrupted in 2015. It is also proposed to focus on strengthening operational forecasting as a basis for the development of fishery management measures. Practical significance: Restoration of the primary database and return to previously well-established methods of fishery management should increase the effectiveness of scientific part in pink salmon fishery of the region.

Studies of the migration of juvenile Pacific salmon in the Savushkina river (Paramushir Island, Northern Kuriles) in 2022

The purpose of the research is to form scientific basis of effective management of salmon fisheries in the Russian Far East.Applied methods: research work was carried out in accordance with standard methods used in fisheries research.Scientific novelty: data on qualitative and quantitative composition of juvenile Pacific salmon migrating from the Savushkina River for rearing in marine waters in May-July 2022. Based on qualitative heterogeneity of juveniles, presence of eco-temporal groups within chum salmon and coho salmon was supposed.Result: data on timing and dynamics of seaward migration of Pacific salmon juveniles, as well as their qualitative and quantitative patterns.Practical relevance: Results of the research would be used in forecasting of commercial catch of Pacific salmon in the Northern Kurils.

Analysis of 2021 pacific salmon fishing season

Analysis of 2021 Pacific salmon fishing season in the Far East of Russia is presented. It is based on data obtained from the Department of Anadromous Fish of Russia and the Far Eastern branches of the FSBSI «VNIRO», as well as the Far Eastern Territorial Administrations of the Federal Agency for Fisheries. Causes of discrepancy between forecasted and actual harvest of Pacific salmon are revealed. Proposals for improving Pacific salmon fishery management of and its scientific support are presented.

Modeling Chinook Salmon Run Timing in the Gulkana River, Alaska Using Environmental Indices

AbstractEnvironmental data from the Gulkana River, in conjunction with in‐season Chinook Salmon Oncorhynchus tshawytscha passage numbers, are among the many tools used by the Alaska Department of Fish and Game to assess in‐season run strength and timing in the upper Copper River drainage. In this study, we refine the modeling of Chinook Salmon run timing by comparing methods based on linear, exponential, and polynomial regressions of marine and freshwater environmental indices for the Gulkana River stock. A range of temporal subsets and measurement techniques for coastal upwelling, air temperature, river discharge, and water temperature was analyzed in a stepwise process to update the in‐season forecast model. Ultimately, Gulkana River water temperature proved to be the most important variable in predicting run timing. A model considering daily maximum water temperature and river discharge can accurately estimate the proportion of the total run that swam upriver before July (pseudo‐R2 = 0.97), allowing for efficient Chinook Salmon fishery management through the latter portion of the run.

Parentage-based tagging and genetic stock identification applied to assessment of mixed-stock fisheries and hatchery broodstocks for Chinook salmon in British Columbia, Canada

Genetic stock identification (GSI) and parentage-based tagging (PBT) are being increasingly applied to salmon fisheries and hatchery broodstock management and assessment in Canada. GSI and PBT with single nucleotide polymorphisms (SNPs) were applied in assessment of 2020 Chinook salmon fisheries and hatchery broodstocks in British Columbia (BC), Canada, with 9234 individuals successfully genotyped in fishery samples and 2250 PBT identifications made (24.4% individual identification rate). As PBT identifications provided age of the individual and sex was determined from a SNP in the SNP panel, it was possible to evaluate sex ratios by age observed in the fishery sampling. Fishery catch sex ratios at age two and three years were male-biased, whereas those at age four and five years were female-biased. The combined age and sex information derived from genetics-based fishery sampling illustrates the ancillary information that becomes available relative to coded-wire tag (CWT) sampling if biological sampling of the catch is not conducted. There were 20,342 individuals genotyped in 65 hatchery broodstocks from which 6080 PBT identifications were made. Population-specific contributions to mixed-stock fisheries and exploitation rates were estimated with CWTs and GSI-PBT technologies for 13 populations, and close agreement of estimated population-specific exploitation rates between CWT and genetic methods for the 13 populations was observed (r2(11)= 0.951, P < 0.001). We conclude that a genetic approach can improve upon the results available from the current CWT program for assessment and management of Chinook salmon fisheries and hatchery broodstocks in BC, as well as provide ancillary information to improve wild Chinook salmon assessment and conservation by providing fishery impacts by conservation unit for any fishery in Canada.

The identification of individuals with hatchery and natural origin in a mixed sample of Amur River chum salmon by Otolith microchemistry

We estimated the proportion of hatchery and natural fall spawning chum salmon returning to the Amur River using chemical markers specific to hatchery-origin fry. We used otolith microchemistry technique to identify fish with artificial origin among returning spawners. First, we found that juveniles of artificial origin had higher values of the Sr:Ca molar ratio of the otoliths’ edge zone compared with juveniles of natural origin, what can be related to the use of rearing feed produced from raw materials of marine origin rich in strontium. Then we observed that most of the spawners from Anyuisky Hatchery and from the Amur River mouth at the start of the spawning migration has also the higher value of Sr:Ca molar ratio of the juvenile zone of otoliths. Also, adults with higher values of the Sr:Ca molar ratio are characterized by a skewed right in the peak of the age distribution. Both, the age structure and phenological shift in the time of spawning migration of individuals with higher value of the used chemical marker corresponds to results of studies on hatchery-produced chum salmon completed at different parts on Northern Pacific. The results of this study will be used in the management of Amur fall chum salmon fisheries, and also demonstrates the necessity of the development of specific measures for increasing the survival of juvenile anadromous salmonids released at large rivers and exposed to prolonged freshwater migration to the ocean. As a further application of the methodology, we plan to identify the markers specific to each of the hatcheries and main spawning tributaries belonging to Amur River catchments. This will be an important step in the evaluation of the contribution of different stocks in mixed fisheries and also in the estimation of the effect of hatchery releases on naturally spawning stocks of Amur fall chum.Following to, our results may indicate the applicability of this approach for the determination of artificial-origin fish in a mixed sample of the Amur fall chum salmon.

Genotyping-in-Thousands by sequencing panel development and application to inform kokanee salmon (Oncorhynchus nerka) fisheries management at multiple scales.

The ability to differentiate life history variants is vital for estimating fisheries management parameters, yet traditional survey methods can be inaccurate in mixed-stock fisheries. Such is the case for kokanee, the freshwater resident form of sockeye salmon (Oncorhynchus nerka), which exhibits various reproductive ecotypes (stream-, shore-, deep-spawning) that co-occur with each other and/or anadromous O. nerka in some systems across their pan-Pacific distribution. Here, we developed a multi-purpose Genotyping-in-Thousands by sequencing (GT-seq) panel of 288 targeted single nucleotide polymorphisms (SNPs) to enable accurate kokanee stock identification by geographic basin, migratory form, and reproductive ecotype across British Columbia, Canada. The GT-seq panel exhibited high self-assignment accuracy (93.3%) and perfect assignment of individuals not included in the baseline to their geographic basin, migratory form, and reproductive ecotype of origin. The GT-seq panel was subsequently applied to Wood Lake, a valuable mixed-stock fishery, revealing high concordance (>98%) with previous assignments to ecotype using microsatellites and TaqMan® SNP genotyping assays, while improving resolution, extending a long-term time-series, and demonstrating the scalability of this approach for this system and others.

Evaluating tag-reliant harvest estimators in Chinook salmon mixed-stock fisheries using simulations

Management of mixed-stock Chinook salmon (Oncorhynchus tshawytscha) fisheries requires balancing fishery access and conservation of vulnerable stocks. Although accurate, timely estimates of stock-specific harvest are crucial in achieving competing objectives, limited numbers of stock assignments (e.g., tag recoveries) can diminish the utility of estimates. We used a flexible simulation approach, applied to both a theoretical and real-world fishery case study, to compare the performance of competing monitoring alternatives and estimators for harvest. We sought to improve accuracy for point estimates of harvest and harvest trajectories over time. Bayesian models provided similarly accurate point estimates to existing models at high levels of data aggregation, generally improved estimates of harvest trajectories at intermediate aggregation, and reliable estimates of uncertainty. Incorporation of time-lagged prior information inconsistently improved estimates of harvest trajectories. Among monitoring alternatives yielding equal increases (33%) in coded wire tag recoveries, increasing tagging rates resulted in the greatest decrease in estimate uncertainty for target stocks (37.5% to 45.3%). Variable performances of mixed-stock harvest estimators suggest their use should considered on a stock- and fishery-specific basis, potentially using a simulation-based approach.

On inter-organizational trust, control and risk in transboundary fisheries governance

Inter-organizational collaboration is often considered essential to transboundary fishery governance, due, in part, to the high levels of task interdependence, the remote and often treacherous conditions, and the limited levels of information available to any policy actor on resource status. In the high seas, Regional Fisheries Management Organizations (RFMOs) are responsible for sustainably managing highly migratory and straddling fish stocks through the implementation of ecosystem-based approaches and ensuring adequate inter-jurisdictional cooperation. A central question facing RFMO governance is therefore how to structure and sustain inter-organizational transboundary collaboration under high uncertainty? This paper presents the case of the North Atlantic Salmon Conservation Organization (NASCO), conceptualized as a strategic alliance between the bureaucratic organizations responsible for north Atlantic salmon fishery management in the member countries. We identify and explain how dimensions of trust, control, and perceived risk have structured the collaborative performance of the alliance. The application of an integrated trust-control-risk framework increases conceptual clarity for how, when and why alliance managers might seek to develop different forms of trust through different management control systems in ways that further multi-actor collaborative network performance. Future research needs are identified, including better understanding how managerial strategies and control mechanisms facilitate inter-organizational trust in transboundary governance settings and mitigate the perceived risks of working together.

Estimation of conservation unit and population contribution to Chinook salmon mixed-stock fisheries in British Columbia, Canada, using direct DNA sequencing for single nucleotide polymorphisms

Determination of population structure and stock identification is a general problem in fisheries assessment and management. Pacific salmon fishery management regimes are evolving to require higher resolution of stock composition on increasingly smaller reporting units. For Chinook salmon (Oncorhynchus tshawytscha), a stock identification baseline comprised of some 125 198 individuals from 369 populations ranging from Russia to California was employed for genetic stock identification (GSI). GSI analysis based on variation at up to 547 single nucleotide polymorphisms (SNPs) was demonstrated to provide accurate estimates of stock composition for 68 conservation units (CUs) in British Columbia, 23 reporting groups in the United States, and one reporting group in Russia. In many instances, accurate population-specific estimates of stock composition within a CU were possible in fishery samples, as well as identifying individuals to some specific populations. A genetics-based assessment system provides an opportunity for conservation-based management of Canadian Chinook salmon.

Parentage-based tagging combined with genetic stock identification is a cost-effective and viable replacement for coded-wire tagging in large-scale assessments of marine Chinook salmon fisheries in British Columbia, Canada.

Wild Pacific salmon, including Chinook salmon Oncorhynchus tshawytscha, have been supplemented with hatchery propagation for over 50 years in support of increased ocean harvest, mitigation for hydroelectric development, and conservation of threatened populations. In Canada, the Wild Salmon Policy for Pacific salmon was established with the goal of maintaining and restoring healthy and diverse Pacific salmon populations, making conservation of wild salmon and their habitats the highest priority for resource management decision‐making. For policy implementation, a new approach to the assessment and management of Chinook salmon and the associated hatchery production and fisheries management are needed. Implementation of genetic stock identification (GSI) and parentage‐based tagging (PBT) for marine fisheries assessment may overcome problems associated with coded‐wire tag‐based (CWT) assessment and management of Chinook salmon fisheries, providing at a minimum information equivalent to that derived from the CWT program. GSI and PBT were used to identify Chinook salmon sampled in 2018 and 2019 marine fisheries (18,819 individuals genotyped) in British Columbia to specific conservation units (CU), populations, and broodyears. Individuals were genotyped at 391 single nucleotide polymorphisms via direct sequencing of amplicons. Very high accuracy of assignment to population and age (>99.5%) via PBT was observed for 1994 Chinook salmon of ages 2–4 years, with a 105,722–individual, 380–population baseline available for assignment. Application of a GSI‐PBT system of identification to individuals in 2019 fisheries provided high‐resolution estimates of stock composition, catch, and exploitation rate by CU or population, with fishery exploitation rates directly comparable to those provided by CWTs for 13 populations. GSI and PBT provide an alternate, cheaper, and more effective method in the assessment and management of Canadian‐origin Chinook salmon relative to CWTs, and an opportunity for a genetics‐based system to replace the current CWT system for salmon assessment.

Opportunities and impediments for use of local data in the management of salmon fisheries

Inman, S. C., J. Esquible, M. L. Jones, W. R. Bechtol, and B. Connors. 2021. Opportunities and impediments for use of local data in the management of salmon fisheries. Ecology and Society 26(2):26. https://doi.org/10.5751/ES-12117-260226

Large-scale parentage-based tagging and genetic stock identification applied in assessing mixed-stock fisheries and hatchery brood stocks for coho salmon in British Columbia, Canada

Direct DNA sequencing is powering a revolution in the application of genetics to resource management, with parentage-based tagging (PBT) increasingly applied to salmon fisheries and hatchery brood stock management and assessment. Genetic stock identification (GSI) and PBT were applied to assessment of 2018 coho salmon (Oncorhynchus kisutch) ocean fisheries and hatchery brood stocks in British Columbia (BC), Canada, with 6391 individuals successfully genotyped in fishery samples and 7805 individuals genotyped in 40 hatchery brood stocks. Population-specific contributions to mixed-stock fisheries and exploitation rates were estimated with coded-wire tags (CWTs) and GSI–PBT technologies for six populations. PBT assignments, verified by CWTs, were 100% accurate for 308 individuals with respect to population of origin and age. There was generally reasonably close agreement of estimated population-specific exploitation rates between CWT and genetic methods. We conclude that a genetic approach can improve upon the results available from the current CWT program for assessment and management of coho salmon fisheries and hatchery brood stocks in BC and provide information critical to aid in implementation of Canada’s Policy for Conservation of Wild Pacific Salmon.

Accurate estimation of conservation unit contribution to coho salmon mixed-stock fisheries in British Columbia, Canada, using direct DNA sequencing for single nucleotide polymorphisms

Determination of population structure and stock identification is a ubiquitous problem in fisheries assessment and management. Pacific salmon fishery management regimes are evolving to require higher resolution of stock composition on increasingly smaller reporting units. For coho salmon (Oncorhynchus kisutch), a stock identification baseline composed of some 57 982 individuals from 332 populations ranging from southeast Russia to California was employed for genetic stock identification (GSI). GSI analysis based upon variation at up to 480 single nucleotide polymorphisms (SNPs) was demonstrated to provide accurate estimates of stock composition for 37 conservation units (CU) in British Columbia, 13 reporting groups in the United States, and one reporting group in Russia. In many instances, accurate population-specific estimates of stock composition within a CU were possible in fishery samples, as well as identifying individuals to some specific populations. A genetics-based assessment system provides an opportunity for conservation-based management of Canadian coho salmon.

Climate effects on size‐at‐age and growth rate of Chinook Salmon (Oncorhynchus tshawytscha) in the Fraser River, Canada

AbstractDecline in size‐at‐age of Chinook Salmon (Oncorhynchus tshawytscha) has been observed for many populations across the entire Northeast Pacific Ocean, and identifying external drivers of this decline is important for sustainable management of these ecologically, economically, and culturally valuable resources. We assessed size‐at‐age of 96,939 Chinook Salmon sampled in the Fraser River watershed (Canada) from 1969 to 2017. A broad decline in size‐at‐age was confirmed across all population aggregates of Fraser River Chinook Salmon, in particular since year 2000. By developing a novel probability‐based approach to calculate age‐ and year‐specific growth rates for Fraser River Chinook Salmon and relating growth rates to environmental conditions in specific years through a machine learning method (boosted regression trees), we were able to disentangle multi‐year effects on size‐at‐age and thus identify environmental factors that were most related to the observed size‐at‐age of Chinook Salmon. Among 10 selected environmental variables, ocean salinity at Entrance Island in spring, the Aleutian Low Pressure Index and the North Pacific Current Bifurcation Index were consistently identified as important contributors for four of the seven age and population aggregate combinations. These top environmental contributors could be incorporated into future stock assessment and forecast models to improve Chinook Salmon fisheries management under climate change.

Ecological thresholds in forecast performance for key United States West Coast Chinook salmon stocks

AbstractPreseason abundance forecasts drive management of US West Coast salmon fisheries, yet little is known about how environmental variability influences forecast performance. We compared forecasts of Chinook salmon (Oncorhynchus tshawytscha) against returns for (i) key California-Oregon ocean fishery stocks and (ii) high priority prey stocks for endangered Southern Resident Killer Whales (Orcinus orca) in Puget Sound, Washington. We explored how well environmental indices (at multiple locations and time lags) explained performance of forecasts based on different methods (i.e. sibling-based, production-based, environment-based, or recent averages), testing for nonlinear threshold dynamics. For the California stocks, no index tested explained &amp;gt;50% of the variation in forecast performance, but spring Pacific Decadal Oscillation and winter North Pacific Index during the year of return explained &amp;gt;40% of the variation for the sibling-based Sacramento Fall Chinook forecast, with nonlinearity and apparent thresholds. This suggests that oceanic conditions experienced by adults (after younger siblings returned) have the most impact on sibling-based forecasts. For Puget Sound stocks, we detected nonlinear/threshold relationships explaining &amp;gt;50% of the variation with multiple indices and lags. Environmental influences on preseason forecasts may create biases that render salmon fisheries management more or less conservative, and therefore could motivate the development of ecosystem-based risk assessments.

Comparison of coded-wire tagging with parentage-based tagging and genetic stock identification in a large-scale coho salmon fisheries application in British Columbia, Canada.

Wild Pacific salmon, including Coho salmon Onchorynchus kisutch, have been supplemented with hatchery propagation for over 50 years in support of increased ocean harvest and conservation of threatened populations. In Canada, the Wild Salmon Policy for Pacific salmon was established with the goal of maintaining and restoring healthy and diverse Pacific salmon populations, making conservation of wild salmon and their habitats the highest priority for resource management decision‐making. A new approach to the assessment and management of wild coho salmon, and the associated hatchery production and fishery management is needed. Implementation of parentage‐based tagging (PBT) may overcome problems associated with coded‐wire tag‐based (CWT) assessment and management of coho salmon fisheries, providing at a minimum information equivalent to that derived from the CWT program. PBT and genetic stock identification (GSI) were used to identify coho salmon sampled in fisheries (8,006 individuals) and escapements (1,692 individuals) in British Columbia to specific conservation units (CU), populations, and broodyears. Individuals were genotyped at 304 single nucleotide polymorphisms (SNPs) via direct sequencing of amplicons. Very high accuracy of assignment to population (100%) via PBT for 543 jack (age 2) assigned to correct age and collection location and 265 coded‐wire tag (CWT, age 3) coho salmon assigned to correct age and release location was observed, with a 40,774—individual, 267—population baseline available for assignment. Coho salmon from un‐CWTed enhanced populations contributed 65% of the catch in southern recreational fisheries in 2017. Application of a PBT‐GSI system of identification to individuals in 2017 fisheries and escapements provided high‐resolution estimates of stock composition, catch, and exploitation rate by CU or population, providing an alternate and more effective method in the assessment and management of Canadian‐origin coho salmon relative to CWTs, and an opportunity for a genetic‐based system to replace the current CWT system for coho salmon assessment.

Valuing recreational salmon fishing at a remote site in Finland: A travel cost analysis

The River Teno is the most visited river for recreational wild salmon fishing in Finland and is one of the most productive wild salmon rivers in Northern Europe. Despite the popularity of recreational fishing in the area, no estimates are available for its economic value. This study uses a travel cost recreation demand model to estimate the recreational value of salmon fishing in the Teno river area. Following a two-step estimation procedure outlined by McConnell, we show that on-site time per trip is endogenous. The estimated consumer surplus per trip ranges from 235 to 338 euros. The estimated total recreational value of salmon fishing in the area is 2.6–3.7 million euros. Also, according to the empirical results, the number of fishing trips per angler is strongly affected by the angler’s previous salmon catch in the Teno river area, which underlines the importance of the proper and sustainable management of recreational salmon fisheries.

Range-wide regional assignment of Atlantic salmon (Salmo salar) using genome wide single-nucleotide polymorphisms

The estimation of stock specific exploitation is imperative to fisheries management and the conservation of biodiversity, particularly in instances where fisheries simultaneously exploit mixtures of stocks. Mixed stock harvests are particularly common in species that have extensive marine migrations, such as Atlantic and Pacific salmon. Here we develop a range-wide genetic baseline for Atlantic salmon (Salmo salar) from North American and European rivers to allow regional assignment of individuals targeted in international mixed stock fisheries. A combination of published data and additional genotyping was used to assemble a dataset of 96 SNPs for 285 range-wide Atlantic salmon populations for regional assignment. Clustering of baseline samples identified 20 North American and eight European reporting groups with mean individual assignment accuracy of 90% (range 70–100%). This baseline was applied to disentangle the stock composition of individuals in a subset of individuals from the West Greenland Atlantic salmon fishery. Genetic mixture analysis revealed that both European and North American individuals originated from multiple regions, with 92% of European individuals originating from the United Kingdom and Ireland, and North American individuals originating from three regions; Gulf of St. Lawrence (28%), Gaspé Peninsula (23%), and coastal Labrador (21%). The baseline represents a significant resource for the management of Atlantic salmon fisheries and the quantification of salmon migration patterns at sea.