The pink salmon genome: Uncovering the genomic consequences of a two-year life cycle

Pink salmon (Oncorhynchus gorbuscha) adults are the smallest of the five Pacific salmon native to the western Pacific Ocean. Pink salmon are also the most abundant of these species and account for a large proportion of the commercial value of the salmon fishery worldwide. A two-year life history of pink salmon generates temporally isolated populations that spawn either in even-years or odd-years. To uncover the influence of this genetic isolation, reference genome assemblies were generated for each year-class and whole genome re-sequencing data was collected from salmon of both year-classes. The salmon were sampled from six Canadian rivers and one Japanese river. At multiple centromeres we identified peaks of Fst between year-classes that were millions of base-pairs long. The largest Fst peak was also associated with a million base-pair chromosomal polymorphism found in the odd-year genome near a centromere. These Fst peaks may be the result of a centromere drive or a combination of reduced recombination and genetic drift, and they could influence speciation. Other regions of the genome influenced by odd-year and even-year temporal isolation and tentatively under selection were mostly associated with genes related to immune function, organ development/maintenance, and behaviour.

The pink salmon genome: uncovering the genomic consequences of a strict two-year life-cycle

Pink salmon (Oncorhynchus gorbuscha) adults are the smallest of the five Pacific salmon native to the western Pacific Ocean. Pink salmon are also the most abundant of these species and account for a large proportion of the commercial value of the salmon fishery worldwide. A strict two-year life-history of most pink salmon generates temporally isolated populations that spawn either in even-years or odd-years. To uncover the influence of this genetic isolation, reference genome assemblies were generated for each year-class and whole genome re-sequencing data was collected from salmon of both year-classes. The salmon were sampled from six Canadian rivers and one Japanese river. At multiple centromeres we identified peaks of Fst between year-classes that were millions of base-pairs long. The largest Fst peak was also associated with a million base-pair chromosomal polymorphism found in the odd-year genome near a centromere. These Fst peaks may be the result of centromere drive or a combination of reduced recombination and genetic drift, and they could influence speciation. Other regions of the genome influenced by odd-year and even-year temporal isolation and tentatively under selection were mostly associated with genes related to immune function, organ development/maintenance, and behaviour.

Understanding barriers, access, and management of marine mixed-stock fisheries in an era of reconciliation: Indigenous-led salmon monitoring in British Columbia

Wild salmon are central to food security, cultural identity, and livelihoods of coastal Indigenous communities. Yet ongoing inequities in governance, declining fish populations, and mixed-stock ocean fisheries may pose challenges for equitable access between Indigenous fishers and other non-Indigenous fishers. We sought to understand current perceptions among Haíłzaqv (Heiltsuk) fishers towards salmon fisheries and their management. We conducted dockside surveys with both Haíłzaqv fishers and sport fishers, and in-depth interviews with Haíłzaqv fishers, community members, and natural resource managers. From these surveys and interviews we quantified satisfaction among both food, social, and ceremonial fishers and visiting recreational fishers with the current salmon fishery and associated social-ecological drivers, and characterized perceptions among Haíłzaqv people of salmon fisheries and management. Second, we synthesized community perceptions of the revitalization of terminal, communally run salmon fisheries within Haíłzaqv territory as a tool for their future salmon management. Finally, we elicited information from Haíłzaqv fishers about the barriers people in their community currently face in accessing salmon fisheries. Our findings suggest that low salmon abundance, increased fishing competition, and high costs associated with participation in marine mixed-stock fisheries currently hinder access and equity for Haíłzaqv fishers. This community-based research can help strengthen local, Indigenous-led management of salmon into the future.

Resources and fishery of Pacific salmon in Magadan region in the beginning of the 21st century

There are two main areas of pacific salmon fishing in the Magadan region: Shelikhova Gulf and Tauiskaya Bay. The main fishing species is pink salmon in the region. Its share of total salmon catch by odd-year returns reaches 85 %. Data on the dynamics of escapement to the spawning grounds of pink salmon of the Shelikhova Gulf and Tauiskaya Bay are presented. The displacement of the level of spawning returns of pink salmon into the Shelihova Gulf with the simultaneous reduction of its returns to the Tauiskaya Bay is shown. Data on the dynamics of the fishing indicators of pink salmon for the two main fishing areas are provided. The Tauiskaya Bay as the main pink salmon fishery area loses its importance is shown. Graphical data on the escapement of producers pink salmon to the spawning grounds are presented and the optimal values of spawning escapements are estimated. Chum salmon is the second largest and most fishing species. Information on the dynamics of the number of returns, catch and escapement to the spawning grounds of chum salmon is given. The indicators of escapement to the spawning areas and their compliance with the optimal passes of salmon producers are analyzed. The issues of the dynamics of returns number, catch and the escapement to the spawning grounds of coho salmon producers are considered. The level of the escapement to the spawning areas is shown and the ratio of actual to optimal values of passes is estimated. The role of coho salmon as an object of industrial fishing and amateur fishing is shown. The extent of fishing press on individual groups of salmon populations is discussed. It is concluded that it is necessary to remove the main salmon fishery from the Tauiskaya Bay to the Shelikhova Gulf.

Mortality of Atlantic salmon after catch and release angling: assessment of a recreational Atlantic salmon fishery in a changing climate

Human activities have the potential to accelerate population-level decline by contributing to climate warming and decreasing the capacity of species to survive warming temperatures. Here we build a predictive model to test interactions between river warming and catch and release mortality in recreational fisheries for Atlantic salmon (Salmo salar) by compiling and analyzing published data. We then test whether warming has occurred in rivers where angling occurs and whether angling opportunities have been restricted through increased river closures due to high water temperatures. We find that catch and release mortalities are low (<0.05) at cool river temperatures (<12 °C). At river temperatures often leading to fishery closures (between 18 and 20 °C), mortalities range from 0.07 to 0.33 (mean = 0.16). River temperatures on the east and southeast coasts of Newfoundland have warmed, leading to an increase in fishery closures in recent years. By contrast, river temperatures in southern Labrador have warmed slightly, with only one documented river closure. Accordingly, increasing temperatures will increase the frequency of river closures and likely result in higher mortality in caught and released Atlantic salmon in rivers that remain open to catch and release angling at warm water temperatures.

The Bristol Bay Salmon Fishery

The Bristol Bay Salmon Fishery. The Bristol Bay salmon fishery is widely regarded as one of the most sustainable in the world. Fish abundance and catch are at record levels, and the fishery provides employment for thousands of people and subsistence food for the local residents. Despite the industrial harvest, the freshwater ecosystems are largely unchanged. The keys to the sustainability are intact freshwater habitat, a management system that puts sustainability before other factors, and limiting the size of the fishing fleet. Both economic and social sustainability are under management that is less direct and, therefore, are more subject to outside influences.

What is “usable” knowledge? Perceived barriers for integrating new knowledge into management of an iconic Canadian fishery

Understanding the perspectives of knowledge users and the demands of their decision-making environment would benefit researchers looking to enhance the utility of the knowledge they generate. Using the Fraser River Pacific salmon fishery as a case study, we investigate the views of 49 government employees and stakeholders regarding the barriers to incorporating new knowledge into fisheries management. Our study uses analysis of qualitative data structured by a knowledge–action framework, which revealed that 90% of respondents perceived the contextual dimension (e.g., institutional structures and norms) as a barrier for incorporating new knowledge, followed by barriers related to the characteristics of knowledge actors (52% of respondents), characteristics of the knowledge (27%), time and timing (27%), knowledge transfer strategies (17%), and relational dimension (8%). The identified barriers have indirect–direct relationship with knowledge producers and appear hierarchical in nature. We note that informal relationships can enable conditions whereby knowledge users can access new knowledge, and knowledge producers can gain insights on users’ needs. We discuss lessons learned from the case, which we believe can be applied more beyond fisheries.