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The collapse of iconic, keystone populations of sockeye (Oncorhynchus nerka) and Chinook (Oncorhynchus tshawytscha) salmon in the Northeast Pacific is of great concern. It is thought that infectious disease may contribute to declines, but little is known about viruses endemic to Pacific salmon. Metatranscriptomic sequencing and surveillance of dead and moribund cultured Chinook salmon revealed a novel arenavirus, reovirus and nidovirus. Sequencing revealed two different arenavirus variants which each infect wild Chinook and sockeye salmon. In situ hybridisation localised arenavirus mostly to blood cells. Population surveys of >6000 wild juvenile Chinook and sockeye salmon showed divergent distributions of viruses, implying different epidemiological processes. The discovery in dead and dying farmed salmon of previously unrecognised viruses that are also widely distributed in wild salmon, emphasizes the potential role that viral disease may play in the population dynamics of wild fish stocks, and the threat that these viruses may pose to aquaculture. Keystone species are animals and plants that play a pivotal role in supporting the ecosystems they live in, making their conservation a high priority. Chinook and sockeye salmon are two such species. These fish play a central role in the coastal ecosystems of the Northeast Pacific, where they have supported Indigenous populations for thousands of years. The last three decades have seen large declines in populations of Chinook and sockeye salmon. One factor that may be involved in these declines is viral infection. In the last ten years, advances in DNA sequencing technologies have led to the discovery of many new viruses, and Mordecai et al. used these technologies to look for new viruses in Pacific salmon. First, Mordecai et al. looked for viruses in dead and dying salmon from farms and discovered three previously unknown viruses. Next, they screened for these viruses in farmed salmon, hatchery salmon and wild salmon to determine their distribution. Two of the viruses were present in fish from the three sources, while one of the viruses was only found in farmed fish. The fact that the three viruses are distributed differently raises questions about how the viruses are transmitted within and between farmed, hatchery and wild salmon populations. These findings will aid salmon-conservation efforts by informing the extent to which these viruses are present in wild salmon populations. Future work will focus on determining the risks these viruses pose to salmon health and investigating the potential for exchange between hatchery, farmed and wild salmon populations. While farmed Pacific salmon may pose some transmission risk to their wild counterparts, they also offer the opportunity to study disease processes that are not readily observable in wild salmon. In turn, such data can be used to develop policies to minimize the impact of these infectious agents and improve the survival of wild salmon populations.

Viral erythrocytic necrosis (VEN) affects over 20 species of marine and anadromous fishes in the North Atlantic and North Pacific Oceans. However, the distribution and strain variation of its viral causative agent, erythrocytic necrosis virus (ENV), has not been well characterized within Pacific salmon. Here, metatranscriptomic sequencing of Chinook salmon revealed that ENV infecting salmon was closely related to ENV from Pacific herring, with inferred amino-acid sequences from Chinook salmon being 99% identical to those reported for herring. Sequence analysis also revealed 89 protein-encoding sequences attributed to ENV, greatly expanding the amount of genetic information available for this virus. High-throughput PCR of over 19,000 fish showed that ENV is widely distributed in the NE Pacific Ocean and was detected in 12 of 16 tested species, including in 27% of herring, 38% of anchovy, 17% of pollock, and 13% of sand lance. Despite frequent detection in marine fish, ENV prevalence was significantly lower in fish from freshwater (0.03%), as assessed with a generalized linear mixed effects model (p = 5.5 × 10−8). Thus, marine fish are likely a reservoir for the virus. High genetic similarity between ENV obtained from salmon and herring also suggests that transmission between these hosts is likely.

We present the first quantitative analyses of dolphinfish (Coryphaena hippurus) foraging habits and trophic interactions with co-occurring yellowfin (Thunnus albacares) and albacore (T. alalunga) tunas in the Southern New England region of the western North Atlantic Ocean. Fish caught by recreational anglers in offshore waters of Massachusetts were sampled during the summers of 2007–2010. Diet analysis revealed that shortfin squid (Illex illecebrosus) and small pelagic crustaceans were principal prey to dolphinfish, yellowfin tuna, and albacore tuna. A wide variety of Sargassum-associated fishes were also important to dolphinfish and yellowfin tuna diets. Dietary (Schoener’s index: 0.82–0.86) and isotopic niche (isotopic ellipse overlap: 53.6–64.7 %) overlap was high, and dolphinfish and tunas occupied equivalent trophic positions (TP = 3.4–3.6). Relative prey size in dolphinfish and yellowfin tuna diets exhibited convergence with ontogeny. Overall, dolphinfish had the greatest isotopic niche width, which was twice as large as yellowfin tuna and three times as large as albacore tuna; dolphinfish also consumed the greatest range of prey sizes. Results quantify dolphinfish trophic interactions in the western Atlantic near the northern extent of their geographical range, and are relevant for ecosystem-based management of the offshore pelagic guild in the context of shifting fish populations and fisheries in response to climate and ecological change.

This paper is a response to Polinski, M. P. et al. Innate antiviral defense demonstrates high energetic efficiency in a bony fish . BMC Biology 19 , 138 (2021). https://doi.org/10.1186/s12915-021-01069-2

Postdocs are a critical transition for early-career researchers. This transient period, between finishing a PhD and finding a permanent position, is when early-career researchers develop independent research programs and establish collaborative relationships that can make a successful career. Traditionally, postdocs physically relocate-sometimes multiple times-for these short-term appointments, which creates challenges that can disproportionately affect members of traditionally underrepresented groups in science, technology, engineering, and mathematics (STEM). However, many research activities involving analytical and quantitative work do not require a physical presence in a lab and can be accomplished remotely. Other fields have embraced remote work, yet many academics have been hesitant to hire remote postdocs. In this article, we present advice to both principal investigators (PIs) and postdocs for successfully navigating a remote position. Using the combined experience of the authors (as either remote postdocs or employers of remote postdocs), we provide a road map to overcome the real (and perceived) obstacles associated with remote work. With planning, communication, and creativity, remote postdocs can be a fully functioning and productive member of a research lab. Further, our rules can be useful for research labs generally and can help foster a more flexible and inclusive environment.

Abstract Rivers, lakes, and wetlands are facing threats that continue to grow in intensity and frequency from climate change, habitat fragmentation, invasive species, changes in food availability, natural disasters, various forms of pollution (e.g., trace metals, light, noise), and emerging infectious diseases. These disruptions to freshwater environments are driving population declines in freshwater fishes as well as threatening migratory species that need freshwater habitats to complete their life cycle. To improve freshwater fish conservation efforts, it is essential to understand the magnitude and nature of the threats fish are currently facing. Here, we present a series of case studies that illustrate the utility of employing physiological methods to assess both the threats facing freshwater fishes, and the conservation efforts being used to help preserve freshwater biodiversity. We present an array of physiological tools that can be used across multiple levels of biological organization, from molecular to population-level, to address a variety of questions. Finally, we share what we view to be pressing questions in freshwater fish conservation physiology and highlight strategies to help bridge gaps across different user groups. Lay Summary Here, we summarize pressing threats facing freshwater fishes and highlight specific physiological tools that can help characterize the nature and magnitude of the threat, as well as the efficacy of mitigation efforts. Case studies illustrate the diversity of ways physiological techniques can improve freshwater fish conservation.

Among Pacific salmon released from gillnets on their way to spawning grounds, those entangled for the longest amount of time, especially females, were very likely to die before spawning. Fish that died earliest were in poorer health than survivors and showed greater activity of several infectious disease causing microbes.AbstractBycatch is a common occurrence in heavily fished areas such as the Fraser River, British Columbia, where fisheries target returning adult Pacific salmon (Oncorhynchus spp.) en route to spawning grounds. The extent to which these encounters reduce fish survival through injury and physiological impairment depends on multiple factors including capture severity, river temperature and infectious agents. In an effort to characterize the mechanisms of post-release mortality and address fishery and managerial concerns regarding specific regulations, wild-caught Early Stuart sockeye salmon (Oncorhynchus nerka) were exposed to either mild (20 s) or severe (20 min) gillnet entanglement and then held at ecologically relevant temperatures throughout their period of river migration (mid–late July) and spawning (early August). Individuals were biopsy sampled immediately after entanglement and at death to measure indicators of stress and immunity, and the infection intensity of 44 potential pathogens. Biopsy alone increased mortality (males: 33%, females: 60%) when compared with non-biopsied controls (males: 7%, females: 15%), indicating high sensitivity to any handling during river migration, especially among females. Mortality did not occur until 5–10 days after entanglement, with severe entanglement resulting in the greatest mortality (males: 62%, females: 90%), followed by mild entanglement (males: 44%, females: 70%). Infection intensities of Flavobacterium psychrophilum and Ceratonova shasta measured at death were greater in fish that died sooner. Physiological indicators of host stress and immunity also differed depending on longevity, and indicated anaerobic metabolism, osmoregulatory failure and altered immune gene regulation in premature mortalities. Together, these results implicate latent effects of entanglement, especially among females, resulting in mortality days or weeks after release. Although any entanglement is potentially detrimental, reducing entanglement durations can improve post-release survival.

Multiple stressors are commonly encountered by wild animals, but their cumulative effects are poorly understood, especially regarding infection development. We conducted a holding study with repeated gill and blood sampling to characterize the effects of cumulative stressors on infection development in adult coho salmon. Treatments included chronic thermal stress (15°C vs. 10°C) and acute gill net entanglement with an air exposure (simulating fisheries bycatch release). The potential loadings of 35 infectious agents and the expression of 17 host immune genes were quantified using high-throughput quantitative polymerase chain reaction, while host physiology was characterized with chemical analysis of blood. Temporal increases in infectious agent richness and loads were concurrent with decreased expression of immune genes in fish sampled in the river. In the laboratory, mortality was minimal in cool water regardless of fishery treatment (<15%). Elevated water temperature under laboratory conditions increased mortality of males and females (8% and 28% mortality, respectively, delayed by >1 wk) and enhanced mortality associated with handling and biopsy (∼40% both sexes). Experimental gillnetting at high temperature further enhanced female mortality (73%). Fish held at high temperature demonstrated heavier infectious agent loads, osmoregulatory impairment, suppressed female maturation, and upregulation of inflammatory and extracellular immune genes. At high temperature, heavy Parvicapsula minibicornis loads were associated with premature mortality. Females exhibited physiological impairment from both stressors after 1 wk, and infection burdens correlated poorly with immune gene regulation compared with males. Cumulative effects of multiple stressors on female mortality are likely a function of physiological impairment and enhanced infections at high temperature.

Emerging diseases are impacting animals under high‐density culture, yet few studies assess their importance to wild populations. Microparasites selected for enhanced virulence in culture settings should be less successful maintaining infectivity in wild populations, as once the host dies, there are limited opportunities to infect new individuals. Instead, moderately virulent microparasites persisting for long periods across multiple environments are of greatest concern. Evolved resistance to endemic microparasites may reduce susceptibilities, but as barriers to microparasite distributions are weakened, and environments become more stressful, unexposed populations may be impacted and pathogenicity enhanced. We provide an overview of the evolutionary and ecological impacts of infectious diseases in wild salmon and suggest ways in which modern technologies can elucidate the microparasites of greatest potential import. We present four case studies that resolve microparasite impacts on adult salmon migration success, impact of river warming on microparasite replication, and infection status on susceptibility to predation. Future health of wild salmon must be considered in a holistic context that includes the cumulative or synergistic impacts of multiple stressors. These approaches will identify populations at greatest risk, critically needed to manage and potentially ameliorate the shifts in current or future trajectories of wild populations.

Sharks are a diverse group of mobile predators that forage across varied spatial scales and have the potential to influence food web dynamics. The ecological consequences of recent declines in shark biomass may extend across broader geographic ranges if shark taxa display common behavioural traits. By tracking the original site of photosynthetic fixation of carbon atoms that were ultimately assimilated into muscle tissues of 5,394 sharks from 114 species, we identify globally consistent biogeographic traits in trophic interactions between sharks found in different habitats. We show that populations of shelf-dwelling sharks derive a substantial proportion of their carbon from regional pelagic sources, but contain individuals that forage within additional isotopically diverse local food webs, such as those supported by terrestrial plant sources, benthic production and macrophytes. In contrast, oceanic sharks seem to use carbon derived from between 30° and 50° of latitude. Global-scale compilations of stable isotope data combined with biogeochemical modelling generate hypotheses regarding animal behaviours that can be tested with other methodological approaches. Carbon isotopic analysis reveals global biogeographic traits in shark trophic interactions, and sheds light on the diverse foraging behaviour of sharks.