Coupling non‐invasive physiological assessments with telemetry to understand inter‐individual variation in behaviour and survivorship of sockeye salmon: development and validation of a technique

Approximately 200 km from the mouth of the Fraser River, British Columbia, Canada, adult sockeye salmon Oncorhynchus nerka , were gastrically implanted with radio transmitters without anaesthetic. Subsets of the transmitter implanted fish were also biopsied which included drawing blood from the caudal peduncle (3 ml), removal of gill tissue (0·03 g) and quantification of energetic status using a microwave fat meter. Several experiments were used to test the hypothesis that the biopsy had a negligible effect on the subsequent survival and migratory behaviour of transmitter implanted fish. In the first experiment, no difference was found in the survival (both 100%) or tag retention (both 100%) between the two treatment groups (transmitter implanted with and without biopsy) when fish were held in pens for 24 h in the marine environment. Similarly, in other experiments where fish were released to the ocean to resume their migratory journey, no statistical differences were found in the travel times of fish in the two treatment groups, or in the proportion of fish that passed in‐river telemetry checkpoints. These results indicated that the handling and biopsy methods produced similar levels of mortality and tag retention as the telemetry treatment alone and that any changes in behaviour between the two treatment groups did not adversely affect migration time. Based upon the evidence provided from the biotelemetry of >300 adult sockeye salmon, it was felt that this general type of approach could be applicable to other fish species.     

Dead fish swimming: a review of research on the early migration and high premature mortality in adult Fraser River sockeye salmon Oncorhynchus nerka

Adult sockeye salmon Oncorhynchus nerka destined for the Fraser River, British Columbia are some of the most economically important populations but changes in the timing of their homeward migration have led to management challenges and conservation concerns. After a directed migration from the open ocean to the coast, this group historically would mill just off shore for 3-6 weeks prior to migrating up the Fraser River. This milling behaviour changed abruptly in 1995 and thereafter, decreasing to only a few days in some years (termed early migration), with dramatic consequences that have necessitated risk-averse management strategies. Early migrating fish consistently suffer extremely high mortality (exceeding 90% in some years) during freshwater migration and on spawning grounds prior to spawning. This synthesis examines multidisciplinary, collaborative research aimed at understanding what triggers early migration, why it results in high mortality, and how fisheries managers can utilize these scientific results. Tissue analyses from thousands of O. nerka captured along their migration trajectory from ocean to spawning grounds, including hundreds that were tracked with biotelemetry, have revealed that early migrants are more reproductively advanced and ill-prepared for osmoregulatory transition upon their entry into fresh water. Gene array profiles indicate that many early migrants are also immunocompromised and stressed, carrying a genomic profile consistent with a viral infection. The causes of these physiological changes are still under investigation. Early migration brings O. nerka into the river when it is 3-6° C warmer than historical norms, which for some late-run populations approaches or exceeds their critical maxima leading to the collapse of metabolic and cardiac scope, and mortality. As peak spawning dates have not changed, the surviving early migrants tend to mill in warm lakes near to spawning areas. These results in the accumulation of many more thermal units and longer exposures to freshwater diseases and parasites compared to fish that delay freshwater entry by milling in the cool ocean environment. Experiments have confirmed that thermally driven processes are a primary cause of mortality for early-entry migrants. The Fraser River late-run O. nerka early migration phenomenon illustrates the complex links that exist between salmonid physiology, behaviour and environment and the pivotal role that water temperature can have on population-specific migration survival.     

Simultaneous biologging of heart rate and acceleration, and their relationships with energy expenditure in free-swimming sockeye salmon (Oncorhynchus nerka)

Monitoring the physiological status and behaviour of free-swimming fishes remains a challenging task, although great promise stems from techniques such as biologging and biotelemetry. Here, implanted data loggers were used to simultaneously measure heart rate (f _H), visceral temperature, and a derivation of acceleration in two groups of wild adult sockeye salmon (Oncorhynchus nerka) held at two different water speeds (slow and fast). Calibration experiments performed with individual fish in a swim tunnel respirometer generated strong relationships between acceleration, f _H, tail beat frequency and energy expenditure over a wide range of swimming velocities. The regression equations were then used to estimate the overall energy expenditure of the groups of fish held at different water speeds. As expected, fish held at faster water speeds exhibited greater f _H and acceleration, and correspondingly a higher estimated energy expenditure than fish held at slower water speeds. These estimates were consistent with gross somatic energy density of fish at death, as determined using proximate analyses of a dorsal tissue sample. Heart rate alone and in combination with acceleration, rather than acceleration alone, provided the most accurate proxies for energy expenditure in these studies. Even so, acceleration provided useful information on the behaviour of fish and may itself prove to be a valuable proxy for energy expenditure under different environmental conditions, using a different derivation of the acceleration data, and/or with further calibration experiments. These results strengthen the possibility that biologging or biotelemetry of f _H and acceleration may be usefully applied to migrating sockeye salmon to monitor physiology and behaviour, and to estimate energy use in the natural environment.     

Testing the synergistic effects of GnRH and testosterone on the reproductive physiology of pre-adult pink salmon Oncorhynchus gorbuscha

To test the hypothesis that the hypothalmic gonadotropin-releasing hormone (GnRH) and testosterone (T) co-treatment stimulates both the hypothalmo–pituitary–gonadal (HPG) and hypothalmo–pituitary–interrenal axes, the reproductive and osmoregulatory responses of pre-adult pink salmon Oncorhynchus gorbuscha were compared after GnRH and T administration either alone or in combination. Relative to controls, neither GnRH nor T treatment resulted in significantly greater ovarian or testicular growth, but co-treatment significantly increased ovarian growth after 5 months. Interestingly, the stimulation was undetectable after 3 months. However, once daily photoperiod began shortening after the summer solstice, c. 2 months before the natural spawning date, GnRH+T-treated females were stimulated to produce larger ovaries. Final fish body length and the size of individual eggs did not differ among treatment groups. GnRH+T eggs, however, showed signs of advanced vitellogenesis relative to GnRH-treated and control eggs, whereas T-treated eggs became atretic. Testis size increased significantly from initial values and most males were spermiating, but this growth and development were independent of hormone treatments. Final plasma ion, metabolite and cortisol concentrations did not differ among treatment groups. It is concluded that GnRH+T co-treatment was effective in stimulating female but not male maturation. GnRH and T treatment, however, presumably had little effect on the hypothalmo–pituitary–interrenal axis as observed by ionoregulatory status.     

Local Knowledge and Conservation of Seagrasses in the Tamil Nadu State of India

Local knowledge systems are not considered in the conservation of fragile seagrass marine ecosystems. In fact, little is known about the utility of seagrasses in local coastal communities. This is intriguing given that some local communities rely on seagrasses to sustain their livelihoods and have relocated their villages to areas with a rich diversity and abundance of seagrasses. The purpose of this study is to assist in conservation efforts regarding seagrasses through identifying Traditional Ecological Knowledge (TEK) from local knowledge systems of seagrasses from 40 coastal communities along the eastern coast of India. We explore the assemblage of scientific and local traditional knowledge concerning the 1. classification of seagrasses (comparing scientific and traditional classification systems), 2. utility of seagrasses, 3. Traditional Ecological Knowledge (TEK) of seagrasses, and 4. current conservation efforts for seagrass ecosystems. Our results indicate that local knowledge systems consist of a complex classification of seagrass diversity that considers the role of seagrasses in the marine ecosystem. This fine-scaled ethno-classification gives rise to five times the number of taxa (10 species = 50 local ethnotaxa), each with a unique role in the ecosystem and utility within coastal communities, including the use of seagrasses for medicine (e.g., treatment of heart conditions, seasickness, etc.), food (nutritious seeds), fertilizer (nutrient rich biomass) and livestock feed (goats and sheep). Local communities are concerned about the loss of seagrass diversity and have considerable local knowledge that is valuable for conservation and restoration plans. This study serves as a case study example of the depth and breadth of local knowledge systems for a particular ecosystem that is in peril.     

Low cardiac and aerobic scope in a coastal population of sockeye salmon Oncorhynchus nerka with a short upriver migration

This study showed that a coastal population (Harrison) of Fraser River sockeye salmon Oncorhynchus nerka had a lower aerobic and cardiac scope compared with interior populations with more challenging upriver spawning migrations, providing additional support to the idea that Fraser River O. nerka populations have adapted physiologically to their local migratory environment.     

The importance of parentage in assessing temperature effects on fish early life history: a review of the experimental literature

Climate change and human development are altering aquatic thermal regimes, highlighting the need to understand how fish fitness may be impacted across a generational boundary. We reviewed experimental temperature studies investigating the links between parents and progeny, asking questions regarding the taxa studied, broodfish used, offspring traits examined, experimental durations and research motivations. We identified forty-one peer-reviewed articles examining the effects of pre-spawning adult temperature holding on offspring. These studies showed a strong focus on the order Salmoniformes (46% of studies) and aquaculturally driven research (66%). The use of wild broodfish was rare (12%) and the majority of experiments (83%) did not examine offspring consequences beyond hatch. We also identified 56 articles investigating how incubation temperature and parental influences affect embryonic and larval development. We demonstrate that these studies are not common in comparison to the majority of incubation thermal experiments that do not employ controlled parental breeding designs. However, 52 out of 56 studies we reviewed reported maternal, paternal or family identity influenced offspring responses to temperature. In characterizing these studies, Salmoniformes were the most studied order (52%), wild broodfish were more commonly used (55%), aquaculture motivations were less evident (23%), and few studies investigated offspring performance or traits beyond endogenous yolk stages. Overall, we suggest it is beneficial to experimentally examine temperature with consideration to parent-progeny relationships. To broaden our current understanding of intergenerational temperature effects, we recommend an increased focus on wild populations, offspring physiological and performance measures, later offspring development stages, and expanding research in non-salmonid species.     

Host-pathogen-environment interactions predict survival outcomes of adult sockeye salmon (Oncorhynchus nerka) released from fisheries

Incorporating host-pathogen(s)-environment axes into management and conservation planning is critical to preserving species in a warming climate. However, the role pathogens play in host stress resilience remains largely unexplored in wild animal populations. We experimentally characterized how independent and cumulative stressors (fisheries handling, high water temperature) and natural infections affected the health and longevity of released wild adult sockeye salmon (Oncorhynchus nerka) in British Columbia, Canada. Returning adults were collected before and after entering the Fraser River, yielding marine- and river-collected groups, respectively (N = 185). Fish were exposed to a mild (seine) or severe (gill net) fishery treatment at collection, and then held in flow-through freshwater tanks for up to four weeks at historical (14°C) or projected migration temperatures (18°C). Using weekly nonlethal gill biopsies and high-throughput qPCR, we quantified loads of up to 46 pathogens with host stress and immune gene expression. Marine-collected fish had less severe infections than river-collected fish, a short migration distance (100 km, 5–7 days) that produced profound infection differences. At 14°C, river-collected fish survived 1–2 weeks less than marine-collected fish. All fish held at 18°C died within 4 weeks unless they experienced minimal handling. Gene expression correlated with infections in river-collected fish, while marine-collected fish were more stressor-responsive. Cumulative stressors were detrimental regardless of infections or collection location, probably due to extreme physiological disturbance. Because river-derived infections correlated with single stressor responses, river entry probably decreases stressor resilience of adult salmon by altering both physiology and pathogen burdens, which redirect host responses toward disease resistance.     

OpenABM-Covid19—An agent-based model for non-pharmaceutical interventions against COVID-19 including contact tracing

SARS-CoV-2 has spread across the world, causing high mortality and unprecedented restrictions on social and economic activity. Policymakers are assessing how best to navigate through the ongoing epidemic, with computational models being used to predict the spread of infection and assess the impact of public health measures. Here, we present OpenABM-Covid19: an agent-based simulation of the epidemic including detailed age-stratification and realistic social networks. By default the model is parameterised to UK demographics and calibrated to the UK epidemic, however, it can easily be re-parameterised for other countries. OpenABM-Covid19 can evaluate non-pharmaceutical interventions, including both manual and digital contact tracing, and vaccination programmes. It can simulate a population of 1 million people in seconds per day, allowing parameter sweeps and formal statistical model-based inference. The code is open-source and has been developed by teams both inside and outside academia, with an emphasis on formal testing, documentation, modularity and transparency. A key feature of OpenABM-Covid19 are its Python and R interfaces, which has allowed scientists and policymakers to simulate dynamic packages of interventions and help compare options to suppress the COVID-19 epidemic.