Impact of parasites on salmon recruitment in the Northeast Atlantic Ocean

A modeling study of the impact of treatment policies on the evolution of resistance in sea lice on salmon farms

Salmonid aquaculture is an important source of nutritious food with more than 2 million tonnes of fish produced each year (Food and Agriculture Organisation of the United Nations, 2019). In most salmon producing countries, sea lice represent a major barrier to the sustainability of salmonid aquaculture. This issue is exacerbated by widespread resistance to chemical treatments on both sides of the Atlantic. Regulation for sea lice management mostly involves reporting lice counts and treatment thresholds, which depending on interpretation may encourage preemptive treatments. We have developed a stochastic simulation model of sea lice infestation including the lice life-cycle, genetic resistance to treatment, a wildlife reservoir, salmon growth and stocking practices in the context of infestation, and coordination of treatment between farms. Farms report infestation levels to a central organisation, and may then cooperate or not when coordinated treatment is triggered. Treatment practice then impacts the level of resistance in the surrounding sea lice population. Our simulation finds that treatment drives selection for resistance and coordination between managers is key. We also find that position in the hydrologically-derived network of farms can impact individual farm infestation levels and the topology of this network can impact overall infestation and resistance. We show how coordination and triggering of treatment alongside varying hydrological topology of farm connections affects the evolution of lice resistance, and thus optimise salmon quality within socio-economic and environmental constraints. Network topology drives infestation levels in cages, treatments, and hence treatment-driven resistance. Thus farmer behaviour may be highly dependent on hydrologically position and local level of infestation.

Direct evidence of increased natural mortality of a wild fish caused by parasite spillback from domestic conspecifics

Parasite spillback from domestic animals can distort the balance between host and parasites in surrounding wildlife, with potential detrimental effects on wild populations. In aquatic environments, parasite spillback from aquaculture to wild salmon is one of the most contentious sustainability debates. In a 19 year time series of release group studies of Atlantic salmon, we demonstrated that (i) the effect of subjecting out-migrating salmon smolts to parasite treatment on marine survival has been reduced over a time, (ii) the relation between salmon lice levels in the out-migration route of the salmon and effect of treatment against the parasite is weak, but also (iii) the return rates in both treated and untreated groups of salmon are negatively correlated with salmon lice levels, and (iv) returns of wild salmon to the region are similarly negatively correlated with salmon lice levels during the out-migration year. Our study suggests that salmon lice can have a large effect on wild salmon populations that is not revealed with randomized control trials using antiparasitic drugs. This should be better accounted for when considering the impacts of farms on wild salmon populations.

The effect of different intensities of the ectoparasitic salmon lice (Lepeophtheirus salmonis) on Atlantic salmon (Salmo salar)

The effect of different intensities of the ectoparasitic salmon lice (Lepeophtheirus salmonis) on stress, growth and the expression of immune and wound healing transcripts in the skin of Atlantic salmon (Salmo salar) was investigated. Lice infection success and survival were similar at the chalimus and preadult stage in the low and high dose group, but infection success and survival were significantly lower in the high than in the low dose group at the adult stage. The expression of investigated transcripts was not correlated to lice intensities, but several of them were significantly differently expressed locally in the skin at the site of lice attachment in infected fish compared to controls. This included an up-regulation of pro-inflammatory markers at the site of lice attachment (e.g., interleukin 1-beta, interleukin 8 and the acute phase protein serum amyloid A), a reduction of markers of adaptive immunity (cluster of differentiation 8-alpha and immunoglobulin M) and decreased expression of the anti-inflammatory cytokine interleukin 10.

Silver Shiner, Notropis photogenis, fecundity and parasite infections during the reproductive period

The reproductive period is a critical part of a species' life-history. Estimating species-specific fecundity can improve demographic models aimed at developing recovery targets for imperilled species. We provide egg diameter and fecundity estimates and develop a length-fecundity relationship for Silver Shiner, Notropis photogenis (Cope,1865), a small-bodied freshwater species listed as Threatened under Canada’s Species at Risk Act. Furthermore, we document the incidence of an acanthocephalan parasite (thorny-headed worm) Leptorhychoides thecatus (Linton, 1891), in the gastrointestinal tract of Silver Shiner, which is the first published record of the parasite in this species. Silver Shiner egg diameters (average ± standard deviation) were 0.61 ± 0.15 mm and ranged from 0.13-0.92 mm. Fecundity ranged from 311-2768 eggs and was significantly higher in age 2-3+ fish (1475 ± 570 eggs) compared to age 1+ fish (576 ± 270 eggs). We highlight that parasite infection negatively impacted the body condition of individuals and that additional work is needed to determine the impact of parasite infestation on reproductive output, recruitment, susceptibility to predation, and survival of Silver Shiner in Canada. The fecundity and egg diameter estimates for Canadian Silver Shiner provided here can be incorporated into future populations modelling for this threatened species.

North American diadromous fishes: Drivers of decline and potential for recovery in the Anthropocene

Diadromous fishes migrate between freshwater and marine habitats to complete their life cycle, a complexity that makes them vulnerable to the adverse effects of current and past human activities on land and in the oceans. Many North American species are critically endangered, and entire populations have been lost. Major factors driving declines include overfishing, pollution, water withdrawals, aquaculture, non-native species, habitat degradation, over-zealous application of hatcheries designed to mitigate effects of other factors, and effects of climate change. Perhaps, the most broadly tractable and effective factors affecting diadromous fishes are removals of the dams that prevent or hinder their migrations, alter their environment, and often favor non-native biotic communities. Future survival of many diadromous fish populations may depend on this.

Research Before Policy: Identifying Gaps in Salmonid Welfare Research That Require Further Study to Inform Evidence-Based Aquaculture Guidelines in Canada

Aquaculture is a growing industry worldwide and Canadian finfish culture is dominated by marine salmonid farming. In part due to increasing public and stakeholder concerns around fish welfare protection, the first-ever Canadian Code of Practice for the Care and Handling of Farmed Salmonids was recently completed, following the National Farm Animal Care Council's (NFACC) rigorous Code development process. During this process, both the Scientific (responsible for reviewing existing literature and producing a peer-reviewed report that informs the Code) and Code Development (a diverse group of stakeholders including aquaculture producers, fish transporters, aquaculture veterinarians, animal welfare advocates, food retailers, government, and researchers) Committees identified research gaps in tandem, as they worked through the literature on salmonid physiology, health, husbandry, and welfare. When those lists are combined with the results of a public "top-of-mind" survey conducted by NFACC, they reveal several overlapping areas of scientific, stakeholder, and public concern where scientific evidence is currently lacking: (1) biodensity; (2) health monitoring and management, with a focus on sea lice infection prevention and management; (3) feed quality and management, particularly whether feed restriction or deprivation has consequences for welfare; (4) enclosure design, especially focused on environmental enrichment provision and lighting design; and (5) slaughter and euthanasia. For each of these five research areas, we provide a brief overview of current research on the topic and outline the specific research gaps present. The final section of this review identifies future research avenues that will help address these research gaps, including using existing paradigms developed by terrestrial animal welfare researchers, developing novel methods for assessing fish welfare, and the validation of new salmonid welfare indices. We conclude that there is no dearth of relevant research to be done in the realm of farmed salmonid welfare that can support crucial evidence-based fish welfare policy development.

Parasite management in aquaculture exerts selection on salmon louse behaviour

The evolution of pest resistance to management strategies is a major challenge for farmed systems. Mitigating the effects of pest adaptation requires identifying the selective pressures imposed by these strategies. In Atlantic salmon (Salmo salar) aquaculture, barriers are used to prevent salmon louse (Lepeophtheirus salmonis) larvae (copepodids) from entering salmon cages. These barriers are effective against shallow-swimming copepodids, but those swimming deeper can pass underneath and infest salmon. Laboratory experiments suggest that depth regulation in copepodids is a variable behavioural trait with a genetic basis. We used biological-hydrodynamic dispersal models to assess how this trait variation alters the dispersion of lice through the ocean environment and into farms. The dispersal of copepodids with 3 behavioural phenotypes (deep, mean or shallow) was modelled over winter-spring and spring-summer periods in a Norwegian fjord system with intensive aquaculture. The infestation pressure of each phenotype on barrier cages was estimated from their modelled depth distributions: copepodids deeper than 10 m were predicted to successfully pass underneath barriers. The deep phenotype was the most abundant below 10 m and reached infestation pressures 3 times higher than that of the mean phenotype. In contrast, the shallow phenotype infestation pressure reached less than half that of the mean phenotype. These differences in relative fitness indicate that barriers can impose strong directional selection on the swimming behaviour of copepodids. The strength of this selection varied seasonally and geographically, with selection for the deep phenotype stronger in winter-spring and at coastal locations than in spring-summer and within fjords. These findings can be applied across farms to slow louse adaptation, by limiting barriers during situations of strong selection, although this must be balanced against trade-offs to short-term efficacy. More broadly, our study highlights new ways in which dispersal models can address evolutionary questions crucial for sustainable parasite management in aquaculture.

Illuminating the planktonic stages of salmon lice: A unique fluorescence signal for rapid identification of a rare copepod in zooplankton assemblages

Monitoring of planktonic salmon louse (Lepeophtheirus salmonis salmonis) abundance and parameterization of key life-history traits has been hindered by labour-intensive and error-prone quantification using traditional light microscopy. Fluorescence illumination has been proposed as a means of improving visualization, but prior to this study adequate investigation of the relevant fluorescence profiles and measurement conditions has not been undertaken. We investigated the fluorescence profiles of L. salmonis and non-target copepod spp. with excitation and emission matrices (200-600 nm) and identified unique fluorescence signals. Fluorescence microscopy using excitation wavelengths of 470 ± 40 nm, and emission wavelengths of 525 ± 50 nm, showed that after 90 days of formalin storage salmon lice have a mean fluorescence intensity that is 2.4 times greater than non-target copepods (copepodid and adult stages). A 7-day heat treatment of 42°C in formalin increased the difference between salmon louse copepodids and non-target copepods to a factor of 3.6, eliminating the need for prolonged storage. Differences in the fluorescence signal and endogenous fluorophores were investigated with respect to variation in sea lice species, age, stage and host fish origin. Under the conditions outlined in this paper, the fluorescence signal was found to be a reliable means of visualizing and differentiating salmon lice from non-target zooplankters. Adaptation of the fluorescence signal would greatly expedite traditional methods of enumerating salmon louse larvae in plankton samples and could provide a means of automated detection.

Climate change-driven disease in sympatric hosts: Temporal dynamics of parasite burden and proliferative kidney disease in wild brown trout and Atlantic salmon

Global climate change is altering the abundance and spread of various parasites, which has important consequences not only for host-parasite interactions but also for the relationships between different host species. Here, we focus on the myxozoan endoparasite Tetracapsuloides bryosalmonae that causes temperature-dependent proliferative kidney disease (PKD) in salmonids. We characterized the temporal changes in the parasite load and the severity of PKD signs (renal hyperplasia, haematocrit) in two sympatric populations of wild brown trout (Salmo trutta) and Atlantic salmon (Salmo salar). We found that both the parasite load and disease signs vary considerably between individuals, species, rivers and sampling periods. We showed that Atlantic salmon was able to slow down the initial parasite proliferation rate and subsequently tolerate high parasite burden without obvious disease signs. In contrast, the initial parasite proliferation rate was much higher in brown trout, which was followed by the development of severe PKD signs. Thus, the speed of parasite proliferation, rather than the absolute number of the parasites in the host kidney, may play an important role in interspecific variation in PKD susceptibility. To conclude, this study illustrates the usefulness of temporal perspective for understanding host defence mechanisms and climate change-mediated impacts in the wild.

Delayed maturity does not offset negative impact afflicted by ectoparasitism in salmon

The negative effects of parasitism on host population dynamics may be mediated by plastic compensatory life-history changes in hosts. Theory predicts that hosts should shift their life-history towards early reproduction in response to virulent pathogens to maximize reproduction before death. However, for sublethal infections that affect growth, hosts whose fecundity is correlated with body size are predicted to shift towards delayed reproduction associated with larger body size and higher fecundity. This has been observed in Atlantic salmon and parasitic sea lice, via mark-recapture studies that recover mature fish from paired groups of control and parasiticide-treated smolts. We investigated whether such louse-induced changes to age at maturity can offset some of the negative effect of mortality on population growth rate in salmon using a structured population matrix model. Model results show that delayed maturity can partially compensate for reduced survival. However, this only occurs when marine survival is moderate to poor and growth conditions at sea are good. Also, the impact of delayed maturity on population growth when parameterizing the model with empirical data is negligible compared with effects of direct mortality. Our model thus suggests that management that works on minimizing the effect of sea lice from fish farms on wild salmon should focus mainly on correctly quantifying the effect of parasite-induced mortality during the smolt stage if the goal is to maximize population growth rate.

Animal migrations and parasitism: reciprocal effects within a unified framework

Migrations, i.e. the recurring, roundtrip movement of animals between distant and distinct habitats, occur among diverse metazoan taxa. Although traditionally linked to avoidance of food shortages, predators or harsh abiotic conditions, there is increasing evidence that parasites may have played a role in the evolution of migration. On the one hand, selective pressures from parasites can favour migratory strategies that allow either avoidance of infections or recovery from them. On the other hand, infected animals incur physiological costs that may limit their migratory abilities, affecting their speed, the timing of their departure or arrival, and/or their condition upon reaching their destination. During migration, reduced immunocompetence as well as exposure to different external conditions and parasite infective stages can influence infection dynamics. Here, we first explore whether parasites represent extra costs for their hosts during migration. We then review how infection dynamics and infection risk are affected by host migration, thereby considering parasites as both causes and consequences of migration. We also evaluate the comparative evidence testing the hypothesis that migratory species harbour a richer parasite fauna than their closest free-living relatives, finding general support for the hypothesis. Then we consider the implications of host migratory behaviour for parasite ecology and evolution, which have received much less attention. Parasites of migratory hosts may achieve much greater spatial dispersal than those of non-migratory hosts, expanding their geographical range, and providing more opportunities for host-switching. Exploiting migratory hosts also exerts pressures on the parasite to adapt its phenology and life-cycle duration, including the timing of major developmental, reproduction and transmission events. Natural selection may even favour parasites that manipulate their host's migratory strategy in ways that can enhance parasite transmission. Finally, we propose a simple integrated framework based on eco-evolutionary feedbacks to consider the reciprocal selection pressures acting on migratory hosts and their parasites. Host migratory strategies and parasite traits evolve in tandem, each acting on the other along two-way causal paths and feedback loops. Their likely adjustments to predicted climate change will be understood best from this coevolutionary perspective.

Bias in self-reported parasite data from the salmon farming industry

Many industries are required to monitor themselves in meeting regulatory policies intended to protect the environment. Self-reporting of environmental performance can place the cost of monitoring on companies rather than taxpayers, but there are obvious risks of bias, often addressed through external audits or inspections. Surprisingly, there have been relatively few empirical analyses of bias in industry self-reported data. Here, we test for bias in reporting of environmental compliance data using a unique data set from Canadian salmon farms, where companies monitor the number of parasitic sea lice on fish in open sea pens, in order to minimize impacts on wild fish in surrounding waters. We fit a hierarchical population-dynamics model to these sea-louse count data using a Bayesian approach. We found that the industry's monthly counts of two sea-louse species, Caligus clemensi and Lepeophtheirus salmonis, increased by a factor of 1.95 (95% credible interval: 1.57, 2.42) and 1.18 (1.06, 1.31), respectively, in months when counts were audited by the federal fisheries department. Consequently, industry sea-louse counts are less likely to trigger costly but mandated delousing treatments intended to avoid sea-louse epidemics in wild juvenile salmon. These results highlight the potential for combining external audits of industry self-reported data with analyses of their reporting to maintain compliance with regulations, achieve intended conservation goals, and build public confidence in the process.

Increasing temperatures accentuate negative fitness consequences of a marine parasite

Infectious diseases are key drivers of wildlife populations and agriculture production, but whether and how climate change will influence disease impacts remains controversial. One of the critical knowledge gaps that prevents resolution of this controversy is a lack of high-quality experimental data, especially in marine systems of significant ecological and economic consequence. Here, we performed a manipulative experiment in which we tested the temperature-dependent effects on Atlantic salmon (Salmo salar) of sea lice (Lepeophtheirus salmonis)—a parasite that can depress the productivity of wild-salmon populations and the profits of the salmon-farming industry. We explored sea-louse impacts on their hosts across a range of temperatures (10, 13, 16, 19, and 22 °C) and infestation levels (zero, ‘low’ (mean abundance ± SE = 1.6 ± 0.1 lice per fish), and ‘high’ infestation (6.8 ± 0.4 lice per fish)). We found that the effects of sea lice on the growth rate, condition, and survival of juvenile Atlantic salmon all worsen with increasing temperature. Our results provide a rare empirical example of how climate change may influence the impacts of marine disease in a key social-ecological system. These findings underscore the importance of considering climate-driven changes to disease impacts in wildlife conservation and agriculture.

A portrait of the immune response to proliferative kidney disease (PKD) in rainbow trout

Proliferative kidney disease (PKD), caused by the myxozoan Tetracapsuloides bryosalmonae, is one of the most serious parasitic diseases of salmonids in which outbreaks cause severe economic constraints for the aquaculture industry and declines of wild species throughout Europe and North America. Given that rainbow trout (Oncorhynchus mykiss) is one of the most widely farmed freshwater fish and an important model species for fish immunology, most of the knowledge on how the fish immune response is affected during PKD is from this organism. Once rainbow trout are infected, PKD pathogenesis results in a chronic kidney immunopathology mediated by decreasing myeloid cells and increasing lymphocytes. Transcriptional studies have revealed the regulation of essential genes related to T-helper (Th)-like functions and a dysregulated B-cell antibody type response. Recent reports have discovered unique details of teleost B-cell differentiation and functionality and characterized the differential immunoglobulin (Ig)-mediated response. These studies have solidified the rainbow trout T. bryosalmonae system as a sophisticated disease model capable of feeding key advances into mainstream immunology and have contributed essential information to design novel parasite disease prevention strategies. In our following perspective, we summarize these efforts to evaluate the immune mechanisms of rainbow trout during PKD pathogenesis.

Sterilization of sea lice eggs with ultraviolet C light: towards a new preventative technique for aquaculture

BACKGROUND

Sea lice infestations on Atlantic salmon (Salmo salar) farms are a considerable burden on the industry and put wild salmonid populations at risk. Frequent delousing treatments are necessary to keep lice densities below allowable limits, but currently viable treatments have drawbacks in terms of financial cost, animal welfare, or environmental impacts. We tested if 254 nm ultraviolet C light (UVC) could function as a new preventative method to suppress reproduction of salmon lice (Lepeophtheirus salmonis) by sterilizing fertilized eggs. We exposed salmon lice eggstrings to a range of UVC intensities and durations to identify effective doses.

RESULTS

A cumulative dose of 0.008 J cm^-2 induced 5% egg mortality, while 95% egg mortality occurred at 0.09 J cm^-2 , indicating that UVC can be effective as a preventative treatment. The total cumulative dose appeared to be more important than the duration or number of individual exposures by which the total dose was achieved.

CONCLUSION

UVC treatment has immediate applications for the salmon aquaculture industry, including for the treatment of wastewater from delousing or other operations. Future work will assess the feasibility of UVC dose delivery on host salmon in sea cage environments that involves little or no fish handling and creates negligible environmental impacts. © 2019 Society of Chemical Industry.

Age of first infection across a range of parasite taxa in a wild mammalian population

Newborn mammals have an immature immune system that cannot sufficiently protect them against infectious diseases. However, variation in the effectiveness of maternal immunity against different parasites may couple with temporal trends in parasite exposure to influence disparities in the timing of infection risk. Determining the relationship between age and infection risk is critical in identifying the portion of a host population that contributes to parasite dynamics, as well as the parasites that regulate host recruitment. However, there are no data directly identifying timing of first infection among parasites in wildlife. Here, we took advantage of a longitudinal dataset, tracking infection status by viruses, bacteria, protists and gastro-intestinal worms in a herd of African buffalo (Syncerus caffer) to ask: how does age of first infection differ among parasite taxa? We found distinct differences in the age of first infection among parasites that aligned with the mode of transmission and parasite taxonomy. Specifically, we found that tick-borne and environmentally transmitted protists were acquired earlier than directly transmitted bacteria and viruses. These results emphasize the importance of understanding infection risk in juveniles, especially in host species where juveniles are purported to sustain parasite persistence and/or where mortality rates of juveniles influence population dynamics.

Effect of cleaner fish on sea lice in Norwegian salmon aquaculture: a national scale data analysis

The salmon aquaculture industry has adopted the use of invertivorous 'cleaner fishes' (CF) for biological control of sea louse infestations on farmed salmon. At present, ~50 million CF are used annually in Norway alone, with variable success in experimental and industrial contexts. We used a national scale database of louse counts, delousing treatments and CF stocking events on Norwegian salmon farms to test for evidence of CF efficacy at 488 sites that completed a grow-out cycle within 2016-2018. Our analysis revealed that sites using more CF over the duration of a grow-out cycle did not have fewer lice on average, likely because CF use is reactive and in proportion to the scale of the louse problem. Over time within sites, we found that (i) sites using more CF early in the grow-out cycle were able to wait slightly longer (conservatively, a 5.2 week delay with 5000 CF stocked week^-1) before conducting the first delousing treatment, and (ii) CF stocking events were followed, on average, by a small reduction in louse population growth rates. However, both effects were small and highly variable, and louse population growth rates remained positive on average, even when large numbers of CF were used (tens of thousands per site). Moreover, effects of CF on louse density tended to be short-lived, likely reflecting mortality and escape of stocked CF. Overall, the data indicate that while some sites consistently obtain good results from CF, there is also widespread suboptimal use. A better understanding of factors affecting CF efficacy in commercial sea cages is required to inform legislation and drive more efficient and ethical use of CF by the salmon aquaculture industry.

The planktonic stages of the salmon louse (Lepeophtheirus salmonis) are tolerant of end-of-century pCO2 concentrations

The copepod Lepeophtheirus salmonis is an obligate ectoparasite of salmonids. Salmon lice are major pests in salmon aquaculture and due to its economic impact Lepeophtheirus salmonis is one of the most well studied species of marine parasite. However, there is limited understanding of how increased concentration of pCO₂ associated with ocean acidification will impact host-parasite relationships. We investigated the effects of increased pCO₂ on growth and metabolic rates in the planktonic stages, rearing L. salmonis from eggs to 12 days post hatch copepodids under three treatment levels: Control (416 µatm), Mid (747 µatm), and High (942 µatm). The pCO₂ treatment had a significant effect on oxygen consumption rate with the High treatment animals exhibiting the greatest respiration. The treatments did not have a significant effect on the other biological endpoints measured (carbon, nitrogen, lipid volume, and fatty acid content). The results indicate that L. salmonis have mechanisms to compensate for increased concentration of pCO₂and that populations will be tolerant of projected future ocean acidification scenarios. The work reported here also describes catabolism during the lecithotrophic development of L. salmonis, information that is not currently available to parameterize models of dispersal and viability of the planktonic free-living stages.

First record of the nematode Echinocephalus pseudouncinatus (Gnathostomatidae, Spirurida) in an edible, commercial host, the pen shell Atrina maura (Bivalvia: Pinnidae)

We describe a nematode infestation of the Atrina maura, the most valuable pen shell fished in Mexico, for the first time. Observations by Mexican authorities indicated that parasites were found encysted in pen shell gonads. The aims of this study included: (i) to identify the parasite morphologically; (ii) to quantify the infestation in different tissues of the pen shell; and (iii) to establish the seasonal variation in gonadal development. During 2015, 10 to 40 pen shells were randomly collected each month from the same commercial bed, and gonads were preserved and processed histologically to establish the seasonal and monthly frequency of infested gonads. A subsample of 35 pen shells was used to identify the parasite and to characterize the infestation of the muscle, mantle, gonad, and digestive gland tissue components. All tissues were dissected, and parasites were collected, photographed, quantified, and adequately preserved for species identification using scanning electron microscopy. Prevalence, intensity of infestation, abundance and crowding data were analyzed by Quantitative Parasitology software and compared monthly and seasonally using a chi test and analysis of means. Results indicated that all parasites were juvenile (second stage) nematodes, Echinocephalus pseudouncinatus. Parasites were found only in muscle and gonad tissues in both male and female pen shells. Hyperpigmentation was observed in the muscle and atretic oocytes with phagocytosis in the gonads. The frequency of infested gonads was significantly higher during winter but was not related to shell size or sex (p > 0.05). A greater number of pen shells were observed to be infested during December and August and during pen shell spawning and development stages. The highest frequency of infested gonads (40%) occurred in December when the lowest temperature and chlorophyll a concentration were recorded. The effects of the biotic and abiotic parameters on this host-pathogen relationship need further research. This nematode species is related to species that are causal agents of gnathostomiasis, which may constitute a health hazard for raw muscle consumers and could affect the reproductive activity of pen shell.

The effectiveness of hyposaline treatments against host-attached salmon lice

Understanding how salinity affects marine parasites is vital to understanding their ecology and treatment, particularly for host-parasite systems that traverse marine and freshwater realms such as the globally important Atlantic salmon (Salmo salar), salmon louse (Lepeophtheirus salmonis) system. Growing concerns for wild fish populations, and decreased efficiencies and burgeoning costs of lice treatments for farmed fish has necessitated more environmentally and socially acceptable delousing procedures, such as hyposaline treatments. The effect of brackish water on L. salmonis following primary attachment is largely unknown, with experimental evidence derived mostly from unattached or newly attached copepodids, or adult stages. We aimed to understand how attached lice respond to hyposaline environments to assess effectiveness as a parasite management strategy and to help better define delousing areas used by wild fish. Louse development at 4, 12, 19 and 26 ppt, and survival at 4 ppt, decreased as exposure times increased, but survival was otherwise unaffected. Subjecting salmon to fluctuating, repeat exposures did not influence efficacy. We confirm that free-swimming stages are susceptible, and show that attached copepodids were more tolerant than previously predicted based on experiments on alternate development stages. These results improve our understanding of the utility of hyposaline treatments in aquaculture and self-treating in wild fish, and could apply to other fish-lice parasite systems. Further, these data are important for models predicting host-parasite interactions and can contribute to predictive models on the transmission dynamics of sea lice from farm to wild fish.

The Use of Kernel Density Estimation With a Bio-Physical Model Provides a Method to Quantify Connectivity Among Salmon Farms: Spatial Planning and Management With Epidemiological Relevance

Connectivity in an aquatic setting is determined by a combination of hydrodynamic circulation and the biology of the organisms driving linkages. These complex processes can be simulated in coupled biological-physical models. The physical model refers to an underlying circulation model defined by spatially-explicit nodes, often incorporating a particle-tracking model. The particles can then be given biological parameters or behaviors (such as maturity and/or survivability rates, diel vertical migrations, avoidance, or seeking behaviors). The output of the bio-physical models can then be used to quantify connectivity among the nodes emitting and/or receiving the particles. Here we propose a method that makes use of kernel density estimation (KDE) on the output of a particle-tracking model, to quantify the infection or infestation pressure (IP) that each node causes on the surrounding area. Because IP is the product of both exposure time and the concentration of infectious agent particles, using KDE (which also combine elements of time and space), more accurately captures IP. This method is especially useful for those interested in infectious agent networks, a situation where IP is a superior measure of connectivity than the probability of particles from each node reaching other nodes. Here we illustrate the method by modeling the connectivity of salmon farms via sea lice larvae in the Broughton Archipelago, British Columbia, Canada. Analysis revealed evidence of two sub-networks of farms connected via a single farm, and evidence that the highest IP from a given emitting farm was often tens of kilometers or more away from that farm. We also classified farms as net emitters, receivers, or balanced, based on their structural role within the network. By better understanding how these salmon farms are connected to each other via their sea lice larvae, we can effectively focus management efforts to minimize the spread of sea lice between farms, advise on future site locations and coordinated treatment efforts, and minimize any impact of farms on juvenile wild salmon. The method has wide applicability for any system where capturing infectious agent networks can provide useful guidance for management or preventative planning decisions.

The Atlantic salmon (Salmo salar) antimicrobial peptide cathelicidin-2 is a molecular host-associated cue for the salmon louse (Lepeophtheirus salmonis)

Chemical signals are a key element of host-parasite interactions. In marine ecosystems, obligate ectoparasites, such as sea lice, use chemical cues and other sensory signals to increase the probability of encountering a host and to identify appropriate hosts on which they depend to complete their life cycle. The chemical compounds that underlie host identification by the sea lice are not fully described or characterized. Here, we report a novel compound - the Atlantic salmon (Salmo salar) antimicrobial peptide cathelicidin-2 (Cath-2) – that acts as an activation cue for the marine parasitic copepod Lepeophtheirus salmonis. L. salmonis were exposed to 0, 7, 70 and 700 ppb of Cath-2 and neural activity, swimming behaviour and gene expression profiles of animals in response to the peptide were evaluated. The neurophysiological, behavioural and transcriptomic results were consistent: L. salmonis detects Cath-2 as a water-soluble peptide released from the skin of salmon, triggering chemosensory neural activity associated with altered swimming behaviour of copepodids exposed to the peptide, and chemosensory-related genes were up-regulated in copepodids exposed to the peptide. L. salmonis are activated by Cath-2, indicating a tight link between this peptide and the salmon louse chemosensory system.

Behavioural responses of infective-stage copepodids of the salmon louse (Lepeophtheirus salmonis, Copepoda:Caligidae) to host-related sensory cues

The salmon louse (Lepeophtheirus salmonis [Krøyer]) is an ectoparasitic copepod that causes disease in farmed Atlantic salmon (Salmo salar) and may play a role in the decline of some wild salmonid populations. Controlling lice infestations is a major cost for the salmon industry; this has stimulated the pursuit of alternative approaches to controlling them. One such approach involves determining, and then disrupting, the sensory cues used by the parasite to find its host. In this context, we examined the behavioural responses of lice copepodids to light flicker-simulating light reflecting from the sides of the salmon host and/or the shadows cast by fish passing overhead-and water-soluble chemicals released from the skin of the salmon. From these observations, we estimate that visual cues such as those presented here would operate at relatively long range (metres to tens of metres). A diffuse host-related olfactory cue stimulated swimming, however, it remains unclear whether olfactory cues provide directional information. The observations presented herein could be used to disrupt the link between the parasite and host fish, using a large number of traps deployed at a distance from a salmon farm, for example, thereby reducing sea lice infestation pressure.

Sea trout adapt their migratory behaviour in response to high salmon lice concentrations

Sea trout face growth-mortality trade-offs when entering the sea to feed. Salmon lice epizootics resulting from aquaculture have shifted these trade-offs, as salmon lice might both increase mortality and reduce growth of sea trout. We studied mortality and behavioural adaptations of wild sea trout in a large-scale experiment with acoustic telemetry in an aquaculture intensive area that was fallowed (emptied of fish) synchronically biannually, creating large variations in salmon lice concentrations. We tagged 310 wild sea trout during 3 years, and gave half of the individuals a prophylaxis against further salmon lice infestation. There was no difference in survival among years or between treatments. In years of high infestation pressure, however, sea trout remained closer to the river outlet, used freshwater (FW) habitats for longer periods and returned earlier to the river than in the low infestation year. This indicates that sea trout adapt their migratory behaviour by actively choosing FW refuges from salmon lice to escape from immediate mortality risk. Nevertheless, simulations show that these adaptations can lead to lost growth opportunities. Reduced growth can increase long-term mortality of sea trout due to prolonged exposure to size-dependent predation risk, lead to lower fecundity and, ultimately, reduce the likelihood of sea migration.

A multivariable assessment of the spatio-temporal distribution of pyrethroids performance on the sea lice Caligus rogercresseyi in Chile

Synthetic pyrethroids have been widely used in Chile to control the sea lice Caligus rogercresseyi, a major ectoparasite of farmed salmon. Although resistance of C. rogercresseyi to pyrethroids has been reported in Chile, there is no information regarding the geographic extent of this problem. In this study we explored the spatial and temporal variation of C. rogercresseyi's response to pyrethroids in Chile from 2012 to 2013. We modeled lice abundance one week after treatment with a linear mixed-effects regression, and then we performed spatial and spatio-temporal cluster analyses on farm-level effects and on treatment-level residuals, respectively. Results indicate there were two areas where the post-treatment lice counts were significantly higher than in the rest of the study area. These spatial clusters remained even once we adjusted for environmental and management predictors, suggesting unmeasured factors (e.g. resistance) were causing the clustering. Further investigation should be carried out to confirm this hypothesis.

Presence of selected pathogens on the gills of five wrasse species in western Norway

The objective of this study was to identify gill pathogens in Labridae (wrasse) species used as cleaner fish to control salmon louse in western Norwegian aquaculture. Wrasse are often moved over long distances, raising issues of fish health, welfare and pathogen transmission. Histological examination and real-time RT-PCR analysis of the gills from Centrolabrus exoletus, Ctenolabrus rupestris, Labrus bergylta, L. mixtus and Symphodus melops revealed several pathogens: a new species of Ichthyobodo, Paramoeba perurans, microsporidia, trichodinids, Hatschekia spp., Candidatus Similichlamydia labri and 2 putative new species of Chlamydiae. Cand. S. labri or closely related bacteria were present on most wrasse specimens. Epitheliocysts on the gills of L. mixtus contained large inclusions (120 µm) with actiniae radiating from the inclusion membrane. A possible member of the Candidatus family Parilichlamydiaceae was present at a high prevalence on the gills of L. mixtus, L. bergylta and C. rupestris. Sequencing the 16S rRNA gene showed 93.9% similarity to Cand. S. labri and 96.8% similarity to Cand. Parilichlamydia carangidicola from the gills of Seriola lalandi. This bacterium probably represents a new species within the order Chlamydiales, family Cand. Parilichlamydiaceae. The other Chlamydiae detected on gills of S. melops could represent a new species in Cand. genus Syngnamydia. Ichthyobodo sp. and Paranucleospora theridion were detected on the gills of nearly all individuals, while Paramoeba spp. were detected on the gills of L. bergylta and L. mixtus. Trichodinids, microsporidia and parasitic copepods had low prevalence. Viral haemorrhagic septicaemia virus was not detected.

Quantitative risk assessment of salmon louse-induced mortality of seaward-migrating post-smolt Atlantic salmon

The Norwegian government recently implemented a new management system to regulate salmon farming in Norway, aiming to promote environmentally sustainable growth in the aquaculture industry. The Norwegian coast has been divided into 13 production zones and the volume of salmonid production in the zones will be regulated based on salmon lice effects on wild salmonids. Here we present a model for assessing salmon louse-induced mortality of seaward-migrating post-smolts of Atlantic salmon. The model quantifies expected salmon lice infestations and louse-induced mortality of migrating post-smolt salmon from 401 salmon rivers draining into Norwegian coastal waters. It is assumed that migrating post-smolts follow the shortest path from river outlets to the high seas, at constant progression rates. During this migration, fish are infested by salmon lice of farm origin according to an empirical infestation model. Furthermore, louse-induced mortality is estimated from the estimated louse infestations. Rivers draining into production zones on the West Coast of Norway were at the highest risk of adverse lice effects. In comparison, rivers draining into northerly production zones, along with the southernmost production zone, were at lower risk. After adjusting for standing stock biomass, estimates of louse-egg output varied by factors of up to 8 between production zones. Correlation between biomass adjusted output of louse infestation and densities of farmed salmon in the production zones suggests that a large-scale density-dependent host-parasite effect is a major driver of louse infestation rates and parasite-induced mortality. The estimates are sensitive to many of the processes in the chain of events in the model. Nevertheless, we argue that the model is suited to assess spatial and temporal risks associated with farm-origin salmon lice.

Migratory animals feel the cost of getting sick: A meta-analysis across species

Migratory animals are widely assumed to play an important role in the long-distance dispersal of parasites, and are frequently implicated in the global spread of zoonotic pathogens such as avian influenzas in birds and Ebola viruses in bats. However, infection imposes physiological and behavioural constraints on hosts that may act to curtail parasite dispersal via changes to migratory timing ("migratory separation") and survival ("migratory culling"). There remains little consensus regarding the frequency and extent to which migratory separation and migratory culling may operate, despite a growing recognition of the importance of these mechanisms in regulating transmission dynamics in migratory animals. We quantitatively reviewed 85 observations extracted from 41 studies to examine how both infection status and infection intensity are related to changes in body stores, refuelling rates, movement capacity, phenology and survival in migratory hosts across taxa. Overall, host infection status was weakly associated with reduced body stores, delayed migration and lower survival, and more strongly associated with reduced movement. Infection intensity was not associated with changes to host body stores, but was associated with moderate negative effects on movement, phenology and survival. In conclusion, we found evidence for negative effects of infection on host phenology and survival, but the effects were relatively small. This may have implications for the extent to which migratory separation and migratory culling act to limit parasite dispersal in migratory systems. We propose a number of recommendations for future research that will further advance our understanding of how migratory separation and migratory culling may shape host-parasite dynamics along migratory routes globally.

Impact of disease on the survival of three commercially fished species

Recent increases in emergent infectious diseases have raised concerns about the sustainability of some marine species. The complexity and expense of studying diseases in marine systems often dictate that conservation and management decisions are made without quantitative data on population-level impacts of disease. Mark-recapture is a powerful, underutilized, tool for calculating impacts of disease on population size and structure, even in the absence of etiological information. We applied logistic regression models to mark-recapture data to obtain estimates of disease-associated mortality rates in three commercially important marine species: snow crab (Chionoecetes opilio) in Newfoundland, Canada, that experience sporadic epizootics of bitter crab disease; striped bass (Morone saxatilis) in the Chesapeake Bay, USA, that experience chronic dermal and visceral mycobacteriosis; and American lobster (Homarus americanus) in the Southern New England stock, that experience chronic epizootic shell disease. All three diseases decreased survival of diseased hosts. Survival of diseased adult male crabs was 1% (0.003-0.022, 95% CI) that of uninfected crabs indicating nearly complete mortality of infected crabs in this life stage. Survival of moderately and severely diseased striped bass (which comprised 15% and 11% of the population, respectively) was 84% (70-100%, 95% CI), and 54% (42-68%, 95% CI) that of healthy striped bass. The disease-adjusted yearly natural mortality rate for striped bass was 0.29, nearly double the previously accepted value, which did not include disease. Survival of moderately and severely diseased lobsters was 30% (15-60%, 95% CI) that of healthy lobsters and survival of mildly diseased lobsters was 45% (27-75%, 95% CI) that of healthy lobsters. High disease mortality in ovigerous females may explain the poor recruitment and rapid declines observed in this population. Stock assessments should account for disease-related mortality when resource management options are evaluated.

'Snorkel' lice barrier technology reduced two co- occurring parasites, the salmon louse (Lepeophtheirus salmonis) and the amoebic gill disease causing agent (Neoparamoeba perurans), in commercial salmon sea-cages

Diverse chemical-free parasite controls are gaining status in Atlantic salmon sea-cage farming. Yet, the intricacies of their use at commercial scale, including effects on co-occurring parasites, are seldom reported. A new salmon lice prevention method involves installing a deep net roof and 'snorkel' lice barrier in cages to shelter salmon from free-living infective larvae which concentrate at shallow depths, and allows salmon to jump and re- inflate their buoyancy-regulating swim bladder by swallowing air. We document use of snorkel cages (10m deep barrier) in commercial farms, where their effects on salmon lice levels, amoebic gill disease (AGD)-related gill scores, the cage environment, fish welfare and farm management practices were compared to standard cages. During an autumn-winter study involving only snorkel cages, high AGD-related gill scores were observed to decline when freshwater was pumped into snorkels, creating a freshwater surface layer for salmon to enter for self-treatment. In a spring-summer study incorporating snorkel and standard cages, snorkel cages were found to reduce new lice infestations by 84%. The deployment of snorkels and intermittent oxygen depletion detected within them in the spring-summer study did not alter fish welfare parameters. Overall, the results suggest snorkel technology has a place in the toolkit of commercial salmon sea-cage farmers co-managing salmon lice and amoebic gill disease outbreaks - two principal parasite issues facing the industry.

Lessons from sea louse and salmon epidemiology

Effective disease management can benefit from mathematical models that identify drivers of epidemiological change and guide decision-making. This is well illustrated in the host-parasite system of sea lice and salmon, which has been modelled extensively due to the economic costs associated with sea louse infections on salmon farms and the conservation concerns associated with sea louse infections on wild salmon. Consequently, a rich modelling literature devoted to sea louse and salmon epidemiology has been developed. We provide a synthesis of the mathematical and statistical models that have been used to study the epidemiology of sea lice and salmon. These studies span both conceptual and tactical models to quantify the effects of infections on host populations and communities, describe and predict patterns of transmission and dispersal, and guide evidence-based management of wild and farmed salmon. As aquaculture production continues to increase, advances made in modelling sea louse and salmon epidemiology should inform the sustainable management of marine resources.

Interaction between migration behaviour and estuarine mortality in cultivated Atlantic salmon Salmo salar smolts

Migration behaviour and estuarine mortality of cultivated Atlantic salmon Salmo salar smolts in a 16 km long estuary were studied using two methods: (1) acoustic telemetry and (2) group tagging in combination with trap nets. Progression rates of surviving individuals through the estuary were relatively slow using both methods [0·38 L_T (total length) s^-1 v. 0·25 L_T  s^-1 ]. In 2012, the progression rate was slow from the river to the estuary (0·55 L_T  s^-1 ) and the first part of the estuary (0·31 L_T  s^-1 ), but increased thereafter (1·45-2·21 L_T  s^-1 ). In 2013, the progression rate was fast from the river to the estuary (4·31 L_T  s^-1 ) but was slower thereafter (0·18-0·91 L_T  s^-1 ). Survival to the fjord was higher in 2012 (47%) compared to 2013 (6%). Fast moving individuals were more likely to migrate successfully through the estuary compared to slower moving individuals. Adult recapture of coded-wire-tagged S. salar was generally low (0·00-0·04%). Mortality hot spots were related to topographically distinct areas such as the river outlet (in 2012) or the sill separating the estuary and the fjord (in 2013). At the sill, an aggregation of cod Gadus morhua predating on cultivated smolts was identified. The results indicate that slow progression rates through the estuary decreases the likelihood of smolts being detected outside the estuary. The highly stochastic and site-specific mortality patterns observed in this study highlight the complexity in extrapolating mortality patterns of single release groups to the entire smolt run of wild S. salar.

Passing a seawater challenge test is not indicative of hatchery-reared Atlantic salmon Salmo salar smolts performing as well at sea as their naturally produced conspecifics

Despite satisfactory reactions to seawater challenge tests indicative of appropriate physiological state, hatchery-reared Atlantic salmon Salmo salar smolts stocked in the Eira River in Norway between 2001 and 2011 performed less well at sea in terms of growth, age at maturity and survival than smolts of natural origin. The mean rates of return to the river for hatchery-reared and naturally produced S. salar were 0·98 and 2·35%. In the Eira River, c. 50 000 hatchery-reared S. salar smolts of local origin were stocked annually to compensate for reduced natural smolt production following regulation for hydroelectric purposes, while a mean of 17 262 smolts were produced naturally in the river. This study demonstrates that, although captive S. salar perform well in seawater challenge tests, hatchery-reared smolts are not necessarily as adaptable to marine life as their naturally produced counterparts. These findings suggest that production of hatchery-reared smolts more similar to naturally produced individuals in morphology, physiology and behaviour will be necessary to improve success of hatchery releases. Where possible, supplementary or alternative measures, including habitat restoration, could be implemented to ensure the long-term viability of wild stocks.

Wild juvenile salmonids in Muchalat Inlet, British Columbia, Canada: factors associated with sea lice prevalence

The Muchalat Inlet, British Columbia, is among the most westerly points at which aquaculture is practiced in Canada. In this paper, we summarise data from over 18000 wild fish sampled at 16 sites over an 8 yr period, between 2004 and 2011. The most prevalent wild species was chum salmon Oncorhynchus keta (82.4%), followed by Chinook O. tshawytscha (10%) and coho O. kisutch (4.3%). However, inter-annual and seasonal variation was evident, and smaller numbers of other Pacific salmon and stickleback species were sporadically observed. A high percentage of wild salmon (~95%) had no sea lice parasites present, with less than 1% of the fish hosting a mobile-stage sea louse. Of the data for which sea lice species were recorded, just over 96% of samples were identified as Lepeophtheirus salmonis. Logistic regression models assessed the association between the presence of lice and a range of independent variables. These models indicated a significant degree of spatial variation, much of which could be explained in terms of salinity levels. There were also important variations through time, both over the season within a year and across years. In addition, coho salmon were significantly more likely (odds ratio = 1.65; 95% CI = 1.20-2.3) to be infected than chum salmon. The protective effect of low salinity was most clearly seen at values lower than 15 psu, although this was dependent on fish species.

Pathogenicity of members of the vibrionaceae family to cultured juvenile sablefish

Sablefish Anoplopoma fimbria are a prized seafood species due to their high oil content and white flaky flesh. Raising these species in culture can help to provide an important source of protein for humans and relief to declining wild fish populations. Understanding the environmental factors that influence the production of Sablefish is important for successful culturing. The significance of host-pathogen interactions in Sablefish culture and the resulting environmental implications are unknown. Pathogens could potentially cause losses of cultured Sablefish stocks due to disease, while Sablefish cultured in net pens may also serve as reservoirs for pathogens and potentially transmit disease to wild fish species. In this initial study, the susceptibility of juvenile Sablefish to three bacterial pathogens from the family Vibrionaceae was examined. Listonella anguillarum, Vibrio ordalii, and V. splendidus can pose serious economic threats to cultured fish and shellfish. Groups of juvenile Sablefish were exposed to five concentrations of each of the pathogens. Sablefish were susceptible to L. anguillarum, but were resistant to V. ordalii and V. splendidus at exposure concentrations of ≤ 1.32 × 10⁷ CFU/mL and ≤ 3.57 × 10⁶ CFU/mL, respectively. The greatest L. anguillarum concentration examined (8.7 × 10⁶ CFU/mL) resulted in 24% mortality in juvenile Sablefish. A 24% loss of Sablefish stock could significantly influence an aquaculture program. As determined by multiple logistic regression, the survival of Sablefish to L. anguillarum exposure was significantly affected by their body mass, and larger fish had a greater probability of survival. Aquaculture operations could employ various strategies to minimize the loss of juvenile Sablefish by accounting for their size and known susceptibilities to pathogens.

Gone with the flow: current velocities mediate parasitic infestation of an aquatic host

Host-parasite interactions are moderated by the environmental conditions of the interaction medium (e.g. air or water). Encounter rate and the time available for a parasite to make physical contact with a host are both influenced by fluid dynamics, yet how they interact is poorly known. Here, we tested whether current velocities altered the initial attachment and post-settlement survival of an ecto-parasitic copepod (Lepeophtheirus salmonis) on Atlantic salmon. Current velocities strongly influenced attachment; infestation levels were 2.5 and 1.3 times higher in moderate than high and low velocity currents, respectively, while current velocities did not affect post-settlement survival. An interplay between a reduced host-parasite encounter rate in a low velocity current and reduced contact time in a high velocity current likely explains this result. Initial parasite attachment position was influenced by an interaction between current velocity and swimming behaviour, likely due to different fin positioning by fish in flows of different velocities. Our results imply that rapid swimming by salmon migrating out of coastal waters, usually described as adaptive against predation, could also be adaptive against parasitism. Infestation rates were also highest at the typical swimming speed of farmed salmon in coastal fish farms, which may be a hitherto unrecognised factor contributing to L. salmonis epidemics.

Emerging infectious diseases of wildlife: a critical perspective

We review the literature to distinguish reports of vertebrate wildlife disease emergence with sufficient evidence, enabling a robust assessment of emergence drivers. For potentially emerging agents that cannot be confirmed, sufficient data on prior absence (or a prior difference in disease dynamics) are frequently lacking. Improved surveillance, particularly for neglected host taxa, geographical regions and infectious agents, would enable more effective management should emergence occur. Exposure to domestic sources of infection and human-assisted exposure to wild sources were identified as the two main drivers of emergence across host taxa; the domestic source was primary for fish while the wild source was primary for other taxa. There was generally insufficient evidence for major roles of other hypothesized drivers of emergence.

Genomic characterization and phylogenetic position of two new species in Rhabdoviridae infecting the parasitic copepod, salmon louse (Lepeophtheirus salmonis)

Several new viruses have emerged during farming of salmonids in the North Atlantic causing large losses to the industry. Still the blood feeding copepod parasite, Lepeophtheirus salmonis, remains the major challenge for the industry. Histological examinations of this parasite have revealed the presence of several virus-like particles including some with morphologies similar to rhabdoviruses. This study is the first description of the genome and target tissues of two new species of rhabdoviruses associated with pathology in the salmon louse. Salmon lice were collected at different Atlantic salmon (Salmo salar) farming sites on the west coast of Norway and prepared for histology, transmission electron microscopy and Illumina sequencing of the complete RNA extracted from these lice. The nearly complete genomes, around 11,600 nucleotides encoding the five typical rhabdovirus genes N, P, M, G and L, of two new species were obtained. The genome sequences, the putative protein sequences, and predicted transcription strategies for the two viruses are presented. Phylogenetic analyses of the putative N and L proteins indicated closest similarity to the Sigmavirus/Dimarhabdoviruses cluster, however, the genomes of both new viruses are significantly diverged with no close affinity to any of the existing rhabdovirus genera. In situ hybridization, targeting the N protein genes, showed that the viruses were present in the same glandular tissues as the observed rhabdovirus-like particles. Both viruses were present in all developmental stages of the salmon louse, and associated with necrosis of glandular tissues in adult lice. As the two viruses were present in eggs and free-living planktonic stages of the salmon louse vertical, transmission of the viruses are suggested. The tissues of the lice host, Atlantic salmon, with the exception of skin at the attachment site for the salmon louse chalimi stages, were negative for these two viruses.

Human-induced evolution caught in action: SNP-array reveals rapid amphi-atlantic spread of pesticide resistance in the salmon ecotoparasite Lepeophtheirus salmonis

Background

The salmon louse, Lepeophtheirus salmonis, is an ectoparasite of salmonids that causes huge economic losses in salmon farming, and has also been causatively linked with declines of wild salmonid populations. Lice control on farms is reliant upon a few groups of pesticides that have all shown time-limited efficiency due to resistance development. However, to date, this example of human-induced evolution is poorly documented at the population level due to the lack of molecular tools. As such, important evolutionary and management questions, linked to the development and dispersal of pesticide resistance in this parasite, remain unanswered. Here, we introduce the first Single Nucleotide Polymorphism (SNP) array for the salmon louse, which includes 6000 markers, and present a population genomic scan using this array on 576 lice from twelve farms distributed across the North Atlantic.

Results

Our results support the hypothesis of a single panmictic population of lice in the Atlantic, and importantly, revealed very strong selective sweeps on linkage groups 1 and 5. These sweeps included candidate genes potentially connected to pesticide resistance. After genotyping a further 576 lice from 12 full sibling families, a genome-wide association analysis established a highly significant association between the major sweep on linkage group 5 and resistance to emamectin benzoate, the most widely used pesticide in salmonid aquaculture for more than a decade.

Conclusions

The analysis of conserved haplotypes across samples from the Atlantic strongly suggests that emamectin benzoate resistance developed at a single source, and rapidly spread across the Atlantic within the period 1999 when the chemical was first introduced, to 2010 when samples for the present study were obtained. These results provide unique insights into the development and spread of pesticide resistance in the marine environment, and identify a small genomic region strongly linked to emamectin benzoate resistance. Finally, these results have highly significant implications for the way pesticide resistance is considered and managed within the aquaculture industry.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-937) contains supplementary material, which is available to authorized users.

Large scale modelling of salmon lice (Lepeophtheirus salmonis) infection pressure based on lice monitoring data from Norwegian salmonid farms

Infection by parasitic sea lice is a substantial problem in industrial scale salmon farming. To control the problem, Norwegian salmonid farms are not permitted to exceed a threshold level of infection on their fish, and farms are required to monitor and report lice levels on a weekly basis to ensure compliance with the regulation. In the present study, we combine the monitoring data with a deterministic model for salmon lice population dynamics to estimate farm production of infectious lice stages. Furthermore, we use an empirical estimate of the relative risk of salmon lice transmission between farms, that depend on inter-farm distances, to estimate the external infection pressure at a farm site, i.e. the infection pressure from infective salmon lice of neighbouring farm origin. Finally, we test whether our estimates of infection pressure from neighbouring farms as well as internal within farm infection pressure, predicts subsequent development of infection in cohorts of farmed salmonids in their initial phase of marine production. We find that estimated external infection pressure is a main predictor of salmon lice population dynamics in newly stocked cohorts of salmonids. Our results emphasize the importance of keeping the production of infectious lice stages at low levels within local networks of salmon farms. Our model can easily be implemented for real time estimation of infection pressure at the national scale, utilizing the masses of data generated through the compulsory lice monitoring in salmon farms. The implementation of such a system should give the salmon industry greater predictability with respect to salmon lice infection levels, and aid the decision making process when the development of new farm sites are planned.

Variation among genotypes in responses to increasing temperature in a marine parasite: evolutionary potential in the face of global warming?

Climates are changing worldwide, and populations are under selection to adapt to these changes. Changing temperature, in particular, can directly impact ectotherms and their parasites, with potential consequences for whole ecosystems. The potential of parasite populations to adapt to climate change largely depends on the amount of genetic variation they possess in their responses to environmental fluctuations. This study is, to our knowledge, the first to look at differences among parasite genotypes in response to temperature, with the goal of quantifying the extent of variation among conspecifics in their responses to increasing temperature. Snails infected with single genotypes of the trematode Maritrema novaezealandensis were sequentially acclimatised to two different temperatures, 'current' (15°C) and 'elevated' (20°C), over long periods. These temperatures are based on current average field conditions in the natural habitat and those predicted to occur during the next few decades. The output and activity of cercariae (free-swimming infective stages emerging from snails) were assessed for each genotype at each temperature. The results indicate that, on average, both cercarial output and activity are higher at the elevated acclimation temperature. More importantly, the output and activity of cercariae are strongly influenced by a genotype-by-temperature interaction, such that different genotypes show different responses to increasing temperature. Both the magnitude and direction (increase or decrease) of responses to temperature varied widely among genotypes. Therefore, there is much potential for natural selection to act on this variation, and predicting how the trematode M. novaezealandensis will respond to the climate changes predicted for the next century will prove challenging.

Modelling the impact of temperature-induced life history plasticity and mate limitation on the epidemic potential of a marine ectoparasite

Temperature is hypothesized to contribute to increased pathogenicity and virulence of many marine diseases. The sea louse (Lepeophtheirus salmonis) is an ectoparasite of salmonids that exhibits strong life-history plasticity in response to temperature; however, the effect of temperature on the epidemiology of this parasite has not been rigorously examined. We used matrix population modelling to examine the influence of temperature on demographic parameters of sea lice parasitizing farmed salmon. Demographically-stochastic population projection matrices were created using parameters from the existing literature on vital rates of sea lice at different fixed temperatures and yearly temperature profiles. In addition, we quantified the effectiveness of a single stage-specific control applied at different times during a year with seasonal temperature changes. We found that the epidemic potential of sea lice increased with temperature due to a decrease in generation time and an increase in the net reproductive rate. In addition, mate limitation constrained population growth more at low temperatures than at high temperatures. Our model predicts that control measures targeting preadults and chalimus are most effective regardless of the temperature. The predictions from this model suggest that temperature can dramatically change vital rates of sea lice and can increase population growth. The results of this study suggest that sea surface temperatures should be considered when choosing salmon farm sites and designing management plans to control sea louse infestations. More broadly, this study demonstrates the utility of matrix population modelling for epidemiological studies.

Salmon lice increase the age of returning Atlantic salmon

The global increase in the production of domestic farmed fish in open net pens has created concerns about the resilience of wild populations owing to shifts in host-parasite systems in coastal ecosystems. However, little is known about the effects of increased parasite abundance on life-history traits in wild fish populations. Here, we report the results of two separate studies in which 379 779 hatchery-reared Atlantic salmon smolts were treated (or not) against salmon lice, marked and released. Adults were later recaptured, and we specifically tested whether the age distribution of the returning spawners was affected by the treatment. The estimates of parasite-induced mortality were 31.9% and 0.6% in the River Vosso and River Dale stock experiments, respectively. Age of returning salmon was on average higher in untreated [corrected] versus untreated fish. The percentages of fish returning after one winter at sea were 37.5% and 29.9% for the treated and untreated groups, respectively. We conclude that salmon lice increase the age of returning salmon, either by affecting their age at maturity or by disproportionately increasing mortality in fish that mature early.