Environmental DNA from multiple pathogens is elevated near active Atlantic salmon farms

The spread of infection from reservoir host populations is a key mechanism for disease emergence and extinction risk and is a management concern for salmon aquaculture and fisheries. Using a quantitative environmental DNA methodology, we assessed pathogen environmental DNA in relation to salmon farms in coastal British Columbia, Canada, by testing for 39 species of salmon pathogens (viral, bacterial, and eukaryotic) in 134 marine environmental samples at 58 salmon farm sites (both active and inactive) over 3 years. Environmental DNA from 22 pathogen species was detected 496 times and species varied in their occurrence among years and sites, likely reflecting variation in environmental factors, other native host species, and strength of association with domesticated Atlantic salmon. Overall, we found that the probability of detecting pathogen environmental DNA (eDNA) was 2.72 (95% CI: 1.48, 5.02) times higher at active versus inactive salmon farm sites and 1.76 (95% CI: 1.28, 2.42) times higher per standard deviation increase in domesticated Atlantic salmon eDNA concentration at a site. If the distribution of pathogen eDNA accurately reflects the distribution of viable pathogens, our findings suggest that salmon farms serve as a potential reservoir for a number of infectious agents; thereby elevating the risk of exposure for wild salmon and other fish species that share the marine environment.

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.

The implementation of rare events logistic regression to predict the distribution of mesophotic hard corals across the main Hawaiian Islands

Predictive habitat suitability models are powerful tools for cost-effective, statistically robust assessment of the environmental drivers of species distributions. The aim of this study was to develop predictive habitat suitability models for two genera of scleractinian corals (Leptoserisand Montipora) found within the mesophotic zone across the main Hawaiian Islands. The mesophotic zone (30–180 m) is challenging to reach, and therefore historically understudied, because it falls between the maximum limit of SCUBA divers and the minimum typical working depth of submersible vehicles. Here, we implement a logistic regression with rare events corrections to account for the scarcity of presence observations within the dataset. These corrections reduced the coefficient error and improved overall prediction success (73.6% and 74.3%) for both original regression models. The final models included depth, rugosity, slope, mean current velocity, and wave height as the best environmental covariates for predicting the occurrence of the two genera in the mesophotic zone. Using an objectively selected theta (“presence”) threshold, the predicted presence probability values (average of 0.051 for Leptoseris and 0.040 for Montipora) were translated to spatially-explicit habitat suitability maps of the main Hawaiian Islands at 25 m grid cell resolution. Our maps are the first of their kind to use extant presence and absence data to examine the habitat preferences of these two dominant mesophotic coral genera across Hawai‘i.

Allee effect from parasite spill-back

The exchange of native pathogens between wild and domesticated animals can lead to novel disease threats to wildlife. However, the dynamics of wild host-parasite systems exposed to a reservoir of domesticated hosts are not well understood. A simple mathematical model reveals that the spill-back of native parasites from domestic to wild hosts may cause a demographic Allee effect in the wild host population. A second model is tailored to the particulars of pink salmon (Oncorhynchus gorbuscha) and salmon lice (Lepeophtheirus salmonis), for which parasite spill-back is a conservation and fishery concern. In both models, parasite spill-back weakens the coupling of parasite and wild host abundance-particularly at low host abundance-causing parasites per host to increase as a wild host population declines. These findings show that parasites shared across host populations have effects analogous to those of generalist predators and can similarly cause an unstable equilibrium in a focal host population that separates persistence and extirpation. Allee effects in wildlife arising from parasite spill-back are likely to be most pronounced in systems where the magnitude of transmission from domestic to wild host populations is high because of high parasite abundance in domestic hosts, prolonged sympatry of domestic and wild hosts, a high transmission coefficient for parasites, long-lived parasite larvae, and proximity of domesticated populations to wildlife migration corridors.

Critical thresholds in sea lice epidemics: evidence, sensitivity and subcritical estimation

Host density thresholds are a fundamental component of the population dynamics of pathogens, but empirical evidence and estimates are lacking. We studied host density thresholds in the dynamics of ectoparasitic sea lice (Lepeophtheirus salmonis) on salmon farms. Empirical examples include a 1994 epidemic in Atlantic Canada and a 2001 epidemic in Pacific Canada. A mathematical model suggests dynamics of lice are governed by a stable endemic equilibrium until the critical host density threshold drops owing to environmental change, or is exceeded by stocking, causing epidemics that require rapid harvest or treatment. Sensitivity analysis of the critical threshold suggests variation in dependence on biotic parameters and high sensitivity to temperature and salinity. We provide a method for estimating the critical threshold from parasite abundances at subcritical host densities and estimate the critical threshold and transmission coefficient for the two epidemics. Host density thresholds may be a fundamental component of disease dynamics in coastal seas where salmon farming occurs.

Sea-cage aquaculture, sea lice, and declines of wild fish

A sea cage, sometimes referred to as a net pen, is an enclosure designed to prevent farm fish from escaping and to protect them from large predators, while allowing a free flow of water through the cage to carry away waste. Farm fish thus share water with wild fish, which enables transmission of parasites, such as sea lice, from wild to farm and farm to wild fishes. Sea lice epidemics, together with recently documented population-level declines of wild salmon in areas of sea-cage farming, are a reminder that sea-cage aquaculture is fundamentally different from terrestrial animal culture. The difference is that sea cages protect farm fish from the usual pathogen-control mechanisms of nature, such as predators, but not from the pathogens themselves. A sea cage thus becomes an unintended pathogen factory. Basic physical theory explains why sea-cage aquaculture causes sea lice on sympatric wild fish to increase and why increased lice burdens cause wild fish to decline, with extirpation as a real possibility. Theory is important to this issue because slow declines of wild fish can be difficult to detect amid large fluctuations from other causes. The important theoretical concepts are equilibrium, host-density effect, reservoir-host effect, and critical stocking level of farmed fish (stocking level at which lice proliferate on farm fish even if wild fish are not present to infect them). I explored these concepts and their implications without mathematics through examples from salmon farming. I also considered whether the lice-control techniques used by sea-cage farmers (medication and shortened grow-out times) are capable of protecting wild fish. Elementary probability showed that W ≈ W* - εF (where W is the abundance of wild fish, W* is the prefarm abundance, F is the abundance of farm fish, and ε is the ratio of lice per farm fish to lice per wild fish). Declines of wild fish can be reduced by short growing cycles for farm fish, medicating farm fish, and keeping farm stocking levels low. Declines can be avoided only by ensuring that wild fish do not share water with farmed fish, either by locating sea cages very far from wild fish or through the use of closed-containment aquaculture systems. These principles are likely to govern any aquaculture system where cage-protected farm hosts and sympatric wild hosts have a common parasite with a direct life cycle.

Sperm whale three-dimensional track, swim orientation, beam pattern, and click levels observed on bottom-mounted hydrophones

In an earlier paper [Nosal and Frazer Appl. Acoust. 61, 1187-1201 (2006)], a sperm whale was tracked in three-dimensions using direct and surface-reflected time differences (DRTD) of clicks recorded on five bottom-mounted hydrophones, a passive method that is robust to timing errors between hydrophones. This paper refines the DRTD method and combines it with a time of (direct) arrival method to improve the accuracy of the track. The position and origin time of each click having been estimated, pitch and yaw are then obtained by assuming the main axis of the whale is tangent to the track. Roll is then found by applying the bent horn model of sperm whale phonation, in which each click is composed of two pulses, p0 and p1, that exit the whale at different points. With instantaneous pitch, roll, and yaw estimated from time differences, amplitudes are then used to estimate the beam patterns of the p0 and p1 pulses. The resulting beam patterns independently confirm those obtained by Zimmer et al. [J. Acoust. Soc. Am. 117, 1473-1485 (2005); 118, 3337-3345 (2005)] with a very different experimental setup. A method for estimating relative click levels is presented and used to find that click levels decrease toward the end of a click series, prior to the "creak" associated with prey capture.

Epizootics of wild fish induced by farm fish

The continuing decline of ocean fisheries and rise of global fish consumption has driven aquaculture growth by 10% annually over the last decade. The association of fish farms with disease emergence in sympatric wild fish stocks remains one of the most controversial and unresolved threats aquaculture poses to coastal ecosystems and fisheries. We report a comprehensive analysis of the spread and impact of farm-origin parasites on the survival of wild fish populations. We mathematically coupled extensive data sets of native parasitic sea lice (Lepeophtheirus salmonis) transmission and pathogenicity on migratory wild juvenile pink (Oncorhynchus gorbuscha) and chum (Oncorhynchus keta) salmon. Farm-origin lice induced 9-95% mortality in several sympatric wild juvenile pink and chum salmon populations. The epizootics arise through a mechanism that is new to our understanding of emerging infectious diseases: fish farms undermine a functional role of host migration in protecting juvenile hosts from parasites associated with adult hosts. Although the migratory life cycles of Pacific salmon naturally separate adults from juveniles, fish farms provide L. salmonis novel access to juvenile hosts, in this case raising infection rates for at least the first approximately 2.5 months of the salmon's marine life (approximately 80 km of the migration route). Spatial segregation between juveniles and adults is common among temperate marine fishes, and as aquaculture continues its rapid growth, this disease mechanism may challenge the sustainability of coastal ecosystems and economies.

Localization of marine mammals near Hawaii using an acoustic propagation model

Humpback whale songs were recorded on six widely spaced receivers of the Pacific Missile Range Facility (PMRF) hydrophone network near Hawaii during March of 2001. These recordings were used to test a new approach to localizing the whales that exploits the time-difference of arrival (time lag) of their calls as measured between receiver pairs in the PMRF network. The usual technique for estimating source position uses the intersection of hyperbolic curves of constant time lag, but a drawback of this approach is its assumption of a constant wave speed and straight-line propagation to associate acoustic travel time with range. In contrast to hyperbolic fixing, the algorithm described here uses an acoustic propagation model to account for waveguide and multipath effects when estimating travel time from hypothesized source positions. A comparison between predicted and measured time lags forms an ambiguity surface, or visual representation of the most probable whale position in a horizontal plane around the array. This is an important benefit because it allows for automated peak extraction to provide a location estimate. Examples of whale localizations using real and simulated data in algorithms of increasing complexity are provided.

Kinetics and mechanics of stem gravitropism in Coprinus cinereus

Using video recordings we have completed the first kinetic analysis of mushroom stem gravitropism. The stem became gravireceptive after completion of meiosis, beginning to bend within 30 minutes of being placed horizontal. Stem bending first occurred in the apical 15% of its length, then the position of the bend moved rapidly towards the base, traversing 40% of stem length in 2.5 h. Meanwhile, the stem elongated by 25%, mostly in its upper half but also in basal regions. If the apex was pinned horizontally the stem base was elevated but overshot the vertical, often curling through more than 300 degrees. When the base was pinned to the horizontal (considered analogous to the normal situation), 90% of the initial bend was compensated as the stem brought its apex accurately upright, rarely overshooting the vertical. The apex had to be free to move for this curvature compensation to occur. Stems transferred to a clinostat after some minutes gravistimulation showed curvature which increased with the length of initial gravistimulation, indicating that continued exposure to the unilateral gravity vector was necessary for continued bending. Such gravistimulated stems which bent on the clinostat subsequently relaxed back towards their original orientation. Reaction kinetics were unaffected by submergence in water, suggesting that mechanical events do not contribute, but submerged stems bent first at the base rather than apex. In air, the gravitropic bend appeared first near the apex and then moved towards the base, suggesting basipetal movement of a signal. In water, the pattern of initial bending was changed (from apex to base) without effect on kinetics. Taken together these results suggest that bending is induced by a diffusing chemical growth factor (whose extracellular propagation is enhanced under water) which emanates from the apical zone of the stem. The apex is also responsible for regulating compensation of the bend so as to bring the tip to the vertical. The nature of this latter stimulus is unknown but it is polarized (the apex must be free to move for the compensation to occur) and it may not require reference to the unilateral gravity vector.

Environmental constraints on sound transmission by humpback whales

Singing humpback whales in Hawaii produce a variety of sounds at high source levels (ca. 185 dB re: 1 microPa), in coastal waters 15-500 m deep. These sounds are attenuated and distorted as they propagate away from a singer, limiting the utilizable range of the sounds. In the current study, simulations based on normal-mode theory were used to investigate how the effects of shallow-water propagation constrain humpback whales' use of sound. It is shown that humpbacks can greatly affect transmission range by adjusting their positions and sounds in response to environmental factors. Source depth, in particular, is shown to be a major determinant of which frequencies propagate the farthest. A preliminary analysis of range-dependent distortion suggests that spectral cues can potentially provide listening whales with information about how far a sound has traveled.

The role of calcium accumulation and the cytoskeleton in the perception and response of Coprinus cinereus to gravity

The role of Ca2+ in the gravitropic perception and/or response mechanism of Coprinus cinereus was examined by treating stipes with inhibitors of Ca2+ transport and calmodulin. Inhibitors had no effect on gravity perception but significantly diminished gravitropism. It is concluded that, under the conditions tested, Ca2+ is not involved in gravity perception by Coprinus stipes, but does contribute to transduction of the gravitropic impulse. The results would be consistent with regulation of the gravitropic bending process requiring accumulation of Ca2+ within a membrane-bound compartment. Treatment of stipes with an actin inhibitor caused a significantly delayed response, a result not observed with the Ca2+ inhibitors. This suggests that cytoskeletal elements may be involved directly in perception of gravity by Coprinus stipes while Ca(2+)-mediated signal transduction may be involved in directing growth differentials.

Gravitational biology of mushrooms: a flow-chart approach to characterising processes and mechanisms

Flow charts are presented which systematise recently published work on gravitropic responses of the mushroom stipe of Coprinus cinereus. The hypothetical model represented by the charts suggests that the meiotic division is a pivotal point in the gravitational biology of the mushroom fruit body. The unilateral gravity vector seems to be required for formation of the tissues in which meiosis normally occurs, and stipes become gravitropically competent only after onset of meiosis. The gravitropism flow-chart also indicates that two signals emanate from the upper regions of the stipe, one promotes the process of gravitropic bending, and is followed by a second signal which compensates for excess bending and adjusts the stipe apex to the vertical. Formalisation of the various observations into flow-charts, even though comparatively simple at the moment, facilitates comparison with other species and concentrates attention on aspects requiring further experimental analysis.

Rapid Determination of the Critical Temperature in Simulated Annealing Inversion

Knowledge of the critical temperature, T(*), the temperature at which a phase change occurs, greatly improves the efficiency of simulated annealing when used for optimization or inversion. A numerical method of accurately determining T(*) in a relatively short computation time has been developed. This method is used to recover the seismic soundspeed profile from wavefield data, a problem in which cycle skipping causes many local minima of the energy function and the averaging of the medium by finite length waves results in many states with similar energies. Computations indicate that it is cost-effective to spend about 80 percent of the computing budget looking for T(*) instead of annealing, and that in the course of finding T(*) many states with energies near the global minimum will also be found. The a posteriori probability distribution of the solution has been constructed from trial solutions generated at T(*).