Application of machine learning to identify predators of stocked fish in Lake Ontario: using acoustic telemetry predation tags to inform management

Understanding predator–prey interactions and food web dynamics is important for ecosystem-based management in aquatic environments, as they experience increasing rates of human-induced changes, such as the addition and removal of fishes. To quantify the post-stocking survival and predation of a prey fish in Lake Ontario, 48 bloater Coregonus hoyi were tagged with acoustic telemetry predation tags and were tracked on an array of 105 acoustic receivers from November 2018 to June 2019. Putative predators of tagged bloater were identified by comparing movement patterns of six species of salmonids (i.e., predators) in Lake Ontario with the post-predated movements of bloater (i.e., prey) using a random forests algorithm, a type of supervised machine learning. A total of 25 bloater (53% of all detected) were consumed by predators on average (± S.D. ) 3.1 ± 2.1 days after release. Post-predation detections of predators occurred for an average (± S.D. ) of 78.9 ± 76.9 days, providing sufficient detection data to classify movement patterns. Tagged lake trout Salvelinus namaycush provided the most reliable classification from behavioural predictor variables (89% success rate) and was identified as the main consumer of bloater (consumed 50%). Movement networks between predicted and tagged lake trout were significantly correlated over a 6 month period, supporting the classification of lake trout as a common bloater predator. This study demonstrated the ability of supervised learning techniques to provide greater insight into the fate of stocked fishes and predator–prey dynamics, and this technique is widely applicable to inform future stocking and other management efforts.     

Survival and migration patterns of naturally and hatchery-reared Atlantic salmon (Salmo salar) smolts in a Lake Ontario tributary using acoustic telemetry

1. Atlantic salmon (Salmo salar) smolts are often stocked into rivers to supplement natural reproduction, yet hatchery-reared fish have lower survival compared to wild conspecifics. However, few studies have assessed riverine migratory performance and survival differences in hatchery and wild smolts, or more specifically naturally reared smolts (hatchery fish released earlier as parr), particularly in rivers with weirs which may further reduce survival.
2. Using acoustic telemetry, including a subset of fish with novel transmitters that identify predation events, we assessed survival and migration patterns of hatchery- (2017: n = 32; 2018: n = 30) and naturally reared Atlantic salmon smolts (2017: n = 8; 2018: n = 30) in a Lake Ontario tributary with two weirs to better understand their ecology and assess the influence of environmental parameters on migration.
3. Naturally reared smolts were 13.9 times more likely to survive than hatchery-reared smolts and mark–recapture models indicated that weirs did not reduce survival for either group. Survival per km was lowest at the release site, indicating pre-migration mortality, and specifically high stocking-related mortality of hatchery-reared smolts. Speed and times of day fish migrated (i.e. migratory performance) did not vary by rearing group, suggesting that the high mortality of hatchery-reared smolts may be due to other factors related to hatchery and stocking operations. Overall mean (± SD) migration speed for smolts was 0.70 ± 0.39 km/hr and movements occurred significantly more frequently at night (18:00–06:00).
4. Smolts were detected in Lake Ontario after they left the river; however, the array in Lake Ontario was not conducive to providing much detail regarding movement patterns. There was no predation of the two predation tags detected in Lake Ontario, indicating that movements were made by smolts and not predators.
5. With ongoing restoration efforts of Atlantic salmon in Lake Ontario, it was important to understand the smolt migration patterns and success of the stocked fish. Our findings of similar migratory performance yet different relative survival of hatchery- and naturally reared smolts help inform management with regards to stocking strategies that could improve Atlantic salmon reintroduction success.

     

Patterns of genetic diversity in Great Lakes bloaters (Coregonus hoyi) with a view to future reintroduction in Lake Ontario

The originally diverse ciscoe fish fauna of the Laurentian Great Lakes has suffered many extinctions and local extirpations. Bloaters (Coregonus hoyi) are presumed extirpated from Lake Ontario and the reintroduction of this deepwater fish is under consideration. Given the demographic fluctuations of this species in the other Great Lakes and its recent intralacustrine origin, we sought to identify a genetically diverse and similar source of C. hoyi via an analysis of genetic diversity and population structure using 10 microsatellite loci. Despite well-documented demographic declines, we found no genetic evidence of bottlenecks in 12 C. hoyi samples from the four potential donor lakes (Huron, Michigan, Superior and Nipigon). By contrast, evidence of bottlenecks in historical samples of C. artedi from Lake Ontario suggested that standard genetic methods frequently used to identify population bottlenecks can only detect very severe and long-lasting demographic declines in naturally large populations. Patterns of genetic differentiation and assignment tests indicated that C. hoyi from Lake Huron and Lake Michigan, which are not differentiated, are genetically most similar to Lake Ontario ciscoes. The small available sample of deepwater ciscoes recently caught in Lake Ontario did not allow determining if these represent a small undetected C. hoyi population or a recent invasion of the deep section by C. artedi. On the basis of genetic criteria, we conclude that C. hoyi from any location within Lake Huron or Lake Michigan would be judicious sources of breeders for reintroducing C. hoyi in Lake Ontario.     

Long-term retention of acoustic telemetry transmitters in temperate predators revealed by predation tags implanted in wild prey fish

Bloater Coregonus hoyi (n = 48) were implanted with V9DT-2x predation transmitters and monitored on 105 acoustic receivers in eastern Lake Ontario for >6 months. Twenty-three predation events were observed, with predator retention of tags ranging from ≤1 to ≥194 days and 30% of retentions lasting >150 days. Long tag retention times raise concerns for acoustic telemetry analysis and the health of piscivorous predators retaining tags.     

Comparing two fish sampling standards over time: largely congruent results but with caveats

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Deciphering lifelong thermal niche using otolith δ18O thermometry within supplemented lake trout (Salvelinus namaycush) populations

1. The selection of thermal habitat by fish is strongly regulated by physiology and behaviour. However, delineation of a species lifelong thermal niche remains technically challenging. Lake trout (Salvelinus namaycush) survival and productivity are recognised as being tightly linked to a somewhat restricted thermal habitat. The factors guiding temperature selection during each life stage remain poorly understood.
2. In this study, we tested the significant factors controlling the realised thermal niche of lake trout from two southern Quebec small boreal lakes that experienced supplementation stocking during the last 20 years. We used oxygen stable isotope (δ¹⁸O) thermometry of otolith calcium carbonates (aragonite) using secondary-ion mass spectrometry to estimate experienced lifelong temperatures. We investigated the thermal habitat of lake trout with known genotypes (local, hybrid, and stocked).
3. Ontogeny and genetic origin influenced temperature selection in both studied lake trout populations. Young-of-the-year consistently used warmer, shallower habitats (10.7 ± 2.6°C, 7.5 m depth) prior to a juvenile transition to colder and deeper waters (8.5 ± 3.3°C, 10 m depth). Stocked lake trout, originating from a genetically distinct ecotype, exhibited a more variable thermal niche, with some individuals consistently using warmer habitat (10.4 ± 1°C) than local fish. Their hybrid progeny also occupied a warmer thermal niche, intermediate to the parental strains. We propose that increased fat content and genetic origin are potential explanatory factors for warmer temperature use.
4. This study reiterates that high-resolution otolith δ¹⁸O thermometry is a uniquely well-suited approach for unravelling the multiple factors that influence lifelong temperature selection in fish. Our results illustrate that the realised thermal niche is influenced by a genetic–environment interaction.

     

Hatchery-reared fish have less consistent behavioral pattern compared to wild individuals,exemplified by red tilefish studied using video observation and acoustic telemetry tracking

The behavior of wild and hatchery-reared red tilefish Branchiostegus japonicus was analyzed using two different methods: video observation and acoustic telemetry tracking. In the laboratory, digging and swimming activity of seven wild and five hatchery-reared fish were recorded for 2–4 days in an experimental aquarium and related to changes in light intensity. The activity of wild individuals increased with light intensity, while hatchery-reared individuals were active during both day and night. In the field, 18 wild and 9 hatchery-reared fish were released and tracked using an acoustic telemetry system during the winter and the summer in Maizuru Bay, Kyoto (Japan). Seven wild and three hatchery-reared fish settled within 2 km of the release point for 21–200 days whilst 11 wild and 6 hatchery-reared fish were detected in the central part of the bay within 13 days. The settled fish demonstrated a diel pattern of behavior; most of them probably stayed outside their burrows in the daytime but inside their burrows during the nighttime. During the winter wild fish tended to stay near the release site for longer periods than the hatchery-reared fish. However, in summer the hatchery-reared fish tended to remain close to the release site for longer than the wild fish. Based on these two experiments, we suggest that the activity of wild red tilefish respond to changes in low levels of light intensity (0–0.1 μmol m⁻² s⁻¹) at dawn and display a diel behavior. Hatchery-reared fish may differ from wild fish with regard to their behavior, response to water temperature and light conditions. Electronic supplementary material Supplementary material is available for this article at and accessible for authorized users     

Influence of acoustics on the collective behaviour of a shoaling freshwater fish

1. Understanding how collective behaviour of animals is influenced by anthropogenic activity is important for their conservation in an increasingly urbanised world. River infrastructure, e.g. for transport and electricity generation, and associated construction and operation, produces sound that can disrupt ecological processes.
2. Adopting a reductionist manipulative experimental approach using Eurasian minnow (Phoxinus phoxinus) as a model shoaling species, we compared the response of individuals and groups of five fish to a broadband acoustic stimulus in a tank containing still water.
3. Four metrics were calculated 10 min immediately before (control–sound stimulus absent) and during the acoustic treatment: (1) swimming speed, (2) persistence of swim paths, (3) cohesion of the group, and (4) orientation of group members.
4. On presentation of the stimulus, groups exhibited a consistent escape response compared to individuals for which behaviour was more variable. Thereafter, individuals swam faster and their swim paths were less persistent than during the control; no difference was observed for groups. Conversely, group integrity became more cohesive and members were more likely to orient in a common direction during the treatment compared to the control.
5. This study provides insight into the importance of collective behaviour of fish in relation to antipredator-like response to anthropogenic noise. Short-term shifts in behaviour are context specific and depend on whether fish are members of a shoal or solitary. The results indicate the potential for negative impacts of unnatural sound on the ecology of shoaling species that inhabit engineered freshwater environments.

     

Riverine, estuarine and marine migratory behaviour and physiology of wild and hatchery-reared coho salmon Oncorhynchus kisutch (Walbaum) smolts descending the Campbell River, BC, Canada

Eighty coho salmon Oncorhynchus kisutch smolts (40 wild and 40 hatchery-reared) were surgically implanted with acoustic transmitters and released into the Quinsam River over 2 days. Differences in physiology, travel time and migratory behaviour were examined between wild and hatchery-reared fish. In addition, tagged and control fish of both wild and hatchery-reared stock were raised for 3 months following surgery to compare survival and tag retention. Detection ranges of the acoustic receivers were tested in the river, estuary and ocean in a variety of flow conditions and tide levels. Receivers were placed in the river, estuary and up to 50 km north and south from the river mouth in the marine environment. Wild smolts were significantly smaller by mass, fork length and condition factor than hatchery-reared smolts and exhibited significantly higher levels of sodium, potassium and chloride in their blood plasma than hatchery-reared smolts. The gill Na⁺K⁺-ATPase activity was also significantly higher in the wild coho smolts at the time of release. Ninety-eight per cent of wild and 80% of hatchery-reared fish survived to the estuary, 8 km downstream of the release site. No difference was found in migration speed, timing or survival between smolts released during daylight and those released after dark. Wild smolts, however, spent less time in the river and estuary, and as a result entered the ocean earlier than hatchery-reared smolts. Average marine swimming speeds for wild smolts were double those of their hatchery-reared counterparts. While hatchery smolts dispersed in both a northward and southward direction upon entering the marine environment, the majority of wild smolts travelled north from the Campbell River estuary. The wild coho salmon smolts were more physiologically fit and ready to enter sea water than the hatchery-reared smolts, and as a result had higher early survival rates and swimming speeds.     

Forecasting the combined effects of anticipated climate change and agricultural conservation practices on fish recruitment dynamics in Lake Erie

1. Many aquatic ecosystems are experiencing multiple anthropogenic stressors that threaten their ability to support ecologically and economically important fish species. Two of the most ubiquitous stressors are climate change and non-point source nutrient pollution.
2. Agricultural conservation practices (ACPs, i.e. farming practices that reduce runoff, prevent erosion, and curb excessive nutrient loading) offer a potential means to mitigate the negative effects of non-point source pollution on fish populations. However, our understanding of how ACP implementation amidst a changing climate will affect fish production in large ecosystems that receive substantial upstream sediment and nutrient inputs remains incomplete.
3. Towards this end, we explored how anticipated climate change and the implementation of realistic ACPs might alter the recruitment dynamics of three fish populations (native walleye Sander vitreus and yellow perch Perca flavescens and invasive white perch Morone americana) in the highly productive, dynamic west basin of Lake Erie. We projected future (2020–2065) recruitment under different combinations of anticipated climate change (n = 2 levels) and ACP implementation (n = 4 levels) in the western Lake Erie catchment using predictive biological models driven by forecasted winter severity, spring warming rate, and Maumee River total phosphorus loads that were generated from linked climate, catchment-hydrology, and agricultural-practice-simulation models.
4. In general, our models projected reduced walleye and yellow perch recruitment whereas invasive white perch recruitment was projected to remain stable or increase relative to the recent past. Our modelling also suggests the potential for trade-offs, as ACP implementation was projected to reduce yellow perch recruitment with anticipated climate change.
5. Overall, our study presents a useful modelling framework to forecast fish recruitment in Lake Erie and elsewhere, as well as offering projections and new avenues of research that could help resource management agencies and policy-makers develop adaptive and resilient management strategies in the face of anticipated climate and land-management change.

     

Monitoring the acoustic activity of an aquatic insect population in relation to temperature,vegetation and noise

1. Acoustic population monitoring is a noninvasive method that can be deployed continuously over long periods of time and at large spatial scales. One of the newly discovered threats acting on biological diversity is anthropogenic noise. High levels of anthropogenic noise occur in aquatic environments, yet their effects on animals living in freshwater habitats have very rarely been investigated.
2. Here, we used acoustic monitoring and automatic detection to assess the acoustic activity of a population of a soniferous freshwater insect.
3. The sounds emitted by the corixid Micronecta scholtzi were recorded in a Mediterranean pond with an array of 12 hydrophones. An automatic analysis based on a measure of the amplitude found in the frequency band of M. scholtzi was developed to assess the level of acoustic activity. We used functional linear models, accounting for the periodicity of the calling behaviour, to estimate the possible effect of temperature, vegetation and a noise due to an immersed engine.
4. The automatic analysis was validated as an efficient method to measure the acoustic activity. The monitoring revealed a clear 24-hr pattern in the acoustic activity of M. scholtzi and three peaks of activity during the morning. Functional linear models revealed negative effects of both temperature and vegetation and showed that an engine noise, played back for 2 hr during the night, elicited an increase in the level of acoustic activity of the population. Moreover, a cross-correlation procedure showed that noise delayed the acoustic activity of the population.
5. Our results suggest that acoustic survey and automatic detection are efficient methods to monitor the acoustic activity of an insect population especially in response to an anthropogenic disturbance.

     

Restoration of naturally reproducing and resident riverine lake sturgeon populations through capture and transfer

The Winnebago System, Wisconsin, is home to one of the largest Lake Sturgeon Acipenser fulvescens populations in North America. Although there are >50 known spawning sites utilized by Lake Sturgeon in the 200 km of the lower Wolf River upstream of Lake Winnebago, the construction of two dams >90 years ago eliminated the ability of Lake Sturgeon to access 18.5 km of river up to their ancestral spawning grounds below Keshena Falls. Given the cultural importance of sturgeon to the Menominee Indian Tribe of Wisconsin, expanded efforts aimed at restoring Lake Sturgeon spawning and a resident population to the upper Wolf River commenced in 2011. To meet these objectives, 100 or more Lake Sturgeon per year were captured below the dams, and transferred upstream to the Wolf River within the Menominee Reservation. All transferred fish were PIT tagged and 245 fish were surgically implanted with 10 year acoustic transmitters to determine spawning locations and monitor post‐release movement. The first five transfer cohorts contained 621 Lake Sturgeon, with spawning activity observed below Keshena Falls each spring following release. Gravid fish transferred within 3 weeks of spawning exhibited higher spawning rates above the upstream dam (70.2% females; 73.9% males) than gravid fish transferred in late fall (41.8% females; 41.2% males). Spawning documented below Keshena Falls and within the Red River represent the first spawning activity at these locations in >100 years. Lake Sturgeon transferred in early fall displayed higher retention rates, 2‐5 years post‐tagging, in the pool upstream of both dams (10.4%) compared to the late fall (3.1%) and spring transfers (7.4%). Natural reproduction was documented through capture of larval Lake Sturgeon immediately below Keshena Falls in 2013. These results demonstrate that capture and transfer can be utilized as a cost‐effective and biologically‐effective tool for Lake Sturgeon spawning stock and population restoration.     

Does river of origin influence the early marine migratory performance of Salmo salar?

The early marine migratory behaviour of two populations of hatchery-reared Atlantic salmon Salmo salar was compared in a common-garden experiment. Post-smolts from a river in a long fjord (Laerdal River, 144 km from the open coastline, n = 79) and a short fjord (Flekke River, 20 km from the open coastline, n = 80) in western Norway were tagged with acoustic transmitters and released during the spring of 2005 and 2006 in the inner part of the Hardangerfjord system (Opo River mouth, 179 km from the open coastline). The migratory behaviour of the tagged fish was monitored by acoustic listening stations in the fjord system up to 167 km from the release site. The Laerdal fish began migrating before the Flekke fish and had higher progression rates in the middle part of the fjord system. A greater number of Laerdal fish was detected along the most direct migratory route and in the outermost part of the Hardangerfjord system, which is indicative of a higher survival. The results from this study demonstrate differences in early marine migratory behaviour between S. salar from two different stocks and suggest that the distance a S. salar population travels to reach the open coastline may influence its early marine migratory behaviour and performance. The selective pressures of marine predation and arrival time at feeding areas in the ocean may be stronger for stocks with a longer inshore migration, creating more efficient migrants over time.     

An evolutionary perspective on the resistance of Daphnia to the epizoic rotifer Brachionus rubens

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Training fish for restocking: refuge and predator training in the hatchery has limited benefits for a marine fish

Large numbers of hatchery-reared fish are released in stocking programmes; however, success is limited by high mortality. Predation is seen as the main cause of deaths but might be reduced by training fish before release to avoid predators and/or use refuge. In this study on a potential restocking species, yellowfin bream Acanthopagrus australis, the effects of predator training and refuge on the behaviour of fish in the hatchery were tested. In the first experiment, juvenile bream were exposed to predatory mangrove jack (Lutjanus argentimaculatus) fed exclusively on bream flesh while housed in tanks with and without refuge. Predator training altered fish behaviour when fish were re-exposed to predators, but the effects were subtle and varied between groups of fish. In contrast, refuge created strong and consistent changes in behaviour, significantly slowing down the amount of time that fish took to consume food. A second experiment focused on the effects of refuge. Bream were trained to use artificial seagrass or house bricks as refuge and then exposed to mangrove jacks in a laboratory predation experiment. When refuge was available, fish significantly slowed down their feeding rate. There was a small, transient increase in survival for fish given seagrass refuges, but this was irrespective of whether the bream were trained to use refuge. The results of this study indicate that the use of refuge may be innate and the benefits of refuge may be available to naive hatchery-reared fish or fish trained to use refuge shortly before release. This suggests that there is potential to improve post-release survival of fingerlings without time-consuming and expensive hatchery training.     

Effects of the presence of a predatory fish and the phenotype of its prey (a shredding shrimp) on leaf litter decomposition

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Migration, growth and survival of wild and hatchery-reared anadromous Arctic charr (Salvelinus alpinus) in Finnmark, Northern Norway

Two groups of anadromous Arctic charr ( Salvelinus alpinus ) (size 200–350 mm) reared in heated water (6–12° C) under simulated natural photoperiod were individually tagged and released in spring 1988. The fish were released at two sites, in the estuary of the River Halselva and in the fjord, 2 km from the river mouth. Growth, timing of migration and survival of these hatchery-reared fish was compared to that of wild anadromous charr of the same size over a 4-year period. The hatchery-reared charr had poorer growth than the wild fish during their first year in sea water. They also resided longer in the sea and had a slightly lower survival than wild fish. During the second year, hatchery-reared charr displayed good growth, and after the third sea-season the fish were ready for slaughter at a size of approximately 800g. The results suggest that the successful development of Arctic charr ranching will be dependent upon production and release strategies that lead to improved migratory and feeding behaviour of the fish during their first season at sea.     

Tag retention and mortality of adult Atlantic salmon Salmo salar gastrically tagged with different sized telemetry transmitters

A batch of 1 sea winter pre‐spawning adult Salmo salar from the Bush river in Northern Ireland, U.K., were gastrically tagged with large (13 mm diameter) and small (9 mm diameter) dummy acoustic telemetry tags alongside untagged control fish. Survival differed between control and tagged fish and the estimated probability of survival by the end of the study for control fish with no tag was 0·94, small tags was 0·90 and large tags was 0·72. Tag loss through regurgitation was slightly higher for fish tagged with larger tags than for fish tagged with smaller tags and the estimated probability of tag loss for fish with a small tag was 0·10 and for large tags was 0·14.     

Acoustic monitoring reveals diversity and surprising dynamics in tropical freshwater soundscapes

1. Freshwater systems are globally threatened and in need of enhanced monitoring and assessment. We applied soundscape recording and analysis—which presents an opportunity for long-term, high-resolution animal community monitoring and assessment—to a freshwater context to better understand the acoustic diversity and dynamics of these systems.
2. We recorded the aquatic soundscape of a Neotropical freshwater swamp in Costa Rica for 23 days in January and February 2015 during the dry season. We classified biological sound types in these recordings and developed measurements of richness and occupancy based on this classification. We also calculated six complementary acoustic indices to assess soundscape diversity and daily and longer-term soundscape dynamics, and we examined correlations between these acoustic indices and sound type metrics.
3. We found rich soundscapes in which biological sounds were almost always present, and we classified 18 sound types that we attribute to aquatic insects. These sound types showed distinct daily patterns and exhibited temporal and spectral acoustic niche partitioning. Sound type richness was most correlated with the number of peaks index (correlation = .36; p < .001), while sound type occupancy was most correlated with the Bioacoustic Index (correlation = .92; p < .001). In contrast to generally high levels of acoustic activity, there were brief (approximately 1 hr), unexpected quiet periods around dawn and dusk.
4. This study represents an early attempt to comprehensively describe tropical freshwater soundscapes in a systematic and quantitative manner. We demonstrate that sound type classification and the quantification of acoustic occupancy capture aspects of soundscape diversity and dynamics that are complementary to those assessed by acoustic indices. Our analyses reveal that the soundscapes of this tropical wetland were diverse and exhibited daily dynamics that differed from those found in other ecosystems.