actel: Standardised analysis of acoustic telemetry data from animals moving through receiver arrays

Effects of coastal development on sawfish movements and the need for marine animal crossing solutions

Although human-made barriers to animal movement are ubiquitous across many types of ecosystems, the science behind these barriers and how to ameliorate their effects lags far behind in marine environments compared with terrestrial and freshwater realms. Using juvenile sawfish in an Australian nursery habitat as a model system, we aimed to assess the effects of a major anthropogenic development on the movement behavior of coastal species. We compared catch rates and movement behavior (via acoustic telemetry) of juvenile green sawfish (Pristis zijsron) before and after a major coastal structure was built in an important nursery habitat. Acoustic tracking and catch data showed that the development did not affect levels of sawfish recruitment in the nursery, but it did constrain movements of juveniles moving throughout the nursery, demonstrating the reluctance of shoreline-associated species to travel around large or unfamiliar coastal structures. Given the current lack of information on human-made movement barriers in the marine environment, these findings highlight the need for further research in this area, and we propose the development of and experimentation with marine animal crossings as an important area of emerging research.

Monitoring post-spawning movement, habitat use, and survival of adult anadromous rainbow smelt using acoustic telemetry in a New Hampshire estuary

Anadromous rainbow smelt (Osmerus mordax, [Mitchill 1814]) are found along the northeast Atlantic coastline of North America, with their range now limited to north of Cape Cod, Massachusetts, USA. Although their anadromous life cycles are described broadly, gaps remain regarding how adult rainbow smelt use estuaries post-spawning, including movement behaviors, habitats used, and specific timing of emigration to coastal waters. In spring 2021, we used acoustic telemetry to characterize movements during and after the spawning season of rainbow smelt captured in tributaries to Great Bay, New Hampshire, USA, a large estuarine system near the southern edge of their range. Forty-four adult rainbow smelt (n = 35 male, n = 9 female) were tagged with Innovasea V5 180-kHz transmitters and an array of 22,180 kHz VR2W receivers were deployed throughout Great Bay to detect movements of tagged fish from March to October 2021. Rainbow smelt were detected 14,186 times on acoustic telemetry receivers, with 41 (93%) of the tagged individuals being detected at least once post-tagging. Individuals were detected moving between tributaries, revealing that rainbow smelt can use multiple rivers during the spawning season (March-April). Mark-recapture Cormack-Jolly-Seber models estimated 83% (95% confidence interval 66%-92%) of rainbow smelt survived to the mainstem Piscataqua River, and a minimum of 50% (22 of 44) reached the seaward-most receivers and were presumed to have survived emigration. Most individuals that survived remained in the estuary for multiple weeks (average = 19.47 ± 1.99 standard error days), displaying extended use of estuarine environments. Downstream movements occurred more frequently during ebb tides and upstream movements with flood tides, possibly a mechanism to reduce energy expenditures. Fish emigrated from the estuary by mid-May to the coastal Gulf of Maine. Our results underscore that rainbow smelt need access to a variety of habitats, including multiple tributaries and high-quality estuarine habitat, to complete their life cycle.

Comparing the migration behavior and survival of Atlantic salmon (Salmo salar) and brown trout (Salmo trutta) smolts

Many organisms rely on migrations between habitats to maximize lifetime fitness, but these migrations can be risky due to a suite of factors. In anadromous salmonids, the smolt migration from fresh water to sea is a critical life stage, during which smolts can experience high mortality from multiple sources. This study investigated the migratory behavior and survival of Atlantic salmon (Salmo salar) and anadromous brown trout (Salmo trutta) smolts during their seaward migration using acoustic telemetry between March and May 2021. Due to the extinction of wild salmon in the River Gudenaa after the construction of the Tange hydropower plant, this study used hatchery-reared salmon originating from a nearby Danish river. A total of 75 hatchery-reared salmon smolts, 75 hatchery-reared trout smolts, and 75 wild trout smolts were tagged with acoustic transmitters and released into River Gudenaa, Denmark. The downstream movements of tagged fish were monitored using acoustic receivers deployed in the river and fjord. Hatchery-reared trout initiated migration first, followed by hatchery-reared salmon, with wild trout being the last to migrate. There was no difference in riverine progression rates among the three smolt groups, but noticeable differences emerged once in the fjord: trout (wild and hatchery) slowed down, whereas hatchery-reared salmon maintained their speed. Riverine migration was predominantly nocturnal for all smolts; however, daytime migration increased at the fjord arrays. Day-of-year significantly influenced diurnal patterns in the river and fjord, where daytime migration increased later in the year. Hatchery-reared salmon and wild trout had reasonably good overall survival from river to sea entry (≥66%), whereas hatchery-reared trout had poor survival (c.26%). The fjord was the major bottleneck for survival of hatchery-reared trout. We found no strong evidence for differences in progression rate or diurnal patterns between wild and hatchery-reared trout to explain the lower survival. This study demonstrates that salmon and trout differ in their life-history strategy already in the post-smolt phase, and that stocking is a sub-optimal strategy to aid wild populations.

The use of predator tags to explain reversal movement patterns in Atlantic salmon smolts (Salmo salar L.)

Acoustic telemetry has seen a rapid increase in utility and sophistication in recent years and is now used extensively to assess the behavior and survival rates of many aquatic animals, including the Atlantic salmon. As part of the salmon's complex life cycle, salmon smolts are thought to make a unidirectional migration from fresh water to the sea, which is initiated by changes in their physiology. However, some tag movement patterns do not conform with this and can be difficult to explain, particularly if the tagged fish has been eaten by a predator. This study combines the use of predator tags with machine learning techniques to understand the fate of migrating salmon smolts and thereby improve estimates for migration success. Over 3 years between 2020 and 2022, 217 salmon smolts (including wild and hatchery-reared ranched fish) were acoustically tagged and released into an embayment on the west coast of Ireland. Some tagged smolts were observed to return from the estuary back into a saline lagoon through which they had already migrated. To distinguish between the movement of a salmon smolt and that of a predator, predator tags were deployed in migrating smolts in 2021 and 2022. The addition of a temperature sensor in 2022 enabled the determination of predator type causing the returning movement. A significant number of predator tags were triggered, and the patterns of movement associated with these triggered tags were then used with two types of machine learning algorithms (hierarchical cluster analysis and random forest) to identify and validate the behavior of smolts tagged without extra sensors. Both models produced the same outputs, grouping smolts tagged with predator tags with smolts tagged without the additional sensors but showing similar movements. A mammalian predator was identified as the cause of most reversal movement, and hatchery-reared ranched smolts were found to be more likely predated upon by this predator than wild smolts within the lake and the estuary. However, overall migration success estimates were similar for both wild and hatchery-reared ranched fish. This study highlights the value of predator tags as an essential tool in the overall validation of detection data.

Multispecies fish tracking across newly created shallow and deep habitats in a forward-restored lake

BACKGROUND

Freshwater fish communities typically thrive in heterogenous ecosystems that offer various abiotic conditions. However, human impact increasingly leads to loss of this natural heterogeneity and its associated rich fish communities. To reverse this trend, we need guidelines on how to effectively restore or recreate habitats for multiple fish species. Lake Markermeer in the Netherlands is a human-created 70,000-ha lake with a uniform 4 m-water depth, steep shorelines, high wind-induced turbidity, and a declining fish community. In 2016, a forward-looking restoration project newly created a 1000-ha five-island archipelago in this degrading lake, which offered new sheltered shallow waters and deep sand excavations to the fish community.

METHODS

In 2020, we assessed how omnivorous and piscivorous fish species used these new habitats by tracking 78 adult fish of five key species across local and lake-scales. We monitored spring arrival of adult fish and assessed local macro-invertebrate and young-of-the-year fish densities.

RESULTS

Adult omnivorous Cyprinidae and piscivorous Percidae arrived at the archipelago in early spring, corresponding with expected spawning movements. During the productive summer season, 12 species of young-of-the-year fish appeared along the sheltered shorelines, with particularly high densities of common roach (Rutilus rutilus) and European perch (Perca fluviatilis). This suggests the sheltered, shallow, vegetated waters formed new suitable spawning and recruitment habitat for the fish community. Despite highest food densities for adult fish in the shallowest habitats (< 2-m), adult fish preferred minimally 2-m deep water. After spawning most Cyprinidae left the archipelago and moved long distances through the lake system, while most Percidae remained resident. This may be related to (1) high densities of young-of-the-year fish as food for piscivores, (2) medium food densities for omnivores compared to elsewhere in the lake-system, or (3) the attractiveness of 30-m deep sand excavations that were newly created and frequently used by one-third of all tracked fish.

CONCLUSIONS

New littoral zones and a deep sand excavation constructed in a uniform shallow lake that lacked these habitat types attracted omnivorous and piscivorous fish species within four years. Both feeding guilds used the littoral zones for reproduction and nursery, and notably piscivorous fish became residents year-round.

ATfiltR: A solution for managing and filtering detections from passive acoustic telemetry data

Acoustic telemetry is a popular and cost-efficient method for tracking the movements of animals in the aquatic ecosystem. But data acquired via acoustic telemetry often contains spurious detections that must be identified and excluded by researchers to ensure valid results. Such data management is difficult as the amount of data collected often surpasses the capabilities of simple spreadsheet applications. ATfiltR is an open-source package programmed in R that allows users to integrate all telemetry data collected into a single file, to conditionally attribute animal data and location data to detections and to filter spurious detections based on customizable rules. Such tool will likely be useful to new researchers in acoustic telemetry and enhance results reproducibility.•ATfiltR compiles telemetry files and identifies and stores all data that was collected outside of your study period (e.g. when your receivers were on land for servicing) elsewhere.•As spurious detections are unlikely to appear sequentially in the data, ATfiltR finds all detections that occurred only once (per receiver or in the whole array) within a user-designated time period and stores them elsewhere.•ATfiltR identifies detections that are impossible given the animals' swimming speeds and the receivers detection range and stores them elsewhere.

Residency and space use estimation methods based on passive acoustic telemetry data

Acoustic telemetry has helped overcome many of the challenges faced when studying the movement ecology of aquatic species, allowing to obtain unprecedented amounts of data. This has made it into one of the most widely used methods nowadays. Many ways to analyse acoustic telemetry data have been made available and deciding on how to analyse the data requires considering the type of research objectives, relevant properties of the data (e.g., resolution, study design, equipment), habits of the study species, researcher experience, among others. To ease this decision process, here we showcase (1) some of the methods used to estimate pseudo-positions and positions from raw acoustic telemetry data, (2) methods to estimate residency and (3) methods to estimate two-dimensional home and occurrence range using geometric or hull-based methods and density-distribution methods, a network-based approach, and three-dimensional methods. We provide examples of some of these were tested using a sample of real data. With this we intend to provide the necessary background for the selection of the method(s) that better fit specific research objectives when using acoustic telemetry.

Non-Lethal Sampling Supports Integrative Movement Research in Freshwater Fish

Freshwater ecosystems and fishes are enormous resources for human uses and biodiversity worldwide. However, anthropogenic climate change and factors such as dams and environmental contaminants threaten these freshwater systems. One way that researchers can address conservation issues in freshwater fishes is via integrative non-lethal movement research. We review different methods for studying movement, such as with acoustic telemetry. Methods for connecting movement and physiology are then reviewed, by using non-lethal tissue biopsies to assay environmental contaminants, isotope composition, protein metabolism, and gene expression. Methods for connecting movement and genetics are reviewed as well, such as by using population genetics or quantitative genetics and genome-wide association studies. We present further considerations for collecting molecular data, the ethical foundations of non-lethal sampling, integrative approaches to research, and management decisions. Ultimately, we argue that non-lethal sampling is effective for conducting integrative, movement-oriented research in freshwater fishes. This research has the potential for addressing critical issues in freshwater systems in the future.