Singing streams: Describing freshwater soundscapes with the help of acoustic indices

1. Understanding soundscapes, that is, the totality of sounds within a location, helps to assess nature in a more holistic way, providing a novel approach to investigating ecosystems. To date, very few studies have investigated freshwater soundscapes in their entirety and none across a broad spatial scale.
2. In this study, we recorded 12 freshwater streams in South East Queensland continuously for three days and calculated three acoustic indices for each minute in each stream. We then used principal component analysis of summary statistics for all three acoustic indices to investigate acoustic properties of each stream and spatial variation in their soundscapes.
3. All streams had a unique soundscape with most exhibiting diurnal variation in acoustic patterns. Across these sites, we identified five distinct groups with similar acoustic characteristics. We found that we could use summary statistics of AIs to describe daytimes across streams as well. Most difference in stream soundscapes was observed during the daytime with significant variation in soundscapes both between hours and among sites.
4. Synthesis and Application. We demonstrate how to characterize stream soundscapes by using simple summary statistics of complex acoustic indices. This technique allows simple and rapid investigation of streams with similar acoustic properties and the capacity to characterize them in a holistic and universal way. While we developed this technique for freshwater streams, it is also applicable to terrestrial and marine soundscapes.

     

Passive acoustic monitoring as a potential tool to survey animal and ecosystem processes in freshwater environments

1. Biodiversity in freshwater habitats is decreasing faster than in any other type of environment, mostly as a result of human activities. Monitoring these losses can help guide mitigation efforts. In most studies, sampling strategies predominantly rely on collecting animal and vegetal specimens. Although these techniques produce valuable data, they are invasive, time-consuming and typically permit only limited spatial and temporal replication. There is need for the development of complementary methods.
2. As observed in other ecosystems, freshwater environments host animals that emit sounds, either to communicate or as a by-product of their activity. The main freshwater soniferous groups are amphibians, fish, and macroinvertebrates (mainly Coleoptera and Hemiptera, but also some Decapoda, Odonata, and Trichoptera). Biophysical processes such as flow or sediment transport also produce sounds, as well as human activities within aquatic ecosystems.
3. Such animals and processes can be recorded, remotely and autonomously, and provide information on local diversity and ecosystem health. Passive acoustic monitoring (PAM) is an emerging method already deployed in terrestrial environments that uses sounds to survey environments. Key advantages of PAM are its non-invasive nature, as well as its ability to record autonomously and over long timescales. All these research topics are the main aims of ecoacoustics, a new scientific discipline investigating the ecological role of sounds.
4. In this paper, we review the sources of sounds present in freshwater environments. We then underline areas of research in which PAM may be helpful emphasising the role of PAM for the development of ecoacoustics. Finally, we present methods used to record and analyse sounds in those environments.
5. Passive acoustics represents a potentially revolutionary development in freshwater ecology, enabling continuous monitoring of dynamic bio-physical processes to inform conservation practitioners and managers.

     

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.

     

FishSounds Version 1.0: A website for the compilation of fish sound production information and recordings

Many fish species use active sound production for communication in numerous behaviors. Additionally, likely all fish can make passive or incidental sounds that may also serve some signal functions. Despite the ecological importance of fish sounds, their evident passive acoustic monitoring applications, and extensive endeavors to document soniferous fish diversity, the fields of bioacoustics and ichthyology have historically lacked an easily accessible, global inventory of known fish sound production. To alleviate this limitation, we developed http://FishSounds.net, a website that compiles and disseminates fish sound production information and recordings. FishSounds Version 1.0 launched in 2021, cataloging documented examinations for active and passive sound production for 1185 fish species from 837 references as well as 239 exemplary audio recordings. FishSounds allows users to search by taxa (e.g., family or common name), geographical distribution (e.g., region or water body), sound type, or reference. We have also made available the code used to create the website, so that it may be used in other data-sharing efforts—acoustic or otherwise. Subsequent versions of the website will update the data and improve the website functionality. FishSounds will advance research into fish behavior, passive acoustic monitoring, and human impacts on underwater soundscapes; serve as a resource for public outreach; and provide the foundation needed to investigate more of the 96% of fish species that lack published examinations of sound production. We further hope the FishSounds design, implementation, and engagement strategies will serve as a model for future data management and sharing efforts.     

Spatio-temporal heterogeneity in river sounds: Disentangling micro- and macro-variation in a chain of waterholes

1. Passive acoustic monitoring is gaining momentum as a viable alternative method to surveying freshwater ecosystems. As part of an emerging field, the spatio-temporal replication levels of these sampling methods need to be standardised. However, in shallow waters, acoustic spatio-temporal patchiness remains virtually unexplored.
2. In this paper, we specifically investigate the spatial heterogeneity in underwater sounds observed within and between waterholes of an ephemeral river at different times of the day and how it could affect sampling in passive acoustic monitoring.
3. We recorded in the Einasleigh River, Queensland in August 2016, using a linear transect of hydrophones mounted on frames. We recorded four times a day: at dawn, midday, dusk, and midnight. To measure different temporal and spectral attributes of the recorded sound, we investigated the mean frequency spectrum and computed acoustic indices.
4. Both mean frequency spectrum and index analyses revealed that the site and diel activity patterns significantly influenced the sounds recorded, even for adjacent sites with similar characteristics along a single river. We found that most of the variation was due to temporal patterns, followed by between-site differences, while within-site differences had limited influence.
5. This study demonstrates high spatio-temporal acoustic variability in freshwater environments, linked to different species or species groups. Decisions about sampling design are vital to obtain adequate representation. This study thus emphasises the need to tailor spatio-temporal settings of a sampling design to the aim of the study, the species and the habitat.

     

Interspecific variation in the response of fish to anthropogenic noise

1. Elevated levels of anthropogenic noise, especially those observed through boating activity, can negatively impact fish species, but it remains unclear which species are most affected and which behavioural metrics are best used in assessing fish responses to underwater noise. The effects of boat sounds on freshwater species are of particular interest because freshwater environments are less studied than the marine realm despite comparably high levels of biodiversity.
2. In the current study, we examine the behavioural responses to boat noise in two freshwater species that differ in their hypothesised response to sound inputs: the spottail shiner (Notropis hudsonius), a species with known hearing specialisations, and the bluegill sunfish (Lepomis macrochirus), a species with more generalised hearing capabilities. Fish were presented with boat noise in a laboratory setting, and their swimming, escape and foraging behaviours were assessed to examine differential responses in relation to hypothesised hearing abilities.
3. Both species showed a decrease in general swimming behaviours but an increase in erratic movements in response to boat noise, indicative of stress responses for both species. Despite the similarities in response based on swimming behaviours however, only spottail shiners exhibited true escape responses to the onset of the noise stimulus, suggesting a more extreme reaction in the species with a more refined hearing ability.
4. Taken together, these results show that freshwater fish can respond to increased levels of anthropogenic noise, but that the severity of the response may differ based on auditory structures and therefore presumed hearing ability. The differences seen between behavioural metrics used (swimming vs. escape responses) also demonstrate how care must be taken in choosing a metric when developing exposure guidelines for underwater sound exposures, as different metrics could lead to differential impact assessments.

     

Pond Acoustic Sampling Scheme: A draft protocol for rapid acoustic data collection in small waterbodies

1. Freshwater conservation is vital to the maintenance of global biodiversity. Ponds are a critical, yet often under‐recognized, part of this, contributing to overall ecosystem functioning and diversity. They provide habitats for a range of aquatic, terrestrial, and amphibious life, often including rare and declining species.
2. Effective, rapid, and accessible survey methods are needed to enable evidence‐based conservation action, but freshwater taxa are often viewed as “difficult”—and few specialist surveyors are available. Datasets on ponds are therefore limited in their spatiotemporal coverage.
3. With the advent of new recording technologies, acoustic survey methods are becoming increasingly available to researchers, citizen scientists, and conservation practitioners. They can be an effective and noninvasive approach for gathering data on target species, assemblages, and environmental variables. However, freshwater applications are lagging behind those in terrestrial and marine spheres, and as an emergent method, research studies have employed a multitude of different sampling protocols.
4. We propose the Pond Acoustic Sampling Scheme (PASS), a simple protocol to allow a standardized minimal sample to be collected rapidly from small waterbodies, alongside environmental and methodological metadata. This sampling scheme can be incorporated into a variety of survey designs and is intended to allow access to a wide range of participants, without requiring complicated or prohibitively expensive equipment.
5. Adoption of this sampling protocol would enable consistent sound recordings to be gathered by researchers and conservation organizations, and allow the development of landscape‐scale surveys, data sharing, and collaboration within an expanding freshwater ecoacoustic community—rather than individual approaches that produce incompatible datasets. The compilation of standardized data would improve the prospects for effective research into the soundscapes of small waterbodies and aid freshwater conservation efforts.

     

Vocalisation Repertoire of Female Bluefin Gurnard (Chelidonichthys kumu) in Captivity: Sound Structure,Context and Vocal Activity

Fish vocalisation is often a major component of underwater soundscapes. Therefore, interpretation of these soundscapes requires an understanding of the vocalisation characteristics of common soniferous fish species. This study of captive female bluefin gurnard, Chelidonichthys kumu, aims to formally characterise their vocalisation sounds and daily pattern of sound production. Four types of sound were produced and characterised, twice as many as previously reported in this species. These sounds fit two aural categories; grunt and growl, the mean peak frequencies for which ranged between 129 to 215 Hz. This species vocalized throughout the 24 hour period at an average rate of (18.5 ± 2.0 sounds fish^-1 h^-1) with an increase in vocalization rate at dawn and dusk. Competitive feeding did not elevate vocalisation as has been found in other gurnard species. Bluefin gurnard are common in coastal waters of New Zealand, Australia and Japan and, given their vocalization rate, are likely to be significant contributors to ambient underwater soundscape in these areas.     

Diurnal variation in freshwater ecoacoustics: Implications for site-level sampling design

1. Ecoacoustic methods are increasingly used to monitor the state of populations and ecosystems. In freshwater environments, they present the clear advantages of being non-invasive, reducing bias, and providing continuous observations instead of only limited sampling snapshots in time. However, similar to standard bioassessment methods, temporal variation and choice of indicators can greatly influence ecoacoustic assessments, highlighting the importance of sampling and analysis design.
2. In this study, we quantified diurnal variation in underwater sound and its effect on sampling regimes for two waterholes in the Einasleigh River, Northern Australia. Recording continuously for 6 days, and subsampling 5 s every 10 min, we found 22 distinct sounds that were emitted by fish, Hemiptera and Coleoptera as well as another 22 of abiotic or unknown origin.
3. Through rarefaction analyses, we found that subsampling the data to 60% of the recorded sound events resulted in capture of most of the 44 identified sound types. Temporal heterogeneity—patchy sound events through time—needs to be considered when maximising detected sound events. Reducing the sampling interval from every 10 min to half-hourly or hourly had a much greater effect on capturing all sound types compared to the number of days recorded or the length of the recording. Overall, only 10–20% of the sound events need to be annotated for most sound types to be described; for example, restricting analysis of the days recorded to only three and the recording interval to 0.5–1 s. Acoustic indices were dominated by three main event types—a diurnally flowing creek, a nocturnal chorus of Hemiptera, as well as a dawn chorus of terapontid fishes.
4. We conclude with two key messages: First, a select group of informative signals can be monitored using very simple methods—namely, converting an audio stream into indices using freely available software. Second, however, to detect less acoustically dominant sound events, manual annotation or single call processing will still be needed. While these findings are encouraging, similar analysis will need to be conducted within other freshwater ecosystems before general conclusions about optimal sampling regimes can be drawn.

     

Salinisation reduces biodiversity in neighbouring freshwater patches in experimental metacommunities

1. Aquatic ecosystems are biodiversity hot spots across many landscapes; therefore, the degradation of these habitats can lead to decreases in biodiversity across multiple scales. Salinisation is a global issue that threatens freshwater ecosystems by reducing water quality and local biodiversity. The effects of salinity on local processes have been studied extensively; however, the effects of salinisation or similar environmental stressors within a metacommunity (a dispersal network of several distinct communities) have not been explored.
2. We tested how the spatial heterogeneity and the environmental contrast between freshwater and saline habitat patches influenced cladoceran biodiversity and species composition at local and regional scales in a metacommunity mesocosm experiment. We defined spatial heterogeneity as the proportion of freshwater to saltwater patches within the metacommunity, ranging from a freshwater-dominated metacommunity to a saltwater-dominated metacommunity. Environmental contrast was defined as the environmental distance between habitat patches along the salinity gradient in which low-contrast metacommunities consisted of freshwater and low-salinity patches and high-contrast metacommunities consisted of freshwater and high-salinity patches.
3. We hypothesised that the α-richness of freshwater patches and metacommunity γ-richness would decrease as freshwater patches became less abundant along the spatial heterogeneity gradient in both low- and high-contrast metacommunities, because there would be fewer freshwater patches that could serve as source populations for declining populations. We hypothesised that low-contrast metacommunities would support more species across the spatial heterogeneity gradient than high-contrast metacommunities, because, via dispersal, low-salinity patches can support halotolerant freshwater species that can mitigate population declines in neighbouring freshwater patches, whereas` high-salinity patches will mostly support halophilic species, providing fewer potential colonisers to freshwater patches.
4. We found that α-richness of freshwater mesocosms and metacommunity γ-richness declined in saline-dominated metacommunities regardless of the environmental contrast between the freshwater and saline mesocosms. We found that environmental contrast influenced freshwater and saline community composition in low-contrast metacommunities by increasing the abundances of species that could tolerate low-salinity environments through dispersal, whereas freshwater and high-salinity communities showed limited interactions through dispersal.
5. Freshwater mesocosms had a disproportionate effect on the local and regional biodiversity in these experimental metacommunities, indicating that habitat identity may be more important than habitat diversity for maintaining biodiversity in some metacommunities. This study further emphasises the importance in maintaining multiple species-rich habitat patches across landscapes, particularly those experiencing landscape-wide habitat degradation.

     

Positive biotic interactions in freshwaters: A review and research directive

1. Positive interspecific interactions such as mutualism, commensalism, and facilitation are globally ubiquitous. Although research on positive interactions in terrestrial and marine systems has progressed over the past few decades, comparatively little is known about them in freshwater ecosystems. However, recent advances have brought the study of positive interactions in freshwater systems to a point where synthesis is warranted.
2. In this review, we catalogue the variety of direct positive interactions described to date in freshwater ecosystems, discuss factors that could influence prevalence and impact of these interactions, and provide a framework for future research.
3. In positive interactions, organisms exchange key resources such as nutrients, protection, transportation, or habitat to a net benefit for at least one participant. A few mutualistic relationships have received research attention to date, namely seed-dispersing fishes, crayfishes and their ectosymbiotic cleaners, and communal-spawning stream fishes. Similarly, only a handful of commensalisms have been studied, primarily phoretic relationships. Facilitation via ecosystem engineering has received more attention, for example habitat modification by beavers and bioturbation by salmon.
4. It is well known that interaction outcomes vary with abiotic and biotic context. However, only a few of studies have examined context dependency in positive interactions in freshwater systems. Likewise, positive interactions incur costs as well as benefits; conceptualising interactions in terms of net cost/benefit to participants will help to clarify complex interactions.
5. It is likely that there are many positive interactions that have yet to be discovered in freshwater systems. To identify these interactions, we encourage inductive natural history studies combined with hypotheses deduced from general ecological models. Research on positive interactions must move beyond small-scale experiments and observational studies and adopt a cross-scale approach. Likewise, we must progress from reducing systems to oversimplified pairwise interactions, toward studying positive interactions in broader community contexts. Positive interactions have been greatly overlooked in applied freshwater ecology, but have great potential for conservation, restoration, and aquaculture.

     

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.

     

Acoustic detection and acoustic habitat characterisation of the critically endangered white-bellied heron (Ardea insignis) in Bhutan

1. Growing developmental activities, such as hydropower construction, farm roads, and other human activities, are affecting the critically endangered white-bellied heron (WBH). Out of a known global population of 60, 28 individuals inhabit the river basin area and freshwater lakes and ponds of Bhutan. Several constraints impede continuous monitoring of endangered species, such as the isolated and cryptic nature of the species and the remoteness of its habitat; to date, there are no long-term reference data or techniques implemented for continuous monitoring of this species.
2. In this study, we designed acoustic detection and habitat characterisation methods using long-duration recordings from three habitat areas in Bhutan. Acoustic indices were extracted and used to implement a species-specific call detector and to generate habitat soundscape representations. Using WBH calls annotated in month-long recordings from a known site, a novel indices-based detector was implemented and tested. A total of 960 hr of continuous audio recordings from three habitats in Bhutan were analysed.
3. We found that a species call detector implemented using a combination of acoustic indices (that includes measures of spectral and temporal entropy and different angles of spectral ridges) has a correct detection rate of 81%. Additionally, visual inspection of the species’ acoustic habitat using long-duration false-colour spectrograms enabled qualitative assessment of acoustic habitat structure and other dominant acoustic events.
4. This study proposes a combined approach of species acoustic detection and habitat soundscape analysis for holistic acoustic monitoring of endangered species. As a direct outcome of this work, we documented acoustic reference data on the critically endangered WBH from multiple habitat areas and have analysed its temporal vocalisation patterns across sites.

     

Egestion rates of microplastic fibres in fish scaled to in situ concentration and fish density

1. Microplastics (particles <5 mm) are commonly found in aquatic organisms across taxonomic groups and ecosystems. However, the egestion rate of microplastics from aquatic organisms and how egestion rates compare to other rates of microplastic movement in the environment are sparsely documented.
2. We fed microplastic fibres to round gobies (Neogobius melanostomus), an abundant, invasive species in the Laurentian Great Lakes. We conducted two trials where round gobies were fed microplastic-containing food either a single time (1 day) or every day over 7 days.
3. There was no difference in microplastic egestion rates from the 1 day or 7 day feeding trials, suggesting no impact of duration of exposure on egestion (exponential decay rate = −0.055 [±0.016 SE] and −0.040 [±0.007 SE], respectively). Turnover time of microplastics (i.e., average time from ingestion to egestion) in the gut ranged from 18.2 to 25.0 hr, similar to published values for other freshwater taxa.
4. We also measured microplastics in the digestive tracts of round gobies collected directly from Lake Michigan, U.S.A. Using published values for round goby density and microplastic concentration at the study sites, we calculated areal egestion rate by round gobies (no. particles m^–2 day^–1), and compared it to riverine microplastic export (no. particles m^–2 day^–1). Both area-based rates were of the same order of magnitude, suggesting that round goby egestion could be an important, and potentially overlooked component of microplastic dynamics at the ecosystem scale.
5. Animal egestion is well-known as a major component of nutrient and carbon cycling. However, direct measurements of microplastic fluxes in the environment that include animal egestion rates are uncommon. An ecosystem ecology approach is needed to meet the emerging challenge of generating microplastic budgets for freshwater environments and elsewhere, thereby informing management and mitigation of plastic pollution at a global scale.

     

Fragmentation promotes the role of dispersal in determining 10 intermittent headwater stream metacommunities

1. Dispersal, defined as the movement of individuals among local communities in a landscape, is a central regional determinant of metacommunity dynamics in ecosystems. Whereas both natural and anthropogenic ecosystem fragmentations can limit dispersal, previous attempts to measure such limitations have faced considerable context dependency, due to a combination of spatial extent and associated environmental variability, the wide range of dispersal modes, and abilities of organisms or variation in network topologies. Therefore, the role dispersal plays compared to local environmental filtering in explaining metacommunity dynamics remains unclear in fragmented dendritic ecosystems.
2. We quantified α- and β-diversity components of invertebrate metacommunities across 10 fragmented headwater stream networks and tested the hypothesis that dispersal is the primary determinant of biodiversity organisation in these dynamic and spatially constrained ecosystems.
3. Alpha-diversity was much lower in intermittent than perennial reaches, even long after rewetting, indicating an overwhelming effect of drying including a legacy effect on local communities.
4. Beta-diversity was never correlated with environmental distances but predominantly explained by spatial distances accounting for river network fragmentation. The nestedness proportion of β-diversity was considerable and reflected compositional differences where communities from intermittent reaches were subsets of perennial reaches.
5. Altogether, these results indicate dispersal as the primary process shaping metacommunity dynamics in these 10 headwater stream networks, where local communities recurrently undergo extinction and recolonisation events. This challenges previous conceptual views that local environment filtering is the main driver of headwater stream metacommunities.
6. As river networks become increasingly fragmented due to global change, our results suggest that some freshwater ecosystems currently driven by local environment filtering could gradually become dispersal-limited. In this perspective, shifts from perennial to intermittent flow regimes represent ecological thresholds that should not be crossed to avoid jeopardising river biodiversity, functional integrity, and the ecosystem services they provide to society.

     

Life history and genetic characterisation of sea trout Salmo trutta in the Adriatic Sea

1. The brown trout Salmo trutta is characterised by both anadromous (sea trout) and resident populations, naturally occurring in Atlantic and Ponto-Caspian rivers. Sea trout are currently considered absent from rivers of the Mediterranean area, probably because of the non-optimal chemical–physical characteristics of the Mediterranean Sea. However, the occasional bycatch of smoltified S. trutta in the Adriatic Sea is well known among fishermen and the biological explanation of this phenomenon is still controversial. The aim of this study was to compare the genetic diversity of freshwater and marine brown trout to try to understand the factors underlying the presence of putative anadromous brown trout in the Adriatic Sea.
2. In this study, we analysed the genetic diversity of: (1) wild brown trout collected from the Esino River (central Italy); (2) a domestic strain of brown trout used for stocking the study area; and (3) a sample of Adriatic sea trout collected near the outlet of the Esino River. Together with genetic analysis, we carried out scale analysis in order to track the freshwater/marine stages of the life cycle in the sea trout samples. The genetic characterisation was carried out by polymerase chain reaction–restriction fragment length polymorphism analysis of the mtDNA fragment ND-5/6 and the nuclear locus LDH-C1* and by genotyping 15 microsatellite loci. The genetic polymorphism obtained was used to investigate intra- and inter-population genetic diversity, rates of genetic introgression between wild and domestic samples and the origin of sea trout specimens by using assignment tests.
3. Our genetic analyses demonstrated that the sea trout analysed in this study are from the domestic strain of Atlantic origin used in central Italy for stocking activities. The level of genetic introgression between native and domestic samples is high in the Esino River. The populations more resilient to introgressive hybridisation appeared to be those living in the portion of the river network dominated by carbonate rocks. Assignment tests (GeneClass) suggest the existence of a link between stocking efforts and the freshwater origin of the sea trout. In addition, data obtained from the analysis of scales, size measurement, and sex determination showed a pattern of smolt age, size, and sex ratio very similar to those observed in other anadromous populations.
4. In conclusion, the present study highlighted that sea trout from the central Adriatic Sea originated from brown trout of Atlantic origin inhabiting the Esino River. Their seaward migratory behaviour could represent a consequence of an active migration instead of a passive displacement by water flow. Our results also showed that traditional stocking practices represent a negative activity for the conservation of the last Mediterranean native S. trutta populations.

     

Automatic detection of fish and tracking of movement for ecology

1. Animal movement studies are conducted to monitor ecosystem health, understand ecological dynamics, and address management and conservation questions. In marine environments, traditional sampling and monitoring methods to measure animal movement are invasive, labor intensive, costly, and limited in the number of individuals that can be feasibly tracked. Automated detection and tracking of small‐scale movements of many animals through cameras are possible but are largely untested in field conditions, hampering applications to ecological questions.
2. Here, we aimed to test the ability of an automated object detection and object tracking pipeline to track small‐scale movement of many individuals in videos. We applied the pipeline to track fish movement in the field and characterize movement behavior. We automated the detection of a common fisheries species (yellowfin bream, Acanthopagrus australis) along a known movement passageway from underwater videos. We then tracked fish movement with three types of tracking algorithms (MOSSE, Seq‐NMS, and SiamMask) and evaluated their accuracy at characterizing movement.
3. We successfully detected yellowfin bream in a multispecies assemblage (F1 score =91%). At least 120 of the 169 individual bream present in videos were correctly identified and tracked. The accuracies among the three tracking architectures varied, with MOSSE and SiamMask achieving an accuracy of 78% and Seq‐NMS 84%.
4. By employing this integrated object detection and tracking pipeline, we demonstrated a noninvasive and reliable approach to studying fish behavior by tracking their movement under field conditions. These cost‐effective technologies provide a means for future studies to scale‐up the analysis of movement across many visual monitoring systems.