Automated acoustic monitoring of endangered common spadefoot toad populations reveals patterns of vocal activity

1. In the context of global amphibian decline, monitoring and restoration programmes are important. Acoustic monitoring is a possible approach for underwater vocalising species like the rapidly declining European common spadefoot toad (Pelobates fuscus). In this study, our aim was to design a dedicated software detector to be used in combination with programmable audio recorders to process the large amount of data generated by long-term acoustic monitoring and to use it for investigating the seasonal and circadian patterns of P. fuscus vocal activity.
2. The software detector targets advertisement calls of the species. Based on acoustic analysis of that call, we developed a detector that utilises both frequency and time features of the calls. Data collected during three breeding seasons in four known or potential P. fuscus breeding sites of north-eastern France were used to build a ground truth in order to test the performance of the detector. Then, we used the detector for analysing four acoustic monitoring campaigns conducted in two different sites over two breeding seasons to gain insight into the seasonal and circadian patterns of vocal activity of this species.
3. Evaluation of the P. fuscus call detector against a ground truth returned false-positive rates below 1.5% and true-positive rates ranging from 53% to 73%. These figures are compatible with long-term monitoring of the presence of the species. Running the software detector on standard hardware, the computation time for post-processing the 360 hr of a typical 3-month monitoring campaign was less than 1 day.
4. The seasonal pattern of P. fuscus underwater vocal activity is more complex than previously recognised. Over the whole ostensible 3-month breeding season, the actual time window for vocalising and breeding can last from a few days up to several weeks and may be split into clearly distinct episodes. When vocalisations occurred at both night- and daytime, the circadian vocal activity of P. fuscus occasionally proceeded uninterrupted for 24 hr but usually a several hour lull occurred immediately prior to sunset. When vocalisations occurred at both night- and daytime, the vocal activity pattern followed a bimodal distribution with a nocturnal highest peak of activity and a second peak occurring in the morning.
5. Our results demonstrate that it is feasible to monitor presence of P. fuscus in north-eastern France using a dedicated software detector combined with programmable audio recorders. Based on the outcomes of the detector applied to long-term audio data sets, we reveal temporal patterns of the vocal activity of the species and subsequently provide recommendations for attended and unattended acoustic monitoring.

     

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.

     

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.

     

Effects of temperature and a piscivorous fish on diel winter behaviour of juvenile brown trout (Salmo trutta)

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Assessing the value of acoustic indices to distinguish species and quantify activity: A case study using frogs

1. Soundscapes can provide information about a wide range of habitats and species through the recording of vocalisations over long temporal scales. Because of the large volumes of data collected, computational approaches, such as the application of acoustic indices, are required to extract useful information from long-duration recordings.
2. Acoustic indices summarise various soundscape features into frequency ranges over defined time intervals and can aid in the visual exploration, detection, and analysis of species vocalisation patterns. Here, we examine the performance of combinations of three acoustic indices commonly used in visual exploration, the acoustic complexity index, the temporal entropy spectrum index, and the event spectrum index, and assess their ability to distinguish species and describe acoustic features commonly used to detect species and analyse activity. Our case study focuses on three frog species with distinct call structures from Bickerton Island, Northern Territory, Australia. Call structure was categorised based on the number of pulses and harmonics.
3. We summarised acoustic activity by calculating acoustic indices in 256 equal-sized bins over the entire the frequency spectrum, for 30-s intervals, and found that acoustic index values could be used to distinguish species and describe acoustic features. The acoustic complexity index was the most effective index for distinguishing species. To describe acoustic features, we examined correlations between acoustic index values and summarised acoustic features, including call rate, total duration, loudness and signal-to-noise ratio. In single-pulsed species with no harmonics, we found spectral index values were significantly and sometimes strongly correlated with acoustic features. In comparison, species with harmonics were found to be weakly and less frequently correlated with acoustic features even if sampled calls were loud and have high signal-to-noise ratio. We suggest that acoustic indices have the potential to describe acoustic features in single-pulsed species but are limited in those with harmonics.
4. We conclude that acoustic indices can be a useful tool to distinguish some anuran species and to broadly understand specific acoustic features used to analyse calling activity over long periods of time.
5. Further research is required to better understand the relationships between acoustic indices and acoustic features to determine the general utility of indices to detect and distinguish audible species and to identify other acoustic features of various taxa.

     

BIOACOUSTIC PUBLICATIONS, 1989

ABSTRACT

Coruros Spalacopus cyanus, social fossorial rodents from Chile, use a complex acoustic repertoire with eleven different true vocalisations and one mechanical sound in various behavioural contexts. The complex of contact calls is particularly well differentiated. Juvenile coruros produced six true vocalisations of which four were structurally identical to adult calls. One vocalisation had components of two adult sounds and one occurred only in juvenile animals. Certain calls from the adult repertoire were lacking. The frequencies of sounds of juveniles were considerably higher than those of adults, with many sounds reaching the ultrasonic range. Nevertheless, pure ultrasonic sounds were not recorded.

The frequencies of the analysed sounds of coruros extended from 0.17 to 20.33 kHz with dominant frequency components between 0.17 and 10 kHz. The acoustic properties of calls are suitable for transmission above and below ground, thus providing further indirect evidence that coruros are not strictly confined to an underground way of life. Indeed, the great variability of frequency ranges, with lower frequencies always being included, reflects a specialisation for communication in variable acoustic environments.

The most distinctive and unique vocalisation of coruros is the long duration musical trilling (lasting up to two minutes), which is a long-distance call emitted in alarm and arousal contexts. Recordings of this call from natural burrows in the field in Chile showed similar structural features to vocalisations from captive colonies in the laboratory.

Our findings provide a further example of matching physical properties of vocalisations to the acoustic conditions of the habitat. However, vocalisations in subterranean rodents consist almost exclusively of short-distance calls, the trilling of coruros being the notable exception. Since the selective pressure of the acoustic environment upon the evolution of short-distance vocalisations is probably minimal, we suggest that during their evolution, subterranean mammals have matched their vocalisations primarily to their hearing range and not directly to the acoustics underground. Hearing probably has been the primary target of natural selection, serving not only for communication but also for detection of predators (and, in carnivores, of prey).     

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.

     

Spawning behaviour of Allis shad Alosa alosa: new insights based on imaging sonar data

Spawning behaviour of Alosa alosa was observed by high resolution imaging sonar. Detected clouds of sexual products and micro bubbles served as a potential indicator of spawning activity. Peak spawning time was between 0130 and 0200 hours at night. Increasing detections over three consecutive nights were consistent with sounds of mating events (bulls) assessed in hearing surveys in parallel to the hydro acoustic detection. In 70% of the analysed mating events there were no additional A. alosa joining the event whilst 70% of the mating events showed one or two A. alosa leaving the cloud. In 31% of the analysed mating events, however, three or more A. alosa were leaving the clouds, indicating that matings are not restricted to a pair. Imaging sonar is suitable for monitoring spawning activity and behaviour of anadromous clupeids in their spawning habitats.     

Large-scale bioacoustic monitoring to elucidate the distribution of a non-native katydid

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BIOACOUSTIC PUBLICATIONS, 1989

ABSTRACT

In order to increase understanding of African elephant vocal communication and to standardise the terminology used to describe vocalisations, this study examined acoustic and temporal characteristics of 983 vocalisations from 2 male and 6 female captive African elephants. Recording collars were used to monitor vocalisations and videotape to simultaneously record behaviour, allowing for unambiguous attribution of sounds to individuals, even in close proximity. Eight acoustically distinct categories of calls were defined in terms of structural characteristics; two of these categories are described for the first time. Low-frequency vocalisations containing infrasonic components were predominant in this localised communication context and showed a gradation of variation in acoustic structure and duration. Most calls were part of temporally closed exchanges between individuals and coincided with short-distance interactions. In addition, male-female choruses and non-musth rumbles from males were documented, suggesting that the African elephant vocal repertoire may be more complex than previously reported.     

Ecoacoustic monitoring of lake sturgeon (Acipenser fulvescens) spawning and its relation to anthropogenic noise

Lake sturgeon (Acipenser fulvescens) are endangered in the Laurentian Great Lakes with increasing binational efforts to establish spawning grounds to aid restoration. While SCUBA surveys can document spawning activity, these are labour-intensive and may disrupt spawning. We used passive acoustic monitoring to quantify spawning sounds of lake sturgeon as a first step to developing remote sensing of sturgeon spawning grounds. Acipenser sp. are known to make a variety of sounds including, “thunders” (aka drums), which have been documented in A. fulvescens during spawning. We quantified drums from a known spawning bed. We recorded 5 different potential sturgeon sounds but only quantified drums as a marker for spawning activity. Drums were low frequency with average frequency peaks at 40 and 92 Hz and a rapid drop-off thereafter. There was no relationship between calling activity and water temperature but calling activity increased as the summer progressed. Call production was most active from 0600 to 1500 h with little calling activity during nighttime recordings. The presence of low frequency boat sounds did correlate with a reduction in maximum calling rate so it is possible that commercial shipping may disrupt sturgeon communication, but more research is necessary to separate correlational from causative effects. These recordings represent a promising approach to map sturgeon spawning activity and show the potential effect of human activity on communication in this threatened species.     

Acoustic activity across a seabird colony reflects patterns of within-colony flight rather than nest density

Passive acoustic monitoring is increasingly being used as a cost-effective way to study wildlife populations, especially those that are difficult to census using conventional methods. Burrow-nesting seabirds are among the most threatened birds globally, but they are also one of the most challenging taxa to census, making them prime candidates for research into such automated monitoring platforms. Passive acoustic monitoring has the potential to determine presence/absence or quantify burrow-nesting populations, but its effectiveness remains unclear. We compared passive acoustic monitoring, tape-playbacks and GPS tracking data to investigate the ability of passive acoustic monitoring to capture unbiased estimates of within-colony variation in nest density for the Manx Shearwater Puffinus puffinus. Variation in acoustic activity across 12 study plots on an island colony was examined in relation to burrow density and environmental factors across 2 years. As predicted fewer calls were recorded when wind speed was high, and on moon-lit nights, but there was no correlation between acoustic activity and the density of breeding birds within the plots as determined by tape-playback surveys. Instead, acoustic indices correlated positively with spatial variation in the in-colony flight activity of breeding individuals detected by GPS. Although passive acoustic monitoring has enormous potential in avian conservation, our results highlight the importance of understanding behaviour when using passive acoustic monitoring to estimate density and distribution.     

Post-stocking movement and survival of hatchery-reared bloater (Coregonus hoyi) reintroduced to Lake Ontario

1. Determining the movement and fate of fishes post-stocking is challenging due to the difficulty in monitoring them, particularly immediately after release. Bloater (Coregonus hoyi; Salmonidae) is a deepwater cisco that has been extirpated from Lake Ontario for several decades and is presently the focus of binational restoration stocking efforts; however, there is limited information to evaluate the efficacy of these efforts. The aim of this study was to examine the initial post-release survival, 3D movement, and behaviour of hatchery-reared bloater stocked in Lake Ontario to expand knowledge of post-stocking ecology of fish and inform stocking practices for deepwater ciscoes.
2. In total, 74 hatchery-reared bloater were tagged with acoustic transmitters with depth and temperature sensors in 2016, 2017, and 2018 and passively monitored on an array of 105 69-kHz acoustic receivers deployed in north-eastern Lake Ontario. Several spatial metrics analysed movements after release to investigate immediate post-stocking survival and behaviour for the first time in a pelagic freshwater forage fish.
3. Estimated survival for tagged bloater was low (≤42%) and detection periods of live bloater ranged from 0.2 to 12.1 days (mean ± SD: 2.9 ± 2.9 days). Following release, tagged bloater dispersed quickly and exhibited an association with deeper water (>40 m). Despite overlap in space use for some bloater, there was no evidence of schooling behaviour. Bloater underwent extensive diel vertical migration from near bottom to within metres of the surface. These results demonstrated that, despite high initial mortality, some hatchery-reared bloater survived the initial stress of release and displayed characteristic behaviour of the species.
4. This study demonstrated the value of acoustic telemetry in restoration efforts and revealed survival and behaviour of bloater that has never been observed at this resolution, providing novel information for the management of reintroduced species. Establishment of a self-sustaining population of bloater will help restore fish native to Lake Ontario thus increasing prey fish diversity, improving ecological integrity and resilience, and serving as a model for the reintroduction and management of other native species throughout the Great Lakes.

     

Ecoacoustics can detect ecosystem responses to environmental water allocations

1. Globally, water abstraction for human consumption and irrigated agriculture leads to significant changes in aquatic ecosystems. To counter these detrimental effects, water releases—often termed environmental water allocations—restore overbank flow or are delivered to artificially disconnected wetlands. While a suite of monitoring methods is available, few programmes track continuous change in biota, mainly because repeated remote site visits can be prohibitively expensive.
2. In this paper, we propose a new approach to environmental flow monitoring, using ecoacoustic methods. We test acoustic monitoring of frog and waterbird responses to environmental water deliveries in the Goulburn Broken, a valley in the southern Murray–Darling river system. Response to three major environmental water deliveries within 2 years was monitored at four sites along Reedy swamp. Every 2 weeks, 30 s were recorded every 30 min, for a total of 24 hr.
3. We used two analysis strategies—manual counts of bird calls, as well as ecoacoustic indices, which describe the sonic properties of the acoustic spectrum at a site. Manual counts demonstrated that water-dependent birds were clearly responding to environmental water deliveries, whereas non-water-dependent species did not show any increases in activity. After restricting the analysis to the dawn chorus of birds and frogs, two acoustic indices (the median amplitude and the acoustic complexity index) showed responses to watering events.
4. Ecoacoustic methods show promise for continuous response monitoring to environmental water allocations. However, the first strategy—manual annotation of calls—might be too labour intensive for standard monitoring programmes. The second strategy—index-based approaches—can also detect ecological responses, although further investigation using control sites is needed. Automated call classifiers are an alternative that is currently being developed for endangered species. We also encourage simultaneous monitoring of the soundscape above and under water.

     

Fine‐scale movements and interactions of platypuses,and the impact of an environmental flushing flow

1. The platypus is a cryptic mammal that inhabits freshwater streams and rivers of eastern Australia. Tracking the movements of wild platypuses has been notoriously difficult due to the animals' morphology and methodological limitations. Knowledge of fine‐scale movements and interactions among individuals remain particularly poorly understood, as do responses to changes in hydrology.
2. We tracked movements of 15 platypuses (six females, nine males) downstream of the Jindabyne Dam on the Snowy River, using externally attached acoustic transmitters (September–November 2017), to assess spatio‐temporal activity patterns among individuals and changes in movement and activity before and after an environmental flushing flow. As the study took place during the breeding season, we expected to observe overlap in area of activity among males and females, but not among males due to increased territoriality during these months. We also anticipated that a large flow event would impact their activity and foraging behaviour, possibly displacing platypuses downstream.
3. Overlaps in area of activity and temporal co‐occurrence within a pool varied among individuals, with two resident males exhibiting some spatial overlap of activity and varying temporal co‐occurrence, despite tracking during the breeding season. All six tracked females were captured in the same pool and appeared to be residents, possibly highlighting preferences for certain habitats during the breeding months.
4. We found no evidence that the movements of adult platypuses were affected by an environmental flushing flow, with no significant changes to area of activity, number of detections, or daily range of movements. However, foraging duration increased in the week after the flow, possibly associated with increased prey availability.
5. These findings suggest that territoriality between males during and after the breeding season may depend on platypus density and resource availability and that pools with high resource availability may support several breeding females.

     

Estimating the spawning activity of fish species using nuclear and mitochondrial environmental DNA concentrations and their ratios

1. During spawning activity, fish release large amounts of sperm and eggs into the water, which has been assumed to cause an increase in environmental DNA (eDNA) levels and nuclear DNA/mitochondrial DNA ratios. To test whether these assumptions are valid and whether nuclear and mitochondrial eDNA analysis can be used to monitor the spawning activity of freshwater fish, we conducted field eDNA surveys and traditional surveys using common carp (Cyprinus carpio), largemouth bass (Micropterus salmoides) and bluegill sunfish (Lepomis macrochirus) as model species.
2. Fish spawning periods were estimated based on age, as estimated using the body lengths of juveniles collected in the Miharu reservoir in Fukushima, Japan. The results showed that the main spawning periods of largemouth bass and bluegill sunfish were from April to July and from July to August, respectively.
3. Field eDNA surveys were conducted in the Hebisawagawa front reservoir, which is connected to the Miharu reservoir. From March to August 2019 and 2020, weekly eDNA sampling was conducted at three sites, and daily sampling was conducted at six sites from 23 June to 3 July 2020. The eDNA concentrations of the nuclear internal transcribed spacer 1 (ITS1) and mitochondrial cytochrome B (CytB), as well as the ITS1/CytB ratio, were measured for each of the three fish in each water sample. Water temperature had a statistically significant effect on eDNA concentration, probably reflecting the relationship between water temperature and spawning.
4. We created generalised additive mixed models to estimate spawning activity periods based on weekly eDNA data. The estimated periods of spawning activity for common carp, largemouth bass and bluegill sunfish were March to May, May to July, and May to August, respectively. The estimated spawning periods coincided with known fish ecology or the results of traditional methods. This method also has been applied to daily eDNA samples, showing the feasibility of high-resolution estimation of spawning activity.
5. For common carp and bluegill sunfish, we were able to estimate the spawning period using this method. Although the method is affected by biomass and the diffusion and degradation of eDNA, it has the potential to accurately estimating spawning activities. These then can be estimated without conducting laborious traditional surveys, facilitating the monitoring of reproduction by rare, invasive or important fishery species. Further research on the diffusion distance and degradation time of the eDNA concentration peak caused by fish spawning activity may improve the accuracy of monitoring.

     

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.