The use of automated acoustic identification software for bat surveys in the neotropics : Gaps and opportunities

As populações de morcegos são conhecidas por serem afetadas por atividades antropogênicas,njá que os Chiroptera é um grupo extremamente diverso que ocupa quase todos os nichos disponíveis no meio terrestre. Assim, os morcegos são considerados bons bioindicadores para monitorar mudanças no meio ambiente, mas seu valor como tal também depende da facilidade de monitorar e detectar tendências demográficas em suas populações. O interesse a longo prazo dos pesquisadores na acústica dos morcegos resulta do fato de que é um método não-invasivo e eficiente em termos de tempo para monitorar os padrões espaço-temporais da diversidade e atividade de morcegos. A análise dos sons emitidos pelos organismos tem sido útil para a aquisição de conhecimento sobre as interações bióticas e abióticas específicas de cada espécie, e sua aplicação na conservação. Além das identificações manuais de chamados de morcegos, existe atualmente no mercado um conjunto de programas automatizados de identificação que utilizam bibliotecas regionais e se apresentam como uma ferramenta eficiente no monitoramento de populações de morcegos. A maioria desses programas não foi validada usando dados de campo. Este estudo avalia a confiabilidade de dois softwares automatizados, SonoChiro e Kaleidoscope Pro, em comparação com identificações manuais de dados de campo coletados da região Neotropical. Houve um baixo nível de concordância entre os dois métodos automatizados ao nível das identificações específicas, razoável ao nível do gênero e satisfatório ao nível a família. Houve também uma diferença significativa entre a proporção de chamados corretamente identificados entre os dois programas ao nível específico. Os principais desafios para o uso de software de identificação automatizada incluem a necessidade de bibliotecas de chamados abrangentes da diversidade existente nas regiões em foco dos estudos; as principais oportunidades, por outro lado, incluem a ampla possibilidade de monitorar os padrões espaço-temporais da atividade de morcegos. Existem ainda fortes lacunas que impedem uma aplicação generalizada de programas automatizados em estudos ecológicos e de conservação de morcegos, mas há potencial de melhoria. Considerando as limitações dos programas automatizados, é discutida uma estrutura para aplicação em estudos ecológicos e de conservação.Bat populations are known to be affected by anthropogenic activities because bats are an extremely diverse group occupying almost all available niches in terrestrial environment. Hence, bats are considered bioindicators to monitor changes in the environment, but their value as such also depends on the ease to monitor and detect demographic trends in their populations. The long term interest of researchers in the acoustic of bats results from the fact that it is a non-invasive, time-efficient methods to monitor spatiotemporal patterns of bat diversity and activity.The analysis of sounds emitted by organisms has been considered useful to gain insight into species-specific biotic and abiotic interactions, which can further be applied to conservation. Besides manual identifications of bat calls, a number of automated species identification programs using regional call classfiers have been introduced into the market as an efficient tool in monitoring of bat populations. Most of these programs have not been validated using field data. This study evaluates the reliability of two automated softwares, SonoChiro and Kaleidoscope Pro, in comparison to manual identifications of field data collected from the Neotropical region. There was low agreement between the two automated methods at the species level, fair agreement at the genus level and moderate agreement at the family level. There was also a significant difference between the proportion of correctly identified calls of the two-automated software at the species level identifications. Major challenges for using automated identification software include the need for comprehensive call libraries of the regions under scope; major opportunities, on the other hand, include the widespread possibility to monitor spatiotemporal patterns of bat activity. Overall, there are serious gaps that preclude a widespread application of automated programs in ecological and conservation studies of bats, but there is a potential for improvement. Considering the limitations of the automated programs, a framework for application in ecological and conservation studies is discussed

Fish sounds and boat noise are prominent soundscape contributors in an urban European estuary

Passive acoustic monitoring is a valuable tool for non-intrusive monitoring of marine environments, also allowing the assessment of underwater noise that can negatively affect marine organisms. Here we provide for the first time, an assessment of noise levels and temporal soundscape patterns for a European estuary. We used several eco-acoustics methodologies to characterize the data collected over six weeks within May 2016 - July 2017 from Tagus estuary. Biophony was the major contributor dominated by fish vocalizations and the main driver for seasonal patterns. Maritime traffic was the major source of anthropogenic noise, with daily patterns monitored using 1584 Hz third-octave band level. This indicator avoided biophony and geophony, unlike other indicators proposed for the EU Marine Strategy Framework Directive. Furthermore, the frequency overlap between anthropophony and biophony demands precautionary actions and calls for further research. This study provides an assessment that will be useful for future monitoring and management strategies.Fundação para a Ciência e Tecnologia - FCTinfo:eu-repo/semantics/publishedVersio

Testing the performances of automated identification of bat echolocation calls:A request for prudence

Echolocating bats are surveyed and studied acoustically with bat detectors routinely and worldwide, yet identification of species from calls often remains ambiguous or impossible due to intraspecific call variation and/or interspecific overlap in call design. To overcome such difficulties and to reduce workload, automated classifiers of echolocation calls have become popular, but their performance has not been tested sufficiently in the field. We examined the absolute performance of two commercially available programs (SonoChiro and Kaleidoscope) and one freeware package (BatClassify). We recorded noise from rain and calls of seven common bat species with Pettersson real-time full spectrum detectors in Sweden. The programs could always (100%) distinguish rain from bat calls, usually (68–100%) identify bats to group (Nyctalus/Vespertilio/Eptesicus, Pipistrellus, Myotis, Plecotus, Barbastella) and usually (83–99%) recognize typical calls of some species whose echolocation pulses are structurally distinct (Pipistrellus pygmaeus, Barbastella barbastellus). Species with less characteristic echolocation calls were not identified reliably, including Vespertilio murinus (16–26%), Myotis spp. (4–93%) and Plecotus auritus (0–89%). All programs showed major although different shortcomings and the often poor performance raising serious concerns about the use of automated classifiers for identification to species level in research and surveys. We highlight the importance of validating output from automated classifiers, and restricting their use to specific situations where identification can be made with high confidence. For comparison we also present the result of a manual identification test on a random subset of the files used to test the programs. It showed a higher classification success but performances were still low for more problematic taxa

Relación entre índices acústicos, duración de las grabaciones y tiempo de procesamiento:Una prueba metodológica

Ecoacoustic approaches have the potential to provide rapid biodiversity assessments and avoid costly fieldwork. Their use in biodiversity studies for improving management and conservation of natural landscapes has grown considerably in recent years. Standardised methods for sampling acoustic information that deliver reliable and consistent results within and between ecosystems are still lacking. Sampling frequency and duration are particularly important considerations because shorter, intermittent recordings mean recorder batteries last longer and data processing is less computationally intensive, but a smaller proportion of the available soundscape is sampled. Here, we compare acoustic indices and processing time for subsamples of increasing duration clipped from 94 one-hour recordings, to test how different acoustic indices behave, in order to identify the minimum sample length required. Our results suggest that short recordings distributed across the survey period accurately represent acoustic patterns, while optimizing data collection and processing. ACI and H are the most stable indices, showing an ideal sampling schedule of ten 1-minute samples in an hour. Although ADI, AEI and NDSI well represent acoustic patterns under the same sampling schedule, these are more robust under continuous recording formats. Such targeted subsampling could greatly reduce data storage and computational power requirements in large-scale and long-term projects

Can soundscape indices be used to reflect biodiversity in an Ecuadorian Andean tropical montane habitat?

The measurement of biodiversity presents a challenging task for conservationists. Traditional ecological descriptors such as species richness, Shannon and Simpson diversities have long been relied on by ecologists to provide an indication of biodiversity, however, the generation of these indices requires manual assessments of local fauna through methods which can often be expensive, time consuming and invasive. Analysis of the Soundscape, the collection of sounds generated by organisms (biophony), humans (anthrophony) and non-biological sounds such as wind and water (geophony), presents new potential for biodiversity sampling. To date, a range of indices have been developed that aim to provide a value relating to acoustic characteristics of an environment, based on the spectral and temporal properties within sound recordings. Several studies have yielded promising results when using the acoustic indices for biodiversity assessments in temperate, and to some extent, tropical habitats. We here aimed to further the current understanding of soundscape indices by investigating how they behave in a tropical habitat of high avifaunal diversity. Point count data for bird species was collected from the Santa Lucia Cloud Forest Reserve, NW Ecuador (0°17'30"N, 78°40'30"W), during Summer 2014, while acoustic recordings were taken simultaneously using a handheld audio recorder. We first analysed the change in bird species composition and diversity along two environmental gradients of habitat disturbance and altitude, and investigated how the acoustic indices behaved along these same gradients. We then explored whether the acoustic indices can be used to estimate biodiversity based on their correlation with traditional ecological indices. From the point count data we found a high turnover in species composition across sample sites. Mean species richness was found to negatively correlate with increasing altitude (p=1.485e-05) and was found to be significantly lower in sites of primary forest than in both secondary forest and silvopasture (p=0.0165). Although each of the acoustic indices showed varying levels of change across the environmental gradients, we found that only four of the eight acoustic indices, the Normalized Difference Soundscape Index (NDSI, p=0.048), spectral entropy Hs, p=0.033), temporal entropy (Ht, p=0.031), and total entropy (H, p=0.031), were found to significantly correlate with species composition. We found that spectral entropy (Hs) and total entropy (H) were the only acoustic indices to significantly correlate with ecological indices, however since the total entropy (H) is developed as a product of the spectral entropy (Hs) we suggest that only the H index should be utilised for biodiversity measurements. We found that while the acoustic indices have the potential to characterise certain features of a habitat or to assist in analysing bird species composition, their use for biodiversity assessment is limited. We would suggest that more work to develop and understand the indices is needed before we can reliably make use of them for measuring biodiversity

Biases of acoustic indices measuring biodiversity in urban areas

Urban green infrastructure, GI (e.g., parks, gardens, green roofs) are potentially important biodiversity habitats, however their full ecological capacity is poorly understood, in part due to the difficulties of monitoring urban wildlife populations. Ecoacoustic surveying is a useful way of monitoring habitats, where acoustic indices (AIs) are used to measure biodiversity by summarising the activity or diversity of biotic sounds. However, the biases introduced to AIs in acoustically complex urban habitats dominated by anthropogenic noise are not well understood. Here we measure the level of activity and diversity of the low (0-12 kHz, l) and high (12-96 kHz, h) frequency biotic, anthropogenic, and geophonic components of 2452 hours of acoustic recordings from 15 sites across Greater London, UK from June to October 2013 based on acoustic and visual analysis of recordings. We used mixed-effects models to compare these measures to those from four commonly used AIs: Acoustic Complexity Index (ACI), Acoustic Diversity Index (ADI), Bioacoustic Index (BI), and Normalised Difference Soundscape Index (NDSI). We found that three AIs (ACIl, BIl, NDSIl) were significantly positively correlated with our measures of bioticl activity and diversity. However, all three were also correlated with anthropogenicl activity, and BIl and NDSIl were correlated with anthropogenicl diversity. All low frequency AIs were correlated with the presence of geophonicl sound. Regarding the high frequency recordings, only one AI (ACIh) was positively correlated with measured biotich activity, but was also positively correlated with anthropogenich activity, and no index was correlated with biotich diversity. The AIs tested here are therefore not suitable for monitoring biodiversity acoustically in anthropogenically dominated habitats without the prior removal of biasing sounds from recordings. However, with further methodological research to overcome some of the limitations identified here, ecoacoustics has enormous potential to facilitate urban biodiversity and ecosystem monitoring at the scales necessary to manage cities in the future

Evaluation of wildlife acoustic survey as a method to estimate bird habitat quality

In the world of birds, the sound says it all. The song, the alarm call, the flight call, and the call for a mate, all makes up a soundscape telling their friends and foes of their condition, mate status and tells the predator that its presence is noticed. In traditional bird monitoring our human ears and eyes are used, with all the pros and cons that comes with the researcher being in situ. But what does the soundscapes of the birds tell us about the habitat quality? If high quality means a habitat with more complex structure, does it mean that the individuals possessing it can spend more time singing for a mate and claim its territory? And less time to call out warning for predators due to the protection the understory and canopy offers? And if so, can we draw the conclusion that their fellow species in open, lower quality habitats, spend more time warning than singing? By comparing the results of traditional bird spotting in six sites outside Uppsala, Sweden, with the recordings of a SM4 soundscape recorder left on each site for 48 hours, it was possible to not only find which species that inhabited the site but also compare the time each species spent on singing vs the time spent on warning for each site. Part from being an ecological survey, of any behavioural difference between habitats, this project was an evaluation of the quality of the recorder SM4 as well as the software Kaleidoscope Pro from Wildlife acoustic. Findings were that the quality of the recordings were high, and that the software is capable of distinguishing between very small differences of song within species. But that the software still needs more examining to see if the issues, such as cutting phrases into far too short fragments of song, can be adjusted by the settings or if it requires more developing of the software to improve the usability of the software’s ability to cluster species. No evidence was found that the quality of the habitat makes the warning more frequent in the open habitats and the singing more consistent in the complex ones.Fåglarnas värld domineras av ljud. Revirhävdande sång, varningsläten, flyktläten och lockrop för en partner, allt vävs samman till den ljudbild som ger vänner och konkurrenter en uppfattning om ens kondition, förhållandestatus och upplyser predatorer om att deras närvaro är upptäckt. Inom traditionell fågelövervakning är det de mänskliga öronen och ögonen som är avgörande, med alla de för- och nackdelar som det innebär att befinna sig in situ. Men vad kan ljudbilden fåglarna skapar säga oss om kvaliteten på habitatet? Om hög kvalitet avser ett område med mer komplex struktur, innebär det att dess invånare kan tillbringa mer tid med att sjunga för att locka en partner och hävda ett territorium än att varna för predatorer eftersom undervegetation och trädkronor erbjuder en högre grad av skydd? Och går det i så fall att dra slutsatsen att deras artfränder i mer öppna habitat, av lägre kvalitet, tvingas tillbringa en större del av tiden att varna för faror än att sjunga? Genom att jämföra resultaten från traditionell fågelövervakning i sex provytor utanför Uppsala, Sverige, med inspelningar gjorda av en SM4-inspelare placerad i varje provyta i 48 timmar, var det möjligt att finna vilka arter som bebor området, men också jämföra tiden varje art tillbringar med att sjunga jämfört med att varna eller locka. Förutom att vara en ekologisk undersökning, som jämför beteendeskillnaderna mellan habitatfläckar av olika kvalitet, var detta projekt också en utvärderingsstudie i kvaliteten hos inspelningsutrustningen SongMeter4 (SM4) och mjukvaran Kaleidoscope Pro från Wildlife acoustics. Kvaliteten på ljudinspelningarna visade sig vara hög och mjukvaran har kapacitet att göra åtskillnad mellan små variationer inom samma art. Dock så konstaterades det att det krävs fler och längre studier för att undersöka om problemen, så som att mjukvaran klippte av strofer i väldigt korta fragment när den klustrade, kan åtgärdas med hjälp av inställningarna eller om det kräver vidare utveckling av mjukvaran för att den ska vara användbar i studier av arter. Inga resultat från den ekologiska undersökningen antyder att individer i habitat av lägre kvalitet skulle tillbringa mer tid med att varna för faror jämfört med att sjunga. Eller att individer i habitatfläckar av högre kvalitet skulle spendera mer tid med att sjunga än att locka och varna

Applying Island Biogeography Theory and Ecoacoustic Approaches to Explore the Species Composition, Richness, and Biodiversity in Northern Temperate Salt Marsh Pools of the Little River Estuary

Salt marsh habitats are prevalent throughout coastal New England and offer a wide rangeof ecological services, including serving as nursery habitats to both transient and resident species, trapping sediment and nutrients to keep pace with rising sea levels, and improving water quality through filtration of runoff. These complex habitats remain poorly understood, especially regarding the biological communities that occupy them. The northern temperate salt marshes that characterize the coast of Northern New England contain northern temperate salt marsh pools (NTSPs) that serve as important wildlife habitats with unique abiotic conditions and biotic communities. The isolated nature of these pools from their estuary mainland, with the exception of inputs from infrequent tidal flooding, allows them to be characterized as islands in the context of island biogeography theory. Here, I assess two island biogeography variables, island size (pool volume) and connectivity (distance of pools from a tidal creek), to determine their effect on the abundance, species richness, and biodiversity of NTSPs. Data from this study indicated that NTSP size is positively correlated with both organism abundance and species richness, while NTSP connectivity is correlated with biodiversity. The monitoring of ecosystems using passive acoustic techniques has gained increasing popularity in recent years, as it is cost effective, and less time intensive than traditional biodiversity surveys. To expedite the process of analyzing recordings, many acoustic indices have been developed to analyze soundscape recordings. During this study, I used passive acoustic methods to monitor 20 NTSPs during the summer of 2021 to determine whether acoustic indices in the R packaged soundecology and seewave (H, BIO, ACI, ADI, AEI, and NDSI) highlight relationships between NTSP soundscapes with the abundance, species richness, and/or biodiversity of their inhabitants. This analysis determined that the AEI index had the strongest correlation with organism abundance and species richness, while only the maximum values produced by the BIO index correlated with NTSP biodiversity. This analysis also determined that the abiotic variable pool volume was positively correlated with ACI and AEI index values, as well as maximum values from the BIO index. While correlations between both biotic and abiotic variables and acoustic indices were found, it is recommended that acoustic indices designed for aquatic use are created, as there are many differences between aquatic and terrestrial soundscapes

The Tallgrass Prairie Soundscape; Employing an Ecoacoustic Approach to Understand Grassland Response to Prescribed Burns and the Spatial and Temporal Patterns of Nechrophilous Invertebrate Communities

Tallgrass prairies are rapidly vanishing biodiversity hotspots for native and endemic species, yet little is known regarding how spatial and temporal variation of prairie soundscapes relates to seasonal changes, disturbance patterns and biological communities. Ecoacoustics, the study of environmental sounds using passive acoustics as a non-invasive tool for investigating ecological complexity, allows for long-term data to be captured without disrupting biological communities. Two studies were carried out by employing ecoacoustic methodology to study grassland carrion food webs and to capture the phenology of a grassland soundscape following a prescribed burn. Both studies were conducted at the Nature Conservancy’s Tallgrass Prairie Preserve (3650’N, 9625’W) and used six acoustic indices to quantify the ratio of technophony to biophony, acoustic complexity, diversity, evenness, entropy, and biological acoustic diversity from over 70,000 sound recordings. Acoustic index values were used to determine the relationship between Nicrophorus burying beetle species composition and the prairie soundscape (Chapter 1) and to determine if prescribed burning changes the composition of the soundscape over time (Chapter 2). In Chapter 1, I found that associations between Nicrophorus burying beetles and the soundscape were unique to particular species, acoustic indices and times of day. For example, N. americanus trap rates showed a positive correlation to areas of increased acoustic complexity specifically at dawn. In addition to positive associations with the soundscape, we found that N. marginatus was consistently negatively correlated to higher levels of biophony, while N. tomentosus was consistently positively correlated to places with higher levels of biophony. Although reproduction of all species examined is dependent upon securing small carrion for reproduction, I found that known habitat and activity segregation of five Nicrophorus beetle species may be reflective of the soundscape. Finally, I show that favorable habitat for a critically endangered necrophilous insect, the American burying beetle (Nicrophorus americanus) can be identified by the acoustic signature extracted from a short temporal window of its grassland ecosystem soundscape. Using the same suite of acoustic indices from Chapter 1, in Chapter 2 I examined acoustic recordings at a much larger time scale to determine distinctive acoustic events driven by biophony and geophony across a 23-week period. In addition to examining acoustic changes over time, I examined differences between 11 burned and unburned pastures. Results from this study indicate that prescribed burning does alter the soundscape, especially early in the post-burn period, but the effects are ameliorated by a significant increase in biophony as the growing and breeding season progressed into the warmer summer months. Both studies demonstrate that passive acoustic recording is a reliable method to assess relationships to acoustic communities over space and time