Time-series forecasting offers novel quantitative measure to assess loud sound event in an urban park with restored prairie

Soundscape ecology and ecoacoustics study the spatiotemporal dynamics of a soundscape and how the dynamics reflect and influence ecological processes in the environment. Soundscape analysis methods employ acoustic recording units (ARUs) that collect acoustic data in study areas over time. Analyzing these data includes computation of several acoustic diversity indices developed to quantify species abundance, richness, or habitat condition through digital audio processing and algorithm adaptations for within-group populations. However, the success of specific indices is often dependent on habitat type and biota richness present and analyzing these data can be challenging due to temporal pseudo-replication. Time-series analytical methods address the inherent problems of temporal autocorrelation for soundscape analyses challenges. Animal population dynamics fluctuate in a variety of ways due to changes in habitat or natural patterns of a landscape and chronic noise exposure, with soundscape phenology patterns evident in terrestrial and aquatic environments. Historical phenological soundscape patterns have been used to predict expected soundscape patterns in long-term studies but limited work has explored how forecasting can quantify changes in short-term studies. We evaluate how forecasting from an acoustic index can be used to quantify change in an acoustic community response to a loud, acute noise. We found that the acoustic community of a Midwestern restored prairie had decreased acoustic community activity after a loud sound event (LSE), a Civil War Reenactment, mainly driven by observed changes in the bird community and quantified using two methods: an automated acoustic index and species richness. Time-series forecasting maybe considered an underutilized tool in analyzing acoustic data whose experimental design can be flawed with temporal autocorrelation. Forecasting using auto ARIMA with acoustic indices could benefit decision makers who consider ecological questions at different time scales.     

Estimating animal population density using passive acoustics

Reliable estimation of the size or density of wild animal populations is very important for effective wildlife management, conservation and ecology. Currently, the most widely used methods for obtaining such estimates involve either sighting animals from transect lines or some form of capture‐recapture on marked or uniquely identifiable individuals. However, many species are difficult to sight, and cannot be easily marked or recaptured. Some of these species produce readily identifiable sounds, providing an opportunity to use passive acoustic data to estimate animal density. In addition, even for species for which other visually based methods are feasible, passive acoustic methods offer the potential for greater detection ranges in some environments (e.g. underwater or in dense forest), and hence potentially better precision. Automated data collection means that surveys can take place at times and in places where it would be too expensive or dangerous to send human observers. Here, we present an overview of animal density estimation using passive acoustic data, a relatively new and fast‐developing field. We review the types of data and methodological approaches currently available to researchers and we provide a framework for acoustics‐based density estimation, illustrated with examples from real‐world case studies. We mention moving sensor platforms (e.g. towed acoustics), but then focus on methods involving sensors at fixed locations, particularly hydrophones to survey marine mammals, as acoustic‐based density estimation research to date has been concentrated in this area. Primary among these are methods based on distance sampling and spatially explicit capture‐recapture. The methods are also applicable to other aquatic and terrestrial sound‐producing taxa. We conclude that, despite being in its infancy, density estimation based on passive acoustic data likely will become an important method for surveying a number of diverse taxa, such as sea mammals, fish, birds, amphibians, and insects, especially in situations where inferences are required over long periods of time. There is considerable work ahead, with several potentially fruitful research areas, including the development of (i) hardware and software for data acquisition, (ii) efficient, calibrated, automated detection and classification systems, and (iii) statistical approaches optimized for this application. Further, survey design will need to be developed, and research is needed on the acoustic behaviour of target species. Fundamental research on vocalization rates and group sizes, and the relation between these and other factors such as season or behaviour state, is critical. Evaluation of the methods under known density scenarios will be important for empirically validating the approaches presented here.     

Comparative bioacoustics: a roadmap for quantifying and comparing animal sounds across diverse taxa

Animals produce a wide array of sounds with highly variable acoustic structures. It is possible to understand the causes and consequences of this variation across taxa with phylogenetic comparative analyses. Acoustic and evolutionary analyses are rapidly increasing in sophistication such that choosing appropriate acoustic and evolutionary approaches is increasingly difficult. However, the correct choice of analysis can have profound effects on output and evolutionary inferences. Here, we identify and address some of the challenges for this growing field by providing a roadmap for quantifying and comparing sound in a phylogenetic context for researchers with a broad range of scientific backgrounds. Sound, as a continuous, multidimensional trait can be particularly challenging to measure because it can be hard to identify variables that can be compared across taxa and it is also no small feat to process and analyse the resulting high-dimensional acoustic data using approaches that are appropriate for subsequent evolutionary analysis. Additionally, terminological inconsistencies and the role of learning in the development of acoustic traits need to be considered. Phylogenetic comparative analyses also have their own sets of caveats to consider. We provide a set of recommendations for delimiting acoustic signals into discrete, comparable acoustic units. We also present a three-stage workflow for extracting relevant acoustic data, including options for multivariate analyses and dimensionality reduction that is compatible with phylogenetic comparative analysis. We then summarize available phylogenetic comparative approaches and how they have been used in comparative bioacoustics, and address the limitations of comparative analyses with behavioural data. Lastly, we recommend how to apply these methods to acoustic data across a range of study systems. In this way, we provide an integrated framework to aid in quantitative analysis of cross-taxa variation in animal sounds for comparative phylogenetic analysis. In addition, we advocate the standardization of acoustic terminology across disciplines and taxa, adoption of automated methods for acoustic feature extraction, and establishment of strong data archival practices for acoustic recordings and data analyses. Combining such practices with our proposed workflow will greatly advance the reproducibility, biological interpretation, and longevity of comparative bioacoustic studies.     

Abiotic noise,call frequency and stream-breeding anuran assemblages

Environmental noise can be an important selective force modulating signal evolution in species with acoustic communication. Many anuran species breed alongside streams; hence, the sound produced by the flowing water is an important source of noise for acoustic communication. Since calling is physiologically very expensive in anurans, and communication is essential for reproduction, we expected adaptations that reduce environmental masking effects and allow acoustic communication in streamside breeders. This basic assumption of the acoustic adaptation hypothesis has not been yet evaluated at a large phylogenetic scale. We combined ahistorical and phylogenetic methods to test whether anuran species that breed alongside streams call at higher frequencies than species that breed away from streams. We compiled primary and secondary data on body size, breeding habitat, and the dominant frequency of the advertisement call for 110 species; 40 of them breed alongside streams and 70 away from streams. Call frequency was slightly higher and body size was significantly smaller in streamside breeding species. After controlling for the effects of body size and phylogenetic signal, only differences in body size persisted between species breeding at both kinds of habitats. Our data suggest that habitat filtering rather than acoustic adaptation explains the high call frequency of stream breeders. Species with large body size, pleiotropically constrained to utter low-frequency calls, would have succeeded less often in establishing viable populations alongside streams, due to the masking effect of low-frequency noise. Thus, small species calling at relatively high frequencies would be more common there. Although our data do not preclude adaptations to noisy habitats in some anuran species, they do not provide support for the acoustic adaptation hypothesis at a wider phylogenetic scale.     

Phylogeny and the evolution of calling songs in Gryllus (Insecta, Orthoptera, Gryllidae)

Acoustic signalling is the most important communication modality for crickets. While it has been studied intensively, few authors have analysed the evolution of cricket acoustic signals within a macroevolutionary perspective, still fewer with respect to its phylogenetic aspects. This may be due in part to the lack of acoustic and phylogenetic data; there are also difficulties involved in applying phylogenetic methods to acoustic data. The most critical aspect may be describing calls using characteristics consistent with current criteria for homology. In this paper we discuss, in relation to the evolution of the North American species of Gryllus , the reliability of these criteria and describe songs using two complementary sets of characters: (i) general structure (carrier frequencies and main temporal features), and (ii) 'special quality' (particular features at a lower structural level).     

A review of big data analysis methods for baleen whale passive acoustic monitoring

Many organizations collect large passive acoustic monitoring (PAM) data sets that need to be efficiently and reliably analyzed. To determine appropriate methods for effective analysis of big PAM data sets, we undertook a literature review of baleen whale PAM analysis methods. Methodologies from 166 studies (published between 2000–2019) were summarized, and a detailed review was performed on the 94 studies that recorded more than 1,000 hr of acoustic data (“big data”). Analysis techniques for extracting baleen whale information from PAM data sets varied depending on the research observed. A spectrum of methodologies was used and ranged from manual analysis of all acoustic data by human experts to completely automated techniques with no manual validation. Based on this assessment, recommendations are provided to encourage robust research methods that are comparable across studies and sectors, achievable across research groups, and consistent with previous work. These include using automated techniques when possible to increase efficiency and repeatability, supplementing automation with manual review to calculate automated detector performance, and increasing consistency in terminology and presentation of results. This work can be used to facilitate discussion for minimum standards and best practices to be implemented in the field of marine mammal PAM.     

Markov models and network analysis reveal sex‐specific differences in the space‐use of a coastal apex predator

Understanding the links between external variables such as habitat and interactions with conspecifics and animal space‐use is fundamental to developing effective management measures. In the marine realm, automated acoustic tracking has become a widely used method for monitoring the movement of free‐ranging animals, yet researchers generally lack robust methods for analysing the resulting spatial‐usage data. In this study, acoustic tracking data from male and female broadnose sevengill sharks Notorynchus cepedianus, collected in a system of coastal embayments in southeast Tasmania were analyzed to examine sex‐specific differences in the sharks’ coastal space‐use and test novel methods for the analysis of acoustic telemetry data. Sex‐specific space‐use of the broadnose sevengill shark from acoustic telemetry data was analysed in two ways: The recently proposed spatial network analysis of between‐receiver movements was employed to identify sex‐specific space‐use patterns. To include the full breadth of temporal information held in the data, movements between receivers were furthermore considered as transitions between states of a Markov chain, with the resulting transition probability matrix allowing the ranking of the relative importance of different parts of the study area. Both spatial network and Markov chain analysis revealed sex‐specific preferences of different sites within the study area. The identification of priority areas differed for the methods, due to the fact that in contrast to network analysis, our Markov chain approach preserves the chronological sequence of detections and accounts for both residency periods and movements. In addition to adding to our knowledge of the ecology of a globally distributed apex predator, this study presents a promising new step towards condensing the vast amounts of information collected with acoustic tracking technology into straightforward results which are directly applicable to the management and conservation of any species that meet the assumptions of our model.     

Who are we sampling? Apparent survival differs between methods in a secretive species

Survival is a fundamental parameter in population dynamics with increasing importance in the management and conservation strategies of wildlife populations. Survival probability in vertebrates is usually estimated by live‐encounter data obtained by means of physical mark–capture–recapture protocols. Non‐invasive acoustic marking relying on individual‐specific features of signals has been alternatively applied as a marking technique, especially in secretive species. Nevertheless, to date no research has compared survival rate estimates obtained by acoustic and physical marking. We estimated half‐yearly and annual survival and recapture rates of a secretive and threatened passerine, the Dupont's lark Chersophilus duponti, using two separate live‐encounter data sets of males collected simultaneously by physical and acoustic marking in the same study area. The separate analysis of both methods led to different model structures, since transient individuals had to be accounted for in the acoustic marking but not in the physical marking data set. Furthermore, while reencounter probabilities did not differ between methods, survival estimates employing physical marking were lower than those obtained acoustically, especially between the postbreeding and the breeding period when the apparent survival of colour‐banded birds was twice as low as for acoustic marking. The combination of marking methods suggested the existence of different subsets of individuals differentially sampled within the population: whereas colour‐banded males seemed to represent the territorial fraction of the population, both resident and floater individuals were probably detected by acoustic marking. Using traditional mark–recapture methods exclusively could have misled our estimates of survival rates, potentially affecting prospective predictions of population dynamics. Acoustic marking has been poorly applied in mark–recapture studies, but might be a powerful complement to obtain accurate estimates of fundamental demographic parameters such as survival and dispersal.     

A tutorial introduction to Bayesian inference for stochastic epidemic models using Markov chain Monte Carlo methods

Recent Bayesian methods for the analysis of infectious disease outbreak data using stochastic epidemic models are reviewed. These methods rely on Markov chain Monte Carlo methods. Both temporal and non-temporal data are considered. The methods are illustrated with a number of examples featuring different models and datasets.     

Parameterizing Spatial Models of Infectious Disease Transmission that Incorporate Infection Time Uncertainty Using Sampling-Based Likelihood Approximations

A class of discrete-time models of infectious disease spread, referred to as individual-level models (ILMs), are typically fitted in a Bayesian Markov chain Monte Carlo (MCMC) framework. These models quantify probabilistic outcomes regarding the risk of infection of susceptible individuals due to various susceptibility and transmissibility factors, including their spatial distance from infectious individuals. The infectious pressure from infected individuals exerted on susceptible individuals is intrinsic to these ILMs. Unfortunately, quantifying this infectious pressure for data sets containing many individuals can be computationally burdensome, leading to a time-consuming likelihood calculation and, thus, computationally prohibitive MCMC-based analysis. This problem worsens when using data augmentation to allow for uncertainty in infection times. In this paper, we develop sampling methods that can be used to calculate a fast, approximate likelihood when fitting such disease models. A simple random sampling approach is initially considered followed by various spatially-stratified schemes. We test and compare the performance of our methods with both simulated data and data from the 2001 foot-and-mouth disease (FMD) epidemic in the U.K. Our results indicate that substantial computation savings can be obtained—albeit, of course, with some information loss—suggesting that such techniques may be of use in the analysis of very large epidemic data sets.     

On parameter estimation in population models II: Multi-dimensional processes and transient dynamics

Recently, a computationally-efficient method was presented for calibrating a wide-class of Markov processes from discrete-sampled abundance data. The method was illustrated with respect to one-dimensional processes and required the assumption of stationarity. Here we demonstrate that the approach may be directly extended to multi-dimensional processes, and two analogous computationally-efficient methods for non-stationary processes are developed. These methods are illustrated with respect to disease and population models, including application to infectious count data from an outbreak of “Russian influenza” (A/USSR/1977 H1N1) in an educational institution. The methodology is also shown to provide an efficient, simple and yet rigorous approach to calibrating disease processes with gamma-distributed infectious period.     

Unrestrained acoustic plethysmograph for measuring specific airway resistance in mice.

An acoustic whole body plethysmograph was developed to estimate specific airway resistance (sRaw) in unrestrained mice. The plethysmograph uses acoustic principles to measure the thoracic breathing pattern and simultaneously measures the airflow entering and/or leaving the plethysmograph. Similarly to traditional methods utilizing a double-chamber plethysmograph, these measurements were combined to estimate sRaw. To evaluate the new system, we placed six conscious A/J mice individually in a whole body plethysmograph (Buxco System) for a 2-min exposure to aerosolized methacholine chloride dissolved in saline (0, 5, 10, and 20 mg/ml), which is known to increase sRaw in mice. Three minutes after exposure, the mice were transferred to the acoustic plethysmograph for 2 min for data collection. The mean baseline value of sRaw was 0.93+/-0.10 cmH2O.s. A dose-dependent increase in sRaw was shown, with an approximate tripling of sRaw at the highest dose. These results demonstrate the ability of the system to estimate sRaw based on plethysmograph airflow and acoustic amplitude.     

Biosensors for the detection of bacteria

This review will consider the role of biosensors towards the detection of infectious bacteria, although non-infectious ones will be considered where necessary. Recently, there has been a heightened interest in developing rapid and reliable methods of detection. This is especially true for detection of organisms involved in bioterrorism, food poisoning, and clinical problems such as antibiotic resistance. Biosensors can assist in achieving these goals, and sensors using several of the different types of transduction modes are discussed: electrochemical, high frequency (surface acoustic wave), and optical. The paper concludes with a discussion of three areas that may make a great impact in the next few years: integrated (lab-on-a-chip) systems, molecular beacons, and aptamers.     

Heard but not seen: an acoustic survey of the African forest elephant population at Kakum Conservation Area, Ghana

This study, designed to survey forest elephants ( Loxodonta africana cyclotis ) at Kakum Conservation Area, Ghana, is the first to apply acoustic methods to elephant abundance estimation and to compare results with independent survey estimates. Nine acoustic sensors gathered sound continuously for 38 days. Low-frequency calling rates have been established as useful elephant abundance indices at a Namibian watering hole and a central African forest clearing. In this study, we estimated elephant population size by applying an abundance index model and detection function developed in central Africa to data from simultaneous sampling periods on Kakum sensors. The sensor array recorded an average of 1.81 calls per 20-min sampling period from an effective detection area averaging 10.27 km². The resulting estimate of 294 elephants (95% CI: 259–329) falls within confidence bounds of recent dung-based surveys. An extended acoustic model, estimating the frequency with which elephants are silent when present, yields an estimate of 350 elephants (95% CI: 315–384). Acoustic survey confidence intervals are at least half as wide as those from dung-based surveys. This study demonstrates that acoustic surveying is a valuable tool for estimating elephant abundance, as well as for detecting other vocal species and anthropogenic noises that may be associated with poaching.     

Near-real-time acoustic monitoring of beaked whales and other cetaceans using a Seaglider™

In most areas, estimating the presence and distribution of cryptic marine mammal species, such as beaked whales, is extremely difficult using traditional observational techniques such as ship-based visual line transect surveys. Because acoustic methods permit detection of animals underwater, at night, and in poor weather conditions, passive acoustic observation has been used increasingly often over the last decade to study marine mammal distribution, abundance, and movements, as well as for mitigation of potentially harmful anthropogenic effects. However, there is demand for new, cost-effective tools that allow scientists to monitor areas of interest autonomously with high temporal and spatial resolution in near-real time. Here we describe an autonomous underwater vehicle--a glider--equipped with an acoustic sensor and onboard data processing capabilities to passively scan an area for marine mammals in near-real time. The glider was tested extensively off the west coast of the Island of Hawai'i, USA. The instrument covered approximately 390 km during three weeks at sea and collected a total of 194 h of acoustic data. Detections of beaked whales were successfully reported to shore in near-real time. Manual analysis of the recorded data revealed a high number of vocalizations of delphinids and sperm whales. Furthermore, the glider collected vocalizations of unknown origin very similar to those made by known species of beaked whales. The instrument developed here can be used to cost-effectively screen areas of interest for marine mammals for several months at a time. The near-real-time detection and reporting capabilities of the glider can help to protect marine mammals during potentially harmful anthropogenic activities such as seismic exploration for sub-sea fossil fuels or naval sonar exercises. Furthermore, the glider is capable of under-ice operation, allowing investigation of otherwise inaccessible polar environments that are critical habitats for many endangered marine mammal species.     

Global mapping of infectious disease

The primary aim of this review was to evaluate the state of knowledge of the geographical distribution of all infectious diseases of clinical significance to humans. A systematic review was conducted to enumerate cartographic progress, with respect to the data available for mapping and the methods currently applied. The results helped define the minimum information requirements for mapping infectious disease occurrence, and a quantitative framework for assessing the mapping opportunities for all infectious diseases. This revealed that of 355 infectious diseases identified, 174 (49%) have a strong rationale for mapping and of these only 7 (4%) had been comprehensively mapped. A variety of ambitions, such as the quantification of the global burden of infectious disease, international biosurveillance, assessing the likelihood of infectious disease outbreaks and exploring the propensity for infectious disease evolution and emergence, are limited by these omissions. An overview of the factors hindering progress in disease cartography is provided. It is argued that rapid improvement in the landscape of infectious diseases mapping can be made by embracing non-conventional data sources, automation of geo-positioning and mapping procedures enabled by machine learning and information technology, respectively, in addition to harnessing labour of the volunteer ‘cognitive surplus’ through crowdsourcing.     

声景生态学研究进展和展望

声景生态学以景观中的声音为研究对象, 探讨其在不同时空维度上的分布和变化模式, 从而揭示自然环境、野生动物和人类活动的相互作用关系。本文通过系统检索声景生态学研究的相关文献, 回顾了该学科的研究框架和研究方法, 总结了目前常用的声学指标, 重点归纳了声景生态学的研究内容, 包括声景组成和各组分间的相互作用, 声景的时空格局, 以及声景生态学在生物多样性监测中的应用。目前, 声景监测中存在的问题主要包括监测的生态系统类型和物种类群有限、声学指标效力有待提高等。建议未来着重推进建立系统性的声景监测网络和数据管理平台, 开发和完善音频数据采集、分析方法和评估指标, 并重视声景数据的采集, 将声景视作一种资源进行研究和保护。     

Can acoustic methods be used to monitor grenadier (Macrouridae) abundance in the Ross Sea region?

Grenadiers Macrourus spp. are the main bycatch species in the exploratory longline fishery for toothfish Dissostichus spp. in the Ross Sea, Antarctica. Ongoing monitoring tools are needed to assess stock status of grenadiers in the Ross Sea and to ensure ecological relationships are maintained. There may be potential to use fisheries acoustic methods to obtain estimates of grenadier abundance. Acoustic data collected during New Zealand??s International Polar Year Census of Marine Life survey in February?CMarch 2008 provide evidence that single targets close to the bottom over the Ross Sea slope are grenadiers. The acoustic target strength distribution of single targets was very similar to that predicted based on the measured size range of grenadiers. There are also positive correlations between acoustic backscatter and trawl and longline catches of grenadiers. Key uncertainties of the acoustic method are mark identification away from the bottom, and technical issues with low signal-to-noise ratio at depths greater than 1000 m and the acoustic dead-zone close to the bottom.     

Acoustic survey of a jellyfish-dominated ecosystem (Mljet Island,Croatia)

Acoustic techniques have been proposed as a new tool to assess jellyfish populations. However, the presence of mixed echoes from jellyfish and other organisms that share their distribution often prevent accurate estimates of their abundance and distribution being obtained. The isolated population of Aurelia inhabiting the Veliko Jezero (Big Lake-BL) of Mljet Island, in the South Adriatic Sea, offered a good opportunity to employ acoustic techniques to assess an entire jellyfish population. During October 2–5, 2006, combined video and acoustic methods were used in BL to determine the vertical distribution of medusae. Two synoptic acoustic surveys were performed during the day and night. In the daylight echograms, medusae were clearly discernible from the acoustic data, and their presence verified by video camera images, as forming a layer of varying density at and below the thermocline (15–30 m). The depth of the jellyfish layer also coincided with the depth of maximum dissolved oxygen concentration. The echointegration of these daylight data enabled quantification the Aurelia population, at a frequency of 120 kHz. In the night echograms, the acoustic signals of Aurelia were at least partially masked by pelagic and demersal fish, which disaggregated from schools and formed a layer associated with a strong thermocline at 15 m. An average target strength (TS) of −76.4 dB was obtained in situ corresponding to a mean length of 10.8 cm and a mean wet weight of 134 g measured from sampled medusae. These results were combined with echo-integration values to provide an estimate of 4,238,602 individuals and a biomass of 568 tons of Aurelia in BL. This study provided a synoptic view of Mljet Lake and illustrated the potential of acoustic surveys of jellyfish populations to contribute to ecosystems studies. Guest editors: K. A. Pitt & J. E. Purcell Jellyfish Blooms: Causes, Consequences, and Recent Advances     

Assessing the accuracy of acoustic seabed classification for mapping coral reef environments in South Florida (Broward County, USA)

The Atlantic coast of Broward County, Florida (USA) is paralleled by a series of progressively deeper, shore-parallel coral reef communities. Two of these reef systems are drowned early Holocene coral reefs of 5 ky and 7 ky uncorrected radiocarbon age. Despite the case of access to these reefs, and their major contribution to the local economy, accurate benthic habitat maps of the area are not available. Ecological studies have shown that different benthic communities (i.e. communities composed of different biological taxa) exist along several spatial gradients on all reefs. Since these studies are limited by time and spatial extent, acoustic surveys with the QTCView V bottom classification system based on a 50 kHz transducer were used as an alternative method of producing habitat maps. From the acoustic data of a 3.1 km(2) survey area, spatial prediction maps were created for the area. These were compared with habitat maps interpreted from in situ data and Laser Airborne Depth Sounder (LADS) bathymetry, in order to ground-truth the remotely sensed data. An error matrix was used to quantitatively determine the accuracy of the acoustically derived spatial prediction model against the maps derived from the in situ and LADS data sets. Confusion analysis of 100 random points showed that the system was able to distinguish areas of reef from areas of rubble and sand with an overall accuracy of 61%. When asked to detect more subtle spatial differences, for example, those between distinct reef communities, the classification was only about 40% accurate. We discuss to what degree a synthesis of acoustic and in situ techniques can provide accurate habitat maps in coral reef environments, and conclude that acoustic methods were able to reflect the spatial extent and composition of at least three different biological communities.