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.     

Mysterious bio-duck sound attributed to the Antarctic minke whale (Balaenoptera bonaerensis)

For decades, the bio-duck sound has been recorded in the Southern Ocean, but the animal producing it has remained a mystery. Heard mainly during austral winter in the Southern Ocean, this ubiquitous sound has been recorded in Antarctic waters and contemporaneously off the Australian west coast. Here, we present conclusive evidence that the bio-duck sound is produced by Antarctic minke whales (Balaenoptera bonaerensis). We analysed data from multi-sensor acoustic recording tags that included intense bio-duck sounds as well as singular downsweeps that have previously been attributed to this species. This finding allows the interpretation of a wealth of long-term acoustic recordings for this previously acoustically concealed species, which will improve our understanding of the distribution, abundance and behaviour of Antarctic minke whales. This is critical information for a species that inhabits a difficult to access sea-ice environment that is changing rapidly in some regions and has been the subject of contentious lethal sampling efforts and ongoing international legal action.     

Estimating the abundance of the critically endangered Baltic Proper harbour porpoise (Phocoena phocoena) population using passive acoustic monitoring

Knowing the abundance of a population is a crucial component to assess its conservation status and develop effective conservation plans. For most cetaceans, abundance estimation is difficult given their cryptic and mobile nature, especially when the population is small and has a transnational distribution. In the Baltic Sea, the number of harbour porpoises (Phocoena phocoena) has collapsed since the mid‐20th century and the Baltic Proper harbour porpoise is listed as Critically Endangered by the IUCN and HELCOM; however, its abundance remains unknown. Here, one of the largest ever passive acoustic monitoring studies was carried out by eight Baltic Sea nations to estimate the abundance of the Baltic Proper harbour porpoise for the first time. By logging porpoise echolocation signals at 298 stations during May 2011–April 2013, calibrating the loggers’ spatial detection performance at sea, and measuring the click rate of tagged individuals, we estimated an abundance of 71–1105 individuals (95% CI, point estimate 491) during May–October within the population''s proposed management border. The small abundance estimate strongly supports that the Baltic Proper harbour porpoise is facing an extremely high risk of extinction, and highlights the need for immediate and efficient conservation actions through international cooperation. It also provides a starting point in monitoring the trend of the population abundance to evaluate the effectiveness of management measures and determine its interactions with the larger neighboring Belt Sea population. Further, we offer evidence that design‐based passive acoustic monitoring can generate reliable estimates of the abundance of rare and cryptic animal populations across large spatial scales.     

Seasonality of Antarctic minke whale (Balaenoptera bonaerensis) calls off the western Antarctic Peninsula

The Antarctic minke whale (Balaenoptera bonaerensis) is a difficult species to study because of its low visual detectability and preference for living within the sea ice habitat, accessible only by ice‐strengthened vessels. Recent identification of the Antarctic minke whale as the source of the seasonally ubiquitous bio‐duck call has allowed the use of this sound, as well as downsweeps, to investigate seasonality trends and diel patterns in Antarctic minke whale call production, and their relationship to sea ice cover. Passive acoustic data were collected using an autonomous Acoustic Recording Package (ARP) off the western Antarctic Peninsula. Bio‐duck calls were classified into four distinct call variants, with one variant having two subtypes. Bio‐duck calls were detected between April and November, with increasing call duration during the austral winter, indicating a strong seasonality in call production. Downsweeps, which were also attributed to Antarctic minke whales, were present throughout most months during the recording period, with a peak in July, and an absence in March and April. Both bio‐duck and downsweeps were significantly correlated with sea ice cover. No diel patterns were observed in bio‐duck calls or in downsweep call production at this site.     

Estimating elephant density using motion-sensitive cameras: challenges,opportunities, and parameters for consideration

With extinction rates far exceeding the natural background rate, reliable monitoring of wildlife populations has become crucial for adaptive management and conservation. Robust monitoring is often labor intensive with high economic costs, particularly in the case of those species that are subject to illegal poaching, such as elephants, which require frequent and accurate population estimates over large spatial scales. Dung counting methods are commonly employed to estimate the density of elephants; however, in the absence of a full survey calibration, these can be unreliable in heterogeneous habitats where dung decay rates may be highly variable. We explored whether motion-sensitive cameras offer a simple, lower cost, and reliable alternative for monitoring in challenging forest environments. We estimated the density of African savanna elephants (Loxodanta africana) in a montane forest using the random encounter model and assessed the importance of surveying parameters for future survey design. We deployed motion-sensitive cameras in 65 locations in the Aberdare Conservation Area in Kenya during June to August in 2015 to 2017, for a survey effort of 967 days, and a mean encounter rate of 0.09 ± 0.29 (SD) images/day. Elephants were captured in 16 locations. Density estimates varied between vegetation types, with estimates ranging from 6.27/km² in shrub, 1.1/km² in forest, 0.53/km² in bamboo (Yushania alpine), and 0.44/km² in the moorlands. The average speed of animal movement and the camera detection zone had the strongest linear associations with density estimates (R = −0.97). The random encounter model has the potential to offer an alternative, or complementary method within the active management framework for monitoring elephant populations in forests at a relatively low cost.     

Seasonal acoustic behavior of blue whales (Balaenoptera musculus) in the Gulf of California,Mexico

Six years of passive acoustic monitoring data from the Gulf of California reveal seasonality and movements for the northeastern Pacific blue whales. Three sites were studied, one from the southern (Punta Pescadero) and two from the northern (Isla Tiburon and Canal de Ballenas) regions. A total of 4,953 h were analyzed, and 15,539 blue whale calls were detected, of which 2,723 (18%) were A calls, 11,249 were B calls (72%), and 1,567 were D calls (10%). A and B calls were produced both as song units (2,524) or AB singular calls (2,026). The high rate of songs and their seasonality suggest that the GC is a winter‐breeding ground. A shift from AB call predominance in winter, to D calls in spring and early summer, especially at the entrance of the GC, suggests the importance of this area for reproduction and foraging. Analysis of calling frequency suggests a clear movement of blue whales from the southern region (Punta Pescadero) to the northern regions (Canal de Ballenas and Isla Tiburon), with subsequent southern movement in March. The seasonality and mobility of blue whales in the Gulf of California, inferred from their calling, contributes to the ecological understanding of this population.     

Local habitat use by botos (Amazon river dolphins,Inia geoffrensis) using passive acoustic methods

We monitored the underwater behavior of botos (Inia geoffrensis) using stereo acoustic data loggers to observe their local habitat use and its diel changes at the Mamirauá Sustainable Development Reserve, Brazil. A‐tags were set at five sites in three different habitat types: Lake (low current), Channel (middle current), and Junction (junction of two channels). The presence index during nighttime was significantly greater than during daytime in the Lake and Junction. Underwater movement was estimated from the changing pattern (trajectory) of the relative angle of the sound source from A‐tags. A staying‐type trajectory was dominant in the Lake, although the prevalence of moving‐type trajectory increased at night. More than 80% of detected trajectories were the staying type in the Junction, while moving‐type trajectories dominated in the Channel. The frequency of click trains was greatest in the Lake, followed by the Junction and Channels. The average interpulse interval, which reflects the mean target distance of echolocation, was shortest in the Lake, followed by the Junction and Channel. These results suggest that the botos used the Lake as their primary habitat for active behaviors like foraging, especially at night, and the Junction as their primary habitat for relatively inactive behaviors at night.     

High cell density fed batch and perfusion processes for stable non-viral expression of secreted alkaline phosphatase (SEAP) using insect cells: comparison to a batch Sf-9-BEV system

The development of insect cells expressing recombinant proteins in a stable continuous manner is an attractive alternative to the BEV system for recombinant protein production. High cell density fed batch and continuous perfusion processes can be designed to maximize the productivity of stably transformed cells. A cell line (Sf-9SEAP) expressing high levels of the reporter protein SEAP stably was obtained by lipid-mediated transfection of Sf-9 insect cells and further selection and screening. The expression of the Sf-9SEAP cells was compared with the BEVS system. It was observed that, the yield obtained in BEVS was similar to the batch Sf-9SEAP at 8 and 7 IU/mL, respectively. The productivity of this foreign gene product with the stable cells was enhanced by bioprocess intensification employing the fed-batch and perfusion modes of culture to increase the cell density in culture. The fed batch process yielded a maximum cell density of 28 x 10(6) cells/mL and 12 IU/mL of SEAP. Further improvements in the productivity could be made using the perfusion process, which demonstrated a stable production rate for extended periods of time. The process was maintained for 43 days, with a steady-state cell density of 17-20 x 10(6) cells/mL and 7 IU/mL SEAP. The total yield obtained in the perfusion process (394 IU) was approximately 22 and 8 times higher than that obtained in a batch (17.6 IU) and fed batch (46.1 IU) process, respectively.