Listen Up! Using Passive Acoustic Monitoring to Help Forest Elephant Conservation

Post provided by Peter H. Wrege

Forest elephant in Gabon

Forest elephant in Gabon

Heard but not seen, populations of forest elephants (Loxodonta cyclotis) are rapidly declining due to ivory poaching. As one of the largest land mammals in the world, this species is surprisingly difficult to observe in the dense forests of Central Africa, but their low frequency rumbles can be recorded. With the autonomous recording afforded by passive acoustic monitoring (PAM) though, we have a window onto forest elephant ecology and behaviour that’s providing data critical to their conservation and survival.

The diverse ways that PAM can contribute to conservation outcomes is growing and while still underappreciated, the availability of relatively inexpensive recorders, increased power efficiency, and powerful techniques to automate the detection of signals have led to an explosion in use. In 2007 there were only about 20 published papers using PAM techniques, but since then over 400 papers have appeared in peer-reviewed journals.

Spectrogram of two forest elephant rumbles. Horizontal line shows the limit of human hearing.

Spectrogram of two forest elephant rumbles. Horizontal line shows the limit of human hearing.

Essentially, PAM is the automatic recording of sounds in a given environment, often for long periods. The trick, and often greatest challenge, is to find the signals of interest (bird calls, elephant rumbles, gunshots) within the recordings. With these signals we can quantify abundance, occupancy and spatial or temporal patterns of activity. Particularly in landscapes or ecosystems where visual observation is difficult (e.g. oceans, rainforests, nocturnal environments) PAM may be uniquely capable of delivering informative and unbiased data. Because PAM is a relatively new method but of considerable interest across the disciplines of ecology, behaviour and conservation, there is huge interest in refining the sampling and statistical methods needed to deal with the peculiarities of acoustic data. Continue reading

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Issue 8.5

Issue 8.5 is now online!

The May issue of Methods is now online!

This issue contains three Applications articles and two Open Access articles. These five papers are freely available to everyone, no subscription required.

MatlabHTK: A software interface to a popular speech recognition system making it possible for non-experts to implement hidden Markov models for bioacoustic signal processing.

 PrimerMiner: The R package PrimerMiner batch downloads DNA barcode gene sequences from BOLD and NCBI databases for specified target taxonomic groups and then applies sequence clustering into operational taxonomic units to reduce biases introduced by the different number of available sequences per species.

 BarcodingR: An integrated software package that provides a comprehensive implementation of species identification methods, including artificial intelligence, fuzzy-set, Bayesian and kmer-based methods, that are not readily available in other packages.

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Microphone Backpacks for Individual-level Acoustic Recordings

To understand the factors shaping vocal communication, we need reliable information about the communicating individuals on different levels. First, vocal behaviour should be recorded from undisturbed animals in meaningful settings. Then we have to separate and assign the individuals’ vocalisations. Finally, the precise timing of vocal events needs to be stored.

Microphone backpacks allow researchers to record the vocal behaviour of individual animals in naturalistic settings – even in acoustically challenging environments! In the video below, Lisa Gill, Nico Adreani and Pietro D’Amelio demonstrate the lightweight radio-transmitter microphone backpacks that have been developed and built at the Max Planck Institute for Ornithology, Seewiesen, Department of Behavioural Neurobiology. They show the attachment and setup of this system in detail, evaluate its behavioural effects, and discuss what makes it so useful for studying vocal communication, especially in small animals.

This video is based on the article ‘A minimum-impact, flexible tool to study vocal communication of small animals with precise individual-level resolution‘ by Gill et al.

 

Issue 8.3

Issue 8.3 is now online!

The March issue of Methods is now online!

This issue contains two Applications articles and one Open Access article. These three papers are freely available to everyone, no subscription required.

 Solo: Solo audio recorders are inexpensive, easy to construct and record audible sound continuously for around 40 days. The paper also has a video tutorial explaining how to assemble the required hardware and comes with a companion website with more information.

 The third dimension: A novel design to obtain three-dimensional data on the movements of aquatic organisms at depths of up to 140m. The set-up consists of two synchronised high-speed cameras fixed to two articulated arms and can be used for any underwater applications that require synchronized video recordings of medium- to large-sized animals.

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Issue 8.2

Issue 8.2 is now online!

The February issue of Methods is now online!

This issue contains four(!) Applications articles and two Open Access articles. These six papers are freely available to everyone – no subscription required.

 Earth Mover’s Distance: The Earth Mover’s Distance (or EMD) is a method commonly used in image retrieval applications. The authors of this paper propose its use to calculate similarity in space use in the framework of movement ecology. This will be helpful for many questions regarding behavioural ecology, wildlife management and conservation.

 warbleR: The R package warbleR is a new package for the analysis of animal acoustic signal structure. It offers functions for downloading avian vocalisations from the open-access online repository Xeno-Canto, displaying the geographic extent of the recordings, manipulating sound files, detecting acoustic signals or importing detected signals from other software, and much more.

– meteR: The open-source R package, meteR directly calculates all of Maximum entropy theory of ecology’s (METE’s) predictions from a variety of data formats; automatically handles approximations and other technical details; and provides high-level plotting and model comparison functions to explore and interrogate models.

– Noise Egg: The Noise Egg is a device that can produce a low-frequency sound, which can be used as an experimental source of noise both in aquaria and in the field. It was developed to study the effects of noise on communication and behaviour in small aquatic animals; however, it could be used for other purposes, such as testing the propagation of certain frequencies in shallow-water habitats.

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Testing the Effects of Underwater Noise on Aquatic Animals

Post provided by Karen de Jong

Most people assume that research equipment is expensive and complicated. But, it doesn’t need to be and the noise egg is a perfect example of this. It consists of a watertight container (as used by scuba divers) and the buzzer from a cellphone and does exactly what it says: it produces low frequency noise. This allows researchers to test the effect of noise on underwater life. It is a small, simple and cheap device that anyone can build.

Why Test Effects of Noise?

A painted goby in front of his nest ©K. de Jong

A painted goby in front of his nest ©K. de Jong

Underwater noise is rapidly increasing due to, for example, boat traffic and offshore wind farms. This can lead to stress for animals and difficulties in communication. Just as people have a hard time communicating in a noisy pub, animals may struggle to get their messages across when background noise is high. A nice description of how animals use sound and how noise may affect this can be found at www.dosits.org

While there is some knowledge on the effect of noise on large aquatic animals, we still know very little about how fish and other small aquatic animals are affected. Such knowledge is vital for management of protected areas. It’s also important to know whether wind farms and boat traffic can affect reproduction in populations of underwater resources such as fish and mussels. The answers to these questions are likely to be species specific, so we’ll need data on a large number of species in different habitats. Continue reading

Animal Density and Acoustic Detection: An Interview with Ben Stevenson

David Warton (University of New South Wales) interviews  interviews  Ben Stevenson (University of St Andrews) about his 2015 Methods in Ecology and Evolution paper ‘A general framework for animal density estimation from acoustic detections across a fixed microphone array’. They also discuss what Ben is currently up to, including an interesting new method for dealing with uncertain identification in capture-recapture, published in Statistical Science as ‘Trace-Contrast Models for Capture–Recapture Without Capture Histories’.

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Issue 7.9

Issue 7.9 is now online!

The September issue of Methods is now online!

This month’s issue contains two Applications articles and three Open Access articles, all of which are freely available.

– Arborist Throw-Line Launcher: A cost-effective and simple alternative for collecting leaves and seeds from tall trees. The authors have also provided some tutorial videos on YouTube.

– ctmm: An R package which implements all of the continuous-time stochastic processes currently in use in the ecological literature and couples them with powerful statistical methods for autocorrelated data adapted from geostatistics and signal processing.

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Biggest Library of Bat Sounds Compiled

Below is a press release about the Methods paper ‘Acoustic identification of Mexican bats based on taxonomic and ecological constraints on call design‘ taken from the University College London.

The Funnel-eared bat (Natalus stramineus)

The Funnel-eared bat (Natalus stramineus)

The biggest library of bat sounds has been compiled to detect bats in Mexico – a country which harbours many of the Earth’s species and has one of the highest rates of species extinction and habitat loss.

An international team led by scientists from UCL, University of Cambridge and the Zoological Society of London, developed the reference call library and a new way of classifying calls to accurately and quickly identify and differentiate between bat species.

It is the first time automatic classification for bat calls has been attempted for a large variety of species, most of them previously noted as hard to identify acoustically. Continue reading

The Overlooked Commotion of Particle Motion in the Ocean

Below is a press release about the Open Access Methods paper ‘Particle motion: the missing link in underwater acoustic ecology‘ taken from the University of Bristol, the University of Exeter and the Centre for Environment, Fisheries  & Aquaculture Science (CEFAS).

Fish and invertebrates predominantly or exclusively detect particle motion.

Fish and invertebrates predominantly or exclusively detect particle motion.

A growing number of studies on the behaviour of aquatic animals are revealing the importance of underwater sound, yet these studies typically overlook the component of sound sensed by most species: particle motion. In response, researchers from the Universities of Bristol, Exeter and Leiden and CEFAS have developed a user-friendly introduction to particle motion, explaining how and when it ought to be measured, and provide open-access analytical tools to maximise its uptake. Continue reading