Summary1. Animals produce sounds for diverse biological functions such as defending territories, attracting mates, deterring predators, navigation, finding food and maintaining contact with members of their social group. Biologists can take advantage of these acoustic behaviours to gain valuable insights into the spatial and temporal scales over which individuals and populations interact. Advances in bioacoustic technology, including the development of autonomous cabled and wireless recording arrays, permit data collection at multiple locations over time. These systems are transforming the way we study individuals and populations of animals and are leading to significant advances in our understandings of the complex interactions between animals and their habitats. 2. Here, we review questions that can be addressed using bioacoustic approaches, by providing a primer on technologies and approaches used to study animals at multiple organizational levels by ecologists, behaviourists and conservation biologists. 3. Spatially dispersed groups of microphones (arrays) enable users to study signal directionality on a small scale or to locate animals and track their movements on a larger scale. 4. Advances in algorithm development can allow users to discriminate among species, sexes, age groups and individuals. 5. With such technology, users can remotely and non-invasively survey populations, describe the soundscape, quantify anthropogenic noise, study species interactions, gain new insights into the social dynamics of sound-producing animals and track the effects of factors such as climate change and habitat fragmentation on phenology and biodiversity. 6. There remain many challenges in the use of acoustic monitoring, including the difficulties in performing signal recognition across taxa. The bioacoustics community should focus on developing a *Correspondence author. E-mail: marmots@ucla.edu 2011, 48, 758-767 doi: 10.1111/j.1365-2664.2011.01993.x Ó 2011 The Authors. Journal of Applied Ecology Ó 2011 British Ecological Society common framework for signal recognition that allows for various species' data to be analysed by any recognition system supporting a set of common standards. 7. Synthesis and applications. Microphone arrays are increasingly used to remotely monitor acoustically active animals. We provide examples from a variety of taxa where acoustic arrays have been used for ecological, behavioural and conservation studies. We discuss the technologies used, the methodologies for automating signal recognition and some of the remaining challenges. We also make recommendations for using this technology to aid in wildlife management. Journal of Applied Ecology

A hidden Markov model ͑HMM͒ system is presented for automatically classifying African elephant vocalizations. The development of the system is motivated by successful models from human speech analysis and recognition. Classification features include frequency-shifted Mel-frequency cepstral coefficients ͑MFCCs͒ and log energy, spectrally motivated features which are commonly used in human speech processing. Experiments, including vocalization type classification and speaker identification, are performed on vocalizations collected from captive elephants in a naturalistic environment. The system classified vocalizations with accuracies of 94.3% and 82.5% for type classification and speaker identification classification experiments, respectively. Classification accuracy, statistical significance tests on the model parameters, and qualitative analysis support the effectiveness and robustness of this approach for vocalization analysis in nonhuman species.

Global climate change (GCC) is projected to bring higher-intensity precipitation and highervariability temperature regimes to the Northeastern United States. The interactive effects of GCC with anthropogenic land use and land cover changes (LULCCs) are unknown for watershed level hydrological dynamics and nutrient fluxes to freshwater lakes. Increased nutrient fluxes can promote harmful algal blooms, also exacerbated by warmer water temperatures due to GCC. To address the complex interactions of climate, land and humans, we developed a cascading integrated assessment model to test the impacts of GCC and LULCC on the hydrological regime, water temperature, water quality, bloom duration and severity through 2040 in transnational Lake Champlain's Missisquoi Bay. Temperature and precipitation inputs were statistically downscaled from four global circulation models (GCMs) for three Representative Concentration Pathways. An agent-based model was used to generate four LULCC scenarios. Combined climate and LULCC scenarios drove a distributed hydrological model to estimate river discharge and nutrient input to the lake. Lake nutrient dynamics were simulated with a 3D hydrodynamic-biogeochemical model. We find accelerated GCC could drastically limit land management options to maintain water quality, but the nature and severity of this impact varies dramatically by GCM and GCC scenario.

Using Hidden Markov Models (HMMs) as a recognition framework for automatic classification of animal vocalizations has a number of benefits, including the ability to handle duration variability through nonlinear time alignment, the ability to incorporate complex language or recognition constraints, and easy extendibility to continuous recognition and detection domains. In this work, we apply HMMs to several different species and bioacoustic tasks using generalized spectral features that can be easily adjusted across species and HMM network topologies suited to each task. This experimental work includes a simple call type classification task using one HMM per vocalization for repertoire analysis of Asian elephants, a language-constrained song recognition task using syllable models as base units for ortolan bunting vocalizations, and a stress stimulus differentiation task in poultry vocalizations using a non-sequential model via a one-state HMM with Gaussian mixtures. Results show strong performance across all tasks and illustrate the flexibility of the HMM framework for a variety of species, vocalization types, and analysis tasks