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Sethi SS, Bick A, Ewers RM, Klinck H, Ramesh V, Tuanmu MN, Coomes DA. Limits to the accurate and generalizable use of soundscapes to monitor biodiversity. Nat Ecol Evol 2023; 7:1373-1378. [PMID: 37524796 PMCID: PMC10482675 DOI: 10.1038/s41559-023-02148-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 07/03/2023] [Indexed: 08/02/2023]
Abstract
Although eco-acoustic monitoring has the potential to deliver biodiversity insight on vast scales, existing analytical approaches behave unpredictably across studies. We collated 8,023 audio recordings with paired manual avifaunal point counts to investigate whether soundscapes could be used to monitor biodiversity across diverse ecosystems. We found that neither univariate indices nor machine learning models were predictive of species richness across datasets but soundscape change was consistently indicative of community change. Our findings indicate that there are no common features of biodiverse soundscapes and that soundscape monitoring should be used cautiously and in conjunction with more reliable in-person ecological surveys.
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Affiliation(s)
- Sarab S Sethi
- Conservation Research Institute and Department of Plant Sciences, University of Cambridge, Cambridge, UK.
- Centre for Biodiversity and Environment Research, University College London, London, UK.
| | - Avery Bick
- Norwegian Institute for Nature Research, Trondheim, Norway
| | - Robert M Ewers
- Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, London, UK
| | - Holger Klinck
- K Lisa Yang Center for Conservation Bioacoustics, Cornell University, Ithaca, NY, USA
| | - Vijay Ramesh
- K Lisa Yang Center for Conservation Bioacoustics, Cornell University, Ithaca, NY, USA
- Project Dhvani, Bangalore, India
| | - Mao-Ning Tuanmu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - David A Coomes
- Conservation Research Institute and Department of Plant Sciences, University of Cambridge, Cambridge, UK
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2
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Lapp S, Stahlman N, Kitzes J. A Quantitative Evaluation of the Performance of the Low-Cost AudioMoth Acoustic Recording Unit. SENSORS (BASEL, SWITZERLAND) 2023; 23:s23115254. [PMID: 37299981 DOI: 10.3390/s23115254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 05/25/2023] [Accepted: 05/28/2023] [Indexed: 06/12/2023]
Abstract
The AudioMoth is a popular autonomous recording unit (ARU) that is widely used to record vocalizing species in the field. Despite its growing use, there have been few quantitative tests on the performance of this recorder. Such information is needed to design effective field surveys and to appropriately analyze recordings made by this device. Here, we report the results of two tests designed to evaluate the performance characteristics of the AudioMoth recorder. First, we performed indoor and outdoor pink noise playback experiments to evaluate how different device settings, orientations, mounting conditions, and housing options affect frequency response patterns. We found little variation in acoustic performance between devices and relatively little effect of placing recorders in a plastic bag for weather protection. The AudioMoth has a mostly flat on-axis response with a boost above 3 kHz, with a generally omnidirectional response that suffers from attenuation behind the recorder, an effect that is accentuated when it is mounted on a tree. Second, we performed battery life tests under a variety of recording frequencies, gain settings, environmental temperatures, and battery types. We found that standard alkaline batteries last for an average of 189 h at room temperature using a 32 kHz sample rate, and that lithium batteries can last for twice as long at freezing temperatures compared to alkaline batteries. This information will aid researchers in both collecting and analyzing recordings generated by the AudioMoth recorder.
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Affiliation(s)
- Sam Lapp
- Department of Biological Sciences, University of Pittsburgh, 103 Clapp Hall, Fifth and Ruskin Avenues, Pittsburgh, PA 15260, USA
| | - Nickolus Stahlman
- Department of Biological Sciences, University of Pittsburgh, 103 Clapp Hall, Fifth and Ruskin Avenues, Pittsburgh, PA 15260, USA
| | - Justin Kitzes
- Department of Biological Sciences, University of Pittsburgh, 103 Clapp Hall, Fifth and Ruskin Avenues, Pittsburgh, PA 15260, USA
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3
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Clink DJ, Kier I, Ahmad AH, Klinck H. A workflow for the automated detection and classification of female gibbon calls from long-term acoustic recordings. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1071640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
Passive acoustic monitoring (PAM) allows for the study of vocal animals on temporal and spatial scales difficult to achieve using only human observers. Recent improvements in recording technology, data storage, and battery capacity have led to increased use of PAM. One of the main obstacles in implementing wide-scale PAM programs is the lack of open-source programs that efficiently process terabytes of sound recordings and do not require large amounts of training data. Here we describe a workflow for detecting, classifying, and visualizing female Northern grey gibbon calls in Sabah, Malaysia. Our approach detects sound events using band-limited energy summation and does binary classification of these events (gibbon female or not) using machine learning algorithms (support vector machine and random forest). We then applied an unsupervised approach (affinity propagation clustering) to see if we could further differentiate between true and false positives or the number of gibbon females in our dataset. We used this workflow to address three questions: (1) does this automated approach provide reliable estimates of temporal patterns of gibbon calling activity; (2) can unsupervised approaches be applied as a post-processing step to improve the performance of the system; and (3) can unsupervised approaches be used to estimate how many female individuals (or clusters) there are in our study area? We found that performance plateaued with >160 clips of training data for each of our two classes. Using optimized settings, our automated approach achieved a satisfactory performance (F1 score ~ 80%). The unsupervised approach did not effectively differentiate between true and false positives or return clusters that appear to correspond to the number of females in our study area. Our results indicate that more work needs to be done before unsupervised approaches can be reliably used to estimate the number of individual animals occupying an area from PAM data. Future work applying these methods across sites and different gibbon species and comparisons to deep learning approaches will be crucial for future gibbon conservation initiatives across Southeast Asia.
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4
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Besson M, Alison J, Bjerge K, Gorochowski TE, Høye TT, Jucker T, Mann HMR, Clements CF. Towards the fully automated monitoring of ecological communities. Ecol Lett 2022; 25:2753-2775. [PMID: 36264848 PMCID: PMC9828790 DOI: 10.1111/ele.14123] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/09/2022] [Accepted: 09/06/2022] [Indexed: 01/12/2023]
Abstract
High-resolution monitoring is fundamental to understand ecosystems dynamics in an era of global change and biodiversity declines. While real-time and automated monitoring of abiotic components has been possible for some time, monitoring biotic components-for example, individual behaviours and traits, and species abundance and distribution-is far more challenging. Recent technological advancements offer potential solutions to achieve this through: (i) increasingly affordable high-throughput recording hardware, which can collect rich multidimensional data, and (ii) increasingly accessible artificial intelligence approaches, which can extract ecological knowledge from large datasets. However, automating the monitoring of facets of ecological communities via such technologies has primarily been achieved at low spatiotemporal resolutions within limited steps of the monitoring workflow. Here, we review existing technologies for data recording and processing that enable automated monitoring of ecological communities. We then present novel frameworks that combine such technologies, forming fully automated pipelines to detect, track, classify and count multiple species, and record behavioural and morphological traits, at resolutions which have previously been impossible to achieve. Based on these rapidly developing technologies, we illustrate a solution to one of the greatest challenges in ecology: the ability to rapidly generate high-resolution, multidimensional and standardised data across complex ecologies.
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Affiliation(s)
- Marc Besson
- School of Biological SciencesUniversity of BristolBristolUK,Sorbonne Université CNRS UMR Biologie des Organismes Marins, BIOMBanyuls‐sur‐MerFrance
| | - Jamie Alison
- Department of EcoscienceAarhus UniversityAarhusDenmark,UK Centre for Ecology & HydrologyBangorUK
| | - Kim Bjerge
- Department of Electrical and Computer EngineeringAarhus UniversityAarhusDenmark
| | - Thomas E. Gorochowski
- School of Biological SciencesUniversity of BristolBristolUK,BrisEngBio, School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | - Toke T. Høye
- Department of EcoscienceAarhus UniversityAarhusDenmark,Arctic Research CentreAarhus UniversityAarhusDenmark
| | - Tommaso Jucker
- School of Biological SciencesUniversity of BristolBristolUK
| | - Hjalte M. R. Mann
- Department of EcoscienceAarhus UniversityAarhusDenmark,Arctic Research CentreAarhus UniversityAarhusDenmark
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5
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Vasconcelos D, Nunes NJ. A Low-Cost Multi-Purpose IoT Sensor for Biologging and Soundscape Activities. SENSORS (BASEL, SWITZERLAND) 2022; 22:7100. [PMID: 36236203 PMCID: PMC9573540 DOI: 10.3390/s22197100] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/12/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
The rapid expansion in miniaturization, usability, energy efficiency, and affordability of Internet of Things (IoT) sensors, integrated with innovations in smart capability, is greatly increasing opportunities in ground-level monitoring of ecosystems at a specific scale using sensor grids. Surrounding sound is a powerful data source for investigating urban and non-urban ecosystem health, and researchers commonly use robust but expensive passive sensors as monitoring equipment to capture it. This paper comprehensively describes the hardware behind our low-cost, small multipurpose prototype, capable of monitoring different environments (e.g., remote locations) with onboard processing power. The device consists of a printed circuit board, microprocessor, local memory, environmental sensor, microphones, optical sensors and LoRa (Long Range) communication systems. The device was successfully used in different use cases, from monitoring mosquitoes enhanced with optical sensors to ocean activities using a hydrophone.
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6
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Oellermann M, Jolles JW, Ortiz D, Seabra R, Wenzel T, Wilson H, Tanner RL. Open Hardware in Science: The Benefits of Open Electronics. Integr Comp Biol 2022; 62:1061-1075. [PMID: 35595471 PMCID: PMC9617215 DOI: 10.1093/icb/icac043] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/30/2022] [Accepted: 05/13/2022] [Indexed: 11/30/2022] Open
Abstract
Openly shared low-cost electronic hardware applications, known as open electronics, have sparked a new open-source movement, with much untapped potential to advance scientific research. Initially designed to appeal to electronic hobbyists, open electronics have formed a global “maker” community and are increasingly used in science and industry. In this perspective article, we review the current costs and benefits of open electronics for use in scientific research ranging from the experimental to the theoretical sciences. We discuss how user-made electronic applications can help (I) individual researchers, by increasing the customization, efficiency, and scalability of experiments, while improving data quantity and quality; (II) scientific institutions, by improving access to customizable high-end technologies, sustainability, visibility, and interdisciplinary collaboration potential; and (III) the scientific community, by improving transparency and reproducibility, helping decouple research capacity from funding, increasing innovation, and improving collaboration potential among researchers and the public. We further discuss how current barriers like poor awareness, knowledge access, and time investments can be resolved by increased documentation and collaboration, and provide guidelines for academics to enter this emerging field. We highlight that open electronics are a promising and powerful tool to help scientific research to become more innovative and reproducible and offer a key practical solution to improve democratic access to science.
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Affiliation(s)
- Michael Oellermann
- Technical University of Munich, TUM School of Life Sciences, Aquatic Systems Biology Unit, Mühlenweg 22, D-85354 Freising, Germany.,University of Tasmania, Institute for Marine and Antarctic Studies, Fisheries and Aquaculture Centre, Private Bag 49, Hobart, TAS 7001, Australia
| | - Jolle W Jolles
- Centre for Research on Ecology and Forestry Applications (CREAF), Campus UAB, Edifici C. 08193 Bellaterra Barcelona, Spain
| | - Diego Ortiz
- INTA, Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Manfredi, Ruta 9 Km 636, 5988, Manfredi, Córdoba, Argentina
| | - Rui Seabra
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - Tobias Wenzel
- Pontificia Universidad Católica de Chile, Institute for Biological and Medical Engineering, Schools of Engineering (IIBM), Medicine and Biological Sciences, Santiago, Chile
| | - Hannah Wilson
- Utah State University, College of Science, Biology Department, 5305 Old Main Hill, Logan, UT, 84321, USA
| | - Richelle L Tanner
- Chapman University, Environmental Science and Policy Program, 1 University Drive, Orange, CA 92866, USA
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7
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MASE: An Instrument Designed to Record Underwater Soundscape. SENSORS 2022; 22:s22093404. [PMID: 35591094 PMCID: PMC9104234 DOI: 10.3390/s22093404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/22/2022] [Accepted: 04/27/2022] [Indexed: 02/01/2023]
Abstract
The study of sound in the natural environment provides interesting information for researchers and policy makers driving conservation policies in our society. The soundscape characterises the biophony, anthrophony and geophony of a particular area. The characterisation of these different sources can lead to changes in ecosystems and we need to identify these parameters in order to make the right decision in relation to the natural environment. These values could be extrapolated and potentially help different areas of ecoacoustic research. Technological advances have enabled the passive acoustic monitoring (PAM) of animal populations in their natural environment. Recordings can be made with little interference, avoiding anthropogenic effects, making it a very effective method for some species such as cetaceans and other marine species in addition to underwater noise studies. Passive acoustic monitoring can be used for population census, but also to understand the effect of human activities on animals. However, recording data over long periods of time requires large storage and processing capacity to handle all the acoustic events generated. In the case of marine environments, the installation of sensors and instruments can be costly in terms of money and maintenance effort. In addition, if they are placed offshore, a data communication problem arises with coverage and bandwidth. In this paper, we propose a low-cost instrument to monitor the soundscape of a marine area using ecoacoustic indices. The instrument is called MASE and provides three echo-acoustic indices at 10 min intervals that are available in real time, which drastically reduces the volume of data generated. It has been operating uninterruptedly for a year and a half since its deployment, except during maintenance periods. MASE has been able to operate uninterruptedly, and maintain an adequate temperature inside while preserving its structural integrity for long periods of time. This has allowed the monitoring and characterisation of the soundscape of the test area in Gando Bay, Gran Canaria Island (Spain) without the need for human intervention to access the data on the instrument itself. Thanks to its integration with an external server, this allows the long-term monitoring of the soundscape, and it is possible to observe changes in the soundscape. In addition, the instrument has made it possible to compare the period of acoustic inactivity during confinement and the return of anthropogenic acoustic activity at sea.
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8
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Heath BE, Sethi SS, Orme CDL, Ewers RM, Picinali L. How index selection, compression, and recording schedule impact the description of ecological soundscapes. Ecol Evol 2021; 11:13206-13217. [PMID: 34646463 PMCID: PMC8495811 DOI: 10.1002/ece3.8042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/17/2021] [Accepted: 06/25/2021] [Indexed: 11/29/2022] Open
Abstract
Acoustic indices derived from environmental soundscape recordings are being used to monitor ecosystem health and vocal animal biodiversity. Soundscape data can quickly become very expensive and difficult to manage, so data compression or temporal down-sampling are sometimes employed to reduce data storage and transmission costs. These parameters vary widely between experiments, with the consequences of this variation remaining mostly unknown.We analyse field recordings from North-Eastern Borneo across a gradient of historical land use. We quantify the impact of experimental parameters (MP3 compression, recording length and temporal subsetting) on soundscape descriptors (Analytical Indices and a convolutional neural net derived AudioSet Fingerprint). Both descriptor types were tested for their robustness to parameter alteration and their usability in a soundscape classification task.We find that compression and recording length both drive considerable variation in calculated index values. However, we find that the effects of this variation and temporal subsetting on the performance of classification models is minor: performance is much more strongly determined by acoustic index choice, with Audioset fingerprinting offering substantially greater (12%-16%) levels of classifier accuracy, precision and recall.We advise using the AudioSet Fingerprint in soundscape analysis, finding superior and consistent performance even on small pools of data. If data storage is a bottleneck to a study, we recommend Variable Bit Rate encoded compression (quality = 0) to reduce file size to 23% file size without affecting most Analytical Index values. The AudioSet Fingerprint can be compressed further to a Constant Bit Rate encoding of 64 kb/s (8% file size) without any detectable effect. These recommendations allow the efficient use of restricted data storage whilst permitting comparability of results between different studies.
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Affiliation(s)
- Becky E. Heath
- Dyson School of Design EngineeringImperial College LondonLondonUK
- Department of Life SciencesImperial College LondonLondonUK
| | - Sarab S. Sethi
- Dyson School of Design EngineeringImperial College LondonLondonUK
- Department of Life SciencesImperial College LondonLondonUK
- Department of MathematicsImperial College LondonLondonUK
| | | | | | - Lorenzo Picinali
- Dyson School of Design EngineeringImperial College LondonLondonUK
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9
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Karlsson ECM, Tay H, Imbun P, Hughes AC. The Kinabalu Recorder, a new passive acoustic and environmental monitoring recorder. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13671] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eva Catharina M. Karlsson
- Center for Integrative Conservation Xishuangbanna Tropical Botanical Garden Chinese Academy of Sciences Menglun PR China
| | | | | | - Alice C. Hughes
- Center for Integrative Conservation Xishuangbanna Tropical Botanical Garden Chinese Academy of Sciences Menglun PR China
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10
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Roe P, Eichinski P, Fuller RA, McDonald PG, Schwarzkopf L, Towsey M, Truskinger A, Tucker D, Watson DM. The Australian Acoustic Observatory. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13660] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Paul Roe
- Faculty of Science Queensland University of Technology Brisbane Qld Australia
| | - Philip Eichinski
- Faculty of Science Queensland University of Technology Brisbane Qld Australia
| | - Richard A. Fuller
- School of Biological Sciences University of Queensland St Lucia Qld Australia
| | - Paul G. McDonald
- Zoology, School of Environmental and Rural Science University of New England Armidale NSW Australia
| | - Lin Schwarzkopf
- College of Science and Engineering James Cook University Townsville Qld Australia
| | - Michael Towsey
- Faculty of Science Queensland University of Technology Brisbane Qld Australia
| | - Anthony Truskinger
- Faculty of Science Queensland University of Technology Brisbane Qld Australia
| | - David Tucker
- Faculty of Science Queensland University of Technology Brisbane Qld Australia
| | - David M. Watson
- School of Environmental Sciences Charles Sturt University Albury NSW Australia
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11
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Towards an ecosystem model of infectious disease. Nat Ecol Evol 2021; 5:907-918. [PMID: 34002048 DOI: 10.1038/s41559-021-01454-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 03/25/2021] [Indexed: 02/03/2023]
Abstract
Increasingly intimate associations between human society and the natural environment are driving the emergence of novel pathogens, with devastating consequences for humans and animals alike. Prior to emergence, these pathogens exist within complex ecological systems that are characterized by trophic interactions between parasites, their hosts and the environment. Predicting how disturbance to these ecological systems places people and animals at risk from emerging pathogens-and the best ways to manage this-remains a significant challenge. Predictive systems ecology models are powerful tools for the reconstruction of ecosystem function but have yet to be considered for modelling infectious disease. Part of this stems from a mistaken tendency to forget about the role that pathogens play in structuring the abundance and interactions of the free-living species favoured by systems ecologists. Here, we explore how developing and applying these more complete systems ecology models at a landscape scale would greatly enhance our understanding of the reciprocal interactions between parasites, pathogens and the environment, placing zoonoses in an ecological context, while identifying key variables and simplifying assumptions that underly pathogen host switching and animal-to-human spillover risk. As well as transforming our understanding of disease ecology, this would also allow us to better direct resources in preparation for future pandemics.
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12
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Jolles JW. Broad‐scale applications of the Raspberry Pi: A review and guide for biologists. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13652] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jolle W. Jolles
- Zukunftskolleg University of Konstanz Konstanz Germany
- Department of Collective Behaviour Max Planck Institute of Animal Behaviour Konstanz Germany
- Centre for Research on Ecology and Forestry Applications (CREAF) Barcelona Spain
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13
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Abstract
Plant phenology is strongly interlinked with ecosystem processes and biodiversity. Like many other aspects of ecosystem functioning, it is affected by habitat and climate change, with both global change drivers altering the timings and frequency of phenological events. As such, there has been an increased focus in recent years to monitor phenology in different biomes. A range of approaches for monitoring phenology have been developed to increase our understanding on its role in ecosystems, ranging from the use of satellites and drones to collection traps, each with their own merits and limitations. Here, we outline the trade-offs between methods (spatial resolution, temporal resolution, cost, data processing), and discuss how their use can be optimised in different environments and for different goals. We also emphasise emerging technologies that will be the focus of monitoring in the years to follow and the challenges of monitoring phenology that still need to be addressed. We conclude that there is a need to integrate studies that incorporate multiple monitoring methods, allowing the strengths of one to compensate for the weaknesses of another, with a view to developing robust methods for upscaling phenological observations from point locations to biome and global scales and reconciling data from varied sources and environments. Such developments are needed if we are to accurately quantify the impacts of a changing world on plant phenology.
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14
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Baker E, Chesmore D. Standardisation of bioacoustic terminology for insects. Biodivers Data J 2020; 8:e54222. [PMID: 32848502 PMCID: PMC7419339 DOI: 10.3897/bdj.8.e54222] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/22/2020] [Indexed: 11/26/2022] Open
Abstract
After reviewing the published literature on sound production in insects, a standardised terminology and controlled vocabularies have been created. This combined terminology has potential for use in automated identification systems, evolutionary studies, and other use cases where the synthesis of bioacoustic traits from the literature is required. An example implementation has been developed for the BioAcoustica platform. It is hoped that future development of controlled vocabularies will become a community effort.
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Affiliation(s)
- Edward Baker
- University of York, York, United Kingdom University of York York United Kingdom
| | - David Chesmore
- University of York, York, United Kingdom University of York York United Kingdom
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15
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Sugai LSM. Pandemics and the Need for Automated Systems for Biodiversity Monitoring. J Wildl Manage 2020; 84:1424-1426. [PMID: 32904967 PMCID: PMC7461419 DOI: 10.1002/jwmg.21946] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 11/30/2022]
Affiliation(s)
- Larissa S M Sugai
- Departamento de Ecologia Universidad Autónoma de Madrid Calle Darwin 2 28049 Madrid Spain
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16
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Proppe DS, Pandit MM, Bridge ES, Jasperse P, Holwerda C. Semi‐portable solar power to facilitate continuous operation of technology in the field. Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13456] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Darren S. Proppe
- School of Natural Sciences St. Edward's University Austin TX USA
- Science Division Calvin University Grand Rapids MI USA
| | - Meelyn M. Pandit
- Department of Biology College of Arts and Sciences University of Oklahoma Norman OK USA
| | - Eli S. Bridge
- Oklahoma Biological Survey University of Oklahoma Norman OK USA
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17
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Hart EE, Fennessy J, Rasmussen HB, Butler-Brown M, Muneza AB, Ciuti S. Precision and performance of an 180g solar-powered GPS device for tracking medium to large-bodied terrestrial mammals. WILDLIFE BIOLOGY 2020. [DOI: 10.2981/wlb.00669] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Emma E. Hart
- E. E. Hart (https://orcid.org/0000-0002-5622-2089) ✉ , Laboratory of Wildlife Ecology and Behaviour, School of Biology and Environmental Science, Univ. College Dublin, Dublin, Ireland
| | - Julian Fennessy
- J. Fennessy, Giraffe Conservation Foundation, Windhoek, Namibia
| | | | - Michael Butler-Brown
- M. Butler-Brown, Dept of Biological Sciences Graduate Program in Ecology, Evolution Ecosystems and Society, Dartmouth College, Hanover, NH, USA
| | - Arthur B. Muneza
- A. B. Muneza, Giraffe Conservation Foundation, Windhoek, Namibia
| | - Simone Ciuti
- S. Ciuti, Laboratory of Wildlife Ecology and Behaviour, School of Biology and Environmental Science, Univ. College Dublin, Dublin, Ireland
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18
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Characterizing soundscapes across diverse ecosystems using a universal acoustic feature set. Proc Natl Acad Sci U S A 2020; 117:17049-17055. [PMID: 32636258 DOI: 10.1073/pnas.2004702117] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Natural habitats are being impacted by human pressures at an alarming rate. Monitoring these ecosystem-level changes often requires labor-intensive surveys that are unable to detect rapid or unanticipated environmental changes. Here we have developed a generalizable, data-driven solution to this challenge using eco-acoustic data. We exploited a convolutional neural network to embed soundscapes from a variety of ecosystems into a common acoustic space. In both supervised and unsupervised modes, this allowed us to accurately quantify variation in habitat quality across space and in biodiversity through time. On the scale of seconds, we learned a typical soundscape model that allowed automatic identification of anomalous sounds in playback experiments, providing a potential route for real-time automated detection of irregular environmental behavior including illegal logging and hunting. Our highly generalizable approach, and the common set of features, will enable scientists to unlock previously hidden insights from acoustic data and offers promise as a backbone technology for global collaborative autonomous ecosystem monitoring efforts.
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19
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Sethi SS, Ewers RM, Jones NS, Signorelli A, Picinali L, Orme CDL. SAFE Acoustics: An open‐source, real‐time eco‐acoustic monitoring network in the tropical rainforests of Borneo. Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13438] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sarab S. Sethi
- Department of Life Sciences Imperial College London London UK
- Department of Mathematics Imperial College London London UK
- Dyson School of Design Engineering Imperial College London London UK
| | - Robert M. Ewers
- Department of Life Sciences Imperial College London London UK
| | - Nick S. Jones
- Department of Mathematics Imperial College London London UK
| | | | - Lorenzo Picinali
- Dyson School of Design Engineering Imperial College London London UK
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Intensity of giraffe locomotor activity is shaped by solar and lunar zeitgebers. Behav Processes 2020; 178:104178. [PMID: 32562740 DOI: 10.1016/j.beproc.2020.104178] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/05/2020] [Accepted: 06/05/2020] [Indexed: 02/07/2023]
Abstract
Natural cycles of light and darkness shift the balance of risks and gains for animals across space and time. Entrainment to photic cycles allows animals to spatiotemporally adapt their behavioural and physiological processes in line with interplaying ecological factors, such as temperature, foraging efficiency and predation risk. Until recently, our understanding of these chronobiological processes was limited by the difficulties of 24 h observations. Technological advances in GPS biotelemetry however are now allowing us unprecedented access to long-term, fine-scale activity data. Here we use data derived from frontline technology to present the first large-scale investigation into the effects of natural fluctuations of light and darkness on the locomotor activity patterns of a threatened African mega-herbivore, the giraffe (Giraffa spp.). Using data from a remote population of Angolan giraffe (G. g. angolensis) in the northern Namib Desert, Namibia, we reveal the first full picture of giraffe chronobiology in a landscape of fear. Furthermore, we present clear evidence of the effect of moonlight on the nocturnal activity patterns of large ungulates. Our results are in line with recent research demonstrating that, rather than a fixed internal representation of time (circadian clock), many surface-dwelling ungulates have plastic activity patterns that are vulnerable to modification by external factors including light and temperature. Relatedly, we highlight important conservation management implications of rising temperatures and increasing light pollution on the chronobiology of surface-dwelling mammals.
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21
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Low-Cost Sensors for Urban Noise Monitoring Networks-A Literature Review. SENSORS 2020; 20:s20082256. [PMID: 32316202 PMCID: PMC7218845 DOI: 10.3390/s20082256] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/10/2020] [Accepted: 04/12/2020] [Indexed: 01/28/2023]
Abstract
Noise pollution reduction in the environment is a major challenge from a societal and health point of view. To implement strategies to improve sound environments, experts need information on existing noise. The first source of information is based on the elaboration of noise maps using software, but with limitations on the realism of the maps obtained, due to numerous calculation assumptions. The second is based on the use of measured data, in particular through professional measurement observatories, but in limited numbers for practical and financial reasons. More recently, numerous technical developments, such as the miniaturization of electronic components, the accessibility of low-cost computing processors and the improved performance of electric batteries, have opened up new prospects for the deployment of low-cost sensor networks for the assessment of sound environments. Over the past fifteen years, the literature has presented numerous experiments in this field, ranging from proof of concept to operational implementation. The purpose of this article is firstly to review the literature, and secondly, to identify the expected technical characteristics of the sensors to address the problem of noise pollution assessment. Lastly, the article will also put forward the challenges that are needed to respond to a massive deployment of low-cost noise sensors.
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22
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Crunchant A, Borchers D, Kühl H, Piel A. Listening and watching: Do camera traps or acoustic sensors more efficiently detect wild chimpanzees in an open habitat? Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13362] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - David Borchers
- Centre for Research into Ecological and Environmental Modelling University of St Andrews St Andrews UK
| | - Hjalmar Kühl
- Max Planck Institute for Evolutionary Anthropology Leipzig Germany
| | - Alex Piel
- Liverpool John Moores University Liverpool UK
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23
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Darras K, Batáry P, Furnas BJ, Grass I, Mulyani YA, Tscharntke T. Autonomous sound recording outperforms human observation for sampling birds: a systematic map and user guide. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2019; 29:e01954. [PMID: 31206926 DOI: 10.1002/eap.1954] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 04/17/2019] [Accepted: 04/23/2019] [Indexed: 06/09/2023]
Abstract
Autonomous sound recording techniques have gained considerable traction in the last decade, but the question remains whether they can replace human observation surveys to sample sonant animals. For birds in particular, survey methods have been tested extensively using point counts and sound recording surveys. Here, we review the latest evidence for this taxon within the frame of a systematic map. We compare sampling effectiveness of these two survey methods, the output variables they produce, and their practicality. When assessed against the standard of point counts, autonomous sound recording proves to be a powerful tool that samples at least as many species. This technology can monitor birds in an exhaustive, standardized, and verifiable way. Moreover, sound recorders give access to entire soundscapes from which new data types can be derived (vocal activity, acoustic indices). Variables such as abundance, density, occupancy, or species richness can be obtained to yield data sets that are comparable to and compatible with point counts. Finally, autonomous sound recorders allow investigations at high temporal and spatial resolution and coverage, which are more cost effective and cannot be achieved by human observations alone, even though small-scale studies might be more cost effective when carried out with point counts. Sound recorders can be deployed in many places, they are more scalable and reliable, making them the better choice for bird surveys in an increasingly data-driven time. We provide an overview of currently available recorders and discuss their specifications to guide future study designs.
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Affiliation(s)
- Kevin Darras
- Agroecology, Department of Crop Sciences, University of Goettingen, Grisebachstrasse 6, 37077, Göttingen, Germany
| | - Péter Batáry
- Agroecology, Department of Crop Sciences, University of Goettingen, Grisebachstrasse 6, 37077, Göttingen, Germany
- Lendület Landscape and Conservation Ecology, Institute of Ecology and Botany, MTA Centre for Ecological Research, Alkotmány u. 2-4, 2163, Vácrátót, Hungary
| | - Brett J Furnas
- Wildlife Investigations Laboratory, California Department of Fish and Wildlife, 1701 Nimbus Road, Suite D, Sacramento, California, 95670, USA
| | - Ingo Grass
- Agroecology, Department of Crop Sciences, University of Goettingen, Grisebachstrasse 6, 37077, Göttingen, Germany
| | - Yeni A Mulyani
- Department of Forest Resources Conservation and Ecotourism, Faculty of Forestry, Bogor Agricultural University, Bogor, Indonesia
| | - Teja Tscharntke
- Agroecology, Department of Crop Sciences, University of Goettingen, Grisebachstrasse 6, 37077, Göttingen, Germany
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Yan X, Zhang H, Li D, Wu D, Zhou S, Sun M, Hu H, Liu X, Mou S, He S, Owen MA, Huang Y. Acoustic recordings provide detailed information regarding the behavior of cryptic wildlife to support conservation translocations. Sci Rep 2019; 9:5172. [PMID: 30914700 PMCID: PMC6435668 DOI: 10.1038/s41598-019-41455-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 02/26/2019] [Indexed: 12/02/2022] Open
Abstract
For translocated animals, behavioral competence may be key to post-release survival. However, monitoring behavior is typically limited to tracking movements or inferring behavior at a gross scale via collar-mounted sensors. Animal-bourne acoustic monitoring may provide a unique opportunity to monitor behavior at a finer scale. The giant panda is an elusive species of Ursid that is vulnerable to extinction. Translocation is an important aspect of the species' recovery, and survival and recruitment for pandas likely hinge on behavioral competence. Here we tested the efficacy of a collar-mounted acoustic recording unit (ARU) to remotely monitor the behavior of panda mothers and their dependent young. We found that trained human listeners could reliably identify 10 behaviors from acoustic recordings. Through visual inspection of spectrograms we further identified 5 behavioral categories that may be detectable by automated pattern recognition, an approach that is essential for the practical application of ARU. These results suggest that ARU are a viable method for remotely observing behaviors, including feeding. With targeted effort directed towards instrumentation and computing advances, ARU could be used to document how behavioral competence supports or challenges post-release survival and recruitment, and allow for research findings to be adaptively integrated into future translocation efforts.
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Affiliation(s)
- Xiao Yan
- China Conservation and Research Centre for the Giant Panda, Wolong, Sichuan, 623006, China
- Key Laboratory of Biodiversity Science and Ecological Engineering of Ministry of Education, School of Life Sciences, Beijing Normal University, Beijing, China
| | - Hemin Zhang
- China Conservation and Research Centre for the Giant Panda, Wolong, Sichuan, 623006, China
| | - Desheng Li
- China Conservation and Research Centre for the Giant Panda, Wolong, Sichuan, 623006, China
| | - Daifu Wu
- China Conservation and Research Centre for the Giant Panda, Wolong, Sichuan, 623006, China.
| | - Shiqiang Zhou
- China Conservation and Research Centre for the Giant Panda, Wolong, Sichuan, 623006, China
| | - Mengmeng Sun
- China Conservation and Research Centre for the Giant Panda, Wolong, Sichuan, 623006, China
| | - Haiping Hu
- China Conservation and Research Centre for the Giant Panda, Wolong, Sichuan, 623006, China
| | - Xiaoqiang Liu
- China Conservation and Research Centre for the Giant Panda, Wolong, Sichuan, 623006, China
| | - Shijie Mou
- China Conservation and Research Centre for the Giant Panda, Wolong, Sichuan, 623006, China
| | - Shengshan He
- China Conservation and Research Centre for the Giant Panda, Wolong, Sichuan, 623006, China
| | - Megan A Owen
- Institute for Conservation Research, San Diego Zoo Global, California, United States.
| | - Yan Huang
- China Conservation and Research Centre for the Giant Panda, Wolong, Sichuan, 623006, China.
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25
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Darras K, Kolbrek B, Knorr A, Meyer V, Zippert M, Wenzel A. Assembling cheap, high-performance microphones for recording terrestrial wildlife: the Sonitor system. F1000Res 2018; 7:1984. [PMID: 30687500 PMCID: PMC6338251 DOI: 10.12688/f1000research.17511.3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/11/2021] [Indexed: 11/20/2022] Open
Abstract
Passive acoustic monitoring of wildlife requires sound recording systems. Several cheap, high-performance, or open-source solutions currently exist for recording soundscapes, but all rely on commercial microphones. Commercial microphones are relatively expensive, specialized for particular taxa, and often have incomplete technical specifications. We designed Sonitor, an open-source microphone system to address all needs of ecologists that sample terrestrial wildlife acoustically. We evaluated the cost and durability of our system and measured trade-offs that are seldom acknowledged but which universally limit microphones' functions: weatherproofing versus sound attenuation, windproofing versus transmission loss after rain, signal loss in long cables, and analog sound amplification versus directivity with acoustic horns. We propose five microphone configurations suiting different budgets (from 8 to 33 EUR per unit), and fulfilling different sound quality and flexibility requirements. The Sonitor system consists of sturdy acoustic sensors that cover the entire sound frequency spectrum of sonant terrestrial wildlife at a fraction of the cost of commercial microphones.
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Affiliation(s)
- Kevin Darras
- Department of Agroecology, University of Göttingen, Göttingen, Niedersachsen, 37077, Germany
| | | | - Andreas Knorr
- Mess-, Steuerungs-, und Regeltechnik, University of Göttingen, Göttingen, Niedersachsen, 37077, Germany
| | - Volker Meyer
- Konstruktion, Geräte- Neuentwicklung, Schreinerei, Schlosserei, University of Göttingen, Göttingen, Niedersachsen, 37077, Germany
| | - Mike Zippert
- Konstruktion, Geräte- Neuentwicklung, Schreinerei, Schlosserei, University of Göttingen, Göttingen, Niedersachsen, 37077, Germany
| | - Arne Wenzel
- Functional Agrobiodiversity, University of Göttingen, Göttingen, Niedersachsen, 37077, Germany
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Gibb R, Browning E, Glover‐Kapfer P, Jones KE. Emerging opportunities and challenges for passive acoustics in ecological assessment and monitoring. Methods Ecol Evol 2018. [DOI: 10.1111/2041-210x.13101] [Citation(s) in RCA: 184] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rory Gibb
- Department of Genetics, Evolution and EnvironmentCentre for Biodiversity and Environment ResearchUniversity College London London UK
| | - Ella Browning
- Department of Genetics, Evolution and EnvironmentCentre for Biodiversity and Environment ResearchUniversity College London London UK
- Institute of ZoologyZoological Society of London London UK
| | - Paul Glover‐Kapfer
- WWF‐UKLiving Planet Centre Woking UK
- Flora & Fauna International David Attenborough Building Cambridge UK
| | - Kate E. Jones
- Department of Genetics, Evolution and EnvironmentCentre for Biodiversity and Environment ResearchUniversity College London London UK
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