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Cauzinille J, Favre B, Marxer R, Rey A. Applying machine learning to primate bioacoustics: Review and perspectives. Am J Primatol 2024:e23666. [PMID: 39120066 DOI: 10.1002/ajp.23666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 06/13/2024] [Accepted: 07/12/2024] [Indexed: 08/10/2024]
Abstract
This paper provides a comprehensive review of the use of computational bioacoustics as well as signal and speech processing techniques in the analysis of primate vocal communication. We explore the potential implications of machine learning and deep learning methods, from the use of simple supervised algorithms to more recent self-supervised models, for processing and analyzing large data sets obtained within the emergence of passive acoustic monitoring approaches. In addition, we discuss the importance of automated primate vocalization analysis in tackling essential questions on animal communication and highlighting the role of comparative linguistics in bioacoustic research. We also examine the challenges associated with data collection and annotation and provide insights into potential solutions. Overall, this review paper runs through a set of common or innovative perspectives and applications of machine learning for primate vocal communication analysis and outlines opportunities for future research in this rapidly developing field.
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Affiliation(s)
- Jules Cauzinille
- LIS, CNRS, Aix-Marseille University, Marseille, France
- CRPN, CNRS, Aix-Marseille University, Marseille, France
- ILCB, Aix-Marseille University, Marseille, France
| | - Benoit Favre
- LIS, CNRS, Aix-Marseille University, Marseille, France
- ILCB, Aix-Marseille University, Marseille, France
| | - Ricard Marxer
- ILCB, Aix-Marseille University, Marseille, France
- LIS, CNRS, Université de Toulon, Toulon, France
| | - Arnaud Rey
- CRPN, CNRS, Aix-Marseille University, Marseille, France
- ILCB, Aix-Marseille University, Marseille, France
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Mitani JC, Abwe E, Campbell G, Giles-Vernick T, Goldberg T, McLennan MR, Preuschoft S, Supriatna J, Marshall AJ. Future coexistence with great apes will require major changes to policy and practice. Nat Hum Behav 2024; 8:632-643. [PMID: 38374442 DOI: 10.1038/s41562-024-01830-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 12/21/2023] [Indexed: 02/21/2024]
Abstract
The great apes-bonobos, chimpanzees, gorillas and orangutans-are critically threatened by human activities. We have destroyed their habitats, hunted them and transmitted fatal diseases to them. Yet we also conduct research on them, try to protect them and live alongside them. They are endangered, and time is running out. Here we outline what must be done to ensure that future generations continue to share this planet with great apes. We urge dialogue with those who live with great apes and interact with them often. We advocate conservation plans that acknowledge the realities of climate change, economic drivers and population growth. We encourage researchers to use technology to minimize risks to great apes. Our proposals will require substantial investment, and we identify ways to generate these funds. We conclude with a discussion of how field researchers might alter their work to protect our closest living relatives more effectively.
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Affiliation(s)
- John C Mitani
- Department of Anthropology, University of Michigan, Ann Arbor, MI, USA.
- Ngogo Chimpanzee Project, Phoenix, AZ, USA.
| | - Ekwoge Abwe
- San Diego Zoo Wildlife Alliance, Escondido, CA, USA
- Cameroon Biodiversity Association, Douala, Cameroon
| | | | - Tamara Giles-Vernick
- Anthropology and Ecology of Disease Emergence Unit, Institut Pasteur/Université Paris Cité, Paris, France
| | - Tony Goldberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - Matthew R McLennan
- Bulindi Chimpanzee and Community Project, Hoima, Uganda
- Faculty of Humanities and Social Sciences, Oxford Brookes University, Oxford, UK
| | | | - Jatna Supriatna
- Department of Biology, Faculty of Mathematics and Sciences, University of Indonesia, Depok, West Java, Indonesia
| | - Andrew J Marshall
- Department of Anthropology, University of Michigan, Ann Arbor, MI, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
- Program in the Environment, University of Michigan, Ann Arbor, MI, USA
- School for Environment and Sustainability, University of Michigan, Ann Arbor, MI, USA
- Program in Computing for the Arts and Sciences, University of Michigan, Ann Arbor, MI, USA
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Batist CH, Dufourq E, Jeantet L, Razafindraibe MN, Randriamanantena F, Baden AL. An integrated passive acoustic monitoring and deep learning pipeline for black-and-white ruffed lemurs (Varecia variegata) in Ranomafana National Park, Madagascar. Am J Primatol 2024; 86:e23599. [PMID: 38244194 DOI: 10.1002/ajp.23599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 01/05/2024] [Accepted: 01/09/2024] [Indexed: 01/22/2024]
Abstract
The urgent need for effective wildlife monitoring solutions in the face of global biodiversity loss has resulted in the emergence of conservation technologies such as passive acoustic monitoring (PAM). While PAM has been extensively used for marine mammals, birds, and bats, its application to primates is limited. Black-and-white ruffed lemurs (Varecia variegata) are a promising species to test PAM with due to their distinctive and loud roar-shrieks. Furthermore, these lemurs are challenging to monitor via traditional methods due to their fragmented and often unpredictable distribution in Madagascar's dense eastern rainforests. Our goal in this study was to develop a machine learning pipeline for automated call detection from PAM data, compare the effectiveness of PAM versus in-person observations, and investigate diel patterns in lemur vocal behavior. We did this study at Mangevo, Ranomafana National Park by concurrently conducting focal follows and deploying autonomous recorders in May-July 2019. We used transfer learning to build a convolutional neural network (optimized for recall) that automated the detection of lemur calls (57-h runtime; recall = 0.94, F1 = 0.70). We found that PAM outperformed in-person observations, saving time, money, and labor while also providing re-analyzable data. Using PAM yielded novel insights into V. variegata diel vocal patterns; we present the first published evidence of nocturnal calling. We developed a graphic user interface and open-sourced data and code, to serve as a resource for primatologists interested in implementing PAM and machine learning. By leveraging the potential of this pipeline, we can address the urgent need for effective primate population surveys to inform conservation strategies.
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Affiliation(s)
- Carly H Batist
- Department of Anthropology, City University of New York (CUNY) Graduate Center, New York, New York, USA
- New York Consortium in Evolutionary Primatology (NYCEP), New York, New York, USA
- Rainforest Connection (RFCx), Katy, Texas, USA
| | - Emmanuel Dufourq
- African Institute for Mathematical Sciences, Muizenberg, South Africa
- Department of Mathematical Sciences, Stellenbosch University, Stellenbosch, South Africa
- National Institute for Theoretical & Computational Sciences, Stellenbosch, South Africa
- African Institute for Mathematical Sciences, Research and Innovation Centre, Kigali, Rwanda
| | - Lorène Jeantet
- African Institute for Mathematical Sciences, Muizenberg, South Africa
- Department of Mathematical Sciences, Stellenbosch University, Stellenbosch, South Africa
- National Institute for Theoretical & Computational Sciences, Stellenbosch, South Africa
| | - Mendrika N Razafindraibe
- Department of Animal Biology, University of Antananarivo, Antananarivo, Madagascar
- Institut International de Science Sociale, Antananarivo, Madagascar
| | | | - Andrea L Baden
- Department of Anthropology, City University of New York (CUNY) Graduate Center, New York, New York, USA
- New York Consortium in Evolutionary Primatology (NYCEP), New York, New York, USA
- Department of Anthropology, Hunter College of City University of New York (CUNY), New York, New York, USA
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Fan YX, Xie PZ, Ma C, Chen T, Ye X, Xu HL, Yang Q, Fan PF. Population size estimates based on GPS telemetry. Zool Res 2024; 45:36-38. [PMID: 38114431 PMCID: PMC10839658 DOI: 10.24272/j.issn.2095-8137.2023.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 09/08/2023] [Indexed: 12/21/2023] Open
Affiliation(s)
- Yu-Xuan Fan
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Pu-Zheng Xie
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Chi Ma
- College of Agriculture and Biological Sciences, Dali, Yunnan 671003, China
| | - Ting Chen
- Neilingding-Futian National Nature Reserve of Guangdong, Shenzhen, Guangdong 518040, China
| | - Xiao Ye
- Neilingding-Futian National Nature Reserve of Guangdong, Shenzhen, Guangdong 518040, China
| | - Hua-Lin Xu
- Neilingding-Futian National Nature Reserve of Guangdong, Shenzhen, Guangdong 518040, China
| | - Qiong Yang
- Neilingding-Futian National Nature Reserve of Guangdong, Shenzhen, Guangdong 518040, China
| | - Peng-Fei Fan
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China. E-mail:
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Gazagne E, Gray RJ, Ratajszczak R, Brotcorne F, Hambuckers A. Unmanned aerial vehicles (UAVs) with thermal infrared (TIR) sensors are effective for monitoring and counting threatened Vietnamese primates. Primates 2023:10.1007/s10329-023-01066-9. [PMID: 37140752 DOI: 10.1007/s10329-023-01066-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 03/28/2023] [Indexed: 05/05/2023]
Abstract
Monitoring the population size of threatened primate species with minimal disturbance is becoming an outstanding requirement for conservation and wildlife management. Drones with thermal infrared (TIR) and visible spectrum (RGB) imaging are increasingly used to survey arboreal primates, but ground-truthing is still required to assess the effectiveness of drone-based count estimates. Our pilot study aims to assess the ability of a drone with both TIR and RGB sensors to detect, count, and identify semi-wild population of four endangered species of langurs and gibbon in the Endangered Primate Rescue Center (EPRC) in northern Vietnam. We found that TIR imagery enabled higher detection rates compared to RGB imagery and obtained an accurate count with the TIR only after four drone flights. We could identify langurs species based on thermal signature at a flight height of 50 m from the ground level (max tree height = 15 m), via size and shape of the body. With TIR imagery, we were able to record inconspicuous behaviors such as foraging and play. While some individuals initially showed flight or avoidance behaviors when the drone was sighted, these behaviors decreased or were absent on following drone surveys. Our study suggests that monitoring and precisely counting langur and gibbon species populations could be successful with the use of thermal drones only.
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Affiliation(s)
- Eva Gazagne
- Unit of Research SPHERES, University of Liège, Quai van Beneden, 22, 4020, Liège, Belgium.
| | - Russell J Gray
- Save Vietnam's Wildlife, Cuc Phuong National Park, Nho Quan, Ninh Binh Province, Vietnam
| | - Radoslaw Ratajszczak
- Endangered Primate Rescue Center, Cuc Phuong National Park, Nho Quan, Ninh Binh Province, Vietnam
| | - Fany Brotcorne
- Unit of Research SPHERES, University of Liège, Quai van Beneden, 22, 4020, Liège, Belgium
| | - Alain Hambuckers
- Unit of Research SPHERES, University of Liège, Quai van Beneden, 22, 4020, Liège, Belgium
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Zambolli AH, Manzano MCR, Honda LK, Rezende GC, Culot L. Performance of autonomous recorders to detect a cryptic and endangered primate species, the black lion-tamarin (Leontopithecus chrysopygus). Am J Primatol 2023; 85:e23454. [PMID: 36415048 DOI: 10.1002/ajp.23454] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/28/2022] [Accepted: 11/05/2022] [Indexed: 11/24/2022]
Abstract
Information about species distribution is important for conservation but the monitoring of populations can demand a high sampling effort with traditional methods (e.g., line transects, sound playback) that are poorly efficient for cryptic primates, such as the black lion tamarin (Leontopithecus chrysopygus). Here we investigated the effectiveness of passive acoustic monitoring (PAM) as an alternative method to identify the presence of vocalizing lion tamarins in the wild. We aimed to: (1) determine the maximum distance at which autonomous recorders (Song Meter 3) and Raven Pro acoustic software can respectively detect and identify lion tamarin long calls emitted by two captive subjects (ex situ study); and (2) determine the sampling effort required to confirm the presence of the species in the wild (in situ study). In captive settings, we recorded lion tamarin long calls with one to two autonomous recorders operating at increasing distances from the animals' enclosure (8-202 m). In a 515 ha forest fragment, we deployed 12 recorders in a grid, 300 m apart from each other, within the estimated 100 ha home range of one group, and let them record for 10 consecutive days, totaling 985 h. In the ex situ study, hand-browsing of spectrograms yielded 298 long calls emitted from 8 to 194 m, and Raven's Template Detector identified 54.6% of them, also emitted from 8 to 194 m. In the in situ study, we manually counted 1115 long calls, and the Raven's Template Detector identified 44.75% of them. Furthermore, the presence of lion tamarins was confirmed within 1 day using four randomly sorted recorders, whereas 5 days on average were necessary with only one device. While specific protocols still need to be developed to determine primate population size using this technology, we concluded that PAM is a promising tool when considering long term costs and benefits.
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Affiliation(s)
- André H Zambolli
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Departamento de Biodiversidade, Laboratório de Primatologia, Rio Claro, São Paulo, Brazil
| | - Maria Carolina R Manzano
- Programa de Pós-Graduação em Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo-USP, São Paulo, Brazil
| | - Laura Kyoko Honda
- Instituto de Biociências, Departamento de Biodiversidade, Laboratório de Ecologia Espacial e Conservação, Universidade Estadual Paulista (UNESP), Rio Claro, São Paulo, Brazil.,Programa de Pós-graduação em Ecologia, Evolução e Biodiversidade, Departamento de Biodiversidade, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro, São Paulo, Brazil
| | - Gabriela C Rezende
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Departamento de Biodiversidade, Laboratório de Primatologia, Rio Claro, São Paulo, Brazil.,Programa de Pós-graduação em Ecologia, Evolução e Biodiversidade, Departamento de Biodiversidade, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro, São Paulo, Brazil.,IPÊ-Instituto de Pesquisas Ecológicas, Nazaré Paulista, São Paulo, Brazil
| | - Laurence Culot
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Departamento de Biodiversidade, Laboratório de Primatologia, Rio Claro, São Paulo, Brazil
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Fasbender D, Yamba U, Keuk K, Hart T, Hart J, Furuichi T. Bonobo social organization at the seasonal forest‐savanna ecotone of the Lomami national park. Am J Primatol 2022; 84:e23448. [DOI: 10.1002/ajp.23448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 08/11/2022] [Accepted: 10/04/2022] [Indexed: 11/07/2022]
Affiliation(s)
- David Fasbender
- Department of Primatology and Wildlife Science, Graduate School of Science Kyoto University Inuyama Japan
| | - Uyulu Yamba
- Institut Congolais pour la Conservation de la Nature Kinshasa Democratic Republic of Congo
| | - Kenneth Keuk
- Department of Primatology and Wildlife Science, Graduate School of Science Kyoto University Inuyama Japan
| | - Terese Hart
- TL2 Project of the Frankfurt Zoological Society Kinshasa Democratic Republic of Congo
| | - John Hart
- TL2 Project of the Frankfurt Zoological Society Kinshasa Democratic Republic of Congo
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Gruber T. An ethical assessment of the use of old and new methods to study sociality in wild animals. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Thibaud Gruber
- Faculty of Psychology and Educational Sciences & Swiss Center for Affective Sciences University of Geneva Geneva Switzerland
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Principal Drivers and Conservation Solutions to the Impending Primate Extinction Crisis: Introduction to the Special Issue. INT J PRIMATOL 2022; 43:1-14. [PMID: 35194270 PMCID: PMC8853428 DOI: 10.1007/s10764-022-00283-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 01/24/2022] [Indexed: 12/20/2022]
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Darras KF, Pérez N, - M, Dilong L, Hanf-Dressler T, Markolf M, Wanger TC. ecoSound-web: an open-source, online platform for ecoacoustics. F1000Res 2020; 9:1224. [PMID: 33274051 PMCID: PMC7682500 DOI: 10.12688/f1000research.26369.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/10/2023] [Indexed: 03/04/2023] Open
Abstract
Passive acoustic monitoring of soundscapes and biodiversity produces vast amounts of audio recordings, but the management and analyses of these raw data present technical challenges. A multitude of software solutions exist, but none can fulfil all purposes required for the management, processing, navigation, analysis, and dissemination of acoustic data. The field of ecoacoustics needs a software tool that is free, evolving, and accessible. We take a step in that direction and present ecoSound-web: an open-source, online platform for ecoacoustics designed and built by ecologists and software engineers. ecoSound-web can be used for storing, organising, and sharing soundscape projects, manually creating and peer-reviewing annotations of soniferous animals and phonies, analysing audio in time and frequency, computing alpha acoustic indices, and providing reference sound libraries for different taxa. We present ecoSound-web's features, structure, and compare it with similar software. We describe its operation mode and the workflow for typical use cases such as the sampling of bird and bat communities, the use of a primate call library, and the analysis of phonies and acoustic indices. ecoSound-web is available from: https://github.com/ecomontec/ecoSound-web.
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Affiliation(s)
- Kevin F.A. Darras
- Computational Landscape Ecology, TU Dresden, Dresden, Sachsen, 01737, Germany
- Agroecology, University of Göttingen, Göttingen, Niedersachsen, 37077, Germany
- Sustainable Agricultural Systems & Engineering Laboratory, School of Engineering, Westlake University, Hangzhou, 310030, China
| | - Noemí Pérez
- Agroecology, University of Göttingen, Göttingen, Niedersachsen, 37077, Germany
| | - Mauladi -
- Department of Information Systems, Universitas Jambi, Jambi, Jambi, 36122, Indonesia
| | - Liu Dilong
- Quality Technology Centre, Nanjing Julong Steel Pipe Co., Ltd., Nanjing, 211800,, China
| | - Tara Hanf-Dressler
- Agroecology, University of Göttingen, Göttingen, Niedersachsen, 37077, Germany
| | - Matthias Markolf
- Behavioral Ecology & Sociobiology Unit, German Primate Centre,, Göttingen, Niedersachsen, 37077, Germany
| | - Thomas C Wanger
- Sustainable Agricultural Systems & Engineering Laboratory, School of Engineering, Westlake University, Hangzhou, 310030, China
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, Westlake University, Hangzhou, China
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