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Wang X, Ma Z, Xing Y, Peng T, Dun X, He Z, Zhang J, Cheng X. Rapid species discrimination of similar insects using hyperspectral imaging and lightweight edge artificial intelligence. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240485. [PMID: 39086830 PMCID: PMC11288683 DOI: 10.1098/rsos.240485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 06/26/2024] [Indexed: 08/02/2024]
Abstract
Species discrimination of insects is an important aspect of ecology and biodiversity research. The traditional methods based on human visual experience and biochemical analysis cannot strike a balance between accuracy and timeliness. Morphological identification using computer vision and machine learning is expected to solve this problem, but image features have poor accuracy for very similar species and usually require complicated networks that are unfriendly to portable edge devices. In this work, we propose a fast and accurate species discrimination method of similar insects using hyperspectral features and lightweight machine learning algorithm. Feature regions selection, feature spectra selection and model quantification are used for the optimization of discriminating network. The experimental results of six similar butterfly species in the genus of Graphium show that, compared with morphological recognition with machine vision, our work achieves a higher accuracy of 92.36 ± 3.04% and a shorter inference time of 0.6 ms, with the tiny-size convolutional neural network deployed on a neural network chip. This study provides a rapid and high-accuracy species discrimination method for insects with high appearance similarity and paves the way for field discriminations using intelligent micro-spectrometer based on on-chip microstructure and artificial intelligence chip.
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Affiliation(s)
- Xuquan Wang
- MOE Key Laboratory of Advanced Micro-Structured Materials, Shanghai200092, People’s Republic of China
- Institute of Precision Optical Engineering, School of Physics Science and Engineering, Tongji University, Shanghai200092, People’s Republic of China
- Frontiers Science Center of Digital Optics, Shanghai200092, People’s Republic of China
| | - Zhiyuan Ma
- MOE Key Laboratory of Advanced Micro-Structured Materials, Shanghai200092, People’s Republic of China
- Institute of Precision Optical Engineering, School of Physics Science and Engineering, Tongji University, Shanghai200092, People’s Republic of China
- Frontiers Science Center of Digital Optics, Shanghai200092, People’s Republic of China
| | - Yujie Xing
- MOE Key Laboratory of Advanced Micro-Structured Materials, Shanghai200092, People’s Republic of China
- Institute of Precision Optical Engineering, School of Physics Science and Engineering, Tongji University, Shanghai200092, People’s Republic of China
- Frontiers Science Center of Digital Optics, Shanghai200092, People’s Republic of China
| | - Tianfan Peng
- MOE Key Laboratory of Advanced Micro-Structured Materials, Shanghai200092, People’s Republic of China
- Institute of Precision Optical Engineering, School of Physics Science and Engineering, Tongji University, Shanghai200092, People’s Republic of China
- Frontiers Science Center of Digital Optics, Shanghai200092, People’s Republic of China
| | - Xiong Dun
- MOE Key Laboratory of Advanced Micro-Structured Materials, Shanghai200092, People’s Republic of China
- Institute of Precision Optical Engineering, School of Physics Science and Engineering, Tongji University, Shanghai200092, People’s Republic of China
- Frontiers Science Center of Digital Optics, Shanghai200092, People’s Republic of China
| | - Zhuqing He
- East China Normal University, Shanghai200241, People’s Republic of China
| | - Jian Zhang
- East China Normal University, Shanghai200241, People’s Republic of China
| | - Xinbin Cheng
- MOE Key Laboratory of Advanced Micro-Structured Materials, Shanghai200092, People’s Republic of China
- Institute of Precision Optical Engineering, School of Physics Science and Engineering, Tongji University, Shanghai200092, People’s Republic of China
- Frontiers Science Center of Digital Optics, Shanghai200092, People’s Republic of China
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Chimeno C, Schmidt S, Hamid H, Narakusumo RP, Peggie D, Balke M, Cancian de Araujo B. DNA barcoding data release for the Phoridae (Insecta, Diptera) of the Halimun-Salak National Park (Java, Indonesia). Biodivers Data J 2023; 11:e104942. [PMID: 37448693 PMCID: PMC10336553 DOI: 10.3897/bdj.11.e104942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/02/2023] [Indexed: 07/15/2023] Open
Abstract
Launched in 2015, the large-scale initiative Indonesian Biodiversity Discovery and Information System (IndoBioSys) is a multidisciplinary German-Indonesian collaboration with the main goal of establishing a standardised framework for species discovery and all associated steps. One aspect of the project includes the application of DNA barcoding for species identification and biodiversity assessments. In this framework, we conducted a large-scale assessment of the insect fauna of the Mount Halimun-Salak National Park which is one of the largest tropical rain-forest ecosystems left in West Java. In this study, we present the results of processing 5,034 specimens of Phoridae (scuttle flies) via DNA barcoding. Despite limited sequencing success, we obtained more than 500 clusters using different algorithms (RESL, ASAP, SpeciesIdentifier). Moreover, Chao statistics indicated that we drastically undersampled all trap sites, implying that the true diversity of Phoridae is, in fact, much higher. With this data release, we hope to shed some light on the hidden diversity of this megadiverse group of flies.
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Affiliation(s)
- Caroline Chimeno
- SNSB-Zoologische Staatssammlung München, München, GermanySNSB-Zoologische Staatssammlung MünchenMünchenGermany
| | - Stefan Schmidt
- SNSB-Zoologische Staatssammlung München, München, GermanySNSB-Zoologische Staatssammlung MünchenMünchenGermany
| | - Hasmiandy Hamid
- Department of Plant Protection, Faculty of Agriculture, Universitas Andalas, Padang, IndonesiaDepartment of Plant Protection, Faculty of Agriculture, Universitas AndalasPadangIndonesia
| | - Raden Pramesa Narakusumo
- Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Cibinong, IndonesiaMuseum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN)CibinongIndonesia
| | - Djunijanti Peggie
- Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Cibinong, IndonesiaMuseum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN)CibinongIndonesia
| | - Michael Balke
- SNSB-Zoologische Staatssammlung München, München, GermanySNSB-Zoologische Staatssammlung MünchenMünchenGermany
| | - Bruno Cancian de Araujo
- SNSB-Zoologische Staatssammlung München, München, GermanySNSB-Zoologische Staatssammlung MünchenMünchenGermany
- LaBI-UFES, Laboratório de Biodiversidade de Insetos, Universidade Federal do Espírito Santo, Vitória, BrazilLaBI-UFES, Laboratório de Biodiversidade de Insetos, Universidade Federal do Espírito SantoVitóriaBrazil
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Arribas P, Andújar C, Bohmann K, deWaard JR, Economo EP, Elbrecht V, Geisen S, Goberna M, Krehenwinkel H, Novotny V, Zinger L, Creedy TJ, Meramveliotakis E, Noguerales V, Overcast I, Morlon H, Papadopoulou A, Vogler AP, Emerson BC. Toward global integration of biodiversity big data: a harmonized metabarcode data generation module for terrestrial arthropods. Gigascience 2022; 11:6646445. [PMID: 35852418 PMCID: PMC9295367 DOI: 10.1093/gigascience/giac065] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 05/04/2022] [Accepted: 06/02/2022] [Indexed: 11/12/2022] Open
Abstract
Metazoan metabarcoding is emerging as an essential strategy for inventorying biodiversity, with diverse projects currently generating massive quantities of community-level data. The potential for integrating across such data sets offers new opportunities to better understand biodiversity and how it might respond to global change. However, large-scale syntheses may be compromised if metabarcoding workflows differ from each other. There are ongoing efforts to improve standardization for the reporting of inventory data. However, harmonization at the stage of generating metabarcode data has yet to be addressed. A modular framework for harmonized data generation offers a pathway to navigate the complex structure of terrestrial metazoan biodiversity. Here, through our collective expertise as practitioners, method developers, and researchers leading metabarcoding initiatives to inventory terrestrial biodiversity, we seek to initiate a harmonized framework for metabarcode data generation, with a terrestrial arthropod module. We develop an initial set of submodules covering the 5 main steps of metabarcode data generation: (i) sample acquisition; (ii) sample processing; (iii) DNA extraction; (iv) polymerase chain reaction amplification, library preparation, and sequencing; and (v) DNA sequence and metadata deposition, providing a backbone for a terrestrial arthropod module. To achieve this, we (i) identified key points for harmonization, (ii) reviewed the current state of the art, and (iii) distilled existing knowledge within submodules, thus promoting best practice by providing guidelines and recommendations to reduce the universe of methodological options. We advocate the adoption and further development of the terrestrial arthropod module. We further encourage the development of modules for other biodiversity fractions as an essential step toward large-scale biodiversity synthesis through harmonization.
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Affiliation(s)
- Paula Arribas
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), 38206 San Cristóbal de la Laguna, Spain
| | - Carmelo Andújar
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), 38206 San Cristóbal de la Laguna, Spain
| | - Kristine Bohmann
- Section for Evolutionary Genomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Jeremy R deWaard
- Centre for Biodiversity Genomics, University of Guelph, N1G2W1 Guelph, Canada.,School of Environmental Sciences, University of Guelph, N1G2W1 Guelph, Canada
| | - Evan P Economo
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, 904-0495 Japan
| | - Vasco Elbrecht
- Centre for Biodiversity Monitoring (ZBM), Zoological Research Museum Alexander Koenig,D-53113 Bonn, Germany
| | - Stefan Geisen
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University and Research, 6708PB Wageningen, The Netherlands
| | - Marta Goberna
- Department of Environment and Agronomy, INIA-CSIC, 28040 Madrid, Spain
| | | | - Vojtech Novotny
- Biology Centre, Czech Academy of Sciences, Institute of Entomology, 37005 Ceske Budejovice, Czech Republic.,Faculty of Science, University of South Bohemia, 37005 Ceske Budejovice, Czech Republic
| | - Lucie Zinger
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France.,Naturalis Biodiversity Center, 2300 RA Leiden, The Netherlands
| | - Thomas J Creedy
- Department of Life Sciences, Natural History Museum, SW7 5BD London, UK
| | | | - Víctor Noguerales
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), 38206 San Cristóbal de la Laguna, Spain
| | - Isaac Overcast
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Hélène Morlon
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Anna Papadopoulou
- Department of Biological Sciences, University of Cyprus, 1678 Nicosia, Cyprus
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, SW7 5BD London, UK.,Department of Life Sciences, Imperial College London, SW7 2AZ London, UK
| | - Brent C Emerson
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), 38206 San Cristóbal de la Laguna, Spain
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Duwe V, Vu L, von Rintelen T, von Raab-Straube E, Schmidt S, Nguyen S, Vu T, Do T, Luu T, Truong V, Di Vincenzo V, Schmidt O, Glöckler F, Jahn R, Lücking R, von Oheimb K, von Oheimb P, Heinze S, Abarca N, Bollendorff S, Borsch T, Buenaventura E, Dang H, Dinh T, Do H, Ehlers S, Freyhof J, Hayden S, Hein P, Hoang T, Hoang D, Hoang S, Kürschner H, Kusber WH, Le H, Le T, Linde M, Mey W, Nguyen H, Nguyen M, Nguyen M, Nguyen D, Nguyen T, Nguyen V, Nguyen D, Ohl M, Parolly G, Pham T, Pham P, Rabe K, Schurian B, Skibbe O, Sulikowska-Drozd A, To Q, Truong T, Zimmermann J, Häuser C. Contributions to the biodiversity of Vietnam – Results of VIETBIO inventory work and field training in Cuc Phuong National Park. Biodivers Data J 2022; 10:e77025. [PMID: 35068979 PMCID: PMC8752577 DOI: 10.3897/bdj.10.e77025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/06/2021] [Indexed: 11/12/2022] Open
Abstract
VIETBIO [Innovative approaches to biodiversity discovery and characterisation in Vietnam] is a bilateral German-Vietnamese research and capacity building project focusing on the development and transfer of new methods and technology towards an integrated biodiversity discovery and monitoring system for Vietnam. Dedicated field training and testing of innovative methodologies were undertaken in Cuc Phuong National Park as part and with support of the project, which led to the new biodiversity data and records made available in this article collection. VIETBIO is a collaboration between the Museum für Naturkunde Berlin – Leibniz Institute for Evolution and Biodiversity Science (MfN), the Botanic Garden and Botanical Museum, Freie Universität Berlin (BGBM) and the Vietnam National Museum of Nature (VNMN), the Institute of Ecology and Biological Resources (IEBR), the Southern Institute of Ecology (SIE), as well as the Institute of Tropical Biology (ITB); all Vietnamese institutions belong to the Vietnam Academy of Science and Technology (VAST). The article collection "VIETBIO" (https://doi.org/10.3897/bdj.coll.63) reports original results of recent biodiversity recording and survey work undertaken in Cuc Phuong National Park, northern Vietnam, under the framework of the VIETBIO project. The collection consist of this “main” cover paper – characterising the study area, the general project approaches and activities, while also giving an extensive overview on previous studies from this area – followed by individual papers for higher taxa as studied during the project. The main purpose is to make primary biodiversity records openly available, including several new and interesting findings for this biodiversity-rich conservation area. All individual data papers with their respective primary records are expected to provide useful baselines for further taxonomic, phylogenetic, ecological and conservation-related studies on the respective taxa and, thus, will be maintained as separate datasets, including separate GUIDs also for further updating.
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Community Structure, Biodiversity and Spatiotemporal Distribution of the Black Flies (Diptera: Simuliidae) Using Malaise Traps on the Highest Mountain in Thailand. INSECTS 2021; 12:insects12060504. [PMID: 34072677 PMCID: PMC8229545 DOI: 10.3390/insects12060504] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 05/26/2021] [Indexed: 11/23/2022]
Abstract
Simple Summary Black flies, also known as buffalo gnats, are major pests to humans and animals. Females of some black fly species serve as vectors for transmitting several pathogens (i.e., filarial nematodes, blood protozoa, viruses, and bacteria) to humans and animals via their bites. In Thailand, some human-biting species are considered as natural vectors of zoonotic onchocerciasis. This study was the first to contribute baseline data on the community structure, biodiversity and spatial and temporal distribution of adult black flies in tropical forests of the highest mountain in northern Thailand, Doi Inthanon National Park, by using malaise traps. Adult black flies were captured monthly at low to high elevation sites, using malaise traps across three seasons during a one-year period. A total of 44 species were identified among 9406 specimens. It was found that species richness was greatest at the mid elevation. Black fly populations peaked in the rainy season at all elevation sites. The findings of this study showed that varied elevations and seasons are important factors that influence the distribution and abundance of black flies in this region. Abstract Black flies form a group of small blood-sucking insects of medical and veterinary importance. This study aimed to investigate the community structure, biodiversity and spatial and temporal distribution of adult black flies in tropical rain forests, by using malaise traps in Doi Inthanon National Park, northern Thailand. Malaise traps were placed along six elevational gradients (400 m to 2500 m, above sea level) at Doi Inthanon National Park, Chiang Mai province, from December 2013 to November 2014. A total of 9406 adult female black flies belonging to five subgenera—Daviesellum (2%), Gomphostilbia (23%), Montisimulium (11%), Nevermannia (16%) and Simulium (48%)—were collected. Among 44 taxa found, S. tenebrosum complex had the highest relative abundance (11.1%), followed by the S. asakoae species-group (9.6%), the S. striatum species-group (7.7%), S. inthanonense (6.6%), S. doipuiense complex (6.4%), S. chomthongense complex (5.3%), S. chumpornense (5.1%) and S. nigrogilvum (4.1%). Two human-biting species—S. nigrogilvum and species in the S. asakoae species-group—were found in all of the collection sites with 100% species occurrence. Species richness was highest at mid elevation (1400 m), which is represented by 19 black fly species. The peak and lowest seasonal abundance was observed in the rainy and hot season, respectively. Seasonal species richness was highest in the cold season, except for that from elevation sites at 700 m, 1700 m and 2500 m. This study revealed that the malaise trap is effective in providing important data for further monitoring of the effects of environmental changes and conservation planning on the biodiversity of black flies in Doi Inthanon National Park.
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Montgomery GA, Belitz MW, Guralnick RP, Tingley MW. Standards and Best Practices for Monitoring and Benchmarking Insects. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2020.579193] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Benchmark studies of insect populations are increasingly relevant and needed amid accelerating concern about insect trends in the Anthropocene. The growing recognition that insect populations may be in decline has given rise to a renewed call for insect population monitoring by scientists, and a desire from the broader public to participate in insect surveys. However, due to the immense diversity of insects and a vast assortment of data collection methods, there is a general lack of standardization in insect monitoring methods, such that a sudden and unplanned expansion of data collection may fail to meet its ecological potential or conservation needs without a coordinated focus on standards and best practices. To begin to address this problem, we provide simple guidelines for maximizing return on proven inventory methods that will provide insect benchmarking data suitable for a variety of ecological responses, including occurrence and distribution, phenology, abundance and biomass, and diversity and species composition. To track these responses, we present seven primary insect sampling methods—malaise trapping, light trapping, pan trapping, pitfall trappings, beating sheets, acoustic monitoring, and active visual surveys—and recommend standards while highlighting examples of model programs. For each method, we discuss key topics such as recommended spatial and temporal scales of sampling, important metadata to track, and degree of replication needed to produce rigorous estimates of ecological responses. We additionally suggest protocols for scalable insect monitoring, from backyards to national parks. Overall, we aim to compile a resource that can be used by diverse individuals and organizations seeking to initiate or improve insect monitoring programs in this era of rapid change.
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