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Meier R, Hartop E, Pylatiuk C, Srivathsan A. Towards holistic insect monitoring: species discovery, description, identification and traits for all insects. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230120. [PMID: 38705187 PMCID: PMC11070263 DOI: 10.1098/rstb.2023.0120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 01/25/2024] [Indexed: 05/07/2024] Open
Abstract
Holistic insect monitoring needs scalable techniques to overcome taxon biases, determine species abundances, and gather functional traits for all species. This requires that we address taxonomic impediments and the paucity of data on abundance, biomass and functional traits. We here outline how these data deficiencies could be addressed at scale. The workflow starts with large-scale barcoding (megabarcoding) of all specimens from mass samples obtained at biomonitoring sites. The barcodes are then used to group the specimens into molecular operational taxonomic units that are subsequently tested/validated as species with a second data source (e.g. morphology). New species are described using barcodes, images and short diagnoses, and abundance data are collected for both new and described species. The specimen images used for species discovery then become the raw material for training artificial intelligence identification algorithms and collecting trait data such as body size, biomass and feeding modes. Additional trait data can be obtained from vouchers by using genomic tools developed by molecular ecologists. Applying this pipeline to a few samples per site will lead to greatly improved insect monitoring regardless of whether the species composition of a sample is determined with images, metabarcoding or megabarcoding. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.
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Affiliation(s)
- Rudolf Meier
- Center for Integrative Biodiversity Discovery, Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
- Institute of Biology, Humboldt University, 10115 Berlin, Germany
| | - Emily Hartop
- Center for Integrative Biodiversity Discovery, Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, NO-7491, Norway
| | - Christian Pylatiuk
- Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Amrita Srivathsan
- Center for Integrative Biodiversity Discovery, Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
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Srivathsan A, Loh RK, Ong EJ, Lee L, Ang Y, Kutty SN, Meier R. Network analysis with either Illumina or MinION reveals that detecting vertebrate species requires metabarcoding of iDNA from a diverse fly community. Mol Ecol 2023; 32:6418-6435. [PMID: 36326295 DOI: 10.1111/mec.16767] [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: 02/16/2022] [Revised: 10/25/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
Abstract
DNA obtained from invertebrates (iDNA) can be metabarcoded in order to survey vertebrate communities. However, little attention has been paid to the interaction between the invertebrate and vertebrate species. Here, we tested for specialization by sampling the dung and carrion fly community of a swamp forest remnant along a disturbance gradient (10 sites: 80-310 m from a road). Approximately, 60% of the baited 407 flies yielded 294 vertebrate identifications based on two COI fragments and 16S. A bipartite network analysis found no statistically significant specialization in the interactions between fly and vertebrate species, but uncommon fly species can carry the signal for vertebrate species that are otherwise difficult to detect with iDNA. A spatial analysis revealed that most of the 20 vertebrate species reported in this study could be detected within 150 m of the road (18 spp.) and that the fly community sourced for iDNA was unexpectedly rich (24 species, 3 families). They carried DNA for rare and common species inhabiting different layers of the forest (ground-dwelling: wild boar, Sunda pangolin, skinks, rats; arboreal: long-tailed macaque, Raffles' banded langur; flying: pin-striped tit-babbler, olive-winged bulbul). All our results were obtained with a new, greatly simplified iDNA protocol that eliminates DNA extraction by obtaining template directly through dissolving fly faeces and regurgitates with water. Lastly, we show that MinION- and Illumina-based metabarcoding yield similar results. We conclude by urging more studies that use different baits and involve experiments that are capable of revealing the dispersal capabilities of the flies carrying the iDNA.
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Affiliation(s)
- Amrita Srivathsan
- Centre for Integrative Biodiversity Discovery, Museum für Naturkunde, Berlin, Germany
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Rebecca Ker Loh
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Elliott James Ong
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Leshon Lee
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Yuchen Ang
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore, Singapore
| | | | - Rudolf Meier
- Centre for Integrative Biodiversity Discovery, Museum für Naturkunde, Berlin, Germany
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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Mancuso CJ, Ehleringer JR, Newsome SD. Examination of amino acid hydrogen isotope measurements of scalp hair for region-of-origin studies. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023; 37:e9442. [PMID: 36411248 PMCID: PMC10518903 DOI: 10.1002/rcm.9442] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/18/2022] [Accepted: 11/19/2022] [Indexed: 06/16/2023]
Abstract
RATIONALE Hydrogen isotope (δ2 H) analysis of keratinaceous bulk tissues has been used in forensic science to reconstruct an individual's travel history or determine their region-of-origin. Here, we use a compound-specific approach to examine patterns of individual amino acid δ2 H values in relation to those of local tap water, bulk scalp hair tissues, and region-of-origin. METHODS We measured δ2 H values of amino acids in anonymously collected scalp hair (n = 67) and tap water from 28 locations in the United States. Samples were hydrolyzed into their constituent amino acids, derivatized alongside in-house reference materials, and analyzed in triplicate using a GC-C-IRMS system. RESULTS Non-essential amino acid (AANESS ) δ2 H values and their corresponding tap water samples varied systematically across continental regions. Hydrogen isotope values of alanine, glutamic acid, and glycine were significantly correlated with tap water and an estimated 42%-51% of the hydrogen atoms in these AANESS were derived from tap water. We used linear discriminate analysis (LDA) to explore regional patterns in scalp hair bulk tissue and amino acid δ2 H values. For the model that included AANESS data, 87% of the variance was explained by the first linear discriminant axis (LD1), and was driven by bulk hair tissue, alanine, and proline. This model had an overall 72% successful reclassification with samples from the south and northwest regions reclassifying correctly 92% and 78% of the time, respectively. For the model that included AAESS data, LD1 explained 81% of the variation and was driven bulk hair, threonine, valine, phenylalanine, and isoleucine. The overall reclassification rate for the model that included AAESS was 70%. CONCLUSIONS Our findings suggest that δ2 H analyses of AANESS and AAESS could help improve geolocation models for human and wildlife forensics by simultaneously providing information about both dietary and tap water inputs of hydrogen to tissue synthesis.
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Affiliation(s)
| | | | - Seth D. Newsome
- University of New Mexico, Department of Biology, Albuquerque, NM 87131
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Butler-Valverde MJ, DeVault TL, Rhodes OE, Beasley JC. Carcass appearance does not influence scavenger avoidance of carnivore carrion. Sci Rep 2022; 12:18842. [PMID: 36344611 PMCID: PMC9640519 DOI: 10.1038/s41598-022-22297-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 10/12/2022] [Indexed: 11/09/2022] Open
Abstract
The selection or avoidance of certain carrion resources by vertebrate scavengers can alter the flow of nutrients in ecosystems. Evidence suggests higher trophic level carrion is scavenged by fewer vertebrate species and persists longer when compared to lower trophic level carrion, although it is unclear how scavengers distinguish between carcasses of varying species. To investigate carnivore carrion avoidance and explore sensory recognition mechanisms in scavenging species, we investigated scavenger use of intact and altered (i.e., skin, head, and feet removed) coyote-Canis latrans (carnivore) and wild pig-Sus scrofa (omnivore) carcasses experimentally placed at the Savannah River Site, SC, USA. We predicted carnivore carcasses would persist longer due to conspecific and intraguild scavenger avoidance. Further, we hypothesized visually modifying carcasses would not reduce avoidance of carnivore carrion, given scavengers likely depend largely on chemical cues when assessing carrion resources. As expected, mammalian carnivores largely avoided scavenging on coyote carcasses, resulting in carnivore carcasses having longer depletion times than wild pig carcasses at intact and altered trials. Therefore, nutrients derived from carnivore carcasses are not as readily incorporated into higher trophic levels and scavengers largely depend on olfactory cues when assessing benefits and risks associated with varying carrion resources.
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Affiliation(s)
- Miranda J. Butler-Valverde
- grid.213876.90000 0004 1936 738XSavannah River Ecology Laboratory, Warnell School of Forestry and Natural Resources, University of Georgia, P.O. Box Drawer E, Aiken, SC 29802 USA
| | - Travis L. DeVault
- grid.213876.90000 0004 1936 738XSavannah River Ecology Laboratory, Warnell School of Forestry and Natural Resources, University of Georgia, P.O. Box Drawer E, Aiken, SC 29802 USA
| | - Olin E. Rhodes
- grid.213876.90000 0004 1936 738XSavannah River Ecology Lab, University of Georgia, P.O. Box Drawer E, Aiken, SC 29802 USA
| | - James C. Beasley
- grid.213876.90000 0004 1936 738XSavannah River Ecology Laboratory, Warnell School of Forestry and Natural Resources, University of Georgia, P.O. Box Drawer E, Aiken, SC 29802 USA
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Butler-Valverde MJ, DeVault TL, Beasley JC. Trophic interactions at avian carcasses: Do scavengers feed on vulture carrion? FOOD WEBS 2022. [DOI: 10.1016/j.fooweb.2022.e00230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Dowling SN, Skaggs CL, Owings CG, Moctar K, Picard CJ, Manicke NE. Insects as Chemical Sensors: Detection of Chemical Warfare Agent Simulants and Hydrolysis Products in the Blow Fly Using LC-MS/MS. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:3535-3543. [PMID: 35188758 DOI: 10.1021/acs.est.1c07381] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In this work, blow flies were investigated as environmental chemical sample collectors following a chemical warfare attack (CWA). Blow flies sample the environment as they search for water and food sources and can be trapped from kilometers away using baited traps. Three species of blow flies were exposed to CWA simulants to determine the persistence and detectability of these compounds under varying environmental conditions. A liquid chromatography mass spectrometry (LC-MS/MS) method was developed to detect CWA simulants and hydrolysis products from fly guts. Flies were exposed to the CWA simulants dimethyl methylphosphonate and diethyl phosphoramidate as well as the pesticide dichlorvos, followed by treatment-dependent temperature and humidity conditions. Flies were sacrificed at intervals within a 14 day postexposure period. Fly guts were extracted and analyzed with the LC-MS/MS method. The amount of CWA simulant in fly guts decreased with time following exposure but were detectable 14 days following exposure, giving a long window of detectability. In addition to the analysis of CWA simulants, isopropyl methylphosphonic acid, the hydrolysis product of sarin, was also detected in blow flies 14 days post exposure. This work demonstrates the potential to obtain valuable samples from remote or access-restricted areas without risking lives.
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Affiliation(s)
- Sarah N Dowling
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Christine L Skaggs
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Charity G Owings
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
- Department of Anthropology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Khadija Moctar
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Christine J Picard
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Nicholas E Manicke
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
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