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      Combining environmental DNA and remote sensing for efficient, fine-scale mapping of arthropod biodiversity

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          Abstract

          Arthropods contribute importantly to ecosystem functioning but remain understudied. This undermines the validity of conservation decisions. Modern methods are now making arthropods easier to study, since arthropods can be mass-trapped, mass-identified, and semi-mass-quantified into ‘many-row (observation), many-column (species)‘ datasets, with homogeneous error, high resolution, and copious environmental-covariate information. These ‘novel community datasets’ let us efficiently generate information on arthropod species distributions, conservation values, uncertainty, and the magnitude and direction of human impacts. We use a DNA-based method (barcode mapping) to produce an arthropod-community dataset from 121 Malaise-trap samples, and combine it with 29 remote-imagery layers using a deep neural net in a joint species distribution model. With this approach, we generate distribution maps for 76 arthropod species across a 225 km 2 temperate-zone forested landscape. We combine the maps to visualize the fine-scale spatial distributions of species richness, community composition, and site irreplaceability. Old-growth forests show distinct community composition and higher species richness, and stream courses have the highest site-irreplaceability values. With this ‘sideways biodiversity modelling’ method, we demonstrate the feasibility of biodiversity mapping at sufficient spatial resolution to inform local management choices, while also being efficient enough to scale up to thousands of square kilometres.

          This article is part of the theme issue ‘Towards a toolkit for global insect biodiversity monitoring’.

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          Biological identifications through DNA barcodes.

          Although much biological research depends upon species diagnoses, taxonomic expertise is collapsing. We are convinced that the sole prospect for a sustainable identification capability lies in the construction of systems that employ DNA sequences as taxon 'barcodes'. We establish that the mitochondrial gene cytochrome c oxidase I (COI) can serve as the core of a global bioidentification system for animals. First, we demonstrate that COI profiles, derived from the low-density sampling of higher taxonomic categories, ordinarily assign newly analysed taxa to the appropriate phylum or order. Second, we demonstrate that species-level assignments can be obtained by creating comprehensive COI profiles. A model COI profile, based upon the analysis of a single individual from each of 200 closely allied species of lepidopterans, was 100% successful in correctly identifying subsequent specimens. When fully developed, a COI identification system will provide a reliable, cost-effective and accessible solution to the current problem of species identification. Its assembly will also generate important new insights into the diversification of life and the rules of molecular evolution.
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            The struggle to govern the commons.

            Human institutions--ways of organizing activities--affect the resilience of the environment. Locally evolved institutional arrangements governed by stable communities and buffered from outside forces have sustained resources successfully for centuries, although they often fail when rapid change occurs. Ideal conditions for governance are increasingly rare. Critical problems, such as transboundary pollution, tropical deforestation, and climate change, are at larger scales and involve nonlocal influences. Promising strategies for addressing these problems include dialogue among interested parties, officials, and scientists; complex, redundant, and layered institutions; a mix of institutional types; and designs that facilitate experimentation, learning, and change.
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              Environmental DNA for wildlife biology and biodiversity monitoring.

              Extraction and identification of DNA from an environmental sample has proven noteworthy recently in detecting and monitoring not only common species, but also those that are endangered, invasive, or elusive. Particular attributes of so-called environmental DNA (eDNA) analysis render it a potent tool for elucidating mechanistic insights in ecological and evolutionary processes. Foremost among these is an improved ability to explore ecosystem-level processes, the generation of quantitative indices for analyses of species, community diversity, and dynamics, and novel opportunities through the use of time-serial samples and unprecedented sensitivity for detecting rare or difficult-to-sample taxa. Although technical challenges remain, here we examine the current frontiers of eDNA, outline key aspects requiring improvement, and suggest future developments and innovations for research. Copyright © 2014 Elsevier Ltd. All rights reserved.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: InvestigationRole: MethodologyRole: Project administrationRole: Writing – review & editing
                Role: InvestigationRole: MethodologyRole: Writing – review & editing
                Role: Project administrationRole: ResourcesRole: SupervisionRole: Writing – review & editing
                Role: Project administrationRole: ResourcesRole: SupervisionRole: Writing – review & editing
                Role: Software
                Role: MethodologyRole: SoftwareRole: ValidationRole: VisualizationRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: ValidationRole: VisualizationRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: ValidationRole: Writing – original draftRole: Writing – review & editing
                Journal
                Philos Trans R Soc Lond B Biol Sci
                Philos Trans R Soc Lond B Biol Sci
                RSTB
                royptb
                Philosophical Transactions of the Royal Society B: Biological Sciences
                The Royal Society
                0962-8436
                1471-2970
                June 24, 2024
                May 6, 2024
                May 6, 2024
                : 379
                : 1904 , Theme issue ‘Towards a toolkit for global insect biodiversity monitoring’ compiled and edited by Roel van Klink, Julie K. Sheard, Toke T. Høye, Tomas Roslin, Leandro A. Do Nascimento and Silke Bauer
                : 20230123
                Affiliations
                [ 1 ] Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, State Key Laboratory of Genetic Resources and Evolution, Chinese Academy of Sciences, , Kunming, Yunnan 650223, People’s Republic of China
                [ 2 ] Kunming Institute of Zoology, Chinese Academy of Sciences, , Kunming, Yunnan 650223, People’s Republic of China
                [ 3 ] Faculty of Biology, University of Duisburg-Essen, , Essen 45141, Germany
                [ 4 ] School of Biological Sciences, University of East Anglia, , Norwich Research Park, Norwich, Norfolk NR47TJ, UK
                [ 5 ] Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, , Corvallis, OR 97331, USA
                [ 6 ] Kunming College of Life Sciences, University of Chinese Academy of Sciences, , Kunming, People’s Republic of China
                [ 7 ] Pacific Northwest Research Station, U.S. Department of Agriculture Forest Service, , Corvallis, OR 97331, USA
                [ 8 ] CSIRO Energy, Lindfield, New South Wales, Australia,
                [ 9 ] School of Biological Sciences, Macquarie University, , Sydney, Australia
                [ 10 ] Theoretical Ecology, University of Regensburg, , Regensburg, Germany
                [ 11 ] Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, , Kunming Yunnan 650223, People’s Republic of China
                Author notes

                One contribution of 23 to a theme issue ‘ Towards a toolkit for global insect biodiversity monitoring’.

                Current address: School of Geography, Geology and the Environment, Keele University, Staffordshire, ST5 5BG, UK.

                Co-first authors.

                Electronic supplementary material is available online at https://doi.org/10.6084/m9.figshare.c.7151335.

                Author information
                http://orcid.org/0000-0002-9020-5098
                http://orcid.org/0000-0001-8551-5609
                Article
                rstb20230123
                10.1098/rstb.2023.0123
                11070265
                38705177
                02030f90-77be-425b-bfc2-038f75668f1b
                © 2024 The Authors.

                Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.

                History
                : August 31, 2023
                : January 31, 2024
                Funding
                Funded by: ARCS Oregon Chapter;
                Funded by: State Key Laboratory of Genetic Resources and Evolution, http://dx.doi.org/10.13039/501100011239;
                Award ID: GREKF19-01, GREKF20-01, GREKF21-01
                Funded by: National Science Foundation LTER;
                Award ID: DEB-1440409, DEB-2025755
                Funded by: sDiv Synthesis Centre;
                Award ID: https://www.idiv.de/en/scom.html
                Funded by: U.S. Department of Agriculture Forest Service;
                Funded by: Key Research Program of Frontier Sciences, CAS;
                Award ID: QYZDY-SSW-SMC024
                Funded by: Leverhulme Trust, http://dx.doi.org/10.13039/501100000275;
                Award ID: RF-2017-342
                Funded by: Strategic Priority Research Program, CAS;
                Award ID: XDA20050202
                Funded by: Pacific Northwest Research Station, http://dx.doi.org/10.13039/100013393;
                Categories
                1001
                60
                69
                Articles
                Research Articles
                Custom metadata
                June 24, 2024

                Philosophy of science
                environmental dna,earth observation,biodiversity indices,systematic conservation planning,forestry,machine learning

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