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      Collective and harmonized high throughput barcoding of insular arthropod biodiversity: Toward a Genomic Observatories Network for islands

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          Abstract

          Current understanding of ecological and evolutionary processes underlying island biodiversity is heavily shaped by empirical data from plants and birds, although arthropods comprise the overwhelming majority of known animal species, and as such can provide key insights into processes governing biodiversity. Novel high throughput sequencing (HTS) approaches are now emerging as powerful tools to overcome limitations in the availability of arthropod biodiversity data, and hence provide insights into these processes. Here, we explored how these tools might be most effectively exploited for comprehensive and comparable inventory and monitoring of insular arthropod biodiversity. We first reviewed the strengths, limitations and potential synergies among existing approaches of high throughput barcode sequencing. We considered how this could be complemented with deep learning approaches applied to image analysis to study arthropod biodiversity. We then explored how these approaches could be implemented within the framework of an island Genomic Observatories Network (iGON) for the advancement of fundamental and applied understanding of island biodiversity. To this end, we identified seven island biology themes at the interface of ecology, evolution and conservation biology, within which collective and harmonized efforts in HTS arthropod inventory could yield significant advances in island biodiversity research.

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          The FAIR Guiding Principles for scientific data management and stewardship

          There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.
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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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              More than 75 percent decline over 27 years in total flying insect biomass in protected areas

              Global declines in insects have sparked wide interest among scientists, politicians, and the general public. Loss of insect diversity and abundance is expected to provoke cascading effects on food webs and to jeopardize ecosystem services. Our understanding of the extent and underlying causes of this decline is based on the abundance of single species or taxonomic groups only, rather than changes in insect biomass which is more relevant for ecological functioning. Here, we used a standardized protocol to measure total insect biomass using Malaise traps, deployed over 27 years in 63 nature protection areas in Germany (96 unique location-year combinations) to infer on the status and trend of local entomofauna. Our analysis estimates a seasonal decline of 76%, and mid-summer decline of 82% in flying insect biomass over the 27 years of study. We show that this decline is apparent regardless of habitat type, while changes in weather, land use, and habitat characteristics cannot explain this overall decline. This yet unrecognized loss of insect biomass must be taken into account in evaluating declines in abundance of species depending on insects as a food source, and ecosystem functioning in the European landscape.
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                Author and article information

                Contributors
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                Journal
                Molecular Ecology
                Molecular Ecology
                Wiley
                0962-1083
                1365-294X
                December 2023
                September 25 2022
                December 2023
                : 32
                : 23
                : 6161-6176
                Affiliations
                [1 ] Island Ecology and Evolution Research Group Institute of Natural Products and Agrobiology (IPNA‐CSIC) San Cristóbal de la Laguna Spain
                [2 ] Centre for Ecology, Evolution and Environmental Changes (cE3c)/Azorean Biodiversity Group, Faculty of Agricultural Sciences and Environment, CHANGE – Global Change and Sustainability Institute University of the Azores Angra do Heroísmo Portugal
                [3 ] Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History Luomus University of Helsinki Helsinki Finland
                [4 ] British Antarctic Survey, NERC Cambridge UK
                [5 ] Department of Zoology University of Johannesburg Auckland Park South Africa
                [6 ] Centre for Biodiversity Genomics University of Guelph Guelph Canada
                [7 ] School of Environmental Sciences University of Guelph Guelph Canada
                [8 ] Biodiversity and Biocomplexity Unit Okinawa Institute of Science and Technology Graduate University Okinawa Japan
                [9 ] Radcliffe Institute for Advanced Study Harvard University Cambridge Massachusetts USA
                [10 ] Department of Environmental Science, Policy and Management University of California, Berkeley Berkeley California USA
                [11 ] Department of Biogeography Trier University Trier Germany
                [12 ] Center for Integrative Biodiversity Discovery Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde Berlin Germany
                [13 ] Department of Biological Sciences National University of Singapore Singapore City Singapore
                [14 ] UMR PVBMT, University of La Réunion Sainte‐Clotilde France
                [15 ] UMR 5174 EDB Laboratoire Évolution & Diversité Biologique Université Paul Sabatier Toulouse III, CNRS, IRD Toulouse France
                [16 ] Global Change Research Group Mediterranean Institut of Advanced Studies (CSIC‐UIB) Mallorca Spain
                [17 ] Department of Life Sciences Natural History Museum London UK
                [18 ] Department of Biological Sciences University of Cyprus Nicosia Cyprus
                [19 ] Département de Biologie, École normale supérieure, Institut de Biologie de l'ENS (IBENS) CNRS, INSERM, Université PSL Paris France
                [20 ] Department of Life Sciences Imperial College London London UK
                Article
                10.1111/mec.16683
                ad3194b0-c3fc-4e2f-9977-a98c1d0d0685
                © 2023

                http://creativecommons.org/licenses/by-nc/4.0/

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