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      Genetic identification of bat species for pathogen surveillance across France

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          Abstract

          With more than 1400 chiropteran species identified to date, bats comprise one-fifth of all mammalian species worldwide. Many studies have associated viral zoonoses with 45 different species of bats in the EU, which cluster within 5 families of bats. For example, the Serotine bats are infected by European Bat 1 Lyssavirus throughout Europe while Myotis bats are shown infected by coronavirus, herpesvirus and paramyxovirus. Correct host species identification is important to increase our knowledge of the ecology and evolutionary pattern of bat viruses in the EU. Bat species identification is commonly determined using morphological keys. Morphological determination of bat species from bat carcasses can be limited in some cases, due to the state of decomposition or nearly indistinguishable morphological features in juvenile bats and can lead to misidentifications. The overall objective of our study was to identify insectivorous bat species using molecular biology tools with the amplification of the partial cytochrome b gene of mitochondrial DNA. Two types of samples were tested in this study, bat wing punches and bat faeces. A total of 163 bat wing punches representing 22 species, and 31 faecal pellets representing 7 species were included in the study. From the 163 bat wing punches tested, a total of 159 were genetically identified from amplification of the partial cyt b gene. All 31 faecal pellets were genetically identified based on the cyt b gene. A comparison between morphological and genetic determination showed 21 misidentifications from the 163 wing punches, representing ~12.5% of misidentifications of morphological determination compared with the genetic method, across 11 species. In addition, genetic determination allowed the identification of 24 out of 25 morphologically non-determined bat samples. Our findings demonstrate the importance of a genetic approach as an efficient and reliable method to identify bat species precisely.

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          Animal mitochondrial genomes.

          Animal mitochondrial DNA is a small, extrachromosomal genome, typically approximately 16 kb in size. With few exceptions, all animal mitochondrial genomes contain the same 37 genes: two for rRNAs, 13 for proteins and 22 for tRNAs. The products of these genes, along with RNAs and proteins imported from the cytoplasm, endow mitochondria with their own systems for DNA replication, transcription, mRNA processing and translation of proteins. The study of these genomes as they function in mitochondrial systems-'mitochondrial genomics'-serves as a model for genome evolution. Furthermore, the comparison of animal mitochondrial gene arrangements has become a very powerful means for inferring ancient evolutionary relationships, since rearrangements appear to be unique, generally rare events that are unlikely to arise independently in separate evolutionary lineages. Complete mitochondrial gene arrangements have been published for 58 chordate species and 29 non-chordate species, and partial arrangements for hundreds of other taxa. This review compares and summarizes these gene arrangements and points out some of the questions that may be addressed by comparing mitochondrial systems.
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            Noninvasive genetic sampling: look before you leap.

            Noninvasive sampling allows genetic studies of free-ranging animals without the need to capture or even observe them, and thus allows questions to be addressed that cannot be answered using conventional methods. Initially, this sampling strategy promised to exploit fully the existing DNA-based technology for studies in ethology, conservation biology and population genetics. However, recent work now indicates the need for a more cautious approach, which includes quantifying the genotyping error rate. Despite this, many of the difficulties of noninvasive sampling will probably be overcome with improved methodology.
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              Geometric morphometrics: Ten years of progress following the ‘revolution’

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                Author and article information

                Contributors
                Role: Formal analysisRole: InvestigationRole: MethodologyRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: Project administrationRole: SupervisionRole: ValidationRole: Writing – original draftRole: Writing – review & editing
                Role: Formal analysisRole: ValidationRole: Writing – original draftRole: Writing – review & editing
                Role: Formal analysisRole: ValidationRole: Writing – original draftRole: Writing – review & editing
                Role: ValidationRole: Writing – original draftRole: Writing – review & editing
                Role: ValidationRole: Writing – original draftRole: Writing – review & editing
                Role: ValidationRole: Writing – original draftRole: Writing – review & editing
                Role: ValidationRole: Writing – original draftRole: Writing – review & editing
                Role: ValidationRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: InvestigationRole: MethodologyRole: SupervisionRole: ValidationRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS One
                plos
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                4 January 2022
                2022
                : 17
                : 1
                : e0261344
                Affiliations
                [1 ] ANSES-Nancy Laboratory for Rabies and Wildlife, WHO Collaborating Centre for Research and Management in Zoonoses Control, OIE Reference Laboratory for Rabies, European Union Reference Laboratory for Rabies, European Union Reference Laboratory for Rabies Serology, Malzéville, France
                [2 ] VetAgro Sup Lyon Laboratory for Leptospira, Marcy l’Etoile, France
                [3 ] UMR ASTRE, CIRAD, INRAE, Université de Montpellier, Montpellier, France
                [4 ] UMR EPIA, INRAE, VetAgro Sup, Theix, France
                [5 ] School of Biology and Environmental Science, Science Centre West, University College Dublin, Dublin, Ireland
                [6 ] CPEPESC Lorraine, Neuves-Maisons, France
                [7 ] GEPMA, Strasbourg, France
                [8 ] LPO Alsace, Rosenwiller, France
                University of Oklahoma Norman Campus: The University of Oklahoma, UNITED STATES
                Author notes

                Competing Interests: No authors have competing interests.

                Author information
                https://orcid.org/0000-0002-0214-4716
                https://orcid.org/0000-0001-7668-1971
                https://orcid.org/0000-0001-9122-9027
                Article
                PONE-D-21-14577
                10.1371/journal.pone.0261344
                8726466
                34982782
                039257a2-ad71-4a58-a5ae-b55cd51ab7b3
                © 2022 Arnaout et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 5 May 2021
                : 1 December 2021
                Page count
                Figures: 1, Tables: 6, Pages: 16
                Funding
                Funded by: French National Agency for Food, Environmental and Occupational Health & Safety
                Funded by: VetAgro Sup laboratory for Leptospira
                This work was supported by the French National Agency for Food, Environmental and Occupational Health & Safety and VetAgro Sup laboratory for Leptospira.
                Categories
                Research Article
                Biology and Life Sciences
                Organisms
                Eukaryota
                Animals
                Vertebrates
                Amniotes
                Mammals
                Bats
                Biology and Life Sciences
                Zoology
                Animals
                Vertebrates
                Amniotes
                Mammals
                Bats
                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Artificial Gene Amplification and Extension
                Polymerase Chain Reaction
                Research and Analysis Methods
                Molecular Biology Techniques
                Artificial Gene Amplification and Extension
                Polymerase Chain Reaction
                Biology and Life Sciences
                Organisms
                Eukaryota
                Animals
                Vertebrates
                Amniotes
                Mammals
                Bats
                Fruit Bats
                Biology and Life Sciences
                Zoology
                Animals
                Vertebrates
                Amniotes
                Mammals
                Bats
                Fruit Bats
                Biology and Life Sciences
                Anatomy
                Animal Anatomy
                Animal Wings
                Medicine and Health Sciences
                Anatomy
                Animal Anatomy
                Animal Wings
                Biology and Life Sciences
                Zoology
                Animal Anatomy
                Animal Wings
                Biology and Life Sciences
                Genetics
                Research and analysis methods
                Database and informatics methods
                Bioinformatics
                Sequence analysis
                BLAST algorithm
                People and places
                Geographical locations
                Europe
                European Union
                France
                Biology and Life Sciences
                Genetics
                Heredity
                Genetic Determinism
                Custom metadata
                All files are available from the Genbank database (accession number(s) MZ066766 to MZ066790). All relevant data are within the manuscript and its Supporting information files.

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