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2,573 results on '"Centre de Biologie pour la Gestion des Populations (UMR CBGP)"'

1. Flat mites (Tenuipalpidae) from Bahia state, Northeastern Brazil - a checklist including new records and an illustrated key to species

Author: Renata S. Nascimento, Kaélem S. Souza, Elisangela A. S. F. Melo, Aline D. Tassi, Elizeu B. Castro, Denise Navia, Renata S. de Mendonça, Ronald Ochoa, Anibal R. Oliveira, Universidade Estadual De Santa Cruz [Brazil] (UESC), University of Florida [Gainesville] (UF), Universidade Estadual Paulista Júlio de Mesquita Filho = São Paulo State University (UNESP), Departamento de Zoologia e Botânica, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), University of Brasilia [Brazil] (UnB), Faculdade de Agronomia e Medicina Veterinária, Universidade de Brasilia [Brasília] (UnB), USDA Agricultural Research Service [Beltsville, Maryland], USDA-ARS : Agricultural Research Service, ARS - Systematic Entomology Laboratory, USDA-ARS : Agricultural Research Service-USDA-ARS : Agricultural Research Service-United States Department of Agriculture, and We thank the 'Coordenação de Aperfeiçoamento de Pessoal de Nível Superior' (CAPES) for the fellowships to RSN (Finance Code 001), and RSM (PNPD/Agronomy Proc. 88882.305808/2018-1), the 'Fundação de Amparo à Pesquisa do Estado de São Paulo' (FAPESP) for the research grant to ADT (Proc. 2018/12252-8 and 2019/25078-9), and UESC, ESALQ, UNESP and USDA for the support.
Subjects: false spider mites, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Brevipalpus, Insect Science, diagnostics, plant viruses, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Taxonomy, diversity
Abstract: International audience; Tenuipalpidae (Trombidiformes: Tetranychoidea) is an economically important family of plant-feeding mites. The family has approximately 1,100 described species in 41 genera with worldwide distribution. Currently, 40 species of Tenuipalpidae have been recorded from Brazil, and prior to this study only 11 were known from Bahia state. Five new species records are presented here for Bahia, making a total of 16 species now known from the state. Brevipalpus is considered the most important genus due to their association with, and ability to transmit, devastating plant viruses. Some diseases caused by viruses transmitted by Brevipalpus mites (VTBs) have already been recorded in the state of Bahia, such as the Passion fruit green spot virus and citrus leprosis. This paper presents a checklist of tenuipalpids reported from the state of Bahia in Brazil, including new records and an illustrated identification key to the species.
Published: 2023

2. Homage to Dr Jean Gutierrez (1936-2023)

Author: Alain Migeon, Maria Navajas, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM)
Subjects: [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Insect Science, Obituary
Abstract: International audience; On January 21, the scientific community, and more particularly that of acarologists and agricultural entomologists, learned with sadness the death of Jean Gutierrez, one of their renowned colleagues.
Published: 2023

3. Unexpected and spatially structured genetic diversity of the relict population of the endangered corsican land snail Tyrrhenaria ceratina

Author: Camus, Louise, Poli, Pedro, Delaugerre, Michel-Jean, Dréano, Stéphane, Cucherat, Xavier, Natali, Christine, Guiller, Annie, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Ecologie et Dynamique des Systèmes Anthropisés - UMR CNRS 7058 (EDYSAN), Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), Conservatoire du Littoral, Ministère de l'Ecologie, Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Bureau d’étude en ingénierie conseil et recherche en environnement, Centre Permanent d’Initiatives pour l’Environnement Ajaccio (CPIE Ajaccio), and This work was supported by the Direction Régionale de l’Environnement de l’Aménagement et du Logement (DREAL) de Corse, and by the Conservatoire du Littoral.
Subjects: [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Population genetics, Conservation biology, Isolation by distance, [SDE]Environmental Sciences, Genetics, Habitat fragmentation, Genetic connectivity, Ecology, Evolution, Behavior and Systematics
Abstract: We thank all the volunteers who realized the sample collection, especially the team of the Centre Permanent d’Initiatives pour l’Environnement d’Ajaccio mobilized for the project “Aio lumacchi, Allez les escargots” funded by Office Français de la Biodiversité and the wardens of the Collectivité Territoriale de Corse. We also thank DREAL Corse for funding support. Handling and sampling of this protected species were performed under permits: Arrêtés préfectoraux 2 A 2018-01-29-001, 2 A 2020-03-25-001 and 2 A-2021-02-25-003.; International audience; Population genetics of threatened species provides information about evolutionary pressures over those populations and thus may inform conservation management strategies. However, conservation genetics still has a low impact on conservation practices. This study's aim is to integrate genetics in the conservation management of the only-known population of an extremely narrow-range endemic Corsican snail-Tyrrhenaria ceratina-, whose distribution area is restricted to the Ricantu site in Corsica. Using non-invasive DNA samples of 210 individuals, we amplified 13 microsatellites loci to assess the population viability, genetic structure and demographic history of the population, along with the estimation of the historical and contemporary gene flow between identified genetic clusters. We also estimated the dispersal ability of the species. Our results showed a surprisingly high genetic diversity, along with a pattern of isolation by distance (IBD) and a strongly spatialized genetic structure. Furthermore, we underlined a low functional connectivity, along with evidence of a recent decline in the population size, which are both likely due to a historical fragmentation between the sampled areas, caused by anthropization. Overall, this study allows to provide a first insight about the functioning of the population, to guide future conservation actions for the species.
Published: 2023

4. Comment on Dunbar et al. (2022) 'Webslinger vs. Dark Knight: First record of a false widow spider Steatoda nobilis preying on a pipistrelle bat in Britain'

Author: Dool, Serena, Uhl, Gabriele, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Universität Greifswald - University of Greifswald, and Zoological Institute and Museum
Subjects: Ecology, [SDV]Life Sciences [q-bio], Ecology, Evolution, Behavior and Systematics
Abstract: We are grateful to the editors for providing us with the opportunity to submit our comment to Web Ecology. The journal which published the original article offered to publish our comment but demanded a EUR 1700 article processing charge (APC) for it.; International audience; A recent publication in Ecosphere claimed to report the first case of a predation event by a theridiid spider on a bat globally and the first case of a member of the genus Steatoda preying on a mammal globally, and the paper concludes with possible implications for public health. Predation is typically understood to mean "capture, kill, and eat". However, none of these aspects had been observed. Moreover, key aspects of bat biology were not taken into account, including that the bat in question was a flightless newborn, the capture of which would require some explanation. We revisit this interesting observation considering both bat and spider ecology.
Published: 2022

5. Late Cenozoic environmental changes drove the diversification of a weevil genus endemic to the Cape Floristic Region

Author: Noémie M.‐C. Hévin, Steffan Hansen, Pia Addison, Laure Benoit, Gael J. Kergoat, Julien Haran, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Université de Poitiers, Stellenbosch University, Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and The first author was supported by a grant from the CBGP laboratory (Montpellier, France) for her Master's degree.
Subjects: biodiversity hotspot, Phlyctinus callosus, [SDV]Life Sciences [q-bio], Genetics, Entiminae, Animal Science and Zoology, sea level oscillations, banded fruit weevil, Molecular Biology, Ecology, Evolution, Behavior and Systematics, allopatric speciation
Abstract: We thank the Western Cape Nature Conservation Board (permit No. CN44-30-4229), the Cape Research Centre (South African National Parks, CRC/2019-2020/012-2012/V1) and Grootbos Private Nature reserve for authorization to collect specimens in the Western Cape province of South Africa.; International audience; The Cape Floristic Region in the Republic of South Africa is a well-recognized hotspot of biodiversity. Although this region is mostly known for its high level of plant diversity and endemicity, it also hosts an understudied and likely diverse arthropod fauna. Here we investigate the evolutionary history and timing of diversification of the apterous weevil genus Phlyctinus (Curculionidae: Entiminae), which is endemic to the coastal area and adjacent mountain ranges of the Cape floristic region and generally associated with sunflower plants (Asteraceae). We use a diverse array of molecular analyses (phylogenetic inference, molecular species delimitation and dating analyses) to analyse a novel molecular dataset of 202 weevil specimens (including 170 Phlyctinus sampled in 60 sites), and sequenced for two mitochondrial and four nuclear gene fragments. Phylogenetic and dating analyses indicate that the genus started diversifying in the late Miocene, with contrasting diversification dynamics for the three inferred clades, which present disjunct distributions. Host plant records and the lack of relatedness of species living in sympatry indicate that the diversification of Phlyctinus was predominantly driven by allopatric (geographic) speciation. We hypothesize that the interplay between topography and recurring cycles of coastline-habitat fragmentation resulting from sea level oscillations spurred the diversification of the most speciose clade, whereas in the two remaining clades populations likely remained connected thus hampering allopatric speciation. Interestingly, this pattern echoes with the role of sea level oscillations as an important driver of the radiation of several lineages in the coastline ecosystems of the Cape Floristic Region.
Published: 2022

6. Capacity of countries to reduce biological invasions

Author: Guillaume Latombe, Hanno Seebens, Bernd Lenzner, Franck Courchamp, Stefan Dullinger, Marina Golivets, Ingolf Kühn, Brian Leung, Núria Roura-Pascual, Emma Cebrian, Wayne Dawson, Christophe Diagne, Jonathan M. Jeschke, Cristian Pérez-Granados, Dietmar Moser, Anna Turbelin, Piero Visconti, Franz Essl, University of Vienna [Vienna], University of Edinburgh, Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Goethe-Universität Frankfurt am Main-Senckenberg – Leibniz Institution for Biodiversity and Earth System Research - Senckenberg Gesellschaft für Naturforschung, Leibniz Association-Leibniz Association, Ecologie Systématique et Evolution (ESE), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), Martin-Luther-University Halle-Wittenberg, Department of Geobotany and Botanical Garden, Martin-Luther-Universität Halle Wittenberg (MLU), McGill University = Université McGill [Montréal, Canada], Universitat de Girona [Girona], Universitat de Girona (UdG), Departament de Ciencies Ambientals, Centre d'Estudis Avançats de Blanes (CEAB), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Institute of Aquatic Ecology, Durham University, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Freie Universität Berlin, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Universidad de Alicante, International Institute for Applied Systems Analysis [Laxenburg] (IIASA), This research was funded through the 2017-2018 Belmont Forum and BiodivERsA joint call for research proposals, under the BiodivScen ERA-Net COFUND programme, and with the funding organisations FWF (project no I 4011-B32–GL, BeL, SD, DM, FE), MCIN/AEI/https://doi.org/10.13039/501100011033 (PCI2018-092966–NRP, CPG, EC), BMBF (16LC1807C–MG, IK, 16LC1807A–HS, 16LC1807B–JMJ) and ANR (NR-18-EBI4-0004–FC, CB, CD, AT)., Universidad de Alicante. Departamento de Ecología, Ecología y Conservación de Poblaciones y Comunidades Animales (ECPCA), Department of Botany and Biodiversity Research, Institute of Biology/Geobotany and Botanical Garden, German Centre for Integrative Biodiversity Research (iDiv), Institute of Biology, Freie Universität Berlin, Berlin, Germany, Departamento de Ecología, Universidad de Alicante, Alicante, Spain, This research was funded through the 2017-2018 Belmont Forum and BiodivERsA joint call for research proposals, under the BiodivScen ERA-Net COFUND programme, and with the funding organisations FWF (project no I 4011-B32-GL, BeL, SD, DM, FE), MCIN/AEI/https://doi.org/10.13039/501100011033 (PCI2018-092966NRP, CPG, EC), BMBF (16LC1807C-MG, IK, 16LC1807A-HS, 16LC1807B-JMJ) and ANR (ANR-18-EBI4-0004-FC, CB, CD, AT).Document Information, and ANR-18-EBI4-0004,AlienScenarios,Developing and applying scenarios of biological invasions for the 21st century(2018)
Subjects: Governance, Global and Planetary Change, Established alien species, Health (social science), Sociology and Political Science, Ecology, [SDV]Life Sciences [q-bio], Geography, Planning and Development, 500 Naturwissenschaften und Mathematik::570 Biowissenschaften, Biologie::570 Biowissenschaften, Biologie, Management, Monitoring, Policy and Law, Lifestyle, Environmental performance, Scenarios, [SDE]Environmental Sciences, Trade, Innovation, Nature and Landscape Conservation
Abstract: Este artículo contiene 19 páginas, 4 figuras, 2 tablas., The extent and impacts of biological invasions on biodiversity are largely shaped by an array of socio-economic and environmental factors, which exhibit high variation among countries. Yet, a global analysis of how these factors vary across countries is currently lacking. Here, we investigate how five broad, country-specific socio-economic and environmental indices (Governance, Trade, Environmental Performance, Lifestyle and Education, Innovation) explain country-level (1) established alien species (EAS) richness of eight taxonomic groups, and (2) proactive or reactive capacity to prevent and manage biological invasions and their impacts. These indices underpin many aspects of the invasion process, including the introduction, establishment, spread and management of alien species. They are also general enough to enable a global comparison across countries, and are therefore essential for defining future scenarios for biological invasions. Models including Trade, Governance, Lifestyle and Education, or a combination of these, best explained EAS richness across taxonomic groups and national proactive or reactive capacity. Historical (1996 or averaged over 1996–2015) levels of Governance and Trade better explained both EAS richness and the capacity of countries to manage invasions than more recent (2015) levels, revealing a historical legacy with important implications for the future of biological invasions. Using Governance and Trade to define a two-dimensional socio-economic space in which the position of a country captures its capacity to address issues of biological invasions, we identified four main clusters of countries in 2015. Most countries had an increase in Trade over the past 25 years, but trajectories were more geographically heterogeneous for Governance. Declines in levels of Governance are concerning as they may be responsible for larger levels of invasions in the future. By identifying the factors influencing EAS richness and the regions most susceptible to changes in these factors, our results provide novel insights to integrate biological invasions into scenarios of biodiversity change to better inform decision-making for policy and the management of biological invasions., This research was funded through the 2017-2018 Belmont Forum and BiodivERsA joint call for research proposals, under the BiodivScen ERA-Net COFUND programme, and with the funding organisations FWF (project no I 4011-B32–GL, BeL, SD, DM, FE), MCIN/AEI/https:// doi. org/ 10. 13039/ 50110 00110 33 (PCI2018-092966– NRP, CPG, EC), BMBF (16LC1807C–MG, IK; 16LC1807A–HS; 16LC1807B–JMJ) and ANR (NR-18-EBI4-0004–FC, CB, CD, AT).
Published: 2022

7. New French tiny spider mites (Prostigmata, Tetranychidae) on a tiny broom

Author: Philippe Auger, Tea Arabuli, Alain Migeon, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Ilia State University [Tbilisi], and Agricultural University of Georgia
Subjects: faunistic survey, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, Arthropoda, alpha taxonomy, Aacriformes, Insect Science, Animalia, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Acari, biodiversity
Abstract: International audience; Two new spider mite species collected in southern France on the tiny broom Genista pulchella are described. The new species, Bryobia (Lyobia) baroni sp. n. and Tenuipalpoides genistearum sp. n are among the smallest known species belonging to the genera Bryobia (Lyobia) and Tenuipalpoides, respectively. In addition, pictures, corrections on body size measurements and additional morphological data of Tenuipalpoides ziziphus are provided.
Published: 2022

8. Novel Gene Rearrangement Pattern in Pachycrepoideus vindemmiae Mitochondrial Genome: New Gene Order in Pteromalidae (Hymenoptera: Chalcidoidea)

Author: Huang, Yixin, Yang, Yuanhan, Qi, Liqing, Hu, Haoyuan, Rasplus, Jean-Yves, Wang, Xu, Anhui Normal University, Key Laboratory of Zoological Systematics and Evolution, Chinese Academy of Agricultural Sciences (CAAS), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), and This work was supported by the National Natural Science Foundation of China (32100355, 32100352), the Natural Science Fund of Anhui Province (1908085QC93) and Natural Science Foundation of Universities of Anhui Province (KJ2020A0094).
Subjects: [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], mitogenome, parasitic lifestyles, phylogenetic position, gene rearrangement, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Pteromalidae
Abstract: All sequences generated during this study have been deposited in the GenBank (https://www.ncbi.nlm.nih.gov/genbank/); International audience; Simple Summary: The mitochondrial genome is a reliable genetic marker for reconstructing phylogeny and Pteromalidae is a diverse and complex family of chalcid wasps, but its evolutionary history is still poorly understood. In this study, we sequenced the mitochondrial genomes of four species (Muscidifurax similadanacus, M. sinesensilla, Nasonia vitripennis, and Pachycrepoideus vindemmiae) of Pteromalidae. Additionally, a phylogenetic hypothesis was reconstructed for the subfamilies of Pteromalidae that includes newly acquired mitogenomes and those deposited inNCBI. We used pairwise breakpoint distances to infer this phylogeny. Our study enriches the overall knowledge on gene rearrangement in Pteromalidae, reveals the evolutionary relationships among several major groups of Pteromalidae, accumulates molecular data for a Pteromalidae phylogeny, and provides a genetic background basis for biological control in agriculture and forestry.Abstract: The mitochondrial genomes of Muscidifurax similadanacus, M. sinesensilla, Nasonia vitripennis, and Pachycrepoideus vindemmiae were sequenced to better understand the structural evolution of Pteromalidae mitogenomes. These newly sequenced mitogenomes all contained 37 genes. Nucleotide composition was AT-biased and the majority of the protein-coding genes exhibited a negative AT skew. All 13 protein-coding genes (PCGs) initiated with the standard start codon of ATN, excepted for nad1 of N. vitripennis, which started with TTG, and terminated with a typical stop codon TAA/TAG or an incomplete stop codon T. All transfer RNA (tRNA) genes were predicted to fold into the typical clover-leaf secondary structures, except for trnS1, which lacks the DHU arm in all species. In P. vindemmiae, trnR and trnQ lack the DHU arm and TΨC arm, respectively. Although most genes under a strong purifying selection, the Ka/Ks value of the atp8 gene of P. vindemmiae was greater than 1, indicating putative positive selection. A novel transposition of trnR in P. vindemmiae was revealed, which was the first of this kind to be reported in Pteromalidae. Two kinds of datasets (PCG12 and AA) and two inference methods (maximum likelihood and Bayesian inference) wereused to reconstruct a phylogenetic hypothesis for the newly sequenced mitogenomes of Pteromalidae and those deposited in GenBank. The topologies obtained recovered the monophyly of the three subfamilies included. Pachyneurinae and Pteromalinae were recovered as sister families, and both appeared sister to Sycophaginae. The pairwise breakpoint distances of mitogenome rearrangements were estimated to infer phylogeny among pteromalid species. The topology obtained was not totally congruent with those reconstructed using the ML and BI methods.
Published: 2023

9. Phytoseiid mites (Acari: Mesostigmata) from Central West Morocco: new records and key to females of all recorded Moroccan species

Author: Zahidi, Abdelaziz, Akchour, Abdellah, Kreiter, Serge, Tixier, Marie-Stéphane, Msanda, Fouad, El Mousadik, Abdelhamid, Faculté des Sciences Agadir (FSA), Université Ibn Zohr [Agadir], Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM)
Subjects: key of females, citrus agrosystems, Arthropoda, [SDV]Life Sciences [q-bio], integrated management, Animalia, weed plants, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Acari, argan forest
Abstract: International audience; Several phytoseiid species are excellent biological control agents for suppressing mite pest populations in many crops and preventing yield losses. This paper aims to improve the knowledge of Phytoseiidae diversity in citrus orchards and argan forest in central western Morocco. The surveys were conducted between April and October during three successive years (2017–2019), in nine conventional citrus orchards covering an area of more than 3,000 hectares and on uncultivated plants in argan forest at an altitude ranging from 150 to 700 meters. Twenty-nine species belonging to 15 genera were found, seven of them being new for the Moroccan fauna: Amblyseius largoensis, A. swirskii, Amblyseiella setosa, Euseius batus, E. dossei, Paragigagnathus molestus, and Cydnoseius negevi. Species of nine genera were found on citrus leaves: Neoseiulus, Amblyseius, Amblyseiella, Transeius, Phytoseiulus, Euseius, Phytoseius, Typhlodromus, and Paraseiulus. Stah AlMadina (24.8%), Ouled Abdellah (15.9%), Nour (14.3%) domains contained a high number (more than 60.2%) of individuals in the collected samples. Malva parviflora, Convolvulus althaeoides, Solanum nigrum, Bryonia dioica, Withania somnifera would be interesting companion plants to be associated in the inter-rows in citrus orchards in this region to ensure sustainability, because they host high densities and diversities of Phytoseiidae. A key of females of all recorded Moroccan species until now is provided.
Published: 2023

10. Endoparasitoid lifestyle promotes endogenization and domestication of dsDNA viruses

Author: Benjamin Guinet, David Lepetit, Sylvain Charlat, Peter N Buhl, David G Notton, Astrid Cruaud, Jean-Yves Rasplus, Julia Stigenberg, Damien M. de Vienne, Boussau Bastien, Julien Varaldi, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Zoological Museum [Copenhagen], Natural History Museum of Denmark, Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Swedish Museum of Natural History (NRM), This work was supported by a grant from the Agence Nationale de la Recherche (ANR) to J.V. (ANR-11-JSV7-0011 Viromics). We also thank the ANR project HORIZON (ANR-17-CE02-0021, S. Charlat) for financial support., ANR-11-JSV7-0011,viromics,Distribution et impact des virus héritables dans une communauté hôtes-parasitoïdes(2011), ANR-17-CE02-0021,Horizon,Patterns and processes of horizontal DNA transfer: an in-depth exploration of the host-parasitoid route(2017), University of Copenhagen = Københavns Universitet (UCPH), Natural Sciences Department, National Museums Collection Centre, 242 West Granton Road, Granton, Edinburgh, EH5 1JA, Department of Zoology, Swedish Museum of Natural History, Box 50007, 104 05 Stockholm, and This work was supported by a grant from the Agence Nationale de la Recherche (ANR) to J.V. (ANR-11-JSV7-0011 Viromics). We also thank the ANR project HORIZON (S. Charlat) for financial support.
Subjects: [SDV]Life Sciences [q-bio], [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], evolutionary biology, Hymenoptera, EVE, dsDNA virus, domestication, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, genomics, horizontal gene transfer, genetics, parasitoid, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: All sequencing data are available at NCBI via the BioProject accession number NCBI: PRJNA826991. All scripts and additional tables as well as all cluster phylogeny figures are available under the github repository : (BenjaminGuinet/Viral-domestication-among-Hymenoptera).; International audience; The accidental endogenization of viral elements within eukaryotic genomes can occasionally provide significant evolutionary benefits, giving rise to their long-term retention, that is, to viral domestication. For instance, in some endoparasitoid wasps (whose immature stages develop inside their hosts), the membrane-fusion property of viruses has been repeatedly domesticated following the ancestral endogenizations of double-stranded DNA viruses. The endogenized genes provide female wasps with a delivery tool to inject virulence factors that are essential to the developmental success of their offspring. Because all known cases of viral domestication involve endoparasitic wasps, we hypothesized that this lifestyle, relying on a close interaction between individuals, may have promoted the endogenization and domestication of viruses. By analyzing the composition of 124 Hymenoptera genomes, spread over the diversity of this clade and including free-living, ecto- and endoparasitoid species, we tested this hypothesis. Our analysis first revealed that double-stranded DNA viruses, in comparisons with other viral genomic structures (ssDNA, dsRNA, ssRNA), are more often integrated (that is, endogenized) and domesticated (that is, retained by selection) than expected from their estimated abundance in insect viral communities. Secondly, our analysis indicates that the rate at which dsDNA viruses are endogenized is higher in endoparasitoids than in ectoparasitoids or free-living hymenopterans, which also translates into more frequent events of domestication. Hence, these results are consistent with the hypothesis that the endoparasitoid lifestyle has facilitated the endogenization of dsDNA viruses, in turn increasing the opportunities of domestications that now play a central role in the biology of many parasitoid lineages.
Published: 2023

11. Metabolic consequences of various fruit-based diets in a generalist insect species

Author: Laure Olazcuaga, Raymonde Baltenweck, Nicolas Leménager, Alessandra Maia-Grondard, Patricia Claudel, Philippe Hugueney, Julien Foucaud, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Colorado State University [Fort Collins] (CSU), Department of Agricultural Biology, Colorado State University, Santé de la vigne et qualité du vin (SVQV), Université de Strasbourg (UNISTRA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and JF was supported by recurrent institutional funding from INRAE. LO acknowledges support from the European Union program FEDER FSE IEJ 2014–2020 (project CPADROL), the INRAE scientific department SPE (AAP-SPE 2016), and the US National Science Foundation (DEB-1930650 to Ruth Hufbauer).
Subjects: ecological specialization, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, generalism, niche breadth, Drosophila suzukii, evolutionary biology, ecology, diet, metabolomics, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy
Abstract: All data & code generated during this study have been deposited in the INRAE dataverse: https://entrepot.recherche.data.gouv.fr/dataset.xhtml?persistentId=doi:10.57745/G4D3PG. The shiny application enabling the exploration and analysis of our complete dataset (PCA, GLM/Elastic Net and associated visualizations) is available here: https://fruitfliesmetabo.shinyapps.io/shiny.; International audience; Most phytophagous insect species exhibit a limited diet breadth and specialize on a few or a single host plant. In contrast, some species display a remarkably large diet breadth, with host plants spanning several families and many species. It is unclear, however, whether this phylogenetic generalism is supported by a generic metabolic use of common host chemical compounds ('metabolic generalism') or alternatively by distinct uses of diet-specific compounds ('multi-host metabolic specialism')? Here, we simultaneously investigated the metabolomes of fruit diets and of individuals of a generalist phytophagous species, Drosophila suzukii, that developed on them. The direct comparison of metabolomes of diets and consumers enabled us to disentangle the metabolic fate of common and rarer dietary compounds. We showed that the consumption of biochemically dissimilar diets resulted in a canalized, generic response from generalist individuals, consistent with the metabolic generalism hypothesis. We also showed that many diet-specific metabolites, such as those related to the particular color, odor, or taste of diets, were not metabolized, and rather accumulated in consumer individuals, even when probably detrimental to fitness. As a result, while individuals were mostly similar across diets, the detection of their particular diet was straightforward. Our study thus supports the view that dietary generalism may emerge from a passive, opportunistic use of various resources, contrary to more widespread views of an active role of adaptation in this process. Such a passive stance towards dietary chemicals, probably costly in the short term, might favor the later evolution of new diet specializations.
Published: 2023

12. Semipermeable species boundaries create opportunities for gene flow and adaptive potential

Author: I. Satokangas, P. Nouhaud, B. Seifert, P. Punttila, R. Schultz, M. M. Jones, J. Sirén, H. Helanterä, J. Kulmuni, Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Senckenberg Museum of Natural History Görlitz, Senckenberg – Leibniz Institution for Biodiversity and Earth System Research - Senckenberg Gesellschaft für Naturforschung, Leibniz Association-Leibniz Association, Finnish Environment Institute (SYKE), HiLIFE - Institute of Biotechnology [Helsinki] (BI), Helsinki Institute of Life Science (HiLIFE), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, University of Oulu, Ecology and Genetics Research Unit, University of Oulu, 90014 Oulu, Tvärminne Zoological Station, Zoological Station, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam [Amsterdam] (UvA), and We thank Natural Resources Institute Finland for access to samples collected during the 10th National Forest Inventory (NFI) of Finland, and Leena Finér and Jouni Kilpeläinen for organising the collection of the NFI ant data. NFI and data collection was funded by the Academy of Finland (#200870 and #114380). Timo Domisch, Pirjo Appelgren, Gergely Várkonyi, Riitta Savolainen and Kari Vepsäläinen provided additional ant samples. We would also like to thank Raphal Martin-Roy for helping to collect the within-nest temperature data, Jaakko Kuurne for involvement in the preliminary mitochondrial data analyses, and the SpecIAnt research group and Perttu Seppä for comments and support. Warm thanks for Martyn James and other Biomedicum Functional Genomics Unit personnel for expertise and advice in genome sequencing, and CSC–ITCenter for Science, Finland, for computational resources. Mirkka Jones and Jukka Sirén acknowledge support from the Academy of Finland's ‘Thriving Nature’ research profiling action. Jonna Kulmuni acknowledges support from the Academy of Finland (#328961, #309580). Ina Satokangas was supported by the Doctoral Programme in Integrative Life Science (University of Helsinki), and Societas pro Fauna et Flora Fennica.
Subjects: [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], speciation, mosaic hybrid zone, hybridisation, Genetics, adaptation, Hymenoptera, Ecology, Evolution, Behavior and Systematics, Formica wood ants
Abstract: International audience; Hybridisation and gene flow can have both deleterious and adaptive consequences for natural populations and species. To better understand the extent of hybridisation in nature and the balance between its beneficial and deleterious outcomes in a changing environment, information on naturally hybridising nonmodel organisms is needed. This requires the characterisation of the structure and extent of natural hybrid zones. Here, we study natural populations of five keystone mound-building wood ant species in the Formica rufa group across Finland. No genomic studies across the species group exist, and the extent of hybridisation and genomic differentiation in sympatry is unknown. Combining genome-wide and morphological data, we demonstrate more extensive hybridisation than was previously detected between all five species in Finland. Specifically, we reveal a mosaic hybrid zone between Formica aquilonia, F. rufa and F. polyctena, comprising further generation hybrid populations. Despite this, we find that F. rufa, F. aquilonia, F. lugubris and F. pratensis form distinct gene pools in Finland. We also find that hybrids occupy warmer microhabitats than the nonadmixed populations of cold-adapted F. aquilonia, and suggest that warm winters and springs, in particular, may benefit hybrids over F. aquilonia, the most abundant F. rufa group species in Finland. In summary, our results indicate that extensive hybridisation may create adaptive potential that could promote wood ant persistence in a changing climate. Additionally, they highlight the potentially significant ecological and evolutionary consequences of extensive mosaic hybrid zones, within which independent hybrid populations face an array of ecological and intrinsic selection pressures.
Published: 2023

13. The worldwide invasion history of a pest ambrosia beetle inferred using population genomics

Author: T. Urvois, C. Perrier, A. Roques, L. Sauné, C. Courtin, H. Kajimura, J. Hulcr, A.I. Cognato, M.-A. Auger-Rozenberg, C. Kerdelhué, Unité de recherche Zoologie Forestière (URZF), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Graduate School of Bioagricultural Sciences, Nagoya University, University of Florida [Gainesville] (UF), Michigan State University [East Lansing], Michigan State University System, SPS KAKENHI, Grant/Award Numbers: 18KK0180 and 20H03026, LIFE project SAMFIX, Grant/Award Number: LIFE17 NAT/IT/000609, National Science Foundation, USDA-Forest Service, Grant/Award Number: 16-CA-11420004-072, and USDA APHIS
Subjects: [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, COI sequencing, Genetics, Genetic clusters, Xylosandrus crassiusculus' invasion history, Invasion route, RAD sequencing, Bioinvasion, Xylosandrus crassiusculus, Ecology, Evolution, Behavior and Systematics
Abstract: Individual RAD sequences files are available in a fq.gz format at the Sequence Read Archive (SRA) (https://www.ncbi.nlm.nih.gov/sra/PRJNA771401). The VCF files Xylosandruscrassiusculus.vcf as well as the popmap used in STACKS' population module and specimens' metadata (e.g. GPS coordinates) are available on Portail Data INRAE (https://doi.org/10.57745/JMT4KD). The Genbank accession numbers for the mitochondrial haplotypes reported in this paper are OK489329 to OK489334.; International audience; Xylosandrus crassiusculus, a fungus-farming wood borer native to Southeastern Asia, is the most rapidly spreading invasive ambrosia species worldwide. Previous studies focusing on its genetic structure suggested the existence of cryptic genetic variation in this species. Yet, these studies used different genetic markers, focused on different geographical areas, and did not include Europe. Our first goal was to determine the worldwide genetic structure of this species based on both mitochondrial and genomic markers. Our second goal was to study X. crassiusculus' invasion history on a global level and identify the origins of the invasion in Europe. We used a COI and RAD sequencing design to characterize 188 and 206 specimens worldwide, building the most comprehensive genetic dataset for any ambrosia beetle to date. The results were largely consistent between markers. Two differentiated genetic clusters were invasive, albeit in different regions of the world. The two markers were inconsistent only for a few specimens found exclusively in Japan. Mainland USA could have acted as a source for further expansion to Canada and Argentina through stepping-stone expansion and bridgehead events. We showed that Europe was only colonized by Cluster 2 through a complex invasion history including several arrivals from multiple origins in the native area, and possibly including bridgehead from the USA. Our results also suggested that Spain .
Published: 2023

14. Molecular Survey of Rodent-Borne Infectious Agents in the Ferlo Region, Senegal

Author: Joa Braïthe Mangombi-Pambou, Laurent Granjon, Fabien Flirden, Mamadou Kane, Youssoupha Niang, Bernard Davoust, Florence Fenollar, Oleg Mediannikov, Centre International de Recherches Médicales de Franceville (CIRMF), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), BIOPASS, ISRA-UCAD, Institut de Recherche pour le Développement (IRD [France-Ouest]), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), This study was supported by the Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, the French National Research Agency under the Investissements d’avenir programme (reference: ANR-10-IAHU-0003) and the fourth Make Our Planet Great Again programme (MOPGA 4). This work was co-funded by the Labex DRIIHM, the French Investissements d’Avenir programme (ANR-11-LABX-0010), which is managed by the ANR., ANR-10-IAHU-0003,Méditerranée Infection,I.H.U. Méditerranée Infection(2010), and ANR-11-LABX-0010,DRIIHM / IRDHEI,Dispositif de recherche interdisciplinaire sur les Interactions Hommes-Milieux(2011)
Subjects: rodents, infectious agents, multiple infections, zoonotic diseases, tick-borne zoonotic disease, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Genetics, Genetics (clinical)
Abstract: International audience; Zoonotic pathogens are responsible for most infectious diseases in humans, with rodents being important reservoir hosts for many of these microorganisms. Rodents, thus, pose a significant threat to public health. Previous studies in Senegal have shown that rodents harbour a diversity of microorganisms, including human pathogens. Our study aimed to monitor the prevalence of infectious agents in outdoor rodents, which can be the cause of epidemics. We screened 125 rodents (both native and expanding) from the Ferlo region, around Widou Thiengoly, for different microorganisms. Analysis, performed on rodent spleens, detected bacteria from the Anaplasmataceae family (20%), Borrelia spp. (10%), Bartonella spp. (24%) and Piroplasmida (2.4%). Prevalences were similar between native and the expanding (Gerbillus nigeriae) species, which has recently colonised the region. We identified Borrelia crocidurae, the agent responsible for tick-borne relapsing fever, which is endemic in Senegal. We also identified two other not-yet-described bacteria of the genera Bartonella and Ehrlichia that were previously reported in Senegalese rodents. Additionally, we found a potential new species, provisionally referred to here as Candidatus Anaplasma ferloense. This study highlights the diversity of infectious agents circulating in rodent populations and the importance of describing potential new species and evaluating their pathogenicity and zoonotic potential.
Published: 2023

15. Exact calculation of the expected SFS in structured populations

Author: Armando Arredondo, Josué Corujo, Camille Noûs, Simon Boitard, Lounès Chikhi, Olivier Mazet, Institut de Mathématiques de Toulouse UMR5219 (IMT), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Cogitamus, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Instituto Gulbenkian de Ciência [Oeiras] (IGC), and Fundação Calouste Gulbenkian
Subjects: [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], [MATH.MATH-GM]Mathematics [math]/General Mathematics [math.GM], structured coalescent, Site frequency spectrum, Markov processes, population structure
Abstract: The Site Frequency Spectrum (SFS), summary statistic of the distribution of derived allele frequencies in a sample of DNA sequences, provides information about genetic variation and can be used to make population inferences. The exact calculation of the expected SFS in panmictic population has been derived in the Markovian coalescent theory for decades, but its generalization to the structured coalescent is hampered by the almost exponential growth of the states space. We propose here a complete algorithmic procedure, from how to build a suitable state space and sort it, to how to take advantage of the sparsity of the rate matrix and to solve numerically the linear system by an iterative method. The simplest case of the symmetricaln-island is then processed to arrive at a ready-to-use demographic parameters inference framework.
Published: 2023

16. Habitat mosaic as a driver of the resilience of native species: The case of the assemblage of small mammals from the city of Franceville, Gabon

Author: J. B. Mangombi‐Pambou, O. Fossati‐Gaschignard, N. N'Dilimabaka, O. Banga Mve‐Ella, N. M. Longo Pendy, S. E. Dibakou, O. Mediannikov, F. Fenollar, E. Leroy, M. Bourgarel, Centre International de Recherches Médicales de Franceville (CIRMF), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Université des Sciences et Techniques de Masuku (USTM), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)
Subjects: urban rodents, [SDV]Life Sciences [q-bio], habitat gradient, central African city, Animal Science and Zoology, community composition, landscape heterogeneity, Ecology, Evolution, Behavior and Systematics, introduced rodents
Abstract: International audience; Rodents (Rodentia) are the most abundant and diverse order of mammals, present in all habitats, including urban areas. The traffic linked to globalisation has favoured their involvement in biological invasions that have an impact on local biodiversity, the economy and human health. In Franceville, Gabon, little is known about the rodent community. We therefore studied the composition and distribution of rodents along a gradient highlighting the heterogeneity of the city's landscape. The three habitat types studied showed no difference in small mammal abundance, while the diversity index was higher in the vegetated habitat (SDI = 0.73) compared to the outdoor (SDI = 0.71) and indoor (SDI = 0.45) habitats. Our work shows the importance of vegetal remnants in the city for the maintenance of native species. It also highlights the impact of introduced species on small mammal assemblages and the need for management to reduce the factors of their proliferation.
Published: 2023

17. Revisiting the historical scenario of a disease dissemination using genetic data and Approximate Bayesian Computation methodology: The case of Pseudocercospora fijiensis invasion in Africa

Author: A. Gilabert, A. Rieux, S. Robert, R. Vitalis, M.‐F. Zapater, C. Abadie, J. Carlier, V. Ravigné, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, This work was supported by the Région Languedoc-Roussillon, the Agence Nationale de la Recherche (project EMERFUNDIS ANR 07-BDIV-003 and EMILE ANR 09-BLAN-0145-01), and French Agropolis Fondation (Labex Agro – Montpellier, BIOFIS project number 1001-001 and Labex Agro –Montpellier, E-SPACE project number 1504-004). VR was funded by the European Union (European Regional Development Fund, ERDF contract GURDT I2016-1731-0006632), the Conseil Régional de La Réunion, and the Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD)., ANR-07-BDIV-0003,EMERFUNDIS,Comprendre les émergences de maladies fongiques de plantes : vers une estimation des risques liés aux changements globaux(2007), ANR-09-BLAN-0145,EMILE,Etude de Méthodes Inférentielles et Logiciels pour l'Evolution(2009), and ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010)
Subjects: Ecology, Approximate Bayesian Computation, population genetics, emerging disease, random forest, Ecology, Evolution, Behavior and Systematics, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Nature and Landscape Conservation
Abstract: Data were produced through the molecular genetic analysis technical facilities of the IFR119 with the help of E. Desmarais and F. Cerqueira. Bioinformatics analyses were performed using the Core Cluster of the Institut Français de Bioinformatique, the MESO@LR-Platform at the University of Montpellier and the INRAE MIGALE bioinformatics facility (doi: 10.15454/1.5572390655343293E12).The microsatellite dataset, template files for Fastsimcoal analyses and R scripts used to generate the tables and figures of the manuscript are deposited in the dryad repository (doi:10.5061/dryad.rn8pk0pgw).; International audience; The reconstruction of geographic and demographic scenarios of dissemination for invasive pathogens of crops is a key step toward improving the management of emerging infectious diseases. Nowadays, the reconstruction of biological invasions typically uses the information of both genetic and historical information to test for different hypotheses of colonization. The Approximate Bayesian Computation framework and its recent Random Forest development (ABC-RF) have been successfully used in evolutionary biology to decipher multiple histories of biological invasions. Yet, for some organisms, typically plant pathogens, historical data may not be reliable notably because of the difficulty to identify the organism and the delay between the introduction and the first mention. We investigated the history of the invasion of Africa by the fungal pathogen of banana Pseudocercospora fijiensis, by testing the historical hypothesis against other plausible hypotheses. We analyzed the genetic structure of eight populations from six eastern and western African countries, using 20 microsatellite markers and tested competing scenarios of population foundation using the ABC-RF methodology. We do find evidence for an invasion front consistent with the historical hypothesis, but also for the existence of another front never mentioned in historical records. We question the historical introduction point of the disease on the continent. Crucially, our results illustrate that even if ABC-RF inferences may sometimes fail to infer a single, well-supported scenario of invasion, they can be helpful in rejecting unlikely scenarios, which can prove much useful to shed light on disease dissemination routes.
Published: 2023

18. Population genetics reveals divergent lineages and ongoing hybridization in a declining migratory fish species complex

Author: Quentin Rougemont, Charles Perrier, Anne-Laure Besnard, Isabelle Lebel, Yann Abdallah, Eric Feunteun, Elodie Réveillac, Emilien Lasne, Anthony Acou, David José Nachón, Fernando Cobo, Guillaume Evanno, Jean-Luc Baglinière, Sophie Launey, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Dynamique et durabilité des écosystèmes : de la source à l’océan (DECOD), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Association Migrateurs Rhône Méditerranée (MRM), Office national de l'eau et des milieux aquatiques (ONEMA), Ministère de l'écologie, du développement durable et de l'énergie-Ministère de l'écologie, du développement durable et de l'énergie, Fédération Nationale de la Pêche en France et de la Protection du Milieu Aquatique, Partenaires INRAE, SCIMABIO Interface SAS, Patrimoine naturel (PatriNat), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Office français de la biodiversité (OFB), Station marine Dinard, Centre De Recherche et d'Enseignement sur les Systèmes Côtiers (CRESCO), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), LIttoral ENvironnement et Sociétés (LIENSs), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS), Pôle OFB-INRAE-Institut Agro-UPPA pour la gestion des migrateurs amphihalins dans leur environnement (MIAME), Université de Pau et des Pays de l'Adour (UPPA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Office français de la biodiversité (OFB)-Institut Agro Rennes Angers, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Universidade de Santiago de Compostela [Spain] (USC ), and This study was funded by the European Regional Development Fund (Transnational program Interreg IV. Atlantic Aquatic Resource Conservation Project)
Subjects: Gene Flow, Population genetics, Speciation, Fishes, Genetic Variation, Bayes Theorem, Invertebrates, Genetics, Population, [SDE]Environmental Sciences, Genetics, Animals, Hybridization, Genetic, Genetic variation, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Genetics (clinical)
Abstract: Deciphering the effects of historical and recent demographic processes responsible for the spatial patterns of genetic diversity and structure is a key objective in evolutionary and conservation biology. Using population genetic analyses, we investigated the demographic history, the contemporary genetic diversity and structure, and the occurrence of hybridization and introgression of two species of anadromous fish with contrasting life history strategies and which have undergone recent demographic declines, the allis shad (Alosa alosa) and the twaite shad (Alosa fallax). We genotyped 706 individuals from 20 rivers and 5 sites at sea in Southern Europe at thirteen microsatellite markers. Genetic structure between populations was lower for the nearly semelparous species A. alosa, which disperses greater distances compared to the iteroparous species, A. fallax. Individuals caught at sea were assigned at the river level for A. fallax and at the region level for A. alosa. Using an approximate Bayesian computation framework, we inferred that the most likely long term historical divergence scenario between both species and lineages involved historical separation followed by secondary contact accompanied by strong population size decline. Accordingly, we found evidence for contemporary hybridization and bidirectional introgression due to gene flow between both species and lineages. Moreover, our results support the existence of at least one distinct species in the Mediterrannean sea: A. agone in Golfe du Lion area, and another divergent lineage in Corsica. Overall, our results shed light on the interplay between historical and recent demographic processes and life history strategies in shaping population genetic diversity and structure of closely related species. The recent demographic decline of these species’ populations and their hybridization should be carefully considered while implementing conservation programs.
Published: 2022

19. Introduction pathways of economically costly invasive alien species

Author: Anna J. Turbelin, Christophe Diagne, Emma J. Hudgins, Desika Moodley, Melina Kourantidou, Ana Novoa, Philip J. Haubrock, Camille Bernery, Rodolphe E. Gozlan, Robert A. Francis, Franck Courchamp, Ecologie Systématique et Evolution (ESE), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Department of Biology, Carleton University (Carleton University), Carleton University, Institute of Botany of the Czech Academy of Sciences (IB / CAS), Czech Academy of Sciences [Prague] (CAS), University of Southern Denmark (SDU), Hellenic Centre for Marine Research (HCMR), Institute of Marine Biological Resources and Inland Waters, Senckenberg Research Institute and Natural History Museum [Frankfurt], Senckenberg – Leibniz Institution for Biodiversity and Earth System Research - Senckenberg Gesellschaft für Naturforschung, Leibniz Association-Leibniz Association, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses [University of South Bohemia] (CENAKVA), Faculty of Fisheries and Protection of Waters [University of South Bohemia], University of South Bohemia -University of South Bohemia, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), King‘s College London, The authors acknowledge the French National Research Agency (ANR-14-CE02-0021) and the BNP-Paribas Foundation Climate Initiative for funding the InvaCost project that allowed the construction of the InvaCost database. The present work was conducted following a workshop funded by the AXA Research Fund Chair of Invasion Biology and is part of the AlienScenario project funded by BiodivERsA and Belmont-Forum call 2018 on biodiversity scenarios. AJT contract comes from the AXA Research Fund Chair of Invasion Biology of University Paris Saclay. CD is funded by the BiodivERsA-Belmont Forum Project 'Alien Scenarios' (BMBF/PT DLR 01LC1807C). AN and DM acknowledge funding from EXPRO Grant No. 19-28807X (Czech Science Foundation) and long-term research development project RVO 67985939 (The Czech Academy of Sciences)., ANR-14-CE02-0021,InvaCosts,Insectes envahissants et leurs couts pour la biodiversité, l'économie et la santé humaine(2014), University of South Bohemia, and The authors acknowledge the French National Research Agency (ANR-14-CE02-0021) and the BNP-Paribas Foundation Climate Initiative for funding the InvaCost project that allowed the construction of the InvaCost database. The present work was conducted following a workshop funded by the AXA Research Fund Chair of Invasion Biology and is part of the AlienScenario project funded by BiodivERsA and Belmont-Forum call 2018 on biodiversity scenarios. AJT contract comes from the AXA Research Fund Chair of Invasion Biology of University Paris Saclay. CD is funded by the BiodivERsA-Belmont Forum Project 'Alien Scenarios' (BMBF/PT DLR 01LC1807C). AN and DM acknowledge funding from EXPRO Grant No. 19-28807X (Czech Science Foundation) and long-term research development project RVO 67985939 (The Czech Academy of Sciences). We also thank John Wilson and the two anonymous reviewers for their stimulating and helpful comments.
Subjects: InvaCost, Monetary impact, Non-native insects, Policy, Ecology, [SDE]Environmental Sciences, Exotic mammals, Invasive alien species, Introduction pathways, Ecology, Evolution, Behavior and Systematics, Management, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy
Abstract: Introduction pathways play a pivotal role in the success of Invasive Alien Species (IAS)—the subset of alien species that have a negative environmental and/or socio-economic impact. Pathways refer to the fundamental processes that leads to the introduction of a species from one geographical location to another—marking the beginning of all alien species invasions. Increased knowledge of pathways is essential to help reduce the number of introductions and impacts of IAS and ultimately improve their management. Here we use the InvaCost database, a comprehensive repository on the global monetary impacts of IAS, combined with pathway data classified using the Convention on Biological Diversity (CBD) hierarchical classification and compiled from CABI Invasive Species Compendium, the Global Invasive Species Database (GISD) and the published literature to address five key points. Data were available for 478 individual IAS. For these, we found that both the total and annual average cost per species introduced through the ‘Stowaway’ (US$144.9bn; US$89.4m) and ‘Contaminant’ pathways (US$99.3bn; US$158.0m) were higher than species introduced primarily through the ‘Escape’ (US$87.4bn; US$25.4m) and ‘Release’ pathways (US$64.2bn; US$16.4m). Second, the recorded costs (both total and average) of species introduced unintentionally was higher than that from species introduced intentionally. Third, insects and mammals, respectively, accounted for the greatest proportion of the total cost of species introduced unintentionally and intentionally respectively, at least of the available records; ‘Stowaway’ had the highest recorded costs in Asia, Central America, North America and Diverse/Unspecified regions. Fourthly, the total cost of a species in a given location is not related to the year of first record of introduction, but time gaps might blur the true pattern. Finally, the total and average cost of IAS were not related to their number of introduction pathways. Although our findings are directly limited by the available data, they provide important material which can contribute to pathway priority measures, notably by complementing studies on pathways associated with ecologically harmful IAS. They also highlight the crucial need to fill the remaining data gaps—something that will be critical in prioritising limited management budgets to combat the current acceleration of species invasions.
Published: 2022

20. MALDI-TOF: A new tool for the identification of Schistosoma cercariae and detection of hybrids

Author: Antoine Huguenin, Julien Kincaid-Smith, Jérôme Depaquit, Jérôme Boissier, Hubert Ferté, Epidémiosurveillance de protozooses à transmission alimentaire et vectorielle (ESCAPE), Université de Reims Champagne-Ardenne (URCA)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Laboratoire de Parasitologie-Mycologie (LPM), IFR 53, Université de Reims Champagne-Ardenne (URCA)-Université de Reims Champagne-Ardenne (URCA)-CHU Maison Blanche-UPRES EA 2070, Interactions Hôtes-Pathogènes-Environnements (IHPE), Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), This research was funded by the program HySWARM (ANR-18-CE35-0001) from the French Research National Agency., and ANR-18-CE35-0001,HySWARM,Hybrid Swarm: rôle de l'hybridation dans les capacités invasives, l'épidémiologie et le diagnostic de la schistosomiase(2018)
Subjects: Infectious Diseases, Public Health, Environmental and Occupational Health, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract: Schistosomiasis is a neglected water-born parasitic disease caused by Schistosoma affecting more than 200 million people. Introgressive hybridization is common among these parasites and raises issues concerning their zoonotic transmission. Morphological identification of Schistosoma cercariae is difficult and does not permit hybrids detection. Our objective was to assess the performance of MALDI-TOF for the specific identification of cercariae in human and non-human Schistosoma and for the detection of hybridization between S. bovis and S. haematobiumSpectra were collected from laboratory reared molluscs infested with strains of S. haematobium, S. mansoni, S. bovis, S. rodhaini and S. bovis x S. haematobium natural (Corsican hybrid) and artificial hybrids. Cluster analysis showed a clear separation between S. haematobium, S. bovis, S. mansoni and S. rodhaini. Corsican hybrids are classified with those of the parental strain of S. haematobium whereas other hybrids formed a distinct cluster. In blind test analysis the developed MALDI-TOF spectral database permits identification of Schistosoma cercariae with high accuracy (94%) and good specificity (S. bovis: 99.59%, S. haematobium 99.56%, S. mansoni and S. rodhaini: 100%). Most misidentifications were between S. haematobium and the Corsican hybrids. The use of machine learning permits to improve the discrimination between these last two taxa, with accuracy, F1 score and Sensitivity/Specificity > 97%. In multivariate analysis the factors associated with obtaining a valid identification score (> 1.7) were absence of ethanol preservation (p < 0.001) and a number of 2-3 cercariae deposited per well (p < 0.001). Also spectra acquired from S. mansoni cercariae are more likely to obtain a valid identification score than those acquired from S. haematobium (pMALDI-TOF is a reliable technique for high-throughput identification of Schistosoma cercariae of medical and veterinary importance and could be useful for field survey in endemic areas.Author SummarySchistosomoses are neglected tropical diseases, affecting approximately 200 million people worldwide. They are transmitted during contact with water contaminated with the infesting stage of the parasite (the cercaria stage). Species-level recognition of cercariae present in water has important implications for field campaigns aimed at eradicating schistosomiasis. In addition, Schistosomes are able to hybridize between different species. Identification of Schistosomes cercariae on microscopy is difficult because of their similarity, and it does not allow hybrids to be distinguished. Molecular biology techniques allow a reliable diagnosis but are expensive. MALDI-TOF is a recent technique that permits an inexpensive identification of micro-organisms in a few minutes. In this paper, we evaluate MALDI-TOF identification of Schistosomes cercariae.We have implemented a database of MALDI-TOF cercariae spectra obtained from parental strains and hybrids of species of medical or veterinary interest, allowing reliable identification with an accuracy of 94%. The identification errors mainly come from confusion between the natural Corsican hybrid (S. haematobium x S. bovis) and S. haematobium. The use of machine learning algorithms permits to obtain an accuracy of more than 97% in the recognition of these two parasites. In conclusion, MALDI-TOF is a promising tool for the identification of Schistosome cercariae.
Published: 2023

21. Economic costs of invasive rodents worldwide: the tip of the iceberg

Author: Diagne, Christophe, Ballesteros-Mejia, Liliana, Cuthbert, Ross, Bodey, Thomas, Fantle-Lepczyk, Jean, Angulo, Elena, Bang, Alok, Dobigny, Gauthier, Courchamp, Franck, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Ecologie Systématique et Evolution (ESE), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institute for Global Food Security [Belfast], Queen's University [Belfast] (QUB), School of Biological Sciences [Aberdeen], University of Aberdeen, Auburn University (AU), Forest Economics and Policy, School of Forestry and Wildlife Science, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Society for Ecology Evolution and Development, Unité Peste - Plague Unit [Antananarivo, Madagascar], Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), This work was supported by the French National Research Agency (ANR-14-CE02-0021) and the BNP-Paribas Foundation Climate Initiative for funding the Invacost project which allowed the construction of the InvaCost database. This work was initiated following a workshop funded by the AXA Research Fund Chair of Invasion Biology. This research was also funded through the 2017-2018 Belmont Forum and BiodivERsA joint call for research proposals, under the BiodivScen ERA-Net COFUND programme. Funds for Elena Angulo and Liliana Ballesteros-Mejia came from the AXA Research Fund Chair of Invasion Biology of University Paris Saclay. Christophe Diagne was funded by the BiodivERsA-Belmont Forum Project ‘‘Alien Scenarios’’ (BMBF/PT DLR 01LC1807C). Ross N. Cuthbert received funding from the Leverhulme Trust (ECF-2021-001). Thomas W. Bodey received funding from the European Union’s Horizon 2020 research and innovation programme Marie Skłodowska-Curie fellowship (Grant No. 747120). Jean Fantle-Lepczyk received travel support to attend the Invacost workshop from Auburn University School of Forestry and Wildlife Sciences., ANR-14-CE02-0021,InvaCosts,Insectes envahissants et leurs couts pour la biodiversité, l'économie et la santé humaine(2014), and Université Paris-Saclay
Subjects: 0106 biological sciences, InvaCost, Natural resource economics, General Neuroscience, 010604 marine biology & hydrobiology, Management expenditures, General Medicine, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 010603 evolutionary biology, 01 natural sciences, Rodents, General Biochemistry, Genetics and Molecular Biology, Iceberg, Damage costs, Monetary impact, Geography, SDG 3 - Good Health and Well-being, Economic cost, [SDE]Environmental Sciences, Reporting bias, General Agricultural and Biological Sciences, SDG 2 - Zero Hunger, health care economics and organizations
Abstract: Background Rodents are among the most notorious invasive alien species worldwide. These invaders have substantially impacted native ecosystems, food production and storage, local infrastructures, human health and well-being. However, the lack of standardized and understandable estimation of their impacts is a serious barrier to raising societal awareness, and hampers effective management interventions at relevant scales. Methods Here, we assessed the economic costs of invasive alien rodents globally in order to help overcome these obstacles. For this purpose, we combined and analysed economic cost data from the InvaCost database—the most up-to-date and comprehensive synthesis of reported invasion costs—and specific complementary searches within and beyond the published literature. Results Our conservative analysis showed that reported costs of rodent invasions reached a conservative total of US$ 3.6 billion between 1930 and 2022 (annually US$ 87.5 million between 1980 and 2022), and were significantly increasing through time. The highest cost reported was for muskrat Ondatra zibethicus (US$ 377.5 million), then unspecified Rattus spp. (US$ 327.8 million), followed by Rattus norvegicus specifically (US$ 156.6 million) and Castor canadensis (US$ 150.4 million). Of the total costs, 87% were damage-related, principally impacting agriculture and predominantly reported in Asia (60%), Europe (19%) and North America (9%). Our study evidenced obvious cost underreporting with only 99 documents gathered globally, clear taxonomic gaps, reliability issues for cost assessment, and skewed breakdowns of costs among regions, sectors and contexts. As a consequence, these reported costs represent only a very small fraction of the expected true cost of rodent invasions (e.g., using a less conservative analytic approach would have led to a global amount more than 80-times higher than estimated here). Conclusions These findings strongly suggest that available information represents a substantial underestimation of the global costs incurred. We offer recommendations for improving estimates of costs to fill these knowledge gaps including: systematic distinction between native and invasive rodents’ impacts; monetizing indirect impacts on human health; and greater integrative and concerted research effort between scientists and stakeholders. Finally, we discuss why and how this approach will stimulate and provide support for proactive and sustainable management strategies in the context of alien rodent invasions, for which biosecurity measures should be amplified globally.
Published: 2023

22. Genome Scan of Rice Landrace Populations Collected Across Time Revealed Climate Changes’ Selective Footprints in the Genes Network Regulating Flowering Time

Author: Nourollah AHMADI, Mamadou Billo BARRY, Julien FROUIN, Miguel de Navascués, Mamadou Aminata Touré, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Développement Adaptatif du Riz [AGAP] (DAR), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut de Recherche Agronomique de Guinée (IRAG), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, and Funding institution: AGROPOLIS Foundation. Grant number: 0900-001-1. Grant recipient: Nourollah Ahmadi.
Subjects: Climate changes, Temporal cline, O. glaberrima, Flowering time, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, Soil Science, Rice, Plant Science, Selection footprint, Genome scan, Agronomy and Crop Science, O. sativa
Abstract: Passport and phenotypic data of the rice accessions studied are provided Additional file 11: Table S1. Genotypic data can be downloaded in HapMap format from http://tropgenedb.cirad.fr/tropgene/JSP/interface.jsp?module=RICE study Genotypes, study type G-panel_GBS_data.; International audience; Analyses of the genetic bases of plant adaptation to climate changes, using genome-scan approaches, are often conducted on natural populations, under hypothesis of out-crossing reproductive regime. We report here on a study based on diachronic sampling (1980 and 2011) of the autogamous crop species, Oryza sativa and Oryza glaberrima, in the tropical forest and the Sudanian savannah of West Africa. First, using historical meteorological data we confirmed changes in temperatures (+ 1 °C on average) and rainfall regime (less predictable and reduced amount) in the target areas. Second, phenotyping the populations for phenology, we observed significantly earlier heading time in the 2010 samples. Third, implementing two genome-scan methods (one of which specially developed for selfing species) on genotyping by sequencing genotypic data of the two populations, we detected 31 independent selection footprints. Gene ontology analysis detected significant enrichment of these selection footprints in genes involved in reproductive processes. Some of them bore known heading time QTLs and genes, including OsGI, Hd1 and OsphyB. This rapid adaptive evolution, originated from subtle changes in the standing variation in genetic network regulating heading time, did not translate into predominance of multilocus genotypes, as it is often the case in selfing plants, and into notable selective sweeps. The high adaptive potential observed results from the multiline genetic structure of the rice landraces, and the rather large and imbricated genetic diversity of the rice meta-population at the farm, the village and the region levels, that hosted the adaptive variants in multiple genetic backgrounds before the advent of the environmental selective pressure. Our results illustrate the evolution of in situ diversity through processes of human and natural selection, and provide a model for rice breeding and cultivars deployment strategies aiming resilience to climate changes. It also calls for further development of population genetic models for adaptation of plant populations to environmental changes. To our best knowledge, this is the first study dealing with climate-changes' selective footprint in crops.
Published: 2023

23. Comparative assessment of heat tolerance in weevils associated with a fire‐prone ecosystem

Author: Marion Javal, John S. Terblanche, Chantelle Smit, Julien Haran, Stellenbosch University, Department of Conservation Ecology and Entomology, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), The authors thank the Western Cape Nature Conservation Board (Permit No. CN44-30-4229) and the Cape Research Centre, South African National Parks (Permit No. CRC/2019-2020/012-2012/V1) for permission to collect specimens in areas under their control. The authors acknowledge Paula Strauss, Gary Beukman, and Michael Lutzeyer for access to the Grootbos Private Nature Reserve and their friendly assistance during sampling. The authors thank Laurene Dubreuil for introducing Julien Haran and Marion Javal to the Montagu region. Henrika Bosua (Stellenbosch University) is warmly thanked for her help with the respirometry measurements. This study was supported by recurring funding from Montpellier University (Marion Javal) and Cirad (Julien Haran)., and Université Paul-Valéry - Montpellier 3 (UPVM)-École pratique des hautes études (EPHE)
Subjects: Coleoptera, Bogert effect, heat knockdown, Ecology, Insect Science, [SDV]Life Sciences [q-bio], fynbos, thermolimit respirometry, insect
Abstract: Data for the HKD experiment is available here: https://doi.org/10.6084/m9.figshare.21647015.; International audience; 1. Fire is an important cause of disturbance which directly shapes many ecosystems worldwide. While the effect of fire on the distribution and regeneration of plant species has been widely documented, little is known on how phytophagous insects are reacting to these disturbances.2. This study explores the survival strategies of various weevil species, a highly diverse phytophagous beetle group in fire-prone ecosystems of the biodiversity hotspot of the Cape Floristic Region in South Africa. More specifically, we investigated how the lifestyle of species (location of larval development, phenology of adults, and flight ability) correlates with heat tolerance. We hypothesized that wingless species in particular will show better tolerance to heat as they have a limited ability to escape fire rapidly and usually remain hidden in the soil.3. The thermal tolerance of a set of sixteen species with divergent lifestyles and geographic distribution was measured using a standard heat knockdown protocol at 48°C. Respirometry was then performed on the most resistant species using a ramping protocol in order to determine CTmax.4. Our results show that the species tested exhibit high variation in thermal tolerance across taxonomic groups, clustering into three modalities: weak, intermediate, and high tolerance to heat stress. In addition, life history traits (diurnal vs. nocturnal adult activity and location of juvenile stages in plant tissues) likely better explain thermal tolerance at the species level than flight ability or the fire-proneness of ecosystems. Finally, results revealed that some non-flying weevil species are highly heat tolerant with CTmax values reaching up to 50.2 and 51.9°C in species among the Ocladiinae and Brachycerinae subfamilies, respectively.5. Climate change is leading to an increase in the impact and frequency of fires. In this context, this study highlights the diversity of strategies developed by arthropods to escape extreme heat in fire prone ecosystems. Further work is necessary to examine the generality of these patterns across other fire prone ecosystems to better understand behavioural compensation and evolutionary responses, especially given the forecast increases in fire driven by drying and warming associated with climate change.
Published: 2023

24. BRC4Env, the Biological Resource Centres for the Environment of AgroBRC-RARe

Author: Bruneau, Sylvia, Artige, Emmanuelle, Faivre-Primot, Céline, Marchand, Frédéric, Mondy, Samuel, Ratié, Céline, Redecker, Dirk, Ris, Nicolas, Starck, Agnes, Warot, Sylvie, Mougin, Christian, Ecologie fonctionnelle et écotoxicologie des agroécosystèmes (ECOSYS), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Agroécologie [Dijon], Université de Bourgogne (UB)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Dijon, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Unité Expérimentale d'Ecologie et d'Ecotoxicologie Aquatique - U3E (Rennes, France) (U3E ), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Info&Sols (Info&Sols), Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), Département ECODIV - INRAE, and Groupe Français de Recherches sur les Pesticides
Subjects: [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences
Abstract: International audience; Le réseau de Centres de Ressources Biologiques BRC4Env (https://www.brc4env.fr/), collecte, caractérise, conserve et distribue des ressources biologiques (matériel biologique et données associées) agro-environnementales. Ces ressources sont ouvertes à la recherche fondamentale et appliquée mobilisant des ressources pour caractériser l’environnement et l’évolution de sa dynamique, ou de proposer des solutions de biocontrôle. Ces ressources biologiques sont échantillonnées à partir d’écosystèmes naturels et cultivés. Elles concernent notamment des sols et les ADNs de leurs communautés microbiennes, des tissus ichtyologiques, des arthropodes et acariens, des hyménoptères parasitoïdes et des champignons mycorhiziens à arbuscule. BRC4Env rend ces ressources disponibles pour les chercheurs du monde académique, mais aussi de l'industrie et de la société civile (ONG...). Ces ressources biologiques sont mobilisables dans le cadre de projets de recherche en écotoxicologie et agroécologie.BRC4Env est un des piliers constitutifs de l'Infrastructure de Recherche nationale « Ressources Agronomiques pour la recherche », AgroBRC-RARe (https://www.agrobrc-rare.org/), co-porté par INRAE, l’IRD et le CIRAD.
Published: 2023

25. Physicochemical Drivers of Zooplankton Seasonal Variability in a West African Lagoon (Nokoué Lagoon, Benin)

Author: Alexis Chaigneau, François Talomonwo Ouinsou, Hervé Hotèkpo Akodogbo, Gauthier Dobigny, Thalasse Tchémangnihodé Avocegan, Fridolin Ubald Dossou-Sognon, Victor Olaègbè Okpeitcha, Metogbe Belfrid Djihouessi, Frédéric Azémar, Laboratoire d'études en Géophysique et océanographie spatiales (LEGOS), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Université d’Abomey-Calavi = University of Abomey Calavi (UAC), IRHOB, Centre de Recherches Halieutiques et Océanologiques du Bénin [Cotonou] (CRHOB), ICMPA-UNESCO Chair, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Laboratoire d'Hydrologie Appliquée (LHA), Institut National de l'Eau (INE), Laboratoire Ecologie Fonctionnelle et Environnement (LEFE), Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), and Field campaigns and instrumentation were supported by IRD. This work is a contribution to the « JEAI SAFUME » project funded by IRD. V. OKPEITCHA was funded by OmiDelta project of the Embassy of the Netherlands in Benin, through a scholarship grant of the National Institute of Water (INE). F. OUINSOU and T. AVOCEGAN received funding from IRD.
Subjects: zooplankton, diversity and abundance, environmental parameters, seasonal variation, Nokoué Lagoon, Ocean Engineering, [SDV.SA.ZOO]Life Sciences [q-bio]/Agricultural sciences/Zootechny, Water Science and Technology, Civil and Structural Engineering
Abstract: International audience; This study aimed to investigate the seasonal variation of zooplankton diversity and abundance in the Nokoué Lagoon in southern Benin. Through extensive sampling, a total of 109 zooplanktonic taxa were identified and quantified. The average zooplankton abundance was found to be 60 individuals per liter, with copepods and rotifers being the most dominant groups, comprising 68.1% and 29.1% of the total abundance, respectively. The key factor identified as driving the structure of the zooplanktonic assemblages was salinity, which showed significant seasonal variation. The results revealed that during the high water period, when the lagoon was filled with fresh water, rotifers were dominant, zooplanktonic diversity was highest, and abundances were quite high. Conversely, during the low water period, when the lagoon was characterized by brackish water, diversity was minimal, and abundance decreased slightly. The study also found that some areas of the lagoon showed high abundances independent of salinity levels, suggesting that other factors such as riverine inputs or the presence of acadjas (home-made brush parks used as fish traps) may also have notable effects on the zooplankton community. Overall, the findings of this study provide valuable insights into the functioning of one of the most biologically productive lagoons in West Africa.
Published: 2023

26. Key innovations and the diversification of Hymenoptera

Author: Bonnie B. Blaimer, Bernardo F. Santos, Astrid Cruaud, Michael W. Gates, Robert R. Kula, István Mikó, Jean-Yves Rasplus, David R. Smith, Elijah J. Talamas, Seán G. Brady, Matthew L. Buffington, Museum für Naturkunde [Berlin], Smithsonian Institution, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), USDA-ARS : Agricultural Research Service, ARS - Systematic Entomology Laboratory, United States Department of Agriculture (USDA), University of New Hampshire (UNH), University of Florida [Gainesville] (UF), and This study was supported by the National Science Foundation (DEB-1555905, S.G.B.) and a Smithsonian Institute for Biodiversity Genomics and Global Genome Initiative grant (S.G.B., M.L.B., and B.B.B.), as well as a grant from the GGI Peer-Review Awards Program (B.F.S.). R.R.K., M.W.G., and M.L.B., as well as part of the sequencing effort, were funded by SEL-ARS. B.B.B. was supported by the Museum für Naturkunde, Berlin, during the analyses and writing stages of this project. J.Y.R. and AC were supported by the INRAe SPE department. B.F.S. was funded by a GGI Peter Buck Postdoctoral Fellowship (Smithsonian Institution) during much of this work. E.J.T. was supported by the Florida Department of Agriculture and Consumer Services, Division of Plant Industry. Open Access funding enabled and organized by Projekt DEAL.
Subjects: [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Multidisciplinary, General Physics and Astronomy, General Chemistry, General Biochemistry, Genetics and Molecular Biology
Abstract: The raw sequence reads newly generated in this study have been deposited in the NCBI Sequence Read Archive under BioProject accession code PRJNA811764 and PRJNA632862. The UCE sequence data from prior publications used in this study are available under BioProject accession codes PRJNA379583, PRJNA248919, PRJNA495844, PRJNA814466, PRJNA606284, PRJNA647791, PRJNA625490, and PRJNA473845; the genome assemblies used in this study are available under accession codes GCA_001444175, GCA_000699045, GCA_000762945, GCA_000696855, GCA_000006295, and GCA_000931545. The raw sequence data can also be accessed using individual accession numbers given in Supplementary Data 1. Source data for this study (assembled contig files, data matrices, tree and log files for phylogenetic analyses; input and output files for FcLM; R code and input and results files for comparative analyses) are available in the Dryad repository at https://doi.org/10.5061/dryad.08kprr54m131. Information on the location of voucher specimens is provided in Supplementary Data 1.; International audience; The order Hymenoptera (wasps, ants, sawflies, and bees) represents one of the most diverse animal lineages, but whether specific key innovations have contributed to its diversification is still unknown. We assembled the largest time-calibrated phylogeny of Hymenoptera to date and investigated the origin and possible correlation of particular morphological and behavioral innovations with diversification in the order: the wasp waist of Apocrita; the stinger of Aculeata; parasitoidism, a specialized form of carnivory; and secondary phytophagy, a reversal to plant-feeding. Here, we show that parasitoidism has been the dominant strategy since the Late Triassic in Hymenoptera, but was not an immediate driver of diversification. Instead, transitions to secondary phytophagy (from parasitoidism) had a major influence on diversification rate in Hymenoptera. Support for the stinger and the wasp waist as key innovations remains equivocal, but these traits may have laid the anatomical and behavioral foundations for adaptations more directly associated with diversification.
Published: 2023

27. Whole-genome sequencing of cryopreserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines

Author: Simon Boitard, Laurence Liaubet, Cyriel Paris, Katia Fève, Patrice Dehais, Alban Bouquet, Juliette Riquet, Marie-José Mercat, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut du Porc (IFIP), This study was supported by the CRB-Anim infrastructure, funded by the French National Research Agency (Grant Number ANR-11-INBS-0003) as part of the Programme d’Investissement d’Avenir. Part of the data were obtained in the Delisus project funded by BIOPORC (ADN, Choice Genetics France, Gene+ and Nucleus breeding organizations and IFIP) and French ANR (ANR-07-GANI-001). The PhD research of CP was conducted as part of the IMAGE project, which recieved funding from the European Union Horizon 2020 Research and Innovative Program under Grant Agreement No. 677353. It was also conducted as part of the Haptitude project, which was funded by the INRA SelGen metaprogramme., ANR-11-INBS-0003,CRB-Anim,Réseau de Centres de Ressources Biologiques pour les animaux domestiques(2011), ANR-07-GANI-0001,DELISUS,An integrated study of the haplotypic variability at the whole genome level on animals finely phenotyped from French porcine populations(2007), and European Project: 677353,H2020,H2020-SFS-2015-2,IMAGE(2016)
Subjects: [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Genetics, Animal Science and Zoology, General Medicine, Ecology, Evolution, Behavior and Systematics
Abstract: Background Numerous genomic scans for positive selection have been performed in livestock species within the last decade, but often a detailed characterization of the detected regions (gene or trait under selection, timing of selection events) is lacking. Cryopreserved resources stored in reproductive or DNA gene banks offer a great opportunity to improve this characterization by providing direct access to recent allele frequency dynamics, thereby differentiating between signatures from recent breeding objectives and those related to more ancient selection constraints. Improved characterization can also be achieved by using next-generation sequencing data, which helps narrowing the size of the detected regions while reducing the number of associated candidate genes. Methods We estimated genetic diversity and detected signatures of recent selection in French Large White pigs by sequencing the genomes of 36 animals from three distinct cryopreserved samples: two recent samples from dam (LWD) and sire (LWS) lines, which had diverged from 1995 and were selected under partly different objectives, and an older sample from 1977 prior to the divergence. Results French LWD and LWS lines have lost approximately 5% of the SNPs that segregated in the 1977 ancestral population. Thirty-eight genomic regions under recent selection were detected in these lines and the corresponding selection events were further classified as convergent between lines (18 regions), divergent between lines (10 regions), specific to the dam line (6 regions) or specific to the sire line (4 regions). Several biological functions were found to be significantly enriched among the genes included in these regions: body size, body weight and growth regardless of the category, early life survival and calcium metabolism more specifically in the signatures in the dam line and lipid and glycogen metabolism more specifically in the signatures in the sire line. Recent selection on IGF2 was confirmed and several other regions were linked to a single candidate gene (ARHGAP10, BMPR1B, GNA14, KATNA1, LPIN1, PKP1, PTH, SEMA3E or ZC3HAV1, among others). Conclusions These results illustrate that sequencing the genome of animals at several recent time points generates considerable insight into the traits, genes and variants under recent selection in a population. This approach could be applied to other livestock populations, e.g. by exploiting the rich biological resources stored in cryobanks.
Published: 2023

28. Inorganic phosphate content does not affect oviposition preference in the invasive pest Drosophila suzukii

Author: Laure Olazcuaga, Robin Guilhot, Jean‐Loup Claret, Nicolas O. Rode, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Colorado State University [Fort Collins] (CSU), L.O. acknowledges support from the European Union program FEFER FSE IEJ 2014-2020 (project CPADROL), the INRAE scientific department SPE (AAP-SPE 2016) and the US National Science Foundation (DEB-1930650 to Ruth Hufbauer). N.O.R. acknowledges support from the CeMEB LabEx/University of Montpellier (ANR-10-LABX-0004)., and ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010)
Subjects: insect behaviour, host choice, spotted-wing drosophila, Insect Science, chemical ecology, oviposition site selection, Agronomy and Crop Science, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy
Abstract: The data and R scripts for our analyses are available at: https://github.com/olazl aure/PhosphorusPreference2022. They are archived on Figshare: https://doi.org/10.6084/m9.figshare.22032500; International audience; The broad variation in host use among polyphagous insects is well documented but still poorly understood. In numerous pest insects, the proximate mechanisms respon-sible for variation in oviposition preference among host plants remain to be eluci-dated. The invasive crop pest, Drosophila suzukii, attacks a wide range of host fruits. Females prefer ovipositing on particular fruit media (blackberry, cherry, blackcurrant) that are rich in phosphorus. As phosphorus is known to be involved in female repro-duction in insect species such as Drosophila, it could drive oviposition preference in D. suzukii. Phosphorus is either present as inorganic or organic phosphate in fruits. As the absolute content in macromolecules associated with phosphate in fruits (i.e. proteins and carbohydrates) do not affect oviposition in D. suzukii, we tested for the effect of inorganic phosphate on oviposition preference. We measured the egg- laying preferences of D. suzukii in a choice environment containing 12 artificial media with increasing content in inorganic phosphate (monopotassium dihydrogen phosphate). In our assay, D. suzukii females did not prefer ovipositing in media with high inorganic phosphate content compared to media with lower inorganic phosphate content. As a confirmation, we verified the previous result of a higher female preference for media made of phosphorus-rich fruits (blackberry, cherry, blackcurrant). The higher prefer-ence for phosphorus- rich fruits could be driven by macromolecules containing phos-phorus (e.g. phospholipids) or by the presence of one or more molecules that do not contain phosphorus, but that happen to be correlated to fruit phosphorus content. Studying the proximate mechanisms driving host use will ultimately help improve the management of D. suzukii and other crop pests
Published: 2023

29. PhylteR: efficient identification of outlier sequences in phylogenomic datasets

Author: Aurore Comte, Théo Tricou, Eric Tannier, Julien Joseph, Aurélie Siberchicot, Simon Penel, Rémi Allio, Frédéric Delsuc, Stéphane Dray, Damien M. de Vienne, Institut Français de Bioinformatique (IFB-CORE), Institut National de Recherche en Informatique et en Automatique (Inria)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), South Green Bioinformatics Platform [Montpellier], Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Work was funded by ANR Grant 18-CE02-0007 (Sthoriz) to DMDV, ANR Grant 19-CE45-0010 (Evoluthon) to ET, and European Research Council grant ERC-2015-CoG-683257 (ConvergeAnt project) to FD. This is also contribution of the Institut des Sciences de l’Evolution (ISEM ) de Montpellier., ANR-18-CE02-0007,STHORIZ,DETECTION DE LA DIVERSITÉ ÉTEINTE ET INCONNUE À L'AIDE DES TRANSFERTS HORIZONTAUX(2018), and ANR-19-CE45-0010,Evoluthon,La vie articifielle comme banc d'essai pour l'évolution moléculaire(2019)
Subjects: [SDV]Life Sciences [q-bio]
Abstract: The documented code of PhylteR is available at https://github.com/damiendevienne/phylter along with a thorough documentation. All data and scripts used in this study are available on the dedicated GitHub repository available at https://github.com/damiendevienne/phylter-data.; In phylogenomics, incongruences between gene trees, resulting from both artifactual and biological reasons, are known to decrease the signal-to-noise ratio and complicate species tree inference. The amount of data handled today in classical phylogenomic analyses precludes manual error detection and removal. However, a simple and efficient way to automate the identification of outlier sequences is still missing.Here, we present PhylteR, a method that allows a rapid and accurate detection of outlier sequences in phylogenomic datasets, i.e. species from individual gene trees that do not follow the general trend. PhylteR relies on DISTATIS, an extension of multidimensional scaling to 3 dimensions to compare multiple distance matrices at once. In PhylteR, distance matrices obtained either directly from multiple sequence alignments or extracted from individual gene phylogenies represent evolutionary distances between species according to each gene.On simulated datasets, we show that PhylteR identifies outliers with more sensitivity and precision than a comparable existing method. On a biological dataset of 14,463 genes for 53 species previously assembled for Carnivora phylogenomics, we show (i) that PhylteR identifies as outliers sequences that can be considered as such by other means, and (ii) that the removal of these sequences improves the concordance between the gene trees and the species tree. Thanks to the generation of numerous graphical outputs, PhylteR also allows for the rapid and easy visual characterisation of the dataset at hand, thus aiding in the precise identification of errors.PhylteR is distributed as an R package on CRAN and as containerized versions (docker and singularity).
Published: 2023

30. Environmental factors driving the abundance of Philaenus spumarius in mesomediterranean habitats of Corsica (France)

Author: Marguerite Chartois, Xavier Mesmin, Ileana Quiquerez, Sabrina Borgomano, Pauline Farigoule, Éric Pierre, Jean-Marc Thuillier, Jean-Claude Streito, François Casabianca, Laetitia Hugot, Jean-Pierre Rossi, Jean-Yves Rasplus, Astrid Cruaud, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Amélioration Génétique et Adaptation des Plantes méditerranéennes et Tropicales Corse - Antenne Corse (AGAP-Corse), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Conservatoire botanique national de Corse / Office de l’environnement de la Corse, Services déconcentrés d'appui à la recherche Corse (SDAR Corse), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), This work was funded by the Collectivité Territoriale de Corse and the European Union Horizon 2020 research and innovation program under Grant Agreement No. 727987 XF-ACTORS., and European Project: 727987,XF-ACTORS
Subjects: Multidisciplinary, [SDE.ES]Environmental Sciences/Environmental and Society
Abstract: Philaenus spumarius (Ps) is considered the main insect vector of the bacterium Xylella fastidiosa (Xf) in Europe. As such, it is a key actor of the Xf pathosystem on which surveillance and management strategies could be implemented. Although research effort has increased in the past years, the ecological factors shaping Ps abundance and distribution across landscapes are still poorly known in most regions of Europe. We selected 64 plots of 500m2 in Corsican semi-natural habitats in which we sampled nymphs and adults of Ps during three years. While local or surrounding vegetation structure (low or high scrubland) had little effect on Ps abundance, we highlighted a positive relationship between Ps abundance and the density of Cistus monspeliensis in the plots. We also found larger populations of Ps in cooler and moister plots. The pattern of host association highlighted here is unique, which calls for more studies on the ecology of Ps in Europe, to help designing surveillance and management strategy for Xf.
Published: 2023

31. Phytoseiidae (Acari: Mesostigmata) in four provinces of Iran

Author: Farazmand, Azadeh, Jalaeian, Mahdi, Kamali, Hashem, Saboori, Alireza, Tixier, Marie-Stéphane, Kreiter, Serge, Agricultural Research, Education and Extension Organisation (AREEO ), Department of Botany, Iranian Research Institute of Plant Protection, Agricultural Research,Education and Extension Organization (ARREO), Rice Research Institute of Iran (RRII), University of Tehran, Department of Plant Protection, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM)
Subjects: taxonomy, Euseius gallicus, phytoseiids, survey, Proprioseiopsis lineatus, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy
Abstract: International audience; The present study reports the results of surveys carried out over a period of two years (2018 and 2020) in four provinces of Iran: Guilan, Razavi Khorasan, Mazandaran, and Sistan and Baluchestan. Twenty-three species from eight genera of Phytoseiidae have been collected, of which two species were newly recorded for Iran, namely: Euseius gallicus and Proprioseiopsis lineatus. Three species, namely Neoseiulus agrestis, Amblyseius obtusus, Typhlodromus (Anthoseius) haiastanius are new records for the Guilan Province. Neoseiulus californicus and Amblyseius swirskii are new records for the Mazandaran Province while Typhlodromus (Anthoseius) haiastanius is a new record for the Razavi Khorasan Province. All species collected in Sistan and Baluchestan are new records for this province. The worldwide distribution and plant hosts of all collected phytoseiids during this study are provided.
Published: 2023

32. A synthesis of biological invasion hypotheses associated with the introduction–naturalisation–invasion continuum

Author: Ella Z. Daly, Olivier Chabrerie, Francois Massol, Benoit Facon, Manon C.M. Hess, Aurélie Tasiemski, Frédéric Grandjean, Matthieu Chauvat, Frédérique Viard, Estelle Forey, Laurent Folcher, Elise Buisson, Thomas Boivin, Sylvie Baltora‐Rosset, Romain Ulmer, Patricia Gibert, Gabrielle Thiébaut, Jelena H. Pantel, Tina Heger, David M. Richardson, David Renault, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Ecologie et Dynamique des Systèmes Anthropisés - UMR CNRS 7058 (EDYSAN), Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Tour du Valat, Research Institute for the conservation of Mediterranean Wetlands, CHU Lille, Ecologie et biologie des interactions (EBI), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Etude et Compréhension de la biodiversité (ECODIV), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Unité de Nématologie (LSV Rennes), Laboratoire de la santé des végétaux (LSV), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Ecologie des Forêts Méditerranéennes (URFM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Universität Duisburg-Essen = University of Duisburg-Essen [Essen], Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Technische Universität München = Technical University of Munich (TUM), Stellenbosch University, Institute of Botany of the Czech Academy of Sciences (IB / CAS), Czech Academy of Sciences [Prague] (CAS), Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), The authors were supported by InEE-CNRS via a funded network dedicated to Biological Invasions (Groupement de Recherche Invasions Biologiques, InvaBio, 2014–2022, CNRS 3647). The research was funded by the ASICS project (ANR-20-EBI5-0004, BiodivERsA, BiodivClim call 2019–2020), and the French Polar Institute Paul-Emile Victor (Project 136 ‘SubAntEco', French Polar Institute). DMR acknowledges support from Mobility 2020 project no. CZ.02.2.69/0.0/0.0/18_053/0017850 (Ministry of Education, Youth and Sports of the Czech Republic) and long-term research development project RVO 67985939 (Czech Academy of Sciences). TH received funding from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation, project number HE 5893/8-1., ANR-20-EBI5-0004,ASICS,ASsessing and mitigating the effects of climate change and biological Invasions on the spatial redistribution of biodiversity in Cold environmentS(2020), RIOU, Christine, ASsessing and mitigating the effects of climate change and biological Invasions on the spatial redistribution of biodiversity in Cold environmentS - - ASICS2020 - ANR-20-EBI5-0004 - BiodivERsA - VALID, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), and University of Duisburg-Essen
Subjects: [SDE] Environmental Sciences, niche, invasion ecology, invasiveness, alien populations, [SDE]Environmental Sciences, hypothesis, dispersal, geographic expansion, Biologie, phenotypic plasticity, Ecology, Evolution, Behavior and Systematics, invasibility
Abstract: International audience; With the advent of the Anthropocene, biological invasions have reached an unprecedented level, and the number of species introductions is still increasing in an ever-changing world. Despite major advances in invasion science, significant debate and lack of clarity remain surrounding the determinants of success of introduced species, the magnitude and dimensions of their impact, and the mechanisms sustaining successful invasions. Empirical studies show divergent impacts of alien populations on ecosystems and contrasting effects of biotic and abiotic factors on the dynamics of alien populations, which hinders the creation of a unified theory of biological invasions. Compounding these issues is the plethora of hypotheses that aim to explain invasion success, which can be unclear and contradictory. We propose a synthesis that categorizes hypotheses along a timeline of invasion. We sorted invasion hypotheses along the invasion timeline, and considered population, community and ecosystem levels. This temporal sorting of invasion concepts shows that each is relevant at a specific stage of the invasion. Although concepts and empirical findings on alien species may appear contradictory, when mapped onto an invasion timeline, they may be combined in a complementary way. An overall scheme is proposed to summarise the theoretical dynamics of ecosystems subjected to invasions. For any given case study, this framework provides a guide through the maze of theories and should help choose the appropriate concepts according to the stage of invasion.
Published: 2023

33. Domestication provides durum wheat with protection from locust herbivory

Author: Marie‐Pierre Chapuis, Nicolas Leménager, Cyril Piou, Pierre Roumet, Héloïse Marche, Julia Centanni, Christophe Estienne, Martin Ecarnot, François Vasseur, Cyrille Violle, Elena Kazakou, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, This work was supported by the DINER project, publicly funded by the Labex CEMEB and funds from the French Agricultural Research Centre for International Development (CIRAD). CV was supported by the European Research Council (ERC) Starting Grant Project StG-2014-639706-CONSTRAINTS. We thank the CEFE (Centre d'Ecologie Fonctionnelle et Evolutive) and the CBGP (Centre de Biologie pour la Gestion des Populations) for providing us access to the LabEx CeMEB plateform 'terrain d'expérience CEFE,' 43°38′20.2′′N 3°51′51.0′′E, and the SEPA plateform, respectively., ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010), and European Project: 639706,H2020,ERC-2014-STG,CONSTRAINTS(2015)
Subjects: Ecology, leaf, nutritional ecology, plant toughness, [SDV]Life Sciences [q-bio], domestication syndrome, Locusta migratoria, functional ecology, Triticum turgidum, cereal crop, pest insects, plant nitrogen content, feeding selection, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation
Abstract: International audience; Lower plant resistance to herbivores following domestication has been suggested as the main cause for higher feeding damage in crops than in wild progenitors. While herbivore compensatory feeding has also been proposed as a possible mechanism for raised damage in crops with low nutritional quality, predictions regarding the effects of plant domestication on nutritional quality for herbivores remain unclear. In particular, data on primary metabolites, even major macronutrients, measured in the organs consumed by herbivores, are scarce. In this study, we used a collection of 10 accessions of wild ancestors and 10 accessions of modern progenies of Triticum turgidum to examine whether feeding damage and selectivity by nymphs of Locusta migratoria primarily depended on five leaf traits related to structural resistance or nutrient profiles. Our results unexpectedly showed that locusts favored wild ancestors over domesticated accessions and that leaf toughness and nitrogen and soluble protein contents increased with the domestication process. Furthermore, the quantitative relationship between soluble protein and digestible carbohydrates was found to poorly meet the specific requirements of the herbivore, in all wheat accessions, both wild and modern. The increase in leaf structural resistance to herbivores in domesticated tetraploid wheat accessions suggested that resource allocation trade-offs between growth and herbivory resistance may have been disrupted by domestication in the vegetative organs of this species. Since domestication did not result in a loss of nutritional quality in the leaves of the tetraploid wheat, our results rather provides evidence for a role of the content of plants in nonnutritive nitrogenous secondary compounds, possibly deterrent or toxic, at least for grasshopper herbivores.
Published: 2023

34. Recent advances in availability and synthesis of the economic costs of biological invasions

Author: Danish A Ahmed, Phillip J Haubrock, Ross N Cuthbert, Alok Bang, Ismael Soto, Paride Balzani, Ali S Tarkan, Rafael L Macêdo, Laís Carneiro, Thomas W Bodey, Francisco J Oficialdegui, Pierre Courtois, Melina Kourantidou, Elena Angulo, Gustavo Heringer, David Renault, Anna J Turbelin, Emma J Hudgins, Chunlong Liu, Showkat A Gojery, Ugo Arbieu, Christophe Diagne, Boris Leroy, Elizabeta Briski, Corey J A Bradshaw, Franck Courchamp, Gulf University for Science and Technology (GUST), Senckenberg Research Institute and Natural History Museum [Frankfurt], Senckenberg – Leibniz Institution for Biodiversity and Earth System Research - Senckenberg Gesellschaft für Naturforschung, Leibniz Association-Leibniz Association, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses [University of South Bohemia] (CENAKVA), Faculty of Fisheries and Protection of Waters [University of South Bohemia], University of South Bohemia -University of South Bohemia, Institute for Global Food Security [Belfast], Queen's University [Belfast] (QUB), Azim Premji University, Society for Ecology Evolution and Development, Mugla Sitki Kocman University, Bournemouth University [Poole] (BU), Universidade Federal do Estado do Rio de Janeiro (UNIRIO), Freie Universität Berlin, Universidade Federal do Parana [Curitiba] (UFPR), Universidade Federal do Paraná (UFPR), University of Aberdeen, Centre d'Economie de l'Environnement - Montpellier (CEE-M), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), University of Southern Denmark (SDU), Aménagement des Usages des Ressources et des Espaces marins et littoraux - Centre de droit et d'économie de la mer (AMURE), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Universidade Federal de Lavras = Federal University of Lavras (UFLA), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Ecologie Systématique et Evolution (ESE), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Natural Resources Canada (NRCan), Great Lakes Forestry Centre, Sault Sainte Marie, Ontario, Department of Biology, Carleton University (Carleton University), Carleton University, Ocean University of China (OUC), Institute of Hydrobiology [Wuhan], Chinese Academy of Sciences [Beijing] (CAS), University of Kashmir, Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Goethe-Universität Frankfurt am Main-Senckenberg – Leibniz Institution for Biodiversity and Earth System Research - Senckenberg Gesellschaft für Naturforschung, Smithsonian Conservation Biology Institute, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Helmholtz Centre for Ocean Research [Kiel] (GEOMAR), Flinders University [Adelaide, Australia], School of Natural Sciences and ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Tasmania, Hobart, Tasmania, 7001, Australia, The InvaCost project was funded by the French National Research Agency (ANR-14-CE02-0021), the BNP-Paribas Foundation Climate Initiative, the AXA Research Fund Chair of Invasion Biology of University Paris Saclay and by the BiodivERsA and Belmont-Forum call 2018 on biodiversity scenarios (AlienScenarios, BMBF/PT DLR 01LC1807C). M.K. received funding from the European Union’s Horizon 2020 research programme under a Marie Skłodowska-Curie grant agreement 899546. C.J.A.B. acknowledges the Australian Research Council (CE170100015) for support. R.N.C. is funded by the Leverhulme Trust (ECF-2021-638001). A.B. acknowledges Azim Premji University’s grants programme (UNIV-RC00326) for support. G.H. was supported by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior — Brasil (Capes) — (001) and the Alexander von Humboldt Foundation., and ANR-14-CE02-0021,InvaCosts,Insectes envahissants et leurs couts pour la biodiversité, l'économie et la santé humaine(2014)
Subjects: environmental management, InvaCost, economic impacts, guiding policy, [SHS.ECO]Humanities and Social Sciences/Economics and Finance, invasive species, [SHS]Humanities and Social Sciences
Abstract: All data presented are available via the invacost R package. Related code and supplementary data available at github.com/cjabradshaw/InvaCostVersionTrends.; International audience; Biological invasions are a global challenge that has received insufficient attention. Recently available cost syntheses have provided policy and decision makers with reliable and up-to-date information on the economic impacts of invasive alien species, aiming to motivate effective management. The resultant InvaCost database is now publicly and freely accessible and enables rapid extraction of monetary cost information globally. This has facilitated knowledge sharing, developed a more integrated and multidisciplinary network of researchers, and forged multidisciplinary collaborations among diverse organisations and stakeholders. Over 50 scientific publications so far have used the database and provided detailed assessments of invasion costs across geographic, taxonomic, and spatio-temporal scales. These studies have been instrumental in guiding policy and legislative decisions, while attracting public and media attention. We provide an overview of the improved availability, reliability, and defragmentation of monetary costs, how this has enhanced invasion science as a discipline, and outline directions for future development
Published: 2023

35. Role of Seaports and Imported Rats in Seoul Hantavirus Circulation, Africa

Author: Guillaume Castel, Claudia Filippone, Caroline Tatard, Jacques Vigan, Gauthier Dobigny, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), European Research Infrastructure on Highly Pathogenic Agents (ERINHA-AISBL), Centre National Hospitalier Universitaire Hubert K. Maga de Cotonou (CNHU-HKM), Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP), and This work was funded by The French National Research Program for Environmental and Occupational Health of Anses (ANSES-22-EST-090) .
Subjects: Microbiology (medical), Orthohantavirus, Internationality, Epidemiology, Seoul, Hantavirus Infections, [SDV]Life Sciences [q-bio], Commerce, Rats, Infectious Diseases, Hemorrhagic Fever with Renal Syndrome, Animals, Humans, Seoul virus
Abstract: International audience; Seoul orthohantavirus (SEOV) is not considered a major public health threat on the continent of Africa. However, Africa is exposed to rodentborne SEOV introduction events through maritime traffic after exponential growth of trade with the rest of the world. Serologic studies have already detected hantavirus antibodies in human populations, and recent investigations have confirmed circulation of hantavirus, including SEOV, in rat populations. Thus, SEOV is a possible emerging zoonotic risk in Africa. Moreover, the range of SEOV could rapidly expand, and transmission to humans could increase because of host switching from the usual brown rat (Rattus norvegicus) species, which is currently invading Africa, to the more widely installed black rat (R. rattus) species. Because of rapid economic development, environmental and climatic changes, and increased international trade, strengthened surveillance is urgently needed to prevent SEOV dissemination among humans in Africa.Rodents are widespread, opportunistic, and competent host reservoirs involved in the maintenance, circulation, and transmission of a wide panel of zoonotic pathogens (1). Rodent-related zoonoses cause up to 400 million human infections worldwide each year (1,2). Among zoonotic pathogens, hantaviruses (order Bunyavirales, family Hantaviridae, genus Orthohantavirus) are among agents considered most likely to emerge and have a global public health impact (3).Hantaviruses are enveloped, negative, single-stranded RNA viruses with a tripartite genome comprised of large, medium, and small segments. Transmitted to humans via inhalation of aerosolized virus in contaminated rodent urine and feces, hantaviruses can cause hemorrhagic fever with renal syndrome (HFRS) or hantavirus pulmonary syndrome (4). Hantaviruses are generally carried by a rodent species host, and geographic distribution of the host can determine the area in which the associated disease occurs among humans. From this perspective, Seoul orthohantavirus (SEOV), identified in South Korea in 1982, deserves special attention because its cosmopolitan host, the Norwegian rat (Rattus norvegicus), also known as the brown rat, has been dispersed worldwide, resulting in a global distribution of the virus today (5). Detection of SEOV is often considered anecdotal and speculated to be driven by sporadic introduction of infected brown rats via transportation but also by pet or laboratory rats (6,7). Diagnosing SEOV in humans remains a challenge due to milder and atypical HFRS pathology (8). However, mild symptoms can progress to acute renal disease associated with HFRS, in which patients experience low blood pressure, acute shock, and acute kidney failure, and the case-fatality rate is ≈1% (9).
Published: 2023

36. Evolution, systematics and historical biogeography of Palparini and Palparidiini antlions (Neuroptera: Myrmeleontidae): Old origin and in situ diversification in Southern Africa

Author: Noémie M.‐C. Hévin, Gael. J. Kergoat, Anne‐Laure Clamens, Bruno Le Ru, Mervyn W. Mansell, Bruno Michel, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Université de Poitiers, Evolution, génomes, comportement et écologie (EGCE), Institut de Recherche pour le Développement (IRD)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), International Centre of Insect Physiology and Ecology (ICIPE), ICIPE, Department of Zoology and Entomology [Pretoria], University of Pretoria [South Africa], Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and Financial support was provided by CIRAD (for B. Michel), INRAE (for G.J. Kergoat), by IRD and ICIPE (for B. Le Ru). Some of the sequencing was also supported by the programme BdV (Project ICONE) supported by a joint CNRS, INRAE, and MNHN consortium and through a collaboration with F.L. Condamine (CNRS, UMR ISEM) as part of another research project.
Subjects: paleoendemism, historical biogeography, Insect Science, Southern Africa, systematics, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Afrotropics, Ecology, Evolution, Behavior and Systematics, antlions, out of Africa
Abstract: Newly generated sequences were deposited in GenBank, and are registered with the following accession numbers: OQ581997–OQ582070(cob), OQ603605–OQ603608(18S), OQ606012–OQ606168(cox1), OQ624960–OQ625111(rrnL), OQ625113–OQ625252(rrnS) and OQ625254–OQ625279(28S) (see Table S2 for details).This study is dedicated to Dr. André Prost, who passed away on February 3, 2023. André Prost was a well-recognized Neuroptera specialist (former secretary of the International Association of Neuropterology), with a special interest for the West African fauna.Merwyn W.Mansell gratefully acknowledges the following organizations and people who contributed to research on antlion diversity in SouthernAfrica: Oppenheimer Generations Research and Conservation, the Tswalu Foundation, and Nicky, Jonathan and Strilli Oppenheimer ,who have actively encouraged and permitted Neuroptera research in their private reserves, Tswalu Kalahari Reserve and Rooipoort; Duncan MacFadyen (Oppenheimer Generations, Head Research and Con-servation), Dylan Smith (Tswalu Kalahari Reserve), who facilitated ourvisits and provided key specimens. Also, (i) the National Parks Boardof South Africa is acknowledged for permits enabling Neuroptera research in the Kalahari Gemsbok National Park (now Kgalagadi Transfrontier Park), the Kruger National Park and Karoo National Park,and the staff of these parks who enabled the visits and provided valuable material: (L.E.O. Braack, A. Braack, H. Braack; Dr S. Joubert), (C.E.O., Kruger Park); (ii) Northern Cape Nature Conservation is thanked for providing permits for the northern Cape region; (iii) the KwaZulu-Natal Parks are acknowledged for permission to work on their reserves. Dr M.K. Seely, Director of the Namib Desert Research Station at Gobabeb is thanked for providing facilities and much scientifico-operation over the years; (iv) the Directorate of Nature Conservation and Recreational Resorts of Namibia are acknowledged for use offacilities at Gobabeb and permission to work in the Namib/NaukluftPark, many years ago. Professor Clarke H. Scholtz (University of Pretoria) is especially thanked for organizing many of the field trips thatprocured important material. Merwyn W. Mansell also gratefullyacknowledges the following people especially, for providing crucial specimens: J.B. Ball (University of Pretoria), A.K. (Tony) Brinkman, A.J.Gardiner, H. de Klerk, P. Hawkes, D.M. Kroon, W. Jubber, A.P. Marais,R.W. Mansell, L.R. Minter, R.G. Oberprieler, H.S Staude, R.D. Stephenand those mentioned in Mansell and Oswald (2023). The JRS Biodiversity Foundation and GBIF are sincerely thanked for funding M.W.Mansell’s Southern African Lacewing project, especially the development of the “Palpares Relational Database” designed by Brian Kenyon,which underpinned the accumulation and collation of much data usedin this presentation, for which he is gratefully acknowledged. Whileworking at icipe (African Insect Science for Food and Health), B. Le Rubenefited from research and collect permits delivered by the KenyaPlant Health Inspectorate Service (KEPHIS) (B. Le Ru thanks A. Kibe,B. Musyoka, L. Ngala, G. Okuku and G. Ong’amo) and the Plant Pro-tection Division of the Ministry of Agriculture of Botswana (B. Le Ru EVOLUTION AND SYSTEMATICS OF PALPARINE ANTLIONS thanks C. Nyakumondiwa, R. Mutamisha and E. Moeng). Bruno Michel also thanks the following people for providing several interesting specimens: B.F. Jacobs (Southern Methodist University, USA), M.Martinez (INRAE) and J.-Y. Rasplus (INRAE). We gratefully acknowledge the late A. Prost for communicating important information on the genusNosa. We are also indebted to the following persons whogave us permission to use pictures they took: S. Akame, T. Cardenos,H. de Klerk, G. Kunz, D. Robertson, H. Robertson, H. Roland, W.Roland and A.T. Schoeman. Laboratory facilities were provided by CBGP in France. We are grateful to the Genotoul bioinformatics platform Toulouse Occitanie (Bioinfo Genotoul, https://doi.org/10.15454/1.5572369328961167E12) for providing help and/or computing and/or storage resources.; International audience; Palparine and palparidiine antlions constitute an emblematic clade of large and occasionally colourful insects that are only distributed in the western portion of the Eastern hemisphere, with about half of the known species diversity occurring exclusively in Southern Africa. Little is known about their evolutionary history, and the boundaries and relationships of most genera are still unresolved. In this study, we analyse a molecular dataset consisting of seven loci (five mitochondrial and two nuclear genes) for 144 antlion species and provide the first phylogenetic hypothesis for a representative sampling of Palparini and Palparidiini (62 Palparini species, representing 15 of the 17 known genera, and all three known Palparidiini species). In addition, we reconstruct their timing of diversification and historical biogeography. The resulting tree indicates that several extant palparine genera are polyphyletic or paraphyletic and provides interesting leads that ought to be helpful for future taxonomic revisions; it also enables us to re-evaluate the taxonomic utility and relevancy of a number of morphological characters that were previously used to define some genera. Molecular dating analyses indicate that the most recent common ancestor of both groups originated about 92 million years ago (Ma) in the Late Cretaceous. Finally, the results of historical biogeography analyses provide strong support for an origin in Southern Africa, which further acted as both a cradle of diversification and a springboard for successive waves of northern dispersals.
Published: 2023

37. Spatiotemporal risk forecasting to improve locust management

Author: Cyril Piou, Lucile Marescot, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), This work was funded by ANR-JCJC (Agence Nationale de la Recherche, Programme Jeunes Chercheuses Jeunes Chercheurs, France) under the PEPPER project (ANR-18-CE32-0010-01)., and ANR-18-CE32-0010,PEPPER,Etude de l'émergence du polyphénisme de phase et des risques associés(2018)
Subjects: [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Insect Science, Ecology, Evolution, Behavior and Systematics
Abstract: We wish to thank the participants of the Symposium on ‘Forecasting Locust Risks’, organized by C. Piou during the 13th International Conference of Orthopterology, in Agadir in March 2019: Ted Deveson, Keith Cressman, Robert A. Cheke, Mohammed F. Smiej, Eduardo Trumper, and Jørgen Aagaard Axelsen. Their inputs and discussion gave a good basis for this review.; International audience; Highlights: • Spatiotemporal forecasting is a key process in the management of locusts. • Forecasts can be used at different risk levels from locust presence to impacts. • Reproducible forecasting systems are still lacking, limiting operationality. • Ecology and human capacities should be at the heart of future forecasting efforts. • Evaluations of forecasting performance need to conducted.Abstract:Locusts are among the most feared agricultural pests. Spatiotemporal forecasting is a key process in their management. The present review aims to 1) set a common language on the subject, 2) evaluate the current methodologies, and 3) identify opportunities to improve forecasting tools. Forecasts can be used to provide reliable predictions on locust presence, reproduction events, gregarization areas, population outbreaks, and potential impacts on agriculture. Statistical approaches are used for the first four objectives, whereas mechanistic approaches are used for the latter. We advocate 1) to build reliable and reproducible spatiotemporal forecasting systems for the impacts on agriculture, 2) to turn scientific studies into operational forecasting systems, and 3) to evaluate the performance of these systems.
Published: 2023

38. Evaluation of 96‐well high‐throughput DNA extraction methods for 16S rRNA gene metabarcoding

Author: Marie‐Pierre Chapuis, Laure Benoit, Maxime Galan, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Département écologie et biodiversité des milieux forestiers, prairiaux et aquatiques (ECODIV), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), MPC and LB were supported by the Insect Microbiome Project, funded by the French Agricultural Research Centre for International Development (CIRAD). Some of the data used in this work were produced through the GenSeq technical facilities of the Institut des Sciences de l'Evolution de Montpellier with the support of LabEx CeMEB, an ANR 'Investissements d'avenir' program (AN-R-1-0-LAB-X-0004)., and ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010)
Subjects: [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], metabarcoding, Genetics, animal, next-generation sequencing, bacteria, 16 rRNA gene, DNA extraction, Ecology, Evolution, Behavior and Systematics, high-throughput, Biotechnology
Abstract: Bacterial abundance data from MiSeq Illumina, Shell script for preprocessing of raw sequences and R scripts for data filtering and analyses were deposited in Cirad data repository (https://dataverse.cirad.fr) and are available from this link: https://doi.org/10.18167/DVN1/D31UAV.; International audience; Gaining meaningful insights into bacterial communities associated with animal hosts requires the provision of high-quality nucleic acids. Although many studies have compared DNA extraction methods for samples with low bacterial biomass (e.g. water) or specific PCR inhibitors (e.g. plants), DNA extraction bias in samples without inherent technical constraint (e.g. animal samples) has received little attention. Furthermore, there is an urgent need to identify a DNA extraction methods in a high-throughput format that decreases the cost and time for processing large numbers of samples. We here evaluated five DNA extraction protocols, using silica membrane-based spin columns and a 96-well microplate format and based on either mechanical or enzymatic lysis or a combination of both, using three bacterial mock communities and Illumina sequencing of the V4 region of the 16SrRNA gene. Our results showed that none of the DNA extraction methods fully eliminated bias associated with unequal lysis efficiencies. However, we identified a DNA extraction method with a lower bias for each mock community standard. Of these methods, those including an enzymatic lysis showed biases specific to some bacteria. Altogether, these results again demonstrate the importance of DNA extraction standardization to be able to compare the microbiome results of different samples. In this attempt, we advise for the use of the 96-well DNeasy Blood and Tissue kit (Qiagen) with a zirconia bead-beating procedure, which optimizes altogether the cost, handling time and bacteria-specific effects associated with enzymatic lysis.
Published: 2023

39. Reconciling fossils with phylogenies reveals the origin and macroevolutionary processes explaining the global cycad biodiversity

Author: Coiro, Mario, Allio, Rémi, Mazet, Nathan, Seyfullah, Leyla, Condamine, Fabien, University of Vienna [Vienna], Department of Palaeontology, Ronin Institute for Independent Scholarship (Ronin Institute), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), MC has been supported by the Austrian Science Fund (FWF), Lise Meitner project no. M3168. The visit of MC to the NRM and the NHM was funded by the European Union's Seventh Framework Programme (FP7/2007-2013) under grant agreement no. 226506 (SYNTHESYS project SE-TAF-5774 and project GB-TAF-5763). The computational results presented have been achieved in part using the Vienna Scientific Cluster (VSC). This project benefited from an Investissements d'Avenir' program managed by the Agence Nationale de la Recherche (CEBA, ref. ANR-10-LABX-0025) and the ANR GAARAnti project (ANR-17-CE31-0009)., ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), ANR-17-CE31-0009,GAARAnti,Pont terrestre 'GAARlandia' vs voies de dispersion à travers les Petites Antilles–Couplage entre dynamique de la subduction et processus de l'évolution des espèces dans le domaine des Caraïbes.(2017), and European Project: 226506,EC:FP7:INFRA,FP7-INFRASTRUCTURES-2008-1,SYNTHESYS(2009)
Subjects: total-evidence analysis, fossil leaves, historical biogeography, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Greenland, Antarctica, Cycadales, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy
Abstract: We dedicate this study to the memory of our esteemed colleague Nathalie S. Nagalingum.; International audience; The determinants of biodiversity patterns can be understood using macroevolutionary analyses. The integration of fossils into phylogenies offers a deeper understanding of processes underlying biodiversity patterns in deep time. Cycadales are considered a relict of a once more diverse and globally distributed group but are restricted to low latitudes today. We still know little about their origin and geographic range evolution. Combining molecular data for extant species and leaf morphological data for extant and fossil species, we study the origin of cycad global biodiversity patterns through Bayesian totalevidence dating analyses. We assess the ancestral geographic origin and trace the historical biogeography of cycads with a time-stratified process-based model. Cycads originated in the Carboniferous on the Laurasian landmass and expanded in Gondwana in the Jurassic. Through now-vanished continental connections, Antarctica and Greenland were crucial biogeographic crossroads for cycad biogeography. Vicariance is an essential speciation mode in the deep and recent past. Their latitudinal span increased in the Jurassic and restrained toward subtropical latitudes in the Neogene in line with biogeographic inferences of high-latitude extirpations. We show the benefits of integrating fossils into phylogenies to estimate ancestral areas of origin and to study evolutionary processes explaining the global distribution of present-day relict groups.
Published: 2023

40. Biological invasions in international seaports: a case study of exotic rodents in Cotonou

Author: Sylvestre Badou, Karmadine Hima, Clément Agbangla, Philippe Gauthier, Antoine A. Missihoun, Gualbert Houéménou, Anne Loiseau, Carine Brouat, Gauthier Dobigny, Ecole Polytechnique d'Abomey Calavi (EPAC), Université d’Abomey-Calavi = University of Abomey Calavi (UAC), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Université Abdou Moumouni [Niamey], Unité Peste - Plague Unit [Antananarivo, Madagascar], Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Sylvestre Badou was granted a Doctoral Research Fellowship (ARTS) by IRD (2019–2022). Data used in this work were produced through the genotyping and sequencing facilities of Labex CeMEB mutualized GenSeq platform (Mediterranean Center for Environment and Biodiversity, Genotyping-Sequencing Platform). This work is part of the PASPort/PPSE project funded by ACP, IRD and ENABEL., and ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010)
Subjects: Urban Studies, Rodent management, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Ecology, Population genetics, Movement, Urban, Invasive rodents Population genetics Movement Urban Rodent management, Invasive rodents
Abstract: Black rat (Rattus rattus), brown rat (Rattus norvegicus), and house mouse (Mus musculus) are known to be among the most common anthropophilic rodent species in cities worldwide. These species are responsible for the destruction of domestic and industrial materials, considerable damage to food stocks as well as zoonotic pathogens circulation and transmission to humans and animals. These invasive species have disseminated in all continents following human-mediated exchanges, especially maritime transports. In particular, seaports appear as privileged rats and mice’s entry points into new regions, thus making them international regulations’ priorities for rodent surveillance and management. Yet, studies on seaport rodents are rare; in particular, investigations on their genetic structure are almost inexistent, thus precluding science-guided interventions. In order to fill such a gap, our study focused on the population genetics of R. rattus, R. norvegicus and M. musculus in the Autonomous Port of Cotonou, Benin. Nine different sites were surveyed for three years. In total, 366 R. rattus, 188 R. norvegicus and 244 M. musculus were genotyped using 18 microsatellites, 16 microsatellites and 17 microsatellites, respectively. Our results show very well-structured genetic clusters in all three species as well as limited impacts of rodent control campaigns. Using comparisons with genotypes from other European, Asian and African countries, we suggest for the first time that settlement of newly introduced individuals may be a rare event. Implications in terms of management units and control and monitoring are discussed.
Published: 2023

41. A new species of Paragigagnathus Amitai and Grinberg (Mesostigmata: Phytoseiidae) from Iran

Author: Alireza Arjmandi-Nezhad, Serge Kreiter, Alireza Saboori, Sultan Ravan, University of Zabol, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), University of Tehran, Department of Plant Protection, Faculty of Agriculture, University of Tehran, Karaj, Iran., and This study was partly supported by University of Zabol, Zabol, Sistan and Baluchestan, Iran and partly from Department of Plant Protection, Faculty of Agriculture, University of Tehran, Karaj, Iran, which is greatly appreciated.
Subjects: [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, new taxon, Arthropoda, Aacriformes, Insect Science, morphology, Tamarix, predatory mites, Animalia, Sistan and Baluchestan, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Acari, Gamasina
Abstract: International audience; Paragigagnathus sistaniensis Kreiter, Arjmandi-Nezhad and Saboori n. sp. belongs to the tribe Neoseiulini, subfamily Amblyseiinae, is described and illustrated, based on females and males. The new species was collected from foliage of tamarisk trees in Sistan region, Sistan and Baluchestan province, southeastern Iran.
Published: 2022

42. Epigenetics and the city: Non‐parallel DNA methylation modifications across pairs of urban‐forest Great tit populations

Author: Aude E. Caizergues, Jeremy Le Luyer, Arnaud Grégoire, Marta Szulkin, Juan‐Carlos Senar, Anne Charmantier, Charles Perrier, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Ecosystèmes Insulaires Océaniens (UMR 241) (EIO), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de la Polynésie Française (UPF)-Institut Louis Malardé [Papeete] (ILM), Institut de Recherche pour le Développement (IRD), University of Warsaw (UW), Centre of New Technologies, Museu de Ciències Naturals de Barcelona, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, European Research Council: Starting grant ERC-2013-StG-337365-SHE (AC), OSU-OREME, Polish National Science Centre grants Sonata BIS 2014/14/E/NZ8/00386 and Opus 2016/21/B/NZ8/03082 (MS), Ministry of Economy and Competitivity, Spanish Research Council grant CGL--2016-79568--C3--3--P (JCS)., and European Project: 337365,EC:FP7:ERC,ERC-2013-StG,SHE(2014)
Subjects: 0106 biological sciences, 0303 health sciences, DNA methylation, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Evolution, urbanization, Original Articles, adaptation, 15. Life on land, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, epigenomics, 11. Sustainability, QH359-425, genomics, Genetics, Original Article, General Agricultural and Biological Sciences, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology
Abstract: DNA sequences: RAD-seq GenBank accessions SRR17125662- SRR17125721, RRBS-seq GenBank accessions SRR17145241-SRR17145300; NCBI project PRJNA786007. Scripts: Github repository https://github.com/AudeCaizergues/Epigenetics_and_the_city.; International audience; Identifying the molecular mechanisms involved in rapid adaptation to novel environments and determining their predictability are central questions in evolutionary biology and pressing issues due to rapid global changes. Complementary to genetic responses to selection, faster epigenetic variations such as modifications of DNA methylation may play a substantial role in rapid adaptation. In the context of rampant urbanization, joint examinations of genomic and epigenomic mechanisms are still lacking. Here, we investigated genomic (SNP) and epigenomic (CpG methylation) responses to urban life in a passerine bird, the Great tit (Parus major). To test whether urban evolution is predictable (i.e. parallel) or involves mostly nonparallel molecular processes among cities, we analysed both SNP and CpG methylation variations across three distinct pairs of city and forest Great tit populations in Europe. Our analyses reveal a polygenic response to urban life, with both many genes putatively under weak divergent selection and multiple differentially methylated regions (DMRs) between forest and city great tits. DMRs mainly overlapped transcription start sites and promotor regions, suggesting their importance in modulating gene expression. Both genomic and epigenomic outliers were found in genomic regions enriched for genes with biological functions related to the nervous system, immunity, or behavioural, hormonal and stress responses. Interestingly, comparisons across the three pairs of city-forest populations suggested little parallelism in both genetic and epigenetic responses. Our results confirm, at both the genetic and epigenetic levels, hypotheses of polygenic and largely nonparallel mechanisms of rapid adaptation in novel environments such as urbanized areas.
Published: 2022

43. Linking genetic, morphological, and behavioural divergence between inland island and mainland deer mice

Author: Joshua M. Miller, Dany Garant, Charles Perrier, Tristan Juette, Joël W. Jameson, Eric Normandeau, Louis Bernatchez, Denis Réale, Département des Sciences Biologiques [Montréal], Université du Québec à Montréal = University of Québec in Montréal (UQAM), MacEwan University, Université de Sherbrooke (UdeS), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Departement de Biologie [Québec], Université Laval [Québec] (ULaval), and This research was funded by a Fonds de Recherche du Québec - Nature et Technologies (FRQNT) team grant to D. Réale, D. Garant, and L. Bernatchez, and by a Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery grant to D. Réale.
Subjects: Gene Flow, 0106 biological sciences, 0303 health sciences, Behavior, Animal, [SDV]Life Sciences [q-bio], Genetic Drift, Genetic Variation, Biological Evolution, 010603 evolutionary biology, 01 natural sciences, Article, 03 medical and health sciences, Peromyscus, parasitic diseases, Genetics, Animals, Genetics (clinical), 030304 developmental biology
Abstract: International audience; The island syndrome hypothesis (ISH) stipulates that, as a result of local selection pressures and restricted gene flow, individuals from island populations should differ from individuals within mainland populations. Specifically, island populations are predicted to contain individuals that are larger, less aggressive, more sociable, and that invest more in their offspring. To date, tests of the ISH have mainly compared oceanic islands to continental sites, and rarely smaller spatial scales such as inland watersheds. Here, using a novel set of genome-wide SNP markers in wild deer mice (Peromyscus maniculatus) we conducted a genomic assessment of predictions underlying the ISH in an inland riverine island system: analysing island-mainland population structure, and quantifying heritability of phenotypes thought to underlie the ISH. We found clear genomic differentiation between the island and mainland populations and moderate to high marker-based heritability estimates for overall variation in traits previously found to differ in line with the ISH between mainland and island locations. F-ST outlier analyses highlighted 12 loci associated with differentiation between mainland and island populations. Together these results suggest that the island populations examined are on independent evolutionary trajectories, the traits considered have a genetic basis (rather than phenotypic variation being solely due to phenotypic plasticity). Coupled with the previous results showing significant phenotypic differentiation between the island and mainland groups in this system, this study suggests that the ISH can hold even on a small spatial scale.
Published: 2021

44. Population genetics as a tool to elucidate pathogen reservoirs: Lessons from Pseudogymnoascus destructans , the causative agent of White‐Nose disease in bats

Author: Nicola M. Fischer, Surendra Ranpal, Gerald Kerth, Serena E. Dool, Sébastien J. Puechmaille, Andrea Altewischer, Universität Greifswald - University of Greifswald, Zoological Institute and Museum, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), and This work was supported by Bat Conservation International (awarded to SJP), the Deutsche Forschungsgemeinschaft (PU 527/2d-1, awarded to SJP), and the Institut Universitaire de France (awarded to SJP). Open access funding enabled and organized by ProjektDEAL.
Subjects: wildlife pathogen, Disease reservoir, [SDV]Life Sciences [q-bio], Population, Population genetics, Zoology, Fungus, Biology, Hibernaculum, Ascomycota, Pseudogymnoascus destructans, Chiroptera, Hibernation, Nose Diseases, Genotype, Genetics, Animals, Humans, fungal pathogen, education, Pathogen, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Ecology, Evolution, Behavior and Systematics, education.field_of_study, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Host (biology), White-Nose syndrome, emerging infectious disease, biology.organism_classification, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Genetics, Population, Mycoses, Emerging infectious disease, Species richness, disease reservoir
Abstract: Emerging infectious diseases pose a major threat to human, animal, and plant health. The risk of species-extinctions increases when pathogens can survive in the absence of the host, for example in environmental reservoirs. However, identifying such reservoirs and modes of infection is often highly challenging. In this study, we investigated the presence and nature of an environmental reservoir for the ascomycete fungus Pseudogymnoascus destructans, the causative agent of white-nose disease. We also characterised the modes and timing of transmission of the pathogen; key elements to better understand the disease dynamics. Using 18 microsatellite markers, we determined the genotypic and genic (based on allele frequencies) differentiation between 1,497 P. destructans isolates collected from nine closely situated hibernacula in North-Eastern Germany. One hibernaculum was the focus of intensive sampling in which both the bats and walls of the site were sampled at regular intervals over five consecutive winter seasons (1,062 isolates). We found significant genic differentiation between sites and few multi-locus genotypes shared across hibernacula (genotypic differentiation). This demonstrates that each hibernaculum has an essentially unique population of the fungus. This would be expected if bats purge viable P. destructans over the summer, preventing the mixing and exchange of the pathogen in maternity colonies, where bats from all of the studied hibernacula meet. Results from the intensively sampled site show higher measures of genotypic richness on walls compared to bats, the absence of genic differentiation between bats and walls, and stable relative abundance of multi-locus genotypes over multiple winter seasons. This clearly implicates hibernacula walls as the main environmental reservoir of the pathogen, from which bats become re-infected annually.
Published: 2021

45. New Phytoseiidae (Acari: Mesostigmata) of Mascareignes and Comoros Archipelagos (Indian Ocean): one new record, three new species groups and description of six new species and of six unknown males

Author: Rose-My Payet, Martial Douin, Reham Abo-Shnaf, Serge Kreiter, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Fonctionnement agroécologique et performances des systèmes de cultures horticoles (UPR HORTSYS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Plant Protection Research Institute (PPRI), Agricultural Research Centre (ARC), 7 Nadi El-Seid Street, Dokii, 12611 Giza, Egypt., Thanks are to the I-SITE Montpellier Université d'Excellence (MUSE) for the international mobility support to the third author for the current work (Explore #2, the MUSE International Mobility program, 2019). Grateful thanks are to UR Hortsys and to the head, Dr Fabrice Le Bellec, who have allowed the second author Rose-My Payet to join the senior author on collection trips and partly funding field collecting trips. Field collections had been made with authorizations of the Government of Union des Comores by letters of the head of INRAPE, Union des Comores (ref. n°18/193/INRAPE/DG and n°18/210/INRAPE/DG, respectively)., European Project: ANR-16-IDEX-0006,MUSE, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: 0106 biological sciences, Systematics, Phytoseiidae, Arthropoda, Aacriformes, Fauna, 010607 zoology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Acariformes, 01 natural sciences, Amblyseius erici Kreiter n. sp, Arachnida, predatory mites, Animalia, survey, Acari, 14. Life underwater, Typhlodromalus baillodi Kreiter n. sp, systematics, Ueckermannseius gutierrezi Kreiter n. sp, Taxonomy, geography, geography.geographical_feature_category, biology, Ecology, Biodiversity, biology.organism_classification, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, Ueckermannseius payetae Kreiter n. sp, 010602 entomology, Insect Science, Mesostigmata, Archipelago, Taxonomy (biology), Paragigagnatus philippei Kreiter n. sp, Ueckermannseius jean-mariei Kreiter n. sp
Abstract: International audience; Faunas of Phytoseiidae of the Mascareignes Archipalago (Réunion, Mauritius and Rodrigues Islands) and of the Comoros Archipelago (Mayotte, Anjouan, Mohéli and Grande Comore Isands) were recently investigated by authors of this paper and results were published in seven already published papers. We described in this eighth paper six species new to science and six unknown males collected during these surveys.
Published: 2021

46. Small terrestrial mammals (Rodentia and Soricomorpha) along a gradient of forest anthropisation (reserves, managed forests, urban parks) in France

Author: Julien Pradel, Marie Bouilloud, Anne Loiseau, Sylvain Piry, Maxime Galan, Emmanuelle Artige, Guillaume Castel, Julien Ferrero, Romain Gallet, Geoffrey Thuel, Nathalie Vieira, Nathalie Charbonnel, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM), This project is funded through the 2018-2019 BiodivERsA joint call for research proposals, under the BiodivERsA3 ERA-Net COFUND programme, and with the funding organisations ANR (France), DFG (Germany), EPA (Ireland), FWO (Belgium) and NCN (Poland)., and European Project: 642420,H2020,H2020-SC5-2014-one-stage,BiodivERsA3(2015)
Subjects: Vertebrata, Tetrapoda, forests, Ecology, Sarcopterygii, Eutheria, global changes, [SDV]Life Sciences [q-bio], urban parks, Rodentia, Amniota, Biota, shrews, Gnathostomata, Osteichthyes, Theria, Soricomorpha, rodents, Mammalia, dilution effect, Animalia, community, Chordata, Ecology, Evolution, Behavior and Systematics, biodiversity
Abstract: Understanding the relationships between wildlife biodiversity and zoonotic infectious diseases in a changing climate is a challenging issue that scientists must address to support further policy actions. We aim at tackling this challenge by focusing on small mammal-borne diseases in temperate forests and large urban green spaces. Small mammals are important reservoirs of zoonotic agents, with a high transmission potential for humans and domestic animals. Forests and large urban green spaces are ecosystems where efforts are undertaken to preserve biodiversity. They are put forward for their contribution to human well-being in addition to other ecosystem services (e.g. provisioning and regulating services). Moreover, forests and large urban green spaces are environments where small mammals are abundant and human/domestic-wildlife interactions are plausible to occur. These environments are, therefore, focal points for conservation management and public health issues. The European Biodiversa BioRodDis project (https://www6.inrae.fr/biodiversa-bioroddis) aims at better understanding the relationships between small terrestrial mammal biodiversity and health in the context of global change and, in particular, of forest anthropisation and urbanisation. Here, we present the data gathered in France. The dataset will enable us to describe the diversity of small terrestrial mammal communities in forested areas corresponding to different levels of anthropisation and to evaluate the variability of this diversity over time, between seasons and years. The dataset contains occurrences of small terrestrial mammals (Rodentia and Soricomorpha) trapped in forested areas in eastern France (administrative Departments: Rhône, Ain, Jura). The sampling sites correspond to different degrees of anthropisation. Forests included in biological reserves are the least anthropised sites. Then, public forests and urban parks experience increasing levels of anthropisation. Data were collected during spring and autumn 2020 (three to four sampling sites), 2021 (six sampling sites) and 2022 (four sampling sites). These variations in the number of sites between years were due to lockdown restrictions in 2020 or to the legal authorisation to trap around biological reserves granted in 2021 only. The capture of animals was carried out in various types of forests (pine, deciduous, mixed) and in different habitats within urban parks (wooded areas, buildings, hay storage yards, riverside vegetation, restaurants, playground for kids, botanical garden, landfills). Animals were captured using live traps that were set on the ground for one to 11 nights. During this study period, 1593 small mammals were trapped and identified. They belong to 15 species, amongst which were nine species of rodents (Muridae, Cricetidae, Gliridae) and six species of shrews (Soricidae). They were weighted (gram) and measured (cm): head-body length, tail length and hind-foot length. Sexual characteristics were also recorded.
Published: 2022

47. From hell's heart I stab at thee! A determined approach towards a monophyletic Pteromalidae and reclassification of Chalcidoidea (Hymenoptera)

Author: Roger Burks, Mircea-Dan Mitroiu, Lucian Fusu, John M. Heraty, Petr Janšta, Steve Heydon, Natalie Dale-Skey Papilloud, Ralph S. Peters, Ekaterina V. Tselikh, James B. Woolley, Simon van Noort, Hannes Baur, Astrid Cruaud, Christopher Darling, Michael Haas, Paul Hanson, Lars Krogmann, Jean-Yves Rasplus, University of California [Riverside] (UC Riverside), University of California (UC), Alexandru Ioan Cuza University of Iași [Romania], Charles University [Prague] (CU), University of California [Davis] (UC Davis), The Natural History Museum [London] (NHM), Zoologisches Forschungsmuseum Alexander Koenig, Zoological Institute of Russian Academy of Sciences, Russian Academy of Sciences [Moscow] (RAS), Texas A&M University [College Station], University of Cape Town, University of Bern, Natural History Museum Bern, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), University of Toronto, Royal Ontario Museum, Stuttgart State Museum of Natural History, Universidad de Costa Rica (UCR), University of Hohenheim, Grant support was provided in part by NSF DEB-1555808 to J. Heraty, J.B. Woolley and M. Yoder. This work was also partly supported by the ANR projects TRIPTIC (ANR-14-CE18-0002) , BIDIME (ANR-19-ECOM-0010) and recurring funding of the INRAE to A. Cruaud and J.Y. Rasplus., ANR-14-CE18-0002,TriPTIC,Trichogramma pour la protection des cultures: Pangénomique, Traits d'histoire de vIe et Capacités d'établissement(2014), and ANR-19-ECOM-0010,Bidime,BIodiversité des trichogrammes, Diversification des produits de biocontrôle et nouveaux Modèles Economiques(2019)
Subjects: Chalcidoidea, Insecta, Arthropoda, Insect Science, [SDV]Life Sciences [q-bio], taxonomic change, Animalia, New family, Biota, Hymenoptera, Ecology, Evolution, Behavior and Systematics, Pteromalidae
Abstract: We thank Daniel Alejandro Aquino (Museo de La Pla- ta) , Fernando H. A. Farache (Rio Verde) , Jeremy Frank (Bishop Museum) , and Ryan Perry (UC Santa Barbara) for helpful photographs of type specimens. We thank Nicole Fisher and Juanita Rodriguez Arrieta (ANIC, Canberra) as well as Christine Lambkin, Chris Burwell and Susan Wright (QM, Brisbane) for the loan of multiple Australian specimens. We acknowledge the Queensland government for collecting permits (WITK18248017-WITK18278817).; International audience; The family Pteromalidae (Hymenoptera: Chalcidoidea) is reviewed with the goal of providing nomenclatural changes and morphological diagnoses in preparation for a new molecular phylogeny and a book on world fauna that will contain keys to identification. Most subfamilies and some tribes of Pteromalidae are elevated to family level or transferred elsewhere in the superfamily. The resulting classification is a compromise, with the aim of preserving the validity and diagnosability of other, well-established families of Chalcidoidea. The following former subfamilies and tribes of Pteromalidae are elevated to family rank: Boucekiidae, Ceidae, Cerocephalidae, Chalcedectidae, Cleonymidae, Coelocybidae, Diparidae, Epichrysomallidae, Eunotidae, Herbertiidae, Hetreulophidae, Heydeniidae, Idioporidae, Lyciscidae, Macromesidae, Melanosomellidae, Moranilidae, Neodiparidae, Ooderidae, Pelecinellidae (senior synonym of Leptofoeninae), Pirenidae, Spalangiidae, and Systasidae. The following subfamilies are transferred from Pteromalidae: Chromeurytominae and Keiraninae to Megastigmidae, Elatoidinae to Neodiparidae, Nefoeninae to Pelecinellidae, and Erotolepsiinae to Spalangiidae. The subfamily Sycophaginae is transferred to Pteromalidae. The formerly incertae sedis tribe Lieparini is abolished and its single genus Liepara is transferred to Coelocybidae. The former tribe Tomocerodini is transferred to Moranilidae and elevated to subfamily status. The former synonym Tridyminae (Pirenidae) is treated as valid. The following former Pteromalidae are removed from the family and, due to phylogenetic uncertainty, placed as incertae sedis subfamilies or genera within Chalcidoidea: Austrosystasinae, Ditropinotellinae, Keryinae, Louriciinae, Micradelinae, Parasaphodinae, Rivasia, and Storeyinae. Within the remaining Pteromalidae, Miscogastrinae and Ormocerinae are confirmed as separate from Pteromalinae, the former tribe Trigonoderini is elevated to subfamily status, the former synonym Pachyneurinae is recognized as a distinct subfamily, and as the senior synonym of Austroterobiinae. The tribe Termolampini is synonymized under Pteromalini, and the tribe Uzkini is synonymized under Colotrechnini. Most former Otitesellinae, Sycoecinae, and Sycoryctinae are retained in the tribe Otitesellini, which is transferred to Pteromalinae, and all other genera of Pteromalinae are treated as Pteromalini. Eriaporidae is synonymized with Pirenidae, with Eriaporinae and Euryischiinae retained as subfamilies. Other nomenclatural acts performed here outside of Pteromalidae are as follows: Calesidae: elevation to family rank. Eulophidae: transfer of Boucekelimini and Platytetracampini to Opheliminae, and abolishment of the tribes Elasmini and Gyrolasomyiini. Baeomorphidae is recognized as the senior synonym of Rotoitidae. Khutelchalcididae is formally excluded from Chalcidoidea and placed as incertae sedis within Apocrita. Metapelmatidae and Neanastatidae are removed from Eupelmidae and treated as distinct families. Eopelma is removed from Eupelmidae and treated as an incertae sedis genus in Chalcidoidea. The following subfamilies and tribes are described as new: Cecidellinae (in Pirenidae), Enoggerinae (incertae sedis in Chalcidoidea), Erixestinae (in Pteromalidae), Eusandalinae (in Eupelmidae), Neapterolelapinae (incertae sedis in Chalcidoidea), Solenurinae (in Lyciscidae), Trisecodinae (in Systasidae), Diconocarini (in Pteromalidae: Miscogastrinae), and Trigonoderopsini (in Pteromalidae: Colotrechninae). A complete generic classification for discussed taxa is provided.
Published: 2022

48. The tribes Kampimodromini Kolodochka and Typhlodromipsini Chant and McMurtry (Mesostigmata: Phytoseiidae) in the Serra do Espinhaço, Brazil, with a key to the Brazilian species of Typhlodromips De Leon

Author: Francisco Ferragut, Denise Navia, Universitat Politècnica de València (UPV), Instituto Agroforestal Mediterraneo (IAM), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), and Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq), Brazil, for granting the fellowship to the second author (DN) (PP, Process N degrees 3121322017-4).
Subjects: taxonomy, Proprioseius, Insect Science, [SDV]Life Sciences [q-bio], neotropical, predatory mites, Neoparaphytoseius, Typhlodromips
Abstract: International audience; Phytoseiid mites of the tribes Kampimodromini and Typhlodromipsini collected from the Serra do Espinhaço (Espinhaço range) are reported here. Two species are proposed as new, Neoparaphytoseius moraesi sp. nov. and Typhlodromips ovametapodalis sp. nov. Typhlodromips constrictatus (El-Banhawy) is redescribed in detail including the first description of the male and the female insemination apparatus. The redescription of the female and the first description of the male and deutonymph of Proprioseius gibbus Moraes and Denmark are given. Complementary descriptions of the females of T. ariri Gondim Jr. and Moraes and T. japi Lofego, Demite and Feres are also included. A key is provided for the separation of the Brazilian species of the genus Typhlodromips.
Published: 2022

49. The evolutionary process of invasion in the fall armyworm (Spodoptera frugiperda)

Author: Sudeeptha Yainna, Wee Tek Tay, Karine Durand, Estelle Fiteni, Frédérique Hilliou, Fabrice Legeai, Anne-Laure Clamens, Sylvie Gimenez, R. Asokan, C. M. Kalleshwaraswamy, Sharanabasappa S. Deshmukh, Robert L. Meagher, Carlos A. Blanco, Pierre Silvie, Thierry Brévault, Anicet Dassou, Gael J. Kergoat, Thomas Walsh, Karl Gordon, Nicolas Nègre, Emmanuelle d’Alençon, Kiwoong Nam, Diversité, Génomes & Interactions Microorganismes - Insectes [Montpellier] (DGIMI), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), Agroécologie et Intensification Durables des cultures annuelles (UPR AIDA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), CSIRO Agriculture and Food (CSIRO), Black Mountain Laboratories, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Indian Institute of Horticultural Research [Bangalore] (ICAR), University of Agricultural and Horticultural Sciences [Shivamogga] (UAHS), USDA-ARS : Agricultural Research Service, USDA Agricultural Research Service [Beltsville, Maryland], Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Plateforme bioinformatique GenOuest [Rennes], Université de Rennes (UR)-Plateforme Génomique Santé Biogenouest®-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), This work (ID 1702-018, given to KN) was publicly funded through ANR (the French National Research Agency) under the 'Investissements d'avenir' programme with the reference ANR-10-LABX-0001 Labex Agro and coordinated by Agropolis Fondation under the frame of I-SITE MUSE (ANR-16-IDEX-0006). In addition, a grant from the department of Sante des Plantes et Environnement at Institut national de la recherche agronomique for KN ( adaptivesv). This work was also financially supported by EUPHRESCO (FAW-spedcom, given to Anne-Nathalie Volkoff) and by CSIRO Health & biosecurity (given to WTT, TW, and KG). SY was supported by a CIRAD-INRAE PhD fellowship. We are grateful to the genotoul bioinformatics platform Toulouse Occitanie (Bioinfo Genotoul, https://doi.org/10.15454/1.557236932896116 7E12) for providing help and/or computing and/or storage resources., ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), and ANR-16-IDEX-0006,MUSE,MUSE(2016)
Subjects: Multidisciplinary, MESH: Humans, MESH: Spodoptera, MESH: Asia, MESH: Africa, Western, Spodoptera frugiperda, MESH: Animals, MESH: Africa, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], MESH: Phylogeny, H10 - Ravageurs des plantes
Abstract: The resequencing dataset generated during the current study is available in the NCBI SRA (Accession Number: PRJNA639295).Computer programming scripts used in this study are available on GitHub (https://github.com/kiwoong-nam/FAW_invasion).; International audience; The fall armyworm (FAW; S podoptera frugiperda ) is one of the major agricultural pest insects. FAW is native to the Americas, and its invasion was first reported in West Africa in 2016. Then it quickly spread through Africa, Asia, and Oceania, becoming one of the main threats to corn production. We analyzed whole genome sequences of 177 FAW individuals from 12 locations on four continents to infer evolutionary processes of invasion. Principal component analysis from the TPI gene and whole genome sequences shows that invasive FAW populations originated from the corn strain. Ancestry coefficient and phylogenetic analyses from the nuclear genome indicate that invasive populations are derived from a single ancestry, distinct from native populations, while the mitochondrial phylogenetic tree supports the hypothesis of multiple introductions. Adaptive evolution specific to invasive populations was observed in detoxification, chemosensory, and digestion genes. We concluded that extant invasive FAW populations originated from the corn strain with potential contributions of adaptive evolution.
Published: 2022

50. Serologic Surveillance for SARS-CoV-2 Infection among Wild Rodents, Europe

Author: Vincent Bourret, Lara Dutra, Hussein Alburkat, Sanna Mäki, Ella Lintunen, Marine Wasniewski, Ravi Kant, Maciej Grzybek, Vinaya Venkat, Hayder Asad, Julien Pradel, Marie Bouilloud, Herwig Leirs, Valeria Carolina Colombo, Vincent Sluydts, Peter Stuart, Andrew McManus, Jana A. Eccard, Jasmin Firozpoor, Christian Imholt, Joanna Nowicka, Aleksander Goll, Nathan Ranc, Guillaume Castel, Nathalie Charbonnel, Tarja Sironen, Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Unité de recherche Comportement et Ecologie de la Faune Sauvage (CEFS), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de la rage et de la faune sauvage de Nancy (LRFSN), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Medical University of Gdańsk, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), University of Antwerp (UA), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Westfälische Wilhelms-Universität Münster = University of Münster (WWU), University of Potsdam = Universität Potsdam, Julius Kühn-Institute, Munster Technological University (MTU), Julius Kühn-Institut (JKI), BiodivErsA3, Our research was funded through the European H2020 (WP 2018-2020) call and the 2018–2019 BiodivERsA joint call for research proposals, under the BiodivErsA3 ERA-Net COFUND program and cofunded by Agence Nationale de la Recherche, Research Foundation–Flanders, National Science Centre, Poland, Deutsche Programme 2021–2030. The National Science Centre, Poland, supported M.G., J.N., and A.G. under the BiodivERsA3 program (2019/31/Z/NZ8/04028).Sampling from Thuringia (Germany) was funded by the DFG Priority Program 1374.Trapping data from this study will be available in Germany in the Biodiversity Exploratories Information System (https://doi.org/10.17616/R32P9Q).Forschungsgemeinschaft, and the EPA Research, European Project: 101052342,Biodiversa+, Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM), funded from Agence Nationale de la Recherche, Research FoundationFlanders, National Science Centre, Poland, Deutsche Forschungsgemeinschaft, and the EPA Research Programme 2021-2030. The National Science Centre, Poland, supported M.G., J.N., and A.G. under the BiodivERsA3 program (2019/31/Z/NZ8/04028). Sampling from Thuringia (Germany) was funded by the DFG Priority Program 1374, European Project: 138572,FCT::,BiodivERsA/2014,BiodivERsA/0001/2014(2015), Medicum, Faculty of Veterinary Medicine, Department of Virology, Emerging Infections Research Group, Faculty Common Matters (Faculty of Medicine), Helsinki One Health (HOH), and Viral Zoonosis Research Unit
Subjects: Microbiology (medical), Epidemiology, serology, Rodentia, serologic tests, Antibodies, Viral, respiratory infections, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, Animals, Humans, viruses, severe acute respiratory infection coronavirus 2, 11832 Microbiology and virology, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, SARS-CoV-2, COVID-19, zoonoses, Europe, Infectious Diseases, serosurveillance, coronavirus disease, 3121 General medicine, internal medicine and other clinical medicine, rodents, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Human medicine, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: We report results from serologic surveillance for exposure to SARS-CoV-2 among 1,237 wild rodents and small mammals across Europe. All samples were negative, with the possible exception of 1. Despite suspected potential for human-to-rodent spillover, no evidence of widespread SARS-CoV-2 circulation in rodent populations has been reported to date.Esitämme tulokset serologisesta tutkimuksesta, jossa seulottiin SARS-CoV-2 tartuntojen varalta 1,237 luonnonvaraista jyrsijää ja piennisäkästä eri puolilta Eurooppaa. Kaikki näytteet olivat negatiivisia, yhtä näytettä lukuun ottamatta. SARS-CoV-2:n läikkymisen ihmisistä jyrsijöihin on arveltu olevan mahdollista, mutta todisteet viruksen laajamittaisesta leviämisestä jyrsijäpopulaatioissa puuttuvat.
Published: 2022

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