Protocols for field and laboratory rodent studies

http://www.ceropath.org/references/rodent_protocols_bookTechnical book"Protocols for field and laboratory rodent studies" present the best practices for the studies of rodents and rodent-borne pathogens and parasites from the field to the laboratory. It aims at covering the different steps of rodent studies: 1) Trapping, 2) Dissection and preparation of tissue samples for pathogens screening, 3) Identification of species, 4) Isolation of helminths, 5) Preparing rodent specimens for collections. This book gathers accurate recommendations and techniques, based on those generally accepted in the literature and adapted from the experience of the different authors during rodent surveys and laboratory work. Its presentation is designed to work in the fields with a clear and colorful organization of each chapter, with: inserts providing definitions and recommendations, protocols detailed step by step, and an emphasis on illustrations with several photographs. This book is a publication generated by the CERoPath project (Community Ecology of Rodents and their Pathogens in a changing environment, www.ceropath.org) funded by the French Ministry of Research from 2008 to 2011

Molecular phylogeny of South-East Asian arboreal murine rodents

peer reviewedRecent phylogenetic studies and taxonomic reviews have led to nearly complete resolution of the phylogenetic divisions within the old world rats and mice (Muridae, Murinae). The Micromys division and Pithecheir division are two notable exceptions where groupings of species into these divisions based on morphology and arboreal lifestyle have not been supported by phylogenetic evidence. Several enigmatic species from these divisions have been missing from molecular studies, preventing a rigorous revision of phylogenetic relationships. In this study, we sequenced for the first time one mitochondrial and three nuclear genes from South-East Asian keystone species of these two arboreal divisions: Hapalomys delacouri (Micromys division), Lenothrix canus and Pithecheir parvus (Pithecheir division). We also complemented the molecular data already available for the two divisions with new data from Sundaic Chiropodomys, Indian Vandeleuria oleracea and the recently described Sulawesian Margaretamys christinae. Using this new phylogenetic framework and molecular dating methodologies, our study allows some more detailed classification of the former Micromys and Pithecheir divisions, while confirming their polyphyletic status. Specifically, the former Micromys division should now be split into four monotypic divisions: Chiropodomys, Hapalomys, Micromys and Vandeleuria divisions. The former Pithecheir division is likely to be refined and restricted to Pithecheir and probably Pithecheirops, whereas Lenothrix and Margaretamys should now be recognized as representatives of the Dacnomys division. Our findings have profound implications with regard to the systematics of Murinae, as well as to the early evolution of murine morphology and dental characters

Insights into Myodes glareolus / Puumala hantavirus interactions from rodent immunogenetics

Nephropathia epidemica (NE) is a mild form of hemorrhagic fever with renal syndrome (HFRS) caused by the hantavirus Puumala (PUUV). In Europe, its distribution is fragmented, whereas the bank vole Myodes glareolus, which is the reservoir of PUUV, is common all over the continent. Determining the causes underlying this heterogeneity is of main importance to better understand and prevent the risks of NE emergence. Besides climatic and ecological hypotheses, we have proposed that the geographic variability of bank vole immune responses to PUUV infection could shape differences in PUUV prevalence, and consequently NE incidence. We have tested this hypothesis by studying polymorphisms and / or expression levels of six candidate genes involved in the immune response to PUUV (DRB-MHC, TNF-alpha promoter, TLR4, TLR7, Mx2, Integrin bêta3) on ten populations of bank voles sampled in the French Ardennes, along a North-South transect including PUUV endemic and non-endemic areas. Signatures of selection have been evidenced for TNF-alpha and Mx2 genes using population genetics (FST scan) and genotype - phenotype association approaches. These genes have antiviral properties but also induce immunological damages, what make them central for driving a balance of resistance / tolerance to PUUV. Bank voles vary in their basal ability to tolerate/resist to PUUV. In high PUUV prevalence areas, TNF-alpha and Mx2 expression seemed down-regulated what suggest selection or phenotypic plasticity for higher tolerance to PUUV, at the benefit of lower immunopathological costs. Some of these results have been confirmed at the European scale.Le campagnol roussâtre Myodes glareolus est le réservoir de l’hantavirus Puumala (PUUV), responsable chez l’Homme d’une forme atténuée de Fièvre Hémorragique à Syndrome Rénal (FHSR), la Néphropathie Épidémique (NE). En Europe, l’incidence de la NE présente, malgré la distribution continue du réservoir, une forte variabilité géographique dont les causes ne sont à ce jour pas identifiées. Aux hypothèses climatiques et paysagères, nous proposons que des facteurs intrinsèques aux campagnols puissent également être impliqués. Une plus forte tolérance à l’infection par le virus PUUV, chez certains campagnols roussâtres, favoriserait la persistance et la transmission de ce virus, ce qui devrait accroître le risque de NE chez l’Homme. Nous avons testé cette hypothèse en étudiant les polymorphismes et/ou les niveaux d'expression de six gènes candidats impliqués dans la réponse immunitaire à PUUV (DRB-CMH, promoteur du TNF-alpha, TLR4, TLR7, Mx2, intégrine bêta3) chez dix populations de campagnols échantillonnées le long d’un axe nord/sud dans les Ardennes françaises, couvrant des zones endémiques et non endémiques à PUUV. Des signatures de sélection ont été détectées pour TNF-alpha et Mx2 grâce à des approches de génétique des populations (scan FST) et d’associations génotypes / phénotypes. Ces gènes codent des protéines dont les propriétés antivirales sont connues, mais qui induisent des coûts immunopathologiques importants. Ils pourraient donc jouer un rôle central dans une balance de tolérance / résistance à PUUV. De plus, dans les zones d’endémie, les gènes TNF-alpha et Mx2 sont sous-exprimés, ce qui suggère l’évolution d’une plus forte tolérance à PUUV, potentiellement au bénéfice d’un moindre coût immunopathologique. Certains de ces résultats ont été confirmés à l’échelle européenn

Concomitant influence of helminth infection and landscape on the distribution of Puumala hantavirus in its reservoir, Myodes glareolus

Peer reviewe

Rodents and risk in the Mekong delta of Vietnam: seroprevalence of selected zoonotic viruses in rodents and humans

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Behavioral responses of terrestrial mammals to COVID-19 lockdowns

COVID-19 lockdowns in early 2020 reduced human mobility, providing an opportunity to disentangle its effects on animals from those of landscape modifications. Using GPS data, we compared movements and road avoidance of 2300 terrestrial mammals (43 species) during the lockdowns to the same period in 2019. Individual responses were variable with no change in average movements or road avoidance behavior, likely due to variable lockdown conditions. However, under strict lockdowns 10-day 95th percentile displacements increased by 73%, suggesting increased landscape permeability. Animals' 1-hour 95th percentile displacements declined by 12% and animals were 36% closer to roads in areas of high human footprint, indicating reduced avoidance during lockdowns. Overall, lockdowns rapidly altered some spatial behaviors, highlighting variable but substantial impacts of human mobility on wildlife worldwide.acceptedVersio

Behavioral responses of terrestrial mammals to COVID-19 lockdowns

COVID-19 lockdowns in early 2020 reduced human mobility, providing an opportunity to disentangle its effects on animals from those of landscape modifications. Using GPS data, we compared movements and road avoidance of 2300 terrestrial mammals (43 species) during the lockdowns to the same period in 2019. Individual responses were variable with no change in average movements or road avoidance behavior, likely due to variable lockdown conditions. However, under strict lockdowns 10-day 95th percentile displacements increased by 73%, suggesting increased landscape permeability. Animals' 1-hour 95th percentile displacements declined by 12% and animals were 36% closer to roads in areas of high human footprint, indicating reduced avoidance during lockdowns. Overall, lockdowns rapidly altered some spatial behaviors, highlighting variable but substantial impacts of human mobility on wildlife worldwide.acceptedVersio

Behavioral responses of terrestrial mammals to COVID-19 lockdowns

DATA AND MATERIALS AVAILABILITY : The full dataset used in the final analyses (33) and associated code (34) are available at Dryad. A subset of the spatial coordinate datasets is available at Zenodo (35). Certain datasets of spatial coordinates will be available only through requests made to the authors due to conservation and Indigenous sovereignty concerns (see table S1 for more information on data use restrictions and contact information for data requests). These sensitive data will be made available upon request to qualified researchers for research purposes, provided that the data use will not threaten the study populations, such as by distribution or publication of the coordinates or detailed maps. Some datasets, such as those overseen by government agencies, have additional legal restrictions on data sharing, and researchers may need to formally apply for data access. Collaborations with data holders are generally encouraged, and in cases where data are held by Indigenous groups or institutions from regions that are under-represented in the global science community, collaboration may be required to ensure inclusion.COVID-19 lockdowns in early 2020 reduced human mobility, providing an opportunity to disentangle its effects on animals from those of landscape modifications. Using GPS data, we compared movements and road avoidance of 2300 terrestrial mammals (43 species) during the lockdowns to the same period in 2019. Individual responses were variable with no change in average movements or road avoidance behavior, likely due to variable lockdown conditions. However, under strict lockdowns 10-day 95th percentile displacements increased by 73%, suggesting increased landscape permeability. Animals’ 1-hour 95th percentile displacements declined by 12% and animals were 36% closer to roads in areas of high human footprint, indicating reduced avoidance during lockdowns. Overall, lockdowns rapidly altered some spatial behaviors, highlighting variable but substantial impacts of human mobility on wildlife worldwide.The Radboud Excellence Initiative, the German Federal Ministry of Education and Research, the National Science Foundation, Serbian Ministry of Education, Science and Technological Development, Dutch Research Council NWO program “Advanced Instrumentation for Wildlife Protection”, Fondation Segré, RZSS, IPE, Greensboro Science Center, Houston Zoo, Jacksonville Zoo and Gardens, Nashville Zoo, Naples Zoo, Reid Park Zoo, Miller Park, WWF, ZCOG, Zoo Miami, Zoo Miami Foundation, Beauval Nature, Greenville Zoo, Riverbanks zoo and garden, SAC Zoo, La Passarelle Conservation, Parc Animalier d’Auvergne, Disney Conservation Fund, Fresno Chaffee zoo, Play for nature, North Florida Wildlife Center, Abilene Zoo, a Liber Ero Fellowship, the Fish and Wildlife Compensation Program, Habitat Conservation Trust Foundation, Teck Coal, and the Grand Teton Association. The collection of Norwegian moose data was funded by the Norwegian Environment Agency, the German Ministry of Education and Research via the SPACES II project ORYCS, the Wyoming Game and Fish Department, Wyoming Game and Fish Commission, Bureau of Land Management, Muley Fanatic Foundation (including Southwest, Kemmerer, Upper Green, and Blue Ridge Chapters), Boone and Crockett Club, Wyoming Wildlife and Natural Resources Trust, Knobloch Family Foundation, Wyoming Animal Damage Management Board, Wyoming Governor’s Big Game License Coalition, Bowhunters of Wyoming, Wyoming Outfitters and Guides Association, Pope and Young Club, US Forest Service, US Fish and Wildlife Service, the Rocky Mountain Elk Foundation, Wyoming Wild Sheep Foundation, Wild Sheep Foundation, Wyoming Wildlife/Livestock Disease Research Partnership, the US National Science Foundation [IOS-1656642 and IOS-1656527, the Spanish Ministry of Economy, Industry and Competitiveness, and by a GRUPIN research grant from the Regional Government of Asturias, Sigrid Rausing Trust, Batubay Özkan, Barbara Watkins, NSERC Discovery Grant, the Federal Aid in Wildlife Restoration act under Pittman-Robertson project, the State University of New York, College of Environmental Science and Forestry, the Ministry of Education, Youth and Sport of the Czech Republic, the Ministry of Agriculture of the Czech Republic, Rufford Foundation, an American Society of Mammalogists African Graduate Student Research Fund, the German Science Foundation, the Israeli Science Foundation, the BSF-NSF, the Ministry of Agriculture, Forestry and Food and Slovenian Research Agency (CRP V1-1626), the Aage V. Jensen Naturfond (project: Kronvildt - viden, værdier og værktøjer), the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy, National Centre for Research and Development in Poland, the Slovenian Research Agency, the David Shepherd Wildlife Foundation, Disney Conservation Fund, Whitley Fund for Nature, Acton Family Giving, Zoo Basel, Columbus, Bioparc de Doué-la-Fontaine, Zoo Dresden, Zoo Idaho, Kolmården Zoo, Korkeasaari Zoo, La Passarelle, Zoo New England, Tierpark Berlin, Tulsa Zoo, the Ministry of Environment and Tourism, Government of Mongolia, the Mongolian Academy of Sciences, the Federal Aid in Wildlife Restoration act and the Illinois Department of Natural Resources, the National Science Foundation, Parks Canada, Natural Sciences and Engineering Research Council, Alberta Environment and Parks, Rocky Mountain Elk Foundation, Safari Club International and Alberta Conservation Association, the Consejo Nacional de Ciencias y Tecnología (CONACYT) of Paraguay, the Norwegian Environment Agency and the Swedish Environmental Protection Agency, EU funded Interreg SI-HR 410 Carnivora Dinarica project, Paklenica and Plitvice Lakes National Parks, UK Wolf Conservation Trust, EURONATUR and Bernd Thies Foundation, the Messerli Foundation in Switzerland and WWF Germany, the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Actions, NASA Ecological Forecasting Program, the Ecotone Telemetry company, the French National Research Agency, LANDTHIRST, grant REPOS awarded by the i-Site MUSE thanks to the “Investissements d’avenir” program, the ANR Mov-It project, the USDA Hatch Act Formula Funding, the Fondation Segre and North American and European Zoos listed at http://www.giantanteater.org/, the Utah Division of Wildlife Resources, the Yellowstone Forever and the National Park Service, Missouri Department of Conservation, Federal Aid in Wildlife Restoration Grant, and State University of New York, various donors to the Botswana Predator Conservation Program, data from collared caribou in the Northwest Territories were made available through funds from the Department of Environment and Natural Resources, Government of the Northwest Territories. The European Research Council Horizon2020, the British Ecological Society, the Paul Jones Family Trust, and the Lord Kelvin Adam Smith fund, the Tanzania Wildlife Research Institute and Tanzania National Parks. The Eastern Shoshone and Northern Arapahoe Fish and Game Department and the Wyoming State Veterinary Laboratory, the Alaska Department of Fish and Game, Kodiak Brown Bear Trust, Rocky Mountain Elk Foundation, Koniag Native Corporation, Old Harbor Native Corporation, Afognak Native Corporation, Ouzinkie Native Corporation, Natives of Kodiak Native Corporation and the State University of New York, College of Environmental Science and Forestry, and the Slovenia Hunters Association and Slovenia Forest Service. F.C. was partly supported by the Resident Visiting Researcher Fellowship, IMéRA/Aix-Marseille Université, Marseille. This work was partially funded by the Center of Advanced Systems Understanding (CASUS), which is financed by Germany’s Federal Ministry of Education and Research (BMBF) and by the Saxon Ministry for Science, Culture and Tourism (SMWK) with tax funds on the basis of the budget approved by the Saxon State Parliament. This article is a contribution of the COVID-19 Bio-Logging Initiative, which is funded in part by the Gordon and Betty Moore Foundation (GBMF9881) and the National Geographic Society.https://www.science.org/journal/sciencehj2023Mammal Research InstituteZoology and Entomolog

Taxonomie intégrative de la tribu des Rattini (Rodentia, Muridae) en Asie du Sud-Est

L’ Asie du Sud-Est est un point chaud de la biodiversité et, dans le même temps, cetterégion est un foyer actif d’émergence ou de réémergence de zoonoses (SRAS, grippesaviaires, leptospirose, roboviroses etc..). Le développement économique sans précédent et lacroissance démographique humaine que connait la zone biogéographique indochinoise sontun moteur de changements considérables des écosystèmes. Dans le contexte du changementglobal, il est primordial de comprendre comment ces modifications environnementalesmodifient les interactions entre les communautés d’hôtes et leurs communautés deparasites/pathogènes afin d’appréhender les transformations du paysage épidémiologique.Certaines espèces, qui sont des réservoirs de zoonoses constituent, de par leur mode de vie etleur statut de gibier des modèles particulièrement intéressants à étudier dans ce cadre. C’est lecas, pour la zone étudiée, des rongeurs et plus particulièrement des représentants de deuxtribus de la sous-famille des Murinae : les Rattini et les Murini. La première partie de cemémoire porte sur ces deux tribus, particulièrement diversifiés en Asie du Sud-Est. L’objectifa été d’étudier la faisabilité d’un outil d’identification web-service innovant basé sur lamorphométrie. Cet outil viendra compléter des réalisations qui lui sont antérieures à savoir :un guide d’identification de terrain et un premier outil web-service basé sur l’identificationmoléculaire. Ces productions formeront un ensemble cohérent d’outils d’identificationpermettant d’offrir à la communauté des personnes désireuses d’étudier les rongeurs de lazone des accès multiples et adaptés à une identification de qualité. Pour la réalisation de cetoutil d’identification morphométrique, nous avons tout d’abord étudié quels sont les facteursintra et inter-spécifiques qui influencent la variation morphologique des espèces de rongeurs.Cette étude, au travers d’une approche de systématique intégrative a ainsi contribué à lastabilisation de la taxonomie des Rattini. L’étude morphométrique est entièrement basée surun jeu de données de six cent soixante individus qui appartiennent à dix-sept espèces.L’ensemble des individus a fait au préalable l’objet d’une identification moléculaire réalisée àl’aide d’un gène mitochondrial. Dans le cadre de la création du web-service morphométrique,les sources d’erreurs relatives à la comparaison de jeux de données produits par desopérateurs différents sont identifiées et encadrées car elles pourraient compromettrel’identification des individus. Des seuils d’assignation sont également définis pour permettre àl’outil de gérer la confrontation avec des espèces qui ne sont pas représentées dans le jeu dedonnées de référence. Dans un second temps nous avons souhaité replacer la disparitémorphologique observée chez les espèces actuelles dans un contexte évolutif. L’objectif étaitde comprendre les patrons macro-évolutifs qui ont potentiellement gouverné la mise en placede la variation morphologique et ainsi d’évaluer le rôle de l’environnement sur celle-ci