Biodiversity Data Journal :
Data Paper (Biosciences)
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Corresponding author: Nathalie Charbonnel (nathalie.charbonnel@inrae.fr)
Academic editor: Miguel Camacho Sanchez
Received: 22 Sep 2022 | Accepted: 22 Nov 2022 | Published: 30 Dec 2022
© 2022 Julien Pradel, Marie Bouilloud, Anne Loiseau, Sylvain Piry, Maxime Galan, Emmanuelle Artige, Guillaume Castel, Julien Ferrero, Romain Gallet, Geoffrey Thuel, Nathalie Vieira, Nathalie Charbonnel
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Pradel J, Bouilloud M, Loiseau A, Piry S, Galan M, Artige E, Castel G, Ferrero J, Gallet R, Thuel G, Vieira N, Charbonnel N (2022) Small terrestrial mammals (Rodentia and Soricomorpha) along a gradient of forest anthropisation (reserves, managed forests, urban parks) in France. Biodiversity Data Journal 10: e95214. https://doi.org/10.3897/BDJ.10.e95214
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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.
rodents, shrews, community, biodiversity, forests, urban parks, global changes, dilution effect
These last centuries, humans have strongly impacted ecosystems, through the development of activities including, amongst others, land-use changes, overexploitation of natural resources including wood or introduction of non-native species (
Anthropisation and, in particular, urbanisation, have led to unprecedented levels of disturbance, disrupting ecological processes, eroding biodiversity and modifying communities towards simplified assemblages (
First, biological diversity alteration may be associated with the disruption of the regulation of pathogen circulation or emergence, including zoonotic ones. Two processes may interact to influence disease risk in anthropised ecosystems. On the one hand, high host diversity can “dilute” pathogen transmission. Such “dilution effect” occurs when the diversity of an ecological community reduces the transmission of a pathogen. It may occur when species vary in their competence (i.e. their ability to harbour and transmit a specific pathogen) and when species diversity limits encounter rates and enhances host regulation (
As such, it is urgent to elucidate the interlinkages between anthropisation and animal community diversity and assemblages, to better predict and prevent zoonotic diseases risk. Several studies have described biodiversity changes for animal communities along anthropisation gradients (e.g.
We provide occurrence data on small mammals (rodents and shrews) surveyed during two years along a gradient of forest anthropisation, including biological reserves, managed forests and urban parks, in eastern France. Small mammals are important reservoirs of zoonotic agents; forests and urban green spaces are environments where small mammals are abundant, human/domestic-wildlife interactions are plausible to occur and efforts are undertaken to preserve biodiversity, while limiting disease risk. These data will hence contribute to advancement of the knowledge of:
This paper provides data collected during the Biodiversa Bioroddis project in France (2020-2022). 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. Public forests and urban parks experience increasing levels of anthropisation. 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.
BioRodDis: Managing BIOdiversity in forests and urban green spaces - Dilution and amplification effects on RODent microbiomes and rodent-borne DISeases
Coordinator: Charbonnel Nathalie
BioRodDis includes occurrence of small terrestrial mammals from forests and urban parks in five countries: Belgium, France, Germany, Ireland and Poland.
The BioRodDis project aims at elucidating the interlinkages between small mammal biodiversity and diseases at local and European scales using standardised assessments of biodiversity and disease risks. In particular, the dilution/amplification effect is assessed by integrating new key research directions, i.e. host microbiome and multiple pathogen diversity levels on one hand, seasonal and multi-annual dynamics on the other hand, including climate change scenarios and interactions with socioeconomic contexts. More information is provided in the website: https://www6.inrae.fr/biodiversa-bioroddis.
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).
This study includes six sampling sites (2 forest reserves, 2 public forests, 2 urban parks) in eastern France (see Figs
General map of the studied areas and their position in France. Localities are indicated by circles, red circles = urban parks; green circles = managed forests; light green circles = protected forests. FRPLTO: Lyon, Parc de la Tête d’Or; FRPDLL: Marcy l'étoile, Domaine Lacroix Laval; FRFCOR: Cormaranche en Bugey; FRFGRI: Arvière, La Griffe au diable; FRFMIG: Mignovillard; FRFGLA: Esserval-Tartre, La Glacière.
Maps of the trapping lines (red points) represented at a local scale for each of the following localities: A- FRPLTO: Lyon, Parc de la Tête d’Or; B- FRPDLL: Marcy l'étoile, Domaine Lacroix Laval; C- FRFCOR: Cormaranche en Bugey; D- FRFGRI: Arvière, La Griffe au diable; E- FRFMIG: Mignovillard; F- FRFGLA: Esserval-Tartre, La Glacière. The landscape around the trapping lines is represented by different colours corresponding to water bodies (blue; corine land cover 5), Forest and semi-natural areas (green, Forest database), artificial areas (grey; corine land cover 1) or other land-cover classes (white).
Small mammals were live-trapped using INRA traps for all rodents and shrews, except rats (an INRA trap is composed of a 160 × 50 × 50-mm aluminium tunnel, coupled with a 150 × 70 × 70-mm plastic rest box). Rats were trapped using meshed traps of 500 x 175 x 175 cm (Fig.
Pictures illustrating the different steps leading to trapping and individual information. A- Preparation of traps (bait, cotton, trap number); B- An INRA trap sets in a forest; C- Meshed trap sets in a urban park; D- Trap checking in the morning (masks and gloves are important to protect animals and humans from zoonotic agents); E- Capture information recorded on a digital tablet (this picture was taken during the lockdown, which explains the mask); F- An INRA trap used to capture small mammals; G- A meshed trap containing a rat (Rattus norvegicus); H- A plastic rest box containing a woodmouse (Apodemus sylvaticus) that is released; I- Disinfection of traps (masks and gloves are important to protect humans from zoonotic agents).
Six to ten lines of 20 INRA live-traps and one meshed trap, with about 3 m interval, were set up so that each sampling locality consisted of a few km2 area (see Table
List of sampling sites including locality (and locationID), coordinates (latitude and longitude of the centroid of the area covered by the traps), the trapping line ID and the landscape type. The number of small mammals trapped and dissected for each site and session (spring 2020; autumn 2020; spring 2021; autumn 2021; spring 2022) is provided.
Locality | LocationID | Centroid_x | Centroid_y | Trapping_LineID | Landscape_type | Number_dissection_session |
Lyon, Parc de la Tête d’Or | FRPLTO | 4.85554195 | 45.77817576 | ASI, CT, CYN, EMB, FAUV, GIF, ILE, IVEL, JDP, LAM, LUZ, MAM, MOM, OBS, PM, PON, PRI, SBO, SBP, SEV, VAC, VOL | Urban park | 84;94;82;124;85 |
Marcy l'etoile, Domaine Lacroix Laval | FRPDLL | 4.72146918 | 45.78982081 | A, Abis, B, C, CREP, D, E, F, G, H, I, PAI, SEL | Urban park | 0;41;96;93;11 |
Cormaranche en Bugey | FRFCOR | 5.62549550 | 45.93477080 | A, AA, AB, AC, AD, B, C, D, E, F, G, H, I, J, K, Kbis, L, M | Managed forest | 29;108;94;95;8 |
Arviere, La Griffe au diable | FRFGRI | 5.75865886 | 45.93370736 | S, T, V, W, X, Y, Z | Protected forest | 0;0;95;41;0 |
Mignovillard | FRFMIG | 6.16343853 | 46.76358715 | A, AA, AC, AD, AG, B, BB, C, CC, D, DD, E, F, G, H, I, J, K, L, M, N, P, Q | Managed forest | 41;81;69;98;25 |
Esserval-Tartre, La Glacière | FRFGLA | 6.02525045 | 46.84288358 | S, T, V, W, X, Y, Z | Protected forest | 0;0;33;66;0 |
All captured animals were determined to species level using morphological criteria in the field or using molecular methods when necessary (CO1 sequencing for Microtus species and shrews,
Fieldwork: The different steps of the fieldwork are detailed in Fig.
Animal dissection: On the day of capture, animals are anaesthetised using isofluorane and euthanised by cervical dislocation, as recommended by
Lastly, all waste products were eliminated using the official incineration process, that is a safe way of destroying hazardous potentially infectious waste, protecting both human and the environment.
The different steps of the dissection are detailed in Fig.
Pictures illustrating the different steps during small mammal dissection. Masks (FFP2), gloves and glasses protect the experimenter who manipulates and dissects the animals. A- All tubes are prepared in advance with unique identifier and datamatrix. One colour is dedicated to each type of sample (e.g. red tip for heart in PBS, purple tip for liver in RNA later). Morphological information was recorded on a paper sheet. Dissection instruments are disinfected between each animal. B- The experimenter is preparing the animal (here a brown rat Rattus norvegicus) for the dissection. C- The experimenter is weighing the animal (here a woodmouse Apodemus sylvaticus) for the dissection. D- A male common vole (Microtus arvalis). E- Tubes corresponding to liver samples, with unique identifiers and datamatrices, stored in a clearly identified box (unique identifier and datamatrix).
Ethical statements: Animal capture and handling have been conducted according to the French and European regulations on care and protection of laboratory animals (French Law 2001-486 issued on 6 June 2001 and Directive 2010/63/EU issued on 22 September 2010). The CBGP laboratory has approval (D-34-169-003) from the Departmental Direction of Population Protection (DDPP, Hérault, France) and from the regional ethical committee (Comite d'Ethique pour l'Expérimentation Animale Languedoc Roussillon), for the sampling of rodents and the storage and use of their tissues.
Molecular analyses: DNA was extracted from kidney using Qiagen DNeasy® Blood & Tissue Kit. The specific identification of Microtus species and shrews was next performed using CO1 sequencing (BatL5310 and R6036R), following
The data were collected in six forested areas in eastern France, within three administrative Departments (Rhône, Ain, Jura).
44.84 and 48.633 Latitude; 2.021 and 7.734 Longitude.
Rank | Scientific Name | Common Name |
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species | Apodemus flavicollis | yellow-necked mouse |
species | Apodemus sylvaticus | woodmouse |
species | Crocidura russula | greater white toothed shrew |
species | Crocidura leucodon | bicoloured shrew |
species | Glis glis | edible dormouse |
species | Microtus agrestis | short-tailed field vole |
species | Microtus subterraneus | European pine vole |
species | Mus musculus | house mouse |
species | Myodes glareolus | bank vole |
species | Neomys fodiens | Eurasian water shrew |
species | Rattus norvegicus | brown rat |
species | Sorex araneus | common Eurasian shrew |
species | Sorex coronatus | crowned shrew |
species | Sorex minutus | Eurasian pygmy shrew |
species | Microtus arvalis | Common vole |
2020-02-25 through 2022-06-03
The dataset contains occurrences of small terrestrial mammals (Rodentia and Soricomorpha) trapped in forested areas in eastern France (administrative Departments: Rhône, Ain, Jura) (
Occurrence (number of individuals) of the small mammal species trapped in the different localities surveyed. FRPLTO: Lyon, Parc de la Tête d’Or; FRPDLL: Marcy l'étoile, Domaine Lacroix Laval; FRFCOR: Cormaranche en Bugey; FRFGRI: Arvière, La Griffe au diable; FRFMIG: Mignovillard; FRFGLA: Esserval-Tartre, La Glacière. The total number of individuals trapped is also indicated for each locality and for each species.
Small mammal species | LocalityID | Total number of individuals | |||||
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FRPLTO | FRPDLL | FRFCOR | FRFGRI | FRFMIG | FRFGLA | ||
Apodemus sp. | 0 | 0 | 0 | 0 | 1 | 0 | 1 |
Soricomorpha | 0 | 1 | 0 | 0 | 1 | 0 | 2 |
Apodemus flavicollis | 0 | 38 | 118 | 51 | 89 | 33 | 329 |
Apodemus sylvaticus | 177 | 108 | 55 | 17 | 43 | 11 | 411 |
Crocidura leucodon | 0 | 0 | 13 | 0 | 17 | 0 | 30 |
Crocidura russula | 83 | 15 | 0 | 0 | 0 | 0 | 98 |
Glis glis | 0 | 0 | 8 | 0 | 9 | 0 | 17 |
Microtus agrestis | 0 | 0 | 2 | 1 | 1 | 0 | 4 |
Microtus arvalis | 29 | 1 | 0 | 1 | 0 | 0 | 31 |
Microtus subterraneus | 0 | 0 | 0 | 1 | 3 | 0 | 4 |
Mus musculus | 89 | 1 | 0 | 0 | 0 | 0 | 90 |
Myodes glareolus | 0 | 77 | 134 | 61 | 138 | 52 | 462 |
Neomys fodiens | 0 | 0 | 2 | 0 | 0 | 1 | 3 |
Rattus norvegicus | 91 | 0 | 0 | 0 | 0 | 0 | 91 |
Sorex araneus | 0 | 0 | 0 | 0 | 3 | 0 | 3 |
Sorex coronatus | 0 | 0 | 2 | 4 | 7 | 2 | 15 |
Sorex minutus | 0 | 0 | 0 | 0 | 2 | 0 | 2 |
Total number of individuals | 469 | 241 | 334 | 136 | 314 | 99 | 1593 |
Total number of species detected | 5 | 6 | 8 | 7 | 10 | 5 | 15 |
Column label | Column description |
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occurrenceID | An identifier for the occurrence (as opposed to a particular digital record of the occurrence). In the absence of a persistent global unique identifier, construct one from a combination of identifiers in the record that will most closely make the occurrenceID globally unique. |
scientificName | The full scientific name, with authorship and date information, if known. When forming part of an Identification, this should be the name in the lowest level taxonomic rank that can be determined. This term should not contain identification qualifications, which should instead be supplied in the IdentificationQualifier term. |
sex | The sex of the biological individual(s) represented in the Occurrence. |
eventDate | The date-time or interval during which an Event occurred. For occurrences, this is the date-time when the event was recorded. Not suitable for a time in a geological context. A variable ("YYYY-MM-DD"). |
measurementType | The nature of the measurement, fact, characteristic or assertion. |
measurementValue | The value of the measurement, fact, characteristic, or assertion. |
measurementUnit | The units associated with the measurementValue. |
countryCode | The standard code for the country in which the Location occurs. |
country | The name of the country or major administrative unit in which the Location occurs. |
locationID | An identifier for the set of location information (data associated with dcterms:Location). May be a global unique identifier or an identifier specific to the dataset. |
locality | The specific description of the place. |
decimalLatitude | The geographic latitude (in decimal degrees, using the spatial reference system given in geodeticDatum) of the geographic centre of a Location. Positive values are north of the Equator, negative values are south of it. Legal values lie between -90 and 90, inclusive. |
decimalLongitude | The geographic longitude (in decimal degrees, using the spatial reference system given in geodeticDatum) of the geographic centre of a Location. Positive values are east of the Greenwich Meridian, negative values are west of it. Legal values lie between -180 and 180, inclusive. |
recordedBy | A person, group or organisation responsible for recording the original Occurrence. |
basisOfRecord | The type of the individual record. |
individualCount | Quantity of a species occurrence, for example, the number of individuals. |
samplingProtocol | Specify how the "Occurrence" records were obtained. |
taxonRank | The taxonomic rank of the supplied scientific name. |
kingdom | The full scientific name specifying the kingdom that the occurrence's scientific name is classified under. |
phylum | The full scientific name specifying the phylum that the occurrence's scientific name is classified under. |
class | The full scientific name specifying the class that the occurrence's scientific name is classified under. |
order | The full scientific name specifying the order that the occurrence's scientific name is classified under. |
family | The full scientific name specifying the family that the occurrence's scientific name is classified under. |
geodeticDatum | The coordinate system and set of reference points upon which the geographic coordinates are based. |
coordinateUncertaintyInMetres | The horizontal distance from the given decimalLatitude and decimalLongitude in metres, describing the smallest circle containing the whole of the Location. |
We are grateful to all the site managers who helped us with the organisation of the fieldwork: D. Sepulveda (ville de Lyon), F. Pradier (ville de Lyon), G. Anfray (zoo du parc de la Tête d'Or, Lyon), S. Chambon-Rouvier and J. Dussert (Domaine de Lacroix-Laval), N. Micoud and C. Leportier (ONF Cormaranche), C. Cambrils and M. Perrez (ONF Mignovillard), as well as colleagues who helped us with mammal trapping: M. Rates (VetAgro sup Lyon), M. Garcia Lopez (Institut Pasteur, VetagroSup Lyon) and M. Rene-Martellet (VetagroSup Lyon) or with further data analyses C. Tatard (CBGP). We thank Sophie Pamerlon (GBIF France) for her help with the GBIF platform.
Julien Pradel - small mammal sampling, species identification, georeferencing, data preparation, manuscript editing
Marie Bouilloud - small mammal sampling, species molecular identification, data preparation
Anne Loiseau - small mammal sampling, species molecular identification
Sylvain Piry - small mammal sampling, species identification, georeferencing, data preparation
Maxime Galan - small mammal sampling
Emmanuelle Artige - small mammal sampling
Guillaume Castel - small mammal sampling
Julien Ferrero - small mammal sampling
Romain Gallet - small mammal sampling
Geoffrey Thuel - small mammal sampling
Nathalie Vieira - small mammal sampling
Nathalie Charbonnel - small mammal sampling, species identification, georeferencing, data preparation, manuscript editing
This Supplementary table details the information gathered during the field sessions. It includes details about the lines and traps set during each field session and for each locality, as well as the results of the trapping detailed for each trap checking. Results can be 'empty open': the trap is open, there is no small mammal in the trap; 'empty closed': for technical issues, the trap is empty and closed, so that it could not have trapped anything; 'not found': the trap is no longer where it has been set (it might have been stolen or moved by large animals, for example). We also provide information on the trap checking, with the preliminary identification of the animal trapped, whether the animal was dead in the trap or released. Note that 67 occurrenceID entries in the occurrence table have no corresponding occurrenceID in this file. This is because these individuals are rats and mice that were trapped by the zoo managers, then frozen and given to us.
Caption : Locality is the specific description of the place; locationID is an identifier for the set of location information (data associated with dcterms:Location); field-sessionID is an identifier for the session of trapping; Trap-settingDate is the date during which traps were set ("YYYY-MM-DD"); Trap-lineID is an identifier for the trap lines; Trap-checkingDate is the date when traps were checked (; Trap-checking-number is the number of a particular trap checking for a given field-sessionID; TrapID is an identifier for the traps, for a given locality and a given field-sessionID; decimalLatitude is the geographic latitude (in decimal degrees, using the spatial reference system given in geodeticDatum) of the trap; decimalLongitude is the geographic longitude (in decimal degrees, using the spatial reference system given in geodeticDatum) of the trap; geodeticDatum is the coordinate system and set of reference points upon which the geographic coordinates are based; coordinateUncertaintyInMetres is the horizontal distance from the given decimalLatitude and decimalLongitude in metres, describing the smallest circle containing the whole of the Location; trapping-result is the result of a given trap checking; FieldObservation includes comments relative to the trap checked (species trapped, individual found alive, dead in the trap, animal released or not…); dissectionDate is the date during which the animal were dissected ("YYYY-MM-DD"); occurrenceID is an identifier for the Occurrence (as opposed to a particular digital record of the occurrence). In the absence of a persistent global unique identifier, construct one from a combination of identifiers in the record that will most closely make the occurrenceID globally unique. This is the same occurrenceID as in the dataset published here and in GBIF.
AP-PCR protocol adapted from Bugarski-Stanojevic et al. (2013) for molecular identification of Apodemus species.