DOI: 10.5281/zenodo.6997317
title: Population dynamics of small mammals in the Jura massif, Franche-Comté, France (1979-2000)

description: Small mammal populations were monitored seasonally from August 1979 to July 2000 according to a stratified sampling plan and using standard trapping, mostly in the area of Septfontaines – Le Souillot, Doubs, France (6.18°E, 46.97°N). The dataset includes 2120 trap lines (90% n = 1912 in the Septfontaines – Le Souillot (LS) area), and 22848 captures (92% n = 20937 in the LS area). <strong>Methods</strong> Small mammals were captured using INRA trap lines. INRA live traps (15 × 5 × 5 cm) are suitable for species of body mass less than 50 g. In a standard way generally applied here,each trap line consisted of 34 live traps spaced 3 meters apart. Trap lines were set up for three nights and checked every morning. Animals were euthanized by cervical dislocation, weighed and dissected for sex, reproductive status and age determination. Liver was examined macroscopically for parasites. Relative age was estimated based on the dry weight of crystalline eye lenses. <em>Caveats:</em> in a very little number of cases (beginning of the study and circumstantial occasions) trap lines were not standard (150 m length, 51 traps, or set up for one or two nights only, etc.). See Codes_Trapline.docx and fields "remarques" (table traplines.txt) and 'observation' (table captures.txt). Sometimes field not informed have been coded "", 99 or NA. Although we did our best to harmonize this in the files uploaded, some inconsistencies might remain. Those issues should be considered carefully before data analysis. Trapping and animal handling was carried out in full accordance with the relevant European guidelines (Directive 86/609/EEC) and national regulations. INRA (<em>Institut National de la Recherche Agronomique</em>), the umbrella organization under which the field work was carried out, created its first ethical committee in 1998. It was therefore impossible to get formal ethical approval prior to the major part of the study. A similar research protocol used from 2014 to 2017 received full approval from the <em>Comité d’Éthique Bisontin en Expérimentation Animale</em> (CEBEA No. 58). <strong>FILE DESCRIPTION</strong> Files traplines.txt, captures.txt and rates.txt are tables of a relational database. They can be linked using the index field 'codeligne' between traplines.txt and captures.txt, and 'codeind' between captures.txt and rates.txt. <strong>Main files</strong> captures.txt codeligne, trapline ID numind, specimen ID for the trap line numcontr, control number (traps were controlled every morning; for 3 successive nights for standard trap lines). E.g. 1 for a specimen captured on the 1st control. numpiege, trap ID in the trap line (1,2,....n). E.g. 34 is the 34th trap in the trap line counted from the beginning. espece, species (see Codes_Sp_Parasites.docx for the codes) poids, wet weight in g sexe, sex (1 male, 2 female) cristallin, dry weight of the two crystalline lens, in 1/10 of mg uterus, uterus diameter foetusd, number of foetuses in the uterus right horn foetusg, number of foetuses in the uterus left horn cicplacd, number of placental scares in the uterus right horn cicplacg, number of placental scares in the uterus left horn corpsjd, number of <em>corpus luteum</em> in the right ovary corpsjg, number of <em>corpus luteum</em> in the left ovary allaitante, milking (1 yes, 0 no) corpsblancd, number of <em>corpus albicans</em> in the right ovary corpsblancg, number of <em>corpus albicans</em> in the left ovary testd, length of the right testicle testg, length of the left testicle vesd, length of the right seminal vesicle vesg, length of the left seminal vesicle diammax, parasite mass great diameter diammin, parasite mass small diameter nombrekyste, parasite cyst number nomlu, parasite species as identified in the field nomanaly, parasite species as identified in the lab observation, remark codeind, specimen ID (codeligne+numind) rates.txt codeind, specimen ID ratepds, spleen weight (1/100 g) remarque, remark traplines.txt codeligne, 8 digits trap line ID. LS891001 = location LS, 89 year, 10 month, 01, trap line ID for this place, year and month. See Codes_Trapline.docx for more details. dept, administrative department (INSEE code) date, date at which the trapline has been set up descripteur1, habitat description, Codes_Trapline.docx descripteur2, habitat description, see Codes_Trapline.docx facies, habitat description, see Codes_Trapline.docx remarque, remark, lati, latitude of the northwest corner of the sampling grid (CRS NTF (Paris) / Lambert zone II, EPSG: 27572), see Codes_Trapline.docx longi, longitude of the northwest corner of the sampling grid (CRS NTF (Paris) / Lambert zone II, EPSG: 27572), see Codes_Trapline.docx precis, precision, the number of Lambert II squares (1km x 1km) composing the square side of the grid, see Codes_Trapline.docx <strong>Supplementary files</strong> bboxlarge.kml, the bounding box including all the area with trap lines that could be geographically located. It takes the precision of the location into account (hence, includes the southeastern extremes of the grid squares (see Codes_Trapline.docx). bboxLS.kml, the bounding box of the study area "LS" (Le Souillot) including all the trap lines that could be geographically located. It takes the precision of the location into account (hence, includes the southeastern extremes of the grid squares, see Codes_Trapline.docx). Those trap lines are the core (90% of the total number of the traplines set) of the research carried out in the area. lineloc.kml, the geographical coordinates of the northwestern corner of the square including each trap line with trapline ID and precision (1, square of 1 x 1 km; 2, square of 2 x 2 km, etc.). Codes_Sp_Parasites.docx, codes of small mammal species and parasite names. Codes_Trapline.docx, codes of trap lines.
description: Pierre Delattre initialized and designed the study in the late 1970s, found financial support, and supervised the works; Patrick Giraudoux reorganized the sampling in 1987, computerized the data and maintained the database. Jean-Pierre Damange and Jean-Pierre Quéré provided technical assistance in the field and in the lab (trapping, dissections, crystalline lens weighing, etc.). All authors participated to field works, occasionally helped by a number of colleagues and students.
description: {"references": ["Giraudoux, P., Villette, P., Qu\u00e9r\u00e9, J.-P., Damange, J.-P., Delattre, P., 2019. Weather influences M. arvalis reproduction but not population dynamics in a 17-year time series. Scientific Reports 9, 13942. https://doi.org/10.1038/s41598-019-50438-z", "Giraudoux, P., Delattre, P., Quere, J.P., Damange, J.P., 1994. Structure and kinetics of rodent populations in a region under agricultural land abandonment. Acta Oecologica 15, 385\u2013400.", "Delattre, P., Giraudoux, P., Quere, J.P., 1990. Cons\u00e9quences \u00e9pid\u00e9miologiques de la r\u00e9ceptivit\u00e9 d'un nouvel h\u00f4te interm\u00e9diaire du T\u00e9nia multiloculaire (Echinococcus multilocularis) et de la localisation spatio-temporelle des rongeurs infest\u00e9s. Compte-Rendus de l'Acad\u00e9mie des Sciences, Paris, III 310, 339\u2013344.", "Delattre, P., Pascal, M., Le Pesteur, M.H., Giraudoux, P., Damange, J.P., 1988. Caract\u00e9ristiques \u00e9cologiques et \u00e9pid\u00e9miologiques de l'Echinococcus multilocularis au cours d'un cycle complet des populations d'un h\u00f4te interm\u00e9diaire (Microtus arvalis). Canadian Journal of Zoology 66, 2740\u20132750.", "LePesteur, M.H., Giraudoux, P., Delattre, P., Damange, J.P., Quere, J.P., 1992. Spatiotemporal distribution of four species of cestodes in a landscape of mid-altitude mountains (Jura, France). Annales de Parasitologie Humaine et Compar\u00e9e 67, 155\u2013160.", "Fichet-Calvet, E., Giraudoux, P., Qu\u00e9r\u00e9, J.-P., Ashford, R.W., Delattre, P., 2003. Is the prevalence of Taenia taeniaeformis in Microtus arvalis dependent on population density? J. Parasitol. 89, 1147\u20131152. https://doi.org/10.1645/GE-3158"]}