Population dynamics of small mammals in the Jura massif, Franche-Comté, France (1979-2000)

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).

Methods

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.

Caveats: 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 (Institut National de la Recherche Agronomique), 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 Comité d’Éthique Bisontin en Expérimentation Animale (CEBEA No. 58).

FILE DESCRIPTION

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.

Main files

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 corpus luteum in the right ovary
• corpsjg, number of corpus luteum in the left ovary
• allaitante, milking (1 yes, 0 no)
• corpsblancd, number of corpus albicans in the right ovary
• corpsblancg, number of corpus albicans 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

Supplementary files

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.