Context: Land-use intensification can alter small mammal community composition and induce loss of genetic variation in remaining populations. Fragmented landscapes favor generalist and synanthropic species, which are potential reservoirs of pathogens and pose risks to agriculture and forestry.

Objectives: This study aimed to evaluate the effects of land-use intensity on small mammal diversity in grassland and forest habitats, as well as on genetic variation patterns driven by geographic (Isolation by Distance) and environmental distance (Isolation by Resistance) factors.

Methods: We analysed differences in small mammal community diversity on grassland and forest plots with varying land-use intensities. Genetic analyses were conducted on Myodes glareolus and Microtus arvalis populations from each habitat, using microsatellites. Maximum Likelihood Population Effects models were employed to elucidate gene flow patterns and significant differences in genetic structure based on land-use intensity.

Results: Small mammal communities in grasslands were significantly less diverse than in forests. Land-use intensity had a significant effect on diversity within grassland but not within forest habitats. M. glareolus showed three genetic groups, while M. arvalis displayed no discernible population structure or landscape-related pattern. Land-use intensity did not significantly influence the genetic structure of either species. Gene flow in M. glareolus is best described by the IBR model.

Conclusion: Land-use intensity significantly affects small mammal community composition, particularly in grasslands. Neither species' genetics is directly impacted by land-use intensity but rather by landscape connectivity and distance. Risk assessments for rodent-borne zoonotic pathogens and crop damage should be framed within a habitat connectivity context.

M. glareolus, caught on forest plots, and M. arvalis, caught on grassland plots, were genetically examined. DNA extraction was performed on tissue samples using Phenol-Chloroform-Isopropanol extraction (Hogan et al., 1986). A set of 12 microsatellite loci for M. glareolus CG13G2, CG5F6, CG16E2, CG17E9, CG7C9, CG15F7, CG12B9, CG13F9, CG5G56, CG12A7 (Rikalainen et al., 2008) and MSCg-15 (Gockel et al., 1997) and a set of 11 microsatellite loci for M. arvalis Ma29, Ma36, Ma54, Ma75, Ma25, Ma30 (Gauffre et al., 2007), Mar012, Mar113, Mar076, Mar080 and Mar016 (Walser & Heckel, 2008) was applied. PCR was performed in a total volume of 15 µl containing a maximum of 24 ng of genomic DNA. Primer concentration varied between 0.15 µM and 0.25 µM in the M. glareolus multiplex system and 0.15 µM and 0.30 µM in the M. arvalis multiplex system. The QIAGEN Multiplex PCR Kit (QIAGEN) was used to perform the Multiplex PCR. The M. glareolus multiplex protocol describes an initial denaturation at 95°C for 5 min, 35 cycles of 94°C for 30 sec, 55°C for 30 sec, 60°C for 90 sec, 72°C for 30 sec, and the final extension at 68°C for 10 min. The M. arvalis multiplex protocol describes an initial denaturation at 95°C for 5 min, 35 cycles of 95°C for 30 sec, 55°C for 90 sec, 72°C for 30 sec, and the final extension at 68°C for 10 min. Fragment sizes were determined by electrophoresis on 4.5% (w/v) denaturing 19:1 acrylamide: bisacrylamide gels on the ABI Prism™ 377 sequencer, using the GeneScan 2.0 software and a ROX-labelled commercial size standard as an internal standard (Applied Biosystems).