Large scale monitoring of terrestrial small mammals using noninvasive sampling and COI barcoding

Abstract Terrestrial small mammals are important elements of the food chain, and like other species affected by climate change. Knowledge about their current distribution is of interest to model future developments and monitoring biodiversity loss. However, their monitoring is challenging due to legal restrictions. Here we document a pilot study testing the performance of a non-invasive monitoring strategy for terrestrial small mammals. It uses baited tubes in the field to collect fecal pellets combined with molecular species identification using COI barcodes. Just over 1000 samples were collected mainly in 2021 in 2506 trap nights, nine areas and 36 specific sites across Germany in habitats located close to waterbodies. COI-PCR products were obtained from 93% of samples and 55% of samples could be assigned to a small mammal species based on high-quality Sanger-Sequences. We found 11 species of Eulipotyphla and Rodentia while local communities were dominated by Apodemus sp. and Clethrionomys glareolus . We showed that the described strategy enables large-scale biomonitoring of small terrestrial mammals as it combines three advantages: 1) welfare of the animals is not affected and therefore time-consuming paperwork to obtain legal permits like for live-trapping is not required, 2) field work can be done by volunteers and 3) molecular species identification can be implemented in the routine work of molecular laboratories. Future tests with tube diameters, bait, timing of placement etc. could increase the “capture” success and demonstrate the applicability of the method to rare species. Also, some training for the involved field workers could be advantageous.