Systematic monitoring of individuals and their abundance over time has become an important tool to provide information for conservation. For genetic monitoring studies, noninvasive sampling has emerged as a valuable approach, particularly so for elusive or rare animals. Here, we present the five-year results of an ongoing noninvasive genetic monitoring of mountain hares (Lepus timidus) in a protected area in the Swiss Alps. We used nuclear microsatellites and a sex marker to identify individuals and assign species to noninvasively collected feces samples. Through including a marker for sex identification, we were able to assess sex-ratio changes and sex-specific demographic parameters over time. Male abundance in the area showed high fluctuations and apparent survival for males was lower than for females. Generally, males and females showed only little temporary migration into and out of the study area. Additionally, using genotyped tissue samples from mountain hares, European hares (Lepus europaeus) and their hybrids, we were able to provide evidence for the first occurrence of a European hare in the study area at an elevation of 2300 m a.s.l. in spring 2016. For future monitoring studies, we suggest to include complementary analysis methods to reliably infer species identities of the individuals analyzed and thus, not only monitor mountain hare individual abundance, but also assess the potential threats given through competitive exclusion by and hybridization with the European hare.

Data originate from a non-invasive sampling of feces of mountain hare, Lepus timidus, collected in the Swiss National Park over a five-year period (2014-2018). DNA was extracted from the fecal samples and genotyped at nuclear microsatellites (simple sequence repeats, SSRs) loci and a sex marker using a multi-tube approach. Based on these sample-specific genetic fingerprints, individual genotypes were determined and population dynamics were derived. Moreover, a comparison with genotypes obtained from tissue samples of L. timidus and European hare (Lepus europaeus) allowed to assign individual genotypes to the respective species or putative hybrids.

Consensus genotypes and sex of samples from three replicated PCRs of noninvasive samples were determined based on a stringent procedure, and missing data occurred in some of the genotypes as marked in the data files (denoted as 0).