Hare's affairs: Lessons learnt from a noninvasive genetic monitoring for tracking mountain hare individuals

Abstract

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 5-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 2,300 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.

Keywords: capture–mark–recapture; conservation; genotyping error rates; lagomorphs; nuclear microsatellites.

FIGURE 1

Origins of tissue samples (left, dots) and location and extent of the study area (right, red) in the Swiss National Park, with systematic sampling points (right, orange circles). On the left, origins of European hare (Lepus europaeus, Le) samples are displayed in blue, mountain hare (Lepus timidus, Lt) samples in dark gray, hybrids (Hb) in black, and samples of unknown species identity in light gray

FIGURE 2

Error rate in the genotyping data obtained for mountain hares (Lepus timidus) based on noninvasive samples, as estimated by the proportional amount of missing replicates in replicate genotypes in each primary sampling period (a) and at each marker (b) and by the amount of false homozygote replicates and consensus heterozygote replicates (c, d). Significance codes refer to differences between sampling periods (a, c) or differences between markers (b, d). Spring sampling sessions are indicated in light gray, and fall sessions are colored dark gray. Values for each marker are given as seasonal averages, and error bars indicate standard errors

FIGURE 3

The mean number of samples collected per mountain hare (Lepus timidus) individual per day with each sampling method across all sampling periods (2014–2018) in the study area in the Swiss Alps. Opportunistic samples were collected whenever a fecal pellet of appropriate condition was detected between systematic sampling points. Values for females are given in red, values for males are in blue, and error bars indicate standard errors of means

FIGURE 4

Overview of the weighted mean of capture (a) and recapture probabilities (b) calculated for the models using capture histories based on systematically collected samples and the whole dataset (systematic and opportunistic), given for male and female mountain hare (Lepus timidus) individuals. Error bars indicate weighted means of standard errors calculated by mark (White & Burnham, 1999)

FIGURE 5

Individual abundance of mountain hare (Lepus timidus) in the study area in each primary sampling period, as given by each of the five best fitting models in mark (White & Burnham, 1999) and as their weighted average. Error bars indicate standard errors as estimated by mark for the model

FIGURE 6

Results of the principal component analysis for genotypes of noninvasive genetic samples (light gray circles) and of tissue samples (triangles). Some samples morphologically assigned to Lepus timidus (Lt, dark gray) showed signs of being assigned to L. europaeus (Le, blue) and vice versa. One hybrid (Hb, black) sample was assigned to L. europaeus, and one hybrid sample was assigned to L. timidus. The sample of unknown origin (Unknown, light gray) was assigned to L. timidus. The large symbols represent the centroids of the defined groups

FIGURE 7

Results of the analysis run in structure (Pritchard et al., 2000): Cluster assignment probabilities are given in gray for Lepus timidus and in blue for L. europaeus. Individual genotypes identified based on noninvasive samples are named with the prefix “NP” and depicted on the left side. The morphological species assignments of tissue samples are given as “Le” for European hares, “Lt” for mountain hares, “Hb” for hybrids, and “NA” for unknown species identity