Combining noninvasive genetics and a new mammalian sex‐linked marker provides new tools to investigate population size, structure and individual behaviour: An application to bats

Abstract

Monitoring wild populations is crucial for their effective management. Noninvasive genetic methods provide robust data from individual free-ranging animals, which can be used in capture-mark-recapture (CMR) models to estimate demographic parameters without capturing or disturbing them. However, sex- and status-specific behaviour, which may lead to differences in detection probabilities, is rarely considered in monitoring. Here, we investigated population size, sex ratio, sex- and status-related behaviour in 19 Rhinolophus hipposideros maternity colonies (Northern France) with a noninvasive genetic CMR approach (using faeces) combined with parentage assignments. The use of the DDX3X/Y-Mam sexual marker designed in this study, which shows inter- and intrachromosomal length polymorphism across placental mammals, together with eight polymorphic microsatellite markers, produced high-quality genetic data with limited genotyping errors and allowed us to reliably distinguish different categories of individuals (males, reproductive and nonreproductive females) and to estimate population sizes. We showed that visual counts represent well-adult female numbers and that population composition in maternity colonies changes dynamically during the summer. Before parturition, colonies mainly harbour pregnant and nonpregnant females with a few visiting males, whereas after parturition, colonies are mainly composed of mothers and their offspring with a few visiting nonmothers and males. Our approach gives deeper insight into sex- and status-specific behaviour, a prerequisite for understanding population dynamics and developing effective monitoring and management strategies. Provided sufficient samples can be obtained, this approach can be readily applied to a wide range of species.

Metabarcoding for the parallel identification of several hundred predators and their prey: Application to bat species diet analysis

“…For all kits, we followed manufacturer's recommendations except for the NucleoSpin 8 Plant II as we used the slight modifications recommended in Zarzoso‐Lacoste et al. ().…”

“…The EZ-10 96 DNA and NucleoSpin 8 Plant II kits provide high-throughput DNA isolation (up to 192 samples in parallel) thanks to a 96-well format unlike the other kits using tube format. For all kits, we followed manufacturer's recommendations except for the NucleoSpin 8 Plant II as we used the slight modifications recommended in Zarzoso-Lacoste et al (2017).…”

Range expansion is associated with increased survival and fecundity in a long-lived bat species

“…In R. hipposideros, females aggregate in the so-called maternity colonies during spring and summer to give birth and raise their single offspring [29,30]. Males can be present in these maternity colonies to a varying extent [34], but we only consider females for the investigation of population dynamics.…”

In silicoand empirical evaluation of twelve COI & 16S metabarcoding primer sets for insectivorous diet analyses

“…DNA extraction was performed according to Zarzoso-Lacoste et al (2018). Briefly, guano samples were frozen at −80°C then bead-beaten for 2 x 30s at 30 Hz on a TissueLyser (Qiagen) using a 5-mm stainless steel bead.…”

“…Briefly, guano samples were frozen at −80°C then bead-beaten for 2 x 30s at 30 Hz on a TissueLyser (Qiagen) using a 5-mm stainless steel bead. DNA was extracted using the NucleoSpin 8 Plant II kit (Macherey Nagel) with the slight modifications recommended in Zarzoso-Lacoste et al (2018).…”