DNA-based identification of small rodent hairs sampled noninvasively in Gabon

Abstract The study of small rodents is challenging because of the difficulty of observing and sampling them in the wild. Although noninvasive approaches have proven effective for large mammals, such an approach has rarely been applied to rodents. Here, we describe a novel noninvasive approach for sampling rodent hairs in tropical forest and caves in Gabon, and present cytochrome b sequence data from hair samples obtained using this technique. Twenty-six unknown rodent hair samples were randomly selected for this study from a larger set of samples collected from 2 sites in Gabon (Lastoursville and Franceville). These samples were captured using 3 types of hair traps made from 20 cm long cylindrical tubes of plastic sheathing composed of either: (i) 50-mm diameter red electric cable; (ii) gray polyvinyl chloride (PVC) pipes; or (iii) a larger PVC pipe of 100-mm diameter. Traps were placed along ~200 m long transects laid either on the forest floor, on tree trunks, or within caves and baited with a tethered palm nut. From this sample subset, we were able to obtain a 429-bp fragment of the mitochondrial cytochrome b gene from 17 samples. Nearly all samples could be identified to the species level using a neighbor-joining tree analysis based on published sequences. Five murid rodents were identified (Praomys petteri, P. missonei, Lophuromys spp., Malacomys longipes, and Grammomys spp.) and 1 Red-legged Sun Squirrel (Heliosciurus rufobrachium). This study shows that it is possible to amplify and sequence hair samples collected noninvasively from small forest rodents in the tropics and that such an approach could provide important genetic data on species that would otherwise be difficult to study.