Noninvasive alternatives for DNA collection from threatened rodents

Abstract

Many rodent species are currently under conservation threat. However, population monitoring and status assessment are extremely challenging because of small body size, low abundance and elusive behavior of rodents. Furthermore, invasive methods of capture and tissue collection commonly used to address such studies can induce an unacceptable amount of stress to sensitive species. As a result, noninvasive techniques have become more widely used, but relatively few studies have applied noninvasive techniques to rodents. Here we present two noninvasive alternatives for the collection of DNA from Franklin's ground squirrels (Poliocitellus franklinii). We compared the quantity, purity and degradation of DNA extracted from plucked hair and fecal pellets to tail snip tissues. We recovered more DNA from tail snips than either plucked hair or fecal pellets. Both hair and fecal pellets recovered DNA with purity ratios similar to tail snips. As expected, DNA recovered from fecal pellets exhibited a high degree of degradation compared to hair and tail tissues. Careful planning of field and laboratory protocols is therefore necessary to compensate for challenges associated with noninvasive tissue types. While there is no tissue that can universally be applied to all research projects, both hair and feces are viable alternatives to traditional invasive procedures and can be applied to threatened and endangered rodent species.

Assessing the efficiency of using passive hair traps as a method for non-invasive sampling from European beavers (Castor fiber L.)

“…Studies on rodent populations are often difficult to perform due to their nocturnal activity (Green et al 2013). Direct observations at night are inefficient, and live-trapping is an expensive and time-consuming process (Alasaad et al 2011).…”

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“…This study suggested the use of fecal matter more promising in comparison to the traditional DNA sources whose collection and use is quite difficult. While there is no tissue that can universally be applied to all research projects, fecal matter is a much more promising alternative to traditional invasive procedures which can be applied to study any species under threat [30] . In accordance to this, this study is a pioneer attempt on reptiles to use fecal pellets as source of DNA.…”

Novel frontier in wildlife monitoring: identification of small rodent species from faecal pellets using Near-Infrared Reflectance Spectroscopy (NIRS)

“…Small rodents are prevalent in ecosystems across the globe, with many species acting as ecosystem engineers (Dickman, 1999) or keystone species (Ims & Fuglei, 2005); with numerous rare species of high conservation value (Green, Ting, Manjerovic, & Mateus-Pinilla, 2013) and many invasive populations with profound effects on ecosystem functioning (Dickman, 1999). Monitoring and research of small rodents is thus a globally salient enterprise for ecosystem management, conservation, forestry and agriculture.…”

“…Monitoring and research of small rodents is thus a globally salient enterprise for ecosystem management, conservation, forestry and agriculture. Yet, obtaining population- or community-level data on small rodents is often challenging, as these small and cryptic animals are elusive (Green et al, 2013) and cost-effective methods for large-scale sampling of their multispecies communities are largely missing (Engeman & Whisson, 2006; Heisler, Somers, & Poulin, 2016). State-of-the-art estimation of small rodent community composition, population size and density, relies on a variety of trapping and indexing efforts, e,g, pitfalls, live-, snap-, hair- or camera traps and systematic incidental observations (Engeman & Whisson, 2006; Soininen, Jensvoll, Killengreen, & Ims, 2015; Fauteux et al, 2018), or on counts of burrows, runways, winter nests, owl pellet contents and faeces (Green et al, 2013; Heisler et al, 2016).…”