DNA persistence in predator saliva from multiple species and methods for optimal recovery from depredated carcasses

Abstract

Molecular forensics is an important component of wildlife research and management. Using DNA from noninvasive samples collected at predation sites, we can identify predator species and obtain individual genotypes, improving our understanding of predator–prey dynamics and impacts of predators on livestock and endangered species. To improve sample collection strategies, we tested two sample collection methods and estimated degradation rates of predator DNA on the carcasses of multiple prey species. We fed carcasses of calves (Bos taurus) and lambs (Ovis aires) to three captive predator species: wolves (Canis lupus), coyotes (C. latrans), and mountain lions (Puma concolor). We swabbed the carcass in the field, as well as removed a piece of hide from the carcasses and then swabbed it in the laboratory. We swabbed all tissue samples through time and attempted to identify the predator involved in the depredation using salivary DNA. We found the most successful approach for yielding viable salivary DNA was removing hide from the prey and swabbing it in the laboratory. As expected, genotyping error increased through time and our ability to obtain complete genotypes decreased over time, the latter falling below 50% after 24 h. We provide guidelines for sampling salivary DNA from tissues of depredated carcasses for maximum probability of detection.

Wildlife whodunnit: forensic identification of predators to inform wildlife management and conservation

“…Mumma et al (2014) similarly investigated most carcasses within 1–2 days of mortality but some investigations occurred up to 6 days post‐mortem, and they also found no effect of the delay on sample retention. Most studies documenting DNA degradation over time have focused on degradation from 0–48 hours since deposition (Blejwas et al 2006, Sundqvist et al 2008, Harms et al 2015, Piaggio et al 2020), a time frame that may be unachievable to access a carcass despite best efforts for many field studies. It is possible that samples degrade in the first 2 days and then stabilize, which could explain the difference between our findings and those of Blejwas et al (2006), Sundqvist et al (2008), Harms et al (2015), and Piaggio et al (2020).…”

“…Most studies documenting DNA degradation over time have focused on degradation from 0–48 hours since deposition (Blejwas et al 2006, Sundqvist et al 2008, Harms et al 2015, Piaggio et al 2020), a time frame that may be unachievable to access a carcass despite best efforts for many field studies. It is possible that samples degrade in the first 2 days and then stabilize, which could explain the difference between our findings and those of Blejwas et al (2006), Sundqvist et al (2008), Harms et al (2015), and Piaggio et al (2020). While our findings suggest that genetic evidence can still be useful even after a long delay, we emphasize that mortalities should be investigated as rapidly as possible because the evidence needed to confirm predation may be destroyed by consumption of the carcass and scavengers have more time to contaminate the site.…”

“…We expected that DNA samples collected with the shortest time since mortality would have less time to degrade and have a higher rate of amplification success (Harms et al 2015, Piaggio et al 2020). We predicted that DNA collected from artificial surfaces (i.e.…”

Application of DNA forensic to identify a problem leopard and its implications for human-leopard conflict mitigation

“…We have followed standard sampling protocols for forensic investigations (Moore et al, 2021), which included aseptically swabbing bite-wound of the victim as soon as he was declared dead. It has been shown that carefully swabbing the bite wounds of carcasses within 24 hours increases the possibilities of obtaining complete genotypes for individual identification of predator species (Piaggio et al, 2020). By preserving the bite-wound in a freezer until lab processing, we successfully ascertained the correct identity of the problem leopard and resolved the case.…”

Straight from the coyote's mouth: genetic identification of prey through oral swabs of predators

“…However, depredation events are rarely witnessed, and direct observation is not a reliable method of identification (Sundqvist et al 2008). Identifying the carnivore involved in a specific depredation event can be difficult, and relies on physical evidence at a kill site, which is often equivocal unless identification is possible from DNA detected from the bite wound (Williams et al 2003, Piaggio et al 2020). Environmental DNA (eDNA) from saliva remaining on prey carcasses at bite wounds has been used to identify the predator at the species level.…”