Molecular forensics in avian conservation: a DNA-based approach for identifying mammalian predators of ground-nesting birds and eggs

Abstract

BackgroundThe greater sage-grouse (Centrocercus urophasianus) is a ground-nesting bird from the Northern Rocky Mountains and a species at risk of extinction in in multiple U.S. states and Canada. Herein we report results from a proof of concept that mitochondrial and nuclear DNAs from mammalian predator saliva could be non-invasively collected from depredated greater sage-grouse eggshells and carcasses and used for predator species identification. Molecular forensic approaches have been applied to identify predators from depredated remains as one strategy to better understand predator–prey dynamics and guide management strategies. This can aid conservation efforts by correctly identifying predators most likely to impact threatened and endangered species. DNA isolated from non-invasive samples around nesting sites (e.g. fecal or hair samples) is one method that can increase the success and accuracy of predator species identification when compared to relying on nest remains alone.ResultsPredator saliva DNA was collected from depredated eggshells and carcasses using swabs. We sequenced two partial fragments of two mitochondrial genes and obtained microsatellite genotypes using canid specific primers for species and individual identification, respectively. Using this multilocus approach we were able to identify predators, at least down to family, from 11 out of 14 nests (79 %) and three out of seven carcasses (47 %). Predators detected most frequently were canids (86 %), while other taxa included rodents, a striped skunk, and cattle. We attempted to match the genotypes of individual coyotes obtained from eggshells and carcasses with those obtained from fecal samples and coyotes collected in the areas, but no genotype matches were found.ConclusionPredation is a main cause of nest failure in ground-nesting birds and can impact reproduction and recruitment. To inform predator management for ground-nesting bird conservation, accurate identification of predator species is necessary. Considering predation can have a high impact on recruitment, predation events are very difficult to observe, and predator species are difficult to identify visually from nest remains, molecular approaches that reduce the need to observe or handle animals offer an additional tool to better understand predator–prey dynamics at nesting sites.Electronic supplementary materialThe online version of this article (doi:10.1186/s13104-015-1797-1) contains supplementary material, which is available to authorized users.

Non-Trapping, Non-Invasive, Rapid Surveillance Sampling Using Tracking Tunnels, Trail Cameras, and eDNA to Determine Presence of Pest Predator Species

“…Similarly, treenesting birds like the endangered 'elepaio (Chasiempis sandwichensis ibidis) are depredated by invasive rats in Hawaii, as evidenced by trail cameras (VanderWerf 2001). Environmental DNA provides another tool for identifying nest predators, which in some cases may be more applicable to certain field situations than other methods (Hopken et al 2016).…”

“…Environmental DNA can be used to identify the predators of depredated bird eggs or carcasses by swabbing saliva from the eggs or carcasses. This technique has proven successful in determining the predators of greater sage grouse (Centrocercus urophasianus) nests: Hopken et al (2016) used two mitochondrial loci to screen for predator DNA from swabs taken from grouse eggs and carcasses (see case studies below for more details).…”

“…This analysis included sequencing two partial fragments of two mitochondrial loci (Cytochrome-b and Control Region) and genotyping eight canid-specific microsatellite loci for canid predator species identification. Additional details for this study are reported in Hopken et al (2016).…”

“…The main nest predator was coyote (Canis latrans; five of the 11), followed by domestic dogs (C. lupus familiaris), and the remaining of the predator identifications included cattle (Bos taurus), striped skunks (Mephitis mephitis), a deer mouse (Peromyscus maniculatus), and a wild canid (Canis sp.) that could not be confidently identified to a lower taxonomic level (Hopken et al 2016).…”

Identifying predators from saliva at kill sites with limited remains

“…A recent study was even able to obtain red fox ( Vulpes vulpes ) or dog saliva from eggshells, successfully identifying the predator in one‐third of the egg samples tested (Dawson et al ). A sage grouse ( Centrocercus urophasianus ) predation study, which identified canid predators to at least family level, actually had greater amplification success from eggshells than from adult carcasses (Hopken et al ).…”