Evaluation of DNA extracted from timber rattlesnake (Cotalus horridus) cloacal and blood swabs for microsatellite genotyping

Genetic research is a key component to modern wildlife conservation, but
it is contingent on the collection of reliable and high-quality genetic
samples. Invasive genetic sampling techniques have potential to negatively
impact individuals, which may be prohibitive when working with threatened
and endangered species. Prior to sample collection, project managers must
try to balance the negative impact on individuals included in the study
with the demand for DNA and the difficulty of obtaining samples. Although
established methods for blood and tissue collection in reptiles meet the
need for high-quantity and quality DNA, they inherently require longer
handling times and more skill to obtain. Thus, non-invasive DNA collection
methods, such as cloacal swabs, may be preferred when animal welfare is a
priority. Cloacal swabs are quicker, easier, require less training and
reduce handling time. To evaluate cloacal swabbing as an alternative to
collecting blood, we obtained both cloacal and blood swabs. We extracted
DNA from cloacal and blood cells that were collected from 23 Timber
Rattlesnakes (Crotalus horridus). We assessed DNA by purity (A260/A280),
concentration, and microsatellite genotyping. Our results show
high-quality DNA can be obtained from both cloacal swabs and blood
samples, but quality and concentration of DNA was significantly lower from
cloacal swabs. Further, degradation and contamination affects the
performance of cloacal DNA when compared to blood DNA in
microsatellite-based genotyping. Although we recommend collecting blood
samples whenever possible to obtain the highest-quality DNA, cloacal swabs
represent a viable alternative for genetic sampling when using
microsatellite loci as genetic markers.