Data from: Evaluating the interaction of faecal pellet deposition rates and DNA degradation rates to optimize sampling design for DNA-based mark-recapture analysis of Sonoran pronghorn

Knowledge of population demographics is important for species management
but can be challenging in low-density, wide-ranging species. Population
monitoring of the endangered Sonoran pronghorn (Antilocapra americana
sonoriensis) is critical for assessing the success of recovery efforts,
and noninvasive DNA sampling (NDS) could be more cost-effective and less
intrusive than traditional methods. We evaluated faecal pellet deposition
rates and faecal DNA degradation rates to maximize sampling efficiency for
DNA-based mark–recapture analyses. Deposition data were collected at five
watering holes using sampling intervals of 1–7 days and averaged one
pellet pile per pronghorn per day. To evaluate nuclear DNA (nDNA)
degradation, 20 faecal samples were exposed to local environmental
conditions and sampled at eight time points from one to 124 days. Average
amplification success rates for six nDNA microsatellite loci were 81% for
samples on day one, 63% by day seven, 2% by day 14 and 0% by day 60. We
evaluated the efficiency of different sampling intervals (1–10 days) by
estimating the number of successful samples, success rate of individual
identification and laboratory costs per successful sample. Cost per
successful sample increased and success and efficiency declined as the
sampling interval increased. Results indicate NDS of faecal pellets is a
feasible method for individual identification, population estimation and
demographic monitoring of Sonoran pronghorn. We recommend collecting
samples >7 days old and estimate that a sampling interval of 4–7
days in summer conditions (i.e. extreme heat and exposure to UV light)
will achieve desired sample sizes for mark–recapture analysis while also
maximizing efficiency.