DOI: 10.5061/dryad.23k27
title: Data from: Balancing sample accumulation and DNA degradation rates to optimize noninvasive genetic sampling of sympatric carnivores

description: Noninvasive genetic sampling, or noninvasive DNA sampling (NDS), can be an
 effective monitoring approach for elusive, wide-ranging species at low
 densities. However, few studies have attempted to maximize sampling
 efficiency. We present a model for combining sample accumulation and DNA
 degradation to identify the most efficient (i.e. minimal cost per
 successful sample) NDS temporal design for capture–recapture analyses. We
 use scat accumulation and faecal DNA degradation rates for two sympatric
 carnivores, kit fox (Vulpes macrotis) and coyote (Canis latrans) across
 two seasons (summer and winter) in Utah, USA, to demonstrate
 implementation of this approach. We estimated scat accumulation rates by
 clearing and surveying transects for scats. We evaluated mitochondrial
 (mtDNA) and nuclear (nDNA) DNA amplification success for faecal DNA
 samples under natural field conditions for 20 fresh scats/species/season
 from &lt;1–112 days. Mean accumulation rates were nearly three times
 greater for coyotes (0.076 scats/km/day) than foxes (0.029 scats/km/day)
 across seasons. Across species and seasons, mtDNA amplification success
 was ≥95% through day 21. Fox nDNA amplification success was ≥70% through
 day 21 across seasons. Coyote nDNA success was ≥70% through day 21 in
 winter, but declined to &lt;50% by day 7 in summer. We identified a
 common temporal sampling frame of approximately 14 days that allowed
 species to be monitored simultaneously, further reducing time, survey
 effort and costs. Our results suggest that when conducting repeated
 surveys for capture–recapture analyses, overall cost-efficiency for NDS
 may be improved with a temporal design that balances field and laboratory
 costs along with deposition and degradation rates.
description: DepositionAnalysisR Script for generalized linear model and contrast analysis for scat accumulation samples collected from September 2012 to July 2012 at Dugway Proving Ground, Utah.dep.dataRaw data for scat accumulation surveys used in the generalized linear model and contrast analyses. Data collected from September 2012 to July 2012 at Dugway Proving Ground, Utah.kitfoxesRaw DNA degradation data for kit fox faecal DNA samples used in the mixed-effects logistic regression models for PCR success, allelic dropout (ADO) and false alleles (FA). Faecal DNA samples collected in 2012 during winter and summer at Dugway Proving Ground, Utah. (Coding: 1 indicates successful PCR amplification, presence of ADO, or presence of FA; 0 indicates failed PCR amplification, no detection of ADO, or no detection of FA)coyotesRaw DNA degradation data for coyote faecal DNA samples used in the mixed-effects logistic regression models for PCR success, allelic dropout (ADO) and false alleles (FA). Faecal DNA samples collected in 2012 during winter and summer at Dugway Proving Ground, Utah. (Coding: 1 indicates successful PCR amplification, presence of ADO, or presence of FA; 0 indicates failed PCR amplification, no detection of ADO, or no detection of FA)lociData on average locus lengths for kit fox and coyote faecal DNA samples used in the mixed-effects logistic regression models for PCR success, allelic dropout (ADO) and false alleles (FA). Faecal DNA samples collected in 2012 during winter and summer at Dugway Proving Ground, Utah.pcrSAS script for the mixed-effects logistic regression models of PCR success for coyote and kit fox faecal DNA samples collected in 2012 during winter and summer at Dugway Proving Ground, Utah.adoSAS script for the mixed-effects logistic regression models of allelic dropout for coyote and kit fox faecal DNA samples collected in 2012 during winter and summer at Dugway Proving Ground, Utah.faSAS script for the mixed-effects logistic regression models of false alleles for coyote and kit fox faecal DNA samples collected in 2012 during winter and summer at Dugway Proving Ground, Utah.