Abstract
Fecal DNA collected noninvasively can provide valuable information about genetic and ecological characteristics. This approach has rarely been used for equids, despite the need for conservation of endangered species and management of abundant feral populations. We examined factors affecting the efficacy of using equid fecal samples for conservation genetics. First, we evaluated two fecal collection methods (paper bag vs. ethanol). Then, we investigated how time since deposition and month of collection impacted microsatellite amplification success and genotyping errors. Between May and November 2014, we collected feral horse fecal samples of known age each month in a feral horse Herd Management Area in western Colorado and documented deterioration in the field with photographs. Samples collected and dried in paper bags had significantly higher amplification rates than those collected and stored in ethanol. There was little difference in the number of loci that amplified per sample between fresh fecal piles and those that had been exposed to the environment for up to 2 months (in samples collected in paper bags). After 2 months of exposure, amplification success declined. When comparing fresh (0–2 months) and old (3–6 months) fecal piles, samples from fresh piles had more matching genotypes across samples, better amplification success and less allelic dropout. Samples defecated during the summer and collected within 2 months of deposition had highest number of genotypes matching among samples, and lowest rates of amplification failure and allelic dropout. Due to the digestive system and amount of fecal material produced by equids, as well as their occurrence in arid ecosystems, we suggest that they are particularly good candidates for noninvasive sampling using fecal DNA.
Highlights
Noninvasive methods such as the use of DNA extracted from fecal samples are increasingly being used to examine occupancy, population size, diet, and even hormones of a wide range of species (Bowser, Diamond, & Addison, 2013; Ernest, Penedo, May, Syvanen, & Boyce, 2000; Macandza, Owen-Smith, & Le Roux, 2014; Oyler- McCance et al, 2018; Powell & Monfort, 2001; Prugh, Ritland, Arthur, & Krebs, 2005; Schoenecker et al, 2014)
Noninvasive sampling of fecal DNA has been used for conservation goals as varied as estimating population sizes of forest elephants (Loxodonta cyclosis, Eggert, Eggert, & Woodruff, 2003; Eggert et al, 2013), identifying hybrids in a reintroduced population of red wolves (Canis rufus, Adams, Kelly, & Waits, 2003), intra-community relationships of bonobos (Pan paniscus, Gerloff, Hartung, Fruth, Hohmann, & Tautz, 1999), and use of resources by individual Sonoran pronghorn (Antilocapra americana sonoriensis, Woodruff, Lukacs, Christianson, & Waits, 2016)
Fecal DNA has been used to inform the conservation of some endangered equid species: the African wild ass (E. africanus, Rosenbom, Costa, Steck, Moehlman, & Beja-Pereira, 2011), Przewalski’s horse (E. ferus przewalskii, Liu et al, 2014a), and Grevy’s zebra, (E. grevyi, Kebede et al, 2014)
Summary
Noninvasive methods such as the use of DNA extracted from fecal samples are increasingly being used to examine occupancy, population size, diet, and even hormones of a wide range of species (Bowser, Diamond, & Addison, 2013; Ernest, Penedo, May, Syvanen, & Boyce, 2000; Macandza, Owen-Smith, & Le Roux, 2014; Oyler- McCance et al, 2018; Powell & Monfort, 2001; Prugh, Ritland, Arthur, & Krebs, 2005; Schoenecker et al, 2014). Several studies have highlighted the advantages of noninvasive sampling compared to traditional methods (Beja-P ereira, Oliveira, Alves, Schwartz, & Luikart, 2009; Kohn & Wayne, 1997; Luikart, Ryman, Tallmon, Schwartz, & Allendorf, 2010), and in some cases they have been shown to be at least as effective at monitoring various parameters, if not more so, than traditional methods The promise of these noninvasive approaches has yet to be fully realized and extends to a wide variety of species for which demographic and other ecological information is needed. The two domesticated equids (horses, Equus ferus caballus, and donkeys, E. africanus asinus) are abundant in feral populations to the point of being considered nuisance species in some places (Garrott & Oli, 2013; Woolnough et al, 2012) For both rare and common equids, conservation and management can be greatly enhanced by understanding genetic characteristics of populations and individuals. Sample collection techniques for herbivores need to be tested and optimized, as factors affecting amplification success of fecal DNA may be different in this group
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