Long-term persistence of horse fecal DNA in the environment makes equids particularly good candidates for non-invasive sampling

Ecology and Evolution
By: , and 



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.

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Additional publication details

Publication type Article
Publication Subtype Journal Article
Title Long-term persistence of horse fecal DNA in the environment makes equids particularly good candidates for non-invasive sampling
Series title Ecology and Evolution
DOI 10.1002/ece3.3956
Volume 8
Issue 8
Year Published 2018
Language English
Publisher Wiley
Contributing office(s) Fort Collins Science Center
Description 12 p.
First page 4053
Last page 4064
Country United States
State Colorado
City Grand Junction
Other Geospatial Little Book Cliffs Wild Horse Herd Management Area
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