Scat as a source of DNA for population monitoring

• Published in: Ecology and evolution Vol. 12; no. 11; pp. e9415 - n/a
• Main Authors: Manning, Jeffrey A., Edwards, Taylor, Clemons, John, Leavitt, Daniel J., Goldberg, Caren S., Culver, Melanie
• Format: Journal Article
• Language: English
• Published: England John Wiley & Sons, Inc 01-11-2022; John Wiley and Sons Inc; Wiley
• Subjects: Amplification; Conservation Genetics; Deoxyribonucleic acid; Desert animals; Deserts; DNA; Environmental conditions; fecal DNA; Feces; Genetic testing; Genotypes; Genotyping; Laboratories; Microsatellites; Mitochondrial DNA; Monitoring; Monitoring methods; non‐invasive sampling; Parks & recreation areas; Populations; reptile; Reptiles; Reptiles & amphibians; scat; Tortoises; United States > US; Arizona; microsatellites; non‐invasive sampling; reptile; fecal DNA; mitochondrial DNA; scat
• ISSN: 2045-7758; 2045-7758
• DOI: 10.1002/ece3.9415

Sampling fecal droppings (scat) to genetically identify individual animals is an established method for monitoring mammal populations and could be highly useful for monitoring reptile populations. Whereas existing protocols for obtaining DNA from reptile scat focus on analyses of whole, fresh scat deposited during animal handling, the collection of scat naturally deposited by reptiles in situ, as required for non‐invasive population monitoring, requires protocols to extract highly degraded DNA. Using surface swabs from such scats can reduce PCR inhibition and increase genotyping success. We report on three related but independently designed studies of DNA analyses from scat swabs of herbivorous reptiles under natural desert conditions: two free‐ranging desert tortoise species (Agassiz's desert tortoise, Gopherus agassizii, California, US, and Morafka's desert tortoise, G. morafkai, Arizona, US) and the common chuckwalla (Sauromalus atar) (Arizona, US, and Sonora, MX). We analyzed samples from both tortoise species with the same set of 16 microsatellites and chuckwalla samples with four mtDNA markers; studies also varied in swab preservation medium and DNA extraction method. Microsatellite amplification success per sample, defined as ≥9 loci with amplification, was 15% for the study of Agassiz's desert tortoise and for the study of 42% Morafka's desert tortoise. For chuckwallas, we successfully amplified and sequenced 50% of samples. We recovered fragments up to 400 bp for tortoises and 980 bp for chuckwallas from scat swab samples. This study indicates that genotypes can successfully be obtained from swabs of scat from herbivorous reptiles collected in the field under natural environmental conditions and emphasizes that repeat amplifications are necessary for the genetic identification of individuals from non‐invasive samples.
Non‐invasive methods for monitoring herbivorous reptile populations would benefit our knowledge of their ecology, space use, and conservation status. Current methods of obtaining fecal DNA for these species have only been demonstrated to work well on fresh scats rather than those found under field conditions. We present a compilation of three independently conducted but similar studies of fecal DNA collected from the common chuckwalla, Agassiz's desert tortoise, and Morafka's desert tortoise to show that swabs of scats obtained under natural conditions have the potential to be used to obtain genotypes for population monitoring.