Pilot study for non-invasive genetic sampling of Cynomys ludovicianus
Abstract: The range and distribution of Cynomys ludovicianus is becoming increasingly constrained and fragmented causing concern for low levels of genetic variation and vulnerability to external threats such as Sylvatic plague and human control. The black-tailed prairie dog has often been regarded as a pest to the farming and ranching industries of the United States Great Plains; however, as a keystone species, the disappearance of the prairie dog throughout the Texas Panhandle region is alarming to conservationists. This pilot study assessed the efficacy of three fecal DNA protocols for purifying C. ludovicianus genomic DNA from colonic mucosal cells isolated from wild fecal samples in order to recognize a reliable method for future non-invasive population surveys. The protocols tested were: Qiagen QIAamp DNA Stool Mini Kit, Zymo Quick-DNA Fecal/Soil Microbe Miniprep Kit, and MPBiomedicals FastDNA Spin Kit for Feces. Approximately 40 fecal pellet samples were collected from a single prairie dog town (~1.6 km2) in Amarillo, Texas, of which 24 suitable samples were used for the extraction protocols. After genomic recoveries were purified from the prairie dog fecal pellets, six microsatellite loci (A104, A711, A8, D1, D6, D12) were tested for PCR amplification. Of the three protocols evaluated for this study, the Zymo Quick-DNA protocol produced both high-quality genomic recovery and attainable PCR. This preliminary study illustrates an effective non-invasive genetic sampling method for future research initiatives pertaining to black-tailed prairie dog conservation.
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