Comparison of protocols for DNA extraction from fecal samples of capuchin monkeys, Sapajus nigritus, and marmosets, Callithrix sp.

Fecal sampling is a non-invasive methodology for obtaining DNA for genetic studies in wild animals. The capuchin monkey, Sapajus nigritus and the invasive marmosets in Southeast Brazil, Callithrix jacchus, C. penicillata, and their hybrids, have been among the targets of these studies. The commercial kits for fecal DNA extraction from feces, still demand a high cost, and to circumvent this situation, homemade protocols can be used. Our objective was to test the protocols of Finger (2015) and Doyle & Doyle (1987) to extract fecal DNA from S. nigritus and Callithrix spp., evaluating their efficiency for PCR and the influence of collection time and storage method. Thirteen fecal samples were collected in Rio de Janeiro in different locations and periods. Three experiments were designed to test the protocols. In test 1, with samples collected in 2015, 2018, and 2019 preserved in 70% ethanol, no DNA was obtained with any protocol. The Finger protocol was also not successful in tests 2 and 3, with samples collected in 2023. The Doyle & Doyle protocol was efficient in tests 2 and 3, with extractions on the day of collection and up to a month of storage at -20°C. Callithrix fecal DNA generated an amplicon in the first PCR, whereas for S. nigritus, only in the second PCR, after dilution of the DNA and probable reduction of inhibitors. The Doyle & Doyle (1987) protocol was efficient for extracting fecal DNA of the species studied from fresh feces or from those stored for up to 30 days at -20°C.