Molecular species identification of scat samples of South American felids and canids

Carnivores play an important role on the ecosystem equilibrium. However, due to habitat loss and fragmentation, their populations have been declining around the world. Together, the elusive behavior and often low population density challenge the data collection. In this way, non-invasive sampling has been considered as an important alternative for information gathering without need of animal capture. Molecular analysis has been essential for precise species identification through non-invasive samples, as scats. However, as DNA from these samples is usually found degraded, the use of more than one marker for a safer identification is critical. In this work, we tested a set of new mini barcoding primers for molecular identification of non-invasive samples for Neotropical felid and canid species. Primers for three mitochondrial DNA regions—rRNA12Ss1, rRNA12Ss2, rRNA16S—were designed for canid and felid species and amplified using fecal samples, while control region and CytB primers were designed only for canids, totaling five mini barcoding primer pairs successfully tested in fecal samples. This study resulted in a very efficient primer set, which represents an important tool for a precise identification of South American carnivores based on non-invasive samples.