Application of DNA barcoding techniques to mammal inventories in the African rain forest: droppings may inform us of the owners

Abstract

The DNA barcoding of fecal samples was used to inventory large- and medium-sized terrestrial mammals in the African rain forest. First, the appropriate DNA region for the genetic identification of various species was determined. Although a region of mitochondrial cytochrome c oxidase I has been commonly used for DNA barcoding, the number of mammal species in which sequences of the region have been registered in the GenBank is limited, with the mitochondrial cytochrome b region (cytb) representing the most appropriate region for this type of analysis. Hence, genetic species identification was conducted using the mitochondrial cytb region for most samples, while the control region was used for small ungulates. We collected 259 fresh fecal samples of mammals in Moukalaba-Doudou National Park, Gabon. More than 70 % of analyzed samples produced sequences. The species was identified by examining the sequence identity between the sample and the identified species and that between the sample and the next closest species, or by constructing a phylogenetic tree containing closely related species. In total, the sequences of 19 mammal species were obtained. A smaller number of species were recorded by DNA barcoding compared to camera traps placed in the study area; however, DNA analyses were effective at discriminating morphologically similar species, such as small ungulates and carnivores, some of which were difficult to identify even when using camera traps. Genetic species identification using feces, in combination with direct observation and/or camera traps, can be useful for the accurate inventory of large- and medium-sized terrestrial mammals.