DNA barcoding meets molecular scatology: short mtDNA sequences for standardized species assignment of carnivore noninvasive samples

Although species assignment of scats is important to study carnivoran biology, there is still no standardized assay for the identification of carnivores worldwide, which would allow large-scale routine assessments and reliable cross-comparison of results. Here we evaluate the potential of two short mtDNA fragments (ATP6 [126 bp] and COI [187 bp]) to serve as standard markers for the Carnivora. Samples of 66 species were sequenced for one or both of these segments. Alignments were complemented with archival sequences, and analyzed with three approaches (tree-based, distance-based and character-based). Intraspecific genetic distances were generally lower than between-species distances, resulting in diagnosable clusters for 86% (ATP6) and and 85% (COI) of the species. Notable exceptions were recently diverged species, most of which could still be identified using diagnostic characters, uniqueness of haplotypes, or by reducing the geographic scope of the comparison. In silico comparative an...