Identifying cryptic mammals with non-invasive methods: an effective
molecular species identification tool to survey southern African
terrestrial carnivores
Abstract
Carnivores play a vital role in ecosystem health and are thus an
important focus for conservation management. Non-invasive methods have
gained traction for carnivore monitoring as they are often elusive and
wide-ranging, making visual counts particularly difficult. Faecal
mini-barcoding combines field collection of scats with genetic analysis
for species identification. Here we assessed the applicability of a
mini-barcode based on the mitochondrial ATP6 gene in southern
Africa. We predicted amplification success based on in silico
evaluation of 34 of the 42 terrestrial carnivore species existing in
southern Africa, including the Congo clawless otter (Aonyx
congicus) for which we contributed a mitochondrial assembly, and tested
amplification success on available reference samples of 23 species. We
expanded the existing ATP6 mini-barcode reference database by
contributing additional sequences for 22 species including the Cape
genet (Genetta tigrina) and the side-striped jackal
(Lupulella adusta), for which no complete mini-barcode sequences
were available on GenBank to date. We furthermore applied the
ATP6 mini-barcode to a scat-based carnivore survey conducted in
2009 in a grassland habitat in Namibia, showing a 94.9% identification
success. Six carnivore species were detected from157 samples and were
predicted to account for 75% of species assemblage. Black-backed
jackals (Canis mesomelas) contributed the majority of faecal
samples (87.2%) and were distributed evenly throughout the area. Scat
samples of the remaining species, including leopard (Panthera
pardus), were distributed along the edge, in proximity to dense
bushland.