Identifying cryptic mammals with non-invasive methods: An effective molecular species identification tool to survey southern African terrestrial carnivores

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 (Lupulell..., , , # Identifying cryptic mammals with non-invasive methods: an effective molecular species identification tool to survey southern African terrestrial carnivores

[https://doi.org/10.5061/dryad.bcc2fqzmt](https://doi.org/10.5061/dryad.bcc2fqzmt)

This dataset includes newly generated mini-barcode reference sequences for Namibian carnivores; a new mitogenome for *Aonyx congicus*; and a curated carnivore sequence fasta alignment for carnivore species identification.

## Description of the data and file structure

* ATP6_NewSequences_Namibia_CheetahConservationFund.fas.txt: includes 26 new reference sequences for the 126 bp *ATP6* mini-barcode with primers ATP6-DF3 and ATP6-DR1. All samples were obtained from Namibian carnivore samples kept at the Cheetah Conservation Fund biobank; details are provided as part of Appendix 2 of the associated manuscript. We verified PCR amplification success of the samples for the mini-barcode, and sequenced them to provide additional reference sequences.

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