Data from: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 (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 from 157 samples and were predicted to account for 75% of the species assemblage. Black-backed jackals (Lupulella 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. # Identifying cryptic mammals with non-invasive methods: an effective molecular species identification tool to survey southern African terrestrial carnivores [doi.org](doi.org) 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. - Aonyx_congicus_612.AciAca_mtDNA2_mtDNA.fa: new mitochondrial genome assembly for the Congo clawless otter (*Aonyx congicus*), using previously reported short reads of *Aonyx congicus* (NCBI SRX15437983; de Ferran et al., 2022) mapped against a mixed reference which included the closest available nuclear (Asian small-clawed otter, *Amblonyx cinereus*, DNA Zoo’s Hi-C assembly) and mitochondrial (African clawless otter, *Aonyx capensis*, NCBI NC046484) references, using the Paleomix pipeline. * ATP6_RepresentativeReferenceDataset.xlsx: includes a subset of 61 sequences which was curated as part of this study for the *ATP6* mini-barcode to provide a tool for species identification of carnivores in southern Africa. The dataset includes one sequence per haplotype[delete: with a minimum of two sequences per species]. Information about sequence origin is provided in Appendix 2 of the associated manuscript. Additional reference sequences that were not included in this alignment as they do not provide additional variation, or are of unknown or non-African origin, are also listed in Appendix 2 of the associated manuscript, with indication of the reference sequence representing them (sequence match). ## Sharing/Access information Data for the RepresentativeReferenceDataset was derived from the following sources: \- GenBank (see Fasta file as well as Appendix 2 for GenBank accession numbers). \- Chaves et al., 2012, and dryad: [doi.org](doi.org) \- this study, sequences submitted to GenBank (see Appendix 2 of the associated manuscript for GenBank accession numbers) or Dryad (see Fasta NewSequences_Namibia_CheetahConservationFund).