Mammal Research

, Volume 64, Issue 1, pp 133–145 | Cite as

How to spot a black-footed cat? Successful application of cross-species markers to identify captive-bred individuals from non-invasive genetic sampling

  • Federica Mattucci
  • Marco Galaverni
  • Cino Pertoldi
  • Elena Fabbri
  • Alexander Sliwa
  • Romolo CanigliaEmail author
Methods Paper


The black-footed cat (Felis nigripes) is the smallest felid of Southern Africa, endemic to the arid steppe and savannah habitats. However, though threatened and characterized by decreasing sizes of its populations, a number of ecological, demographic, sanitary, and genetic aspects, essential for the long-term conservation of the species, still remain poorly known. Non-invasive genetic sampling may represent an appropriate and cost-effective tool to fill this lack of information. Thus, for the first time so far, we developed a protocol for species and individual identification of black-footed cats, starting from markers originally designed for the domestic cat and from 23 non-invasively collected samples of captive-bred individuals. We then tested its genotyping efficiency and reliability for future applications in non-invasive genetic monitoring programs of the wild populations. Most of the samples (65%), corresponding to 15 individuals, were successfully genotyped at 316 bp of the mtDNA ND5 and at nine autosomal microsatellites. We detected two black-footed cat mtDNA ND5 haplotypes that were clearly distinguishable from all the other wild and domestic felids. All microsatellites were polymorphic and showed low error rates, probabilities of identity < 0.001 and a mean observed heterozygosity HO = 0.68. Subsequent approximate Bayesian computation simulations confirmed that black-footed cats and African and European wildcats likely experienced sequential population splittings that started during the Late Pliocene and continued through the Early Pleistocene. Our study provided the first reliable and cost-effective molecular multilocus characterization of non-invasively collected samples of black-footed cats. Though solely tested on captive-bred individuals, our method could be applied to design and implement effective long-term monitoring and conservation plans of poorly investigated black-footed cat wild populations.


Black-footed cats Conservation genetics Felids Phylogenetics Genetic variability Microsatellites mtDNA Non-invasive genetic sampling 



We are grateful to Sofie Nielsen, the Hoedspruit Endangered Species Centre and the Cat Conservation Trust, for the sample collection and to Stefano Anile, Ettore Randi (University of Bologna), and Nadia Mucci (ISPRA) for their useful suggestions on the manuscript.

Funding information

The study was supported by the Danish Natural Science Research Council grant number: 21-01-0526, 21-03-0125, and 95095995 by the Aalborg Zoo Conservation Foundation (AZCF) for CP and by the Italian Institute for Environmental Protection and Research (ISPRA, Istituto Superiore per la Protezione e la Ricerca Ambientale).

Supplementary material

13364_2018_407_MOESM1_ESM.xlsx (20 kb)
ESM 1 (XLSX 19.7 kb)
13364_2018_407_MOESM2_ESM.pdf (52 kb)
ESM 2 Identification of the optimal number of genetic clusters. Rates of increase in the posterior probability LnP(K) between consecutive K used to estimate the most likely number of genetic groups K in the data. (PDF 52.1 kb)
13364_2018_407_MOESM3_ESM.pdf (188 kb)
ESM 3 Model checking. Pre-evaluation of scenario-prior combinations; direct and logistic regression comparison methods of the estimated posterior probabilities among the tree scenarios (Scenario 1 in light blue, Scenario 2 in red and Scenario 3 in green); and fit of the selected best scenario (Scenario 1 in light blue) with the observed data. PCA I and II were plotted using 10.000 data points. (PDF 188 kb)


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Copyright information

© Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland 2018

Authors and Affiliations

  • Federica Mattucci
    • 1
  • Marco Galaverni
    • 2
  • Cino Pertoldi
    • 3
    • 4
  • Elena Fabbri
    • 1
  • Alexander Sliwa
    • 5
  • Romolo Caniglia
    • 1
    Email author
  1. 1.Area per la Genetica della ConservazioneISPRAOzzano dell’EmiliaItaly
  2. 2.Area ConservazioneWWF ItaliaRomeItaly
  3. 3.Department of Chemistry and BioscienceAalborg UniversityAalborg ØstDenmark
  4. 4.Aalborg ZooAalborg ØstDenmark
  5. 5.Kölner ZooKölnGermany

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