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Species-specific mitochondrial DNA markers for identification of non-invasive samples from sympatric carnivores in the Iberian Peninsula

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Abstract

Genetic species identification of non-invasively collected samples has become an important tool in ecological research, management and conservation and wildlife forensics. This is especially true for carnivores, due to their elusive nature, and is crucial when several ecologically and phylogenetically close species, with similar faeces, hairs, bones and/or pelts, occur in sympatry. This is the case of the Iberian Peninsula, a region with a carnivore community of 16 species—about two-thirds of the European carnivore fauna. Here we present a simple, efficient and reliable PCR-based protocol, using a novel set of species-specific primers, for the unambiguous identification to species of non-invasively collected samples or forensic materials from Iberian carnivores. For each species, from the consensus of all cytochrome b haplotypes, found here and previously reported, we designed species-specific primer pairs for short fragments, the most likely to persist in low-quantity and degraded DNA samples. The predicted specificity of each primer pair was assessed through PCR of positive DNA extracts from the carnivore species, from an exhaustive array of potential prey and from humans. The robustness of PCR amplification for non-invasively sampled DNA was tested with scat samples. The primers did not produce false positives and correctly identified all carnivore samples to the species level. In comparison with sequencing and PCR-RFLP assays, our method is, respectively, cost- and time-effective, and is especially suited for monitoring surveys targeting multiple populations/species. It also introduces an approach that works for a whole community of carnivores living sympatrically over a large geographic area.

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Acknowledgements

We thank the members of the carnivore ecology and conservation research group at the CBA, headed by Margarida Santos-Reis, as well as BRISA for their fundamental contributions to the collection of carnivore biological samples maintained at the institution. We are also grateful to Armando Loureiro (BTVS-PNPG, ICN, Portugal) for carnivore samples from northern Portugal; Margarida Fernandes (ICN, Portugal) and Maria da Graça Ramalhinho (MNHN, Portugal) for Iberian lynx samples; Deodália Dias, Maria do Mar Oom, Maria da Luz Mathias, Octávio Paulo and Maria Manuela Coelho, for samples of prey species; Francisco Palomares and Ana Piriz (Doñana Biological Station), Benjamín Gómez-Moliner (University of the Basque Country), Márcia Barbosa (University of Extremadura), Filipa Alves (University of Barcelona), Trinidad Pérez (University of Oviedo) for samples from Spain; Miia Varanka (Ranua Wildlife Park), Hanna Sitek (Poznan Zoo), Alexandra Tsekhanskaya (Kharkiv Zoo) and Irina Skiba (St. Petersburg Zoo) for providing additional valuable samples. We acknowledge financial support from the Fundação para a Ciência e a Tecnologia, research project POCTI/2000/BSE/407888.

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Authors and Affiliations

  1. Centro de Biologia Ambiental, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Edifício C2 3° Piso, 1749-016, Lisboa, Portugal

    Carlos A. Fernandes, Catarina Ginja, Iris Pereira & Margarida Santos-Reis

  2. Biodiversity and Ecological Processes Group, Cardiff University, Cardiff, CF10 3US, UK

    Carlos A. Fernandes & Michael W. Bruford

  3. Centro de Genética e Biologia Molecular, Universidade de Lisboa, Campo Grande Edifício ICAT, 1749-016, Lisboa, Portugal

    Rogério Tenreiro

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  1. Carlos A. Fernandes
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  2. Catarina Ginja
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  4. Rogério Tenreiro
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  6. Margarida Santos-Reis
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Correspondence to Carlos A. Fernandes.

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Fernandes, C.A., Ginja, C., Pereira, I. et al. Species-specific mitochondrial DNA markers for identification of non-invasive samples from sympatric carnivores in the Iberian Peninsula. Conserv Genet 9, 681–690 (2008). https://doi.org/10.1007/s10592-007-9364-5

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