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Mammal Research

, Volume 62, Issue 4, pp 405–411 | Cite as

A novel real-time TaqMan™ PCR assay for simultaneous detection of Neotropical fox species using noninvasive samples based on cytochrome c oxidase subunit II

  • M. CosseEmail author
  • F. Grattarola
  • N. Mannise
Methods Paper
  • 117 Downloads

Abstract

Strategies to evaluate and monitor elusive mammal species require the development of genetic techniques and their application to unambiguous biological material for ecological and genetic studies. In order to assess cytochrome c oxidase subunit II gene inter- and intraspecific variations, we compared sequences from different Neotropical canids and domestic dogs. We developed a primer pair to amplify a 154-bp fragment of this gene and a species-specific multiplex TaqMan™ assay for accurate identification of two native fox species occurring in sympatry in South America, the crab-eating fox (Cerdocyon thous) and the pampas fox (Lycalopex gymnocercus). The assays can also distinguish domestic dogs (Canis lupus familiaris) from both wild foxes. The use of different fluorescent reporter dyes for species identification in a multiplex probe PCR-RT assay reduces labor and costs. The methodology presented in this study demonstrates an efficient approach to enable high-performance analysis and represents a reliable cost-effective tool for molecular ecology research to monitor the wild canid populations by noninvasive genetic sampling. This standardized assay will allow large-scale high-throughput analyses in a routine and reliable way.

Keywords

mtDNA COII gene Molecular ecology Canid Biodiversity monitoring Uruguay 

Notes

Acknowledgements

The research was supported by Programa de Desarrollo de las Ciencias Básicas (PEDECIBA) and grant from Agencia Nacional de Investigación e Innovación (ANII) (FCE_2_20011_1_5700). The authors wish to thank the Monitoreo participativo de fauna en Paso Centurión EFI-UdelaR team, and Cabo Polonio forest ranger team (SNAP) and to acknowledge sample contribution from C. Máspoli, C. Aristimuño, C. Prigioni, M. Baptista, A. Saralegi, O. Lussich, N. Hernandez and C. Pérez, and José M. Venzal.

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Copyright information

© Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland 2017

Authors and Affiliations

  1. 1.Genética de la Conservación, Departamento de Biodiversidad y Genética – IIBCE/MECMontevideoUruguay

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