Acta Theriologica

, Volume 59, Issue 4, pp 511–520 | Cite as

Procedures to genotype problematic non-invasive otter (Lutra lutra) samples

  • Laura Lerone
  • Chiara Mengoni
  • Giuseppe Maria Carpaneto
  • Ettore Randi
  • Anna Loy
Original Paper
First Online:
Received:
Accepted:

Abstract

Non-invasive genetics is a powerful tool in wildlife research and monitoring, especially when dealing with elusive and rare species such as the Eurasian otter (Lutra lutra). Nevertheless, otter DNA obtained from scats and anal secretions appears to be exposed to very quick degradation processes, and the success rate in DNA amplification is lower than in other carnivores. We collected 191 samples from April to September 2011 along the river Sangro basin (Italy) which was recently re-colonized by the Eurasian otter. Using two sets of microsatellite loci (six Lut and seven OT loci), we investigated the influence of sample type and age, collection time, storage time, temperature and humidity on genotyping success and amplification success. We also tested the efficacy of different DNA extraction kits and storage buffer mediums. Finally, we compared amplification success rate, allelic dropout and false allele rates for each locus. We obtained a mean amplification success rate of 79.0 % and a genotyping success rate of 35.1 %. Fresh pure jellies yielded the highest amplification success and genotyping rate. Six microsatellite loci should be theoretically sufficient to distinguish the individual unrelated otters (PID = 0.001), while 13 loci were needed to distinguish sibling otters (PIDsibs = 0.002) in our population. We identified 11 otters, and molecular sexing ascertained the presence of five males, four females and two uncertain individuals. Generalized linear models highlighted a significant influence of sample type and age, temperature and humidity both on genotyping and amplification success.

Keywords

Allelic dropout Amplification success Faecal DNA Lutra lutra Microsatellites Non-invasive genetic sampling 
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Notes

Acknowledgments

We thank Prof. C. Pertoldi and the anonymous reviewer for their precious advices which greatly improved the manuscript. We also thank A. Brambilla, A. Leone, L. Nelli, A. Palladini, R. Caniglia, F. Davoli, E. Fabbri, F. Mattucci and N. Mucci for their suggestions and constant support.

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Copyright information

© Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland 2014

Authors and Affiliations

  • Laura Lerone
    • 1
  • Chiara Mengoni
    • 2
  • Giuseppe Maria Carpaneto
    • 1
  • Ettore Randi
    • 2
    • 3
  • Anna Loy
    • 4
  1. 1.Department of Environmental BiologyRoma Tre UniversityRomeItaly
  2. 2.Laboratorio di GeneticaIstituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA)Ozzano EmiliaItaly
  3. 3.Department 18/Section of Environmental EngineeringAalborg UniversityAalborgDenmark
  4. 4.Environmetrics LaboratoryUniversity of MolisePescheItaly

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