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

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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.

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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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Authors and Affiliations

  1. Department of Environmental Biology, Roma Tre University, 00146, Rome, Italy

    Laura Lerone & Giuseppe Maria Carpaneto

  2. Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Via Ca’ Fornacetta 9, Ozzano Emilia, 40064, Bologna, Italy

    Chiara Mengoni & Ettore Randi

  3. Department 18/Section of Environmental Engineering, Aalborg University, Sohngårdsholmsvej 57, Aalborg, 9000, Denmark

    Ettore Randi

  4. Environmetrics Laboratory, University of Molise, Pesche, 86090, Italy

    Anna Loy

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  1. Laura Lerone
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Correspondence to Laura Lerone.

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Communicated by: Cino Pertoldi

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Lerone, L., Mengoni, C., Carpaneto, G.M. et al. Procedures to genotype problematic non-invasive otter (Lutra lutra) samples. Acta Theriol 59, 511–520 (2014). https://doi.org/10.1007/s13364-014-0195-8

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