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An empirical approach for reliable microsatellite genotyping of wolf DNA from multiple noninvasive sources

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An Erratum to this article was published on 19 October 2006

Abstract

Wildlife management and conservation take advantage of the possibility to study free-living populations by collecting and analysing noninvasive samples. Nevertheless, the commonly adopted approaches, aimed at preventing results being affected by genotyping errors, considerably limit the applicability of noninvasive genotyping. An empirical approach is presented for achieving a reliable data set of wolf (Canis lupus) genotypes from multiple sources of DNA collected in a monitored population. This method relies on the relationship between sample quality and amplification outcome, which is ultimately related to the occurrence of typing errors (allelic dropout, false alleles). After DNA extraction, templates are amplified once at each locus and a conservative rating system (Q-score) is adopted to define the quality of single-locus amplifications. A significant relationship was found between quality scores and error rate (ER) (r 2=0.982). Thus it was possible to predict the chance a genotype has of being affected by errors on the basis of its Q-score. Genotypes not reaching a satisfactory confidence level can either be replicated to become reliable or excluded from the data set. Accordingly, in the present case study, 48–73% of all single-locus and 51–53% of all multilocus (ML) genotypes reached a sufficient (99 and 95%, respectively) reliability level after a single amplification per locus. Despite the possible decrease in overall yield, this method could provide a good compromise between accuracy in genotyping and effectiveness in screening large data sets for long-term or large-scale population surveys. However, to achieve complete and reliable data sets, replicated amplifications are necessary for those samples and loci providing poor results.

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Acknowledgements

We wish to thank all the people who participated in the wolf monitoring program in the province of Arezzo, among whom we are particularly grateful to Elisa Avanzinelli, Alessia Viviani, Andrea Gazzola, Paolo Lamberti and Luca Mattioli. We also thank Francesca Di Benedetto for her contribution to lab activities and James Burge for linguistic revision. Suggestions by the associate editor and two anonymous reviewers allowed to improve the final draft of the manuscript. Financial support was provided by the Provincial Administration of Arezzo and by the Italian Ministry of University and Research (COFIN 2003, # prot. 2003053710).

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Authors and Affiliations

  1. Department of Zoology and Anthropology, University of Sassari, Via Muroni 25, I-07100, Sassari, Italy

    Massimo Scandura, Claudia Capitani, Laura Iacolina & Apollonio Marco

  2. Lehrstuhl für Verhaltensforschung, Universität Bielefeld, Morgenbreede 45, D-33615, Bielefeld, Germany

    Massimo Scandura

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  1. Massimo Scandura
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  2. Claudia Capitani
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  3. Laura Iacolina
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  4. Apollonio Marco
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Correspondence to Massimo Scandura.

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An erratum to this article can be found at http://dx.doi.org/10.1007/s10592-006-9216-8

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Scandura, M., Capitani, C., Iacolina, L. et al. An empirical approach for reliable microsatellite genotyping of wolf DNA from multiple noninvasive sources. Conserv Genet 7, 813–823 (2006). https://doi.org/10.1007/s10592-005-9106-5

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  • DOI: https://doi.org/10.1007/s10592-005-9106-5

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