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Determination of the minimum number of microsatellite markers for individual genotyping in wild boar (Sus scrofa) using a test with close relatives

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Abstract

In the context of developing a noninvasive, practicable method for population size estimation in wild boar, we present a stepwise procedure to reduce the number of required microsatellite markers for individual genotyping. Step1: an initial marker set of 12 microsatellite loci was tested for species specificity with nontarget DNA and resulted in an exclusion of two markers. Step 2: a variability test regarding heterozygosity and deviations from Hardy–Weinberg equilibrium led to the rejection of two further markers. Step 3: the remaining eight markers were tested for transferability across populations with three separate wild boar sample sets. Step 4: on the basis of probability of identity values, a reduction from eight to five markers was possible. Step 5: a novel test using tissue samples from female wild boars and their embryos provided evidence that four variable microsatellite markers and one sex marker are sufficient for individual identification of close relatives. Step 6: feces samples were finally used to estimate PCR (PS) and genotyping success (GS). In conclusion, we recommend a specific four-marker combination with both PS and GS >50% for a reliable individual identification in noninvasive population size estimation of wild boar.

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Acknowledgements

We thank C. Ebert, D. Huckschlag and U. Hohmann from the Research Institute of Forest Ecology and Forestry, Rhineland-Palatinate and G. Sodeikat and O. Keuling from the Institute of Wildlife Research in Hannover for the collection of samples. Furthermore, we thank T. Bürgi for technical advices and C. Wallnisch, J. Schürings and B. Müller for lab assistance as well as S. Baldauf for statistical support with the lme models. This project was supported by the Foundation “Rheinland-Pfalz für Innovation”, and the Ministry for Environment and Forestry, Rhineland-Palatinate. KK was supported through a two-year PhD scholarship from the Lotto Foundation Rhineland-Palatinate.

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Authors and Affiliations

  1. Institute for Environmental Sciences, University of Koblenz-Landau, Fortstr. 7, 76829, Landau, Germany

    K. Kolodziej, K. Theissinger, H. K. Schulz & R. Schulz

  2. Institute for Evolutionary Biology and Ecology, University of Bonn, An der Immenburg 1, 53121, Bonn, Germany

    J. Brün

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  1. K. Kolodziej
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  2. K. Theissinger
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  3. J. Brün
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  4. H. K. Schulz
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  5. R. Schulz
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Correspondence to K. Kolodziej or K. Theissinger.

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Communicated by P. C. Alves

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Kolodziej, K., Theissinger, K., Brün, J. et al. Determination of the minimum number of microsatellite markers for individual genotyping in wild boar (Sus scrofa) using a test with close relatives. Eur J Wildl Res 58, 621–628 (2012). https://doi.org/10.1007/s10344-011-0588-9

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  • DOI: https://doi.org/10.1007/s10344-011-0588-9

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