A factorial design experiment as a pilot study for noninvasive genetic sampling

Authors

  • SHARON RENAN,

    1. Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 85104, Israel
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    • These authors contributed equally to this work.

  • EDITH SPEYER,

    1. Mitrani Department of Desert Ecology, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sde Boqer Campus, Midreshet Ben-Gurion 84990, Israel
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    • These authors contributed equally to this work.

  • NAAMA SHAHAR,

    1. Mitrani Department of Desert Ecology, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sde Boqer Campus, Midreshet Ben-Gurion 84990, Israel
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  • TOMER GUETA,

    1. Mitrani Department of Desert Ecology, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sde Boqer Campus, Midreshet Ben-Gurion 84990, Israel
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  • ALAN R. TEMPLETON,

    1. Department of Biology, Washington University, St. Louis, MO 63130, USA
    2. Department of Evolutionary and Environmental Ecology, University of Haifa, Haifa 31905, Israel
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  • SHIRLI BAR-DAVID

    1. Mitrani Department of Desert Ecology, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sde Boqer Campus, Midreshet Ben-Gurion 84990, Israel
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S. Renan, Fax: 972-8-6596772; E-mail: pazsh@post.bgu.ac.il

Abstract

Noninvasive genetic sampling has increasingly been used in ecological and conservation studies during the last decade. A major part of the noninvasive genetic literature is dedicated to the search for optimal protocols, by comparing different methods of collection, preservation and extraction of DNA from noninvasive materials. However, the lack of quantitative comparisons among these studies and the possibility that different methods are optimal for different systems make it difficult to decide which protocol to use. Moreover, most studies that have compared different methods focused on a single factor – collection, preservation or extraction – while there could be interactions between these factors. We designed a factorial experiment, as a pilot study, aimed at exploring the effect of several collection, preservation and extraction methods, and the interactions between them, on the quality and amplification success of DNA obtained from Asiatic wild ass (Equus hemionus) faeces in Israel. The amplification success rates of one mitochondrial DNA and four microsatellite markers differed substantially as a function of collection, preservation and extraction methods and their interactions. The most efficient combination for our system integrated the use of swabs as a collection method with preservation at −20 °C and with the Qiagen DNA Stool Kit with modifications as the DNA extraction method. The significant interaction found between the collection, preservation methods and the extraction methods reinforces the importance of conducting a factorial design experiment, rather than examining each factor separately, as a pilot study before initiating a full-scale noninvasive research project.

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