How to Overcome Genotyping Errors in Non-Invasive Genetic Mark-Recapture Population Size Estimation—A Review of Available Methods Illustrated by a Case Study

Simone Lampa, Klaus Henle, Reinhard Klenke, Marion Hoehn, Bernd GRUBER

    Research output: Contribution to journalReview article

    34 Citations (Scopus)

    Abstract

    The main goal of non-invasive genetic capture-mark-recapture (CMR) analysis is to gain an unbiased and reliable population size estimate of species that cannot be sampled directly. The method has become an important and widely used tool to research and manage wildlife populations. However, researchers have to struggle with low amplification success rates and genotyping errors, which substantially bias subsequent analysis. To receive reliable results and to minimize the time and costs required for non-invasive microsatellite genotyping, one must carefully choose a species-specific sampling design, methods that maximize the amount of template DNA, and methods that could overcome genotyping errors, especially when using low-quality samples. This article reviews the literature and the pros and cons of the main methods used along the process described above. The review is strengthened by a case study on Eurasian otters (Lutra lutra) using feces; we tested several methods for their appropriateness to accommodate for genotyping errors. Based on this method testing, we demonstrated that high genotyping error rates are the key problem in this process leading to a severely flawed dataset if no consensus genotype is formed. However, even if generating consensus genotypes minimizes errors dramatically, we show that it may not achieve a definite eradication of all errors, which results in overestimated population sizes if conventional estimators are used. In conjunction with these findings, we offer a step-by-step protocol for non-invasive genetic CMR studies to achieve a reliable estimate of population sizes in the presence of high genotyping error rates.
    Original languageEnglish
    Pages (from-to)1490-1511
    Number of pages22
    JournalThe Journal of Wildlife Management
    Volume77
    Issue number8
    DOIs
    Publication statusPublished - 2013

    Fingerprint

    population size
    case studies
    genotype
    testing method
    design method
    methodology
    feces
    Lutra lutra
    amplification
    mark-recapture studies
    DNA
    genotyping
    genotyping errors
    method
    wildlife
    sampling
    researchers
    cost
    microsatellite repeats
    rate

    Cite this

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    abstract = "The main goal of non-invasive genetic capture-mark-recapture (CMR) analysis is to gain an unbiased and reliable population size estimate of species that cannot be sampled directly. The method has become an important and widely used tool to research and manage wildlife populations. However, researchers have to struggle with low amplification success rates and genotyping errors, which substantially bias subsequent analysis. To receive reliable results and to minimize the time and costs required for non-invasive microsatellite genotyping, one must carefully choose a species-specific sampling design, methods that maximize the amount of template DNA, and methods that could overcome genotyping errors, especially when using low-quality samples. This article reviews the literature and the pros and cons of the main methods used along the process described above. The review is strengthened by a case study on Eurasian otters (Lutra lutra) using feces; we tested several methods for their appropriateness to accommodate for genotyping errors. Based on this method testing, we demonstrated that high genotyping error rates are the key problem in this process leading to a severely flawed dataset if no consensus genotype is formed. However, even if generating consensus genotypes minimizes errors dramatically, we show that it may not achieve a definite eradication of all errors, which results in overestimated population sizes if conventional estimators are used. In conjunction with these findings, we offer a step-by-step protocol for non-invasive genetic CMR studies to achieve a reliable estimate of population sizes in the presence of high genotyping error rates.",
    keywords = "capture-mark-recapture (CMR), consensus genotypes, Eurasian otter (Lutra lutra), fecal DNA, microsatellites, screening approach.",
    author = "Simone Lampa and Klaus Henle and Reinhard Klenke and Marion Hoehn and Bernd GRUBER",
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    How to Overcome Genotyping Errors in Non-Invasive Genetic Mark-Recapture Population Size Estimation—A Review of Available Methods Illustrated by a Case Study. / Lampa, Simone; Henle, Klaus; Klenke, Reinhard; Hoehn, Marion; GRUBER, Bernd.

    In: The Journal of Wildlife Management, Vol. 77, No. 8, 2013, p. 1490-1511.

    Research output: Contribution to journalReview article

    TY - JOUR

    T1 - How to Overcome Genotyping Errors in Non-Invasive Genetic Mark-Recapture Population Size Estimation—A Review of Available Methods Illustrated by a Case Study

    AU - Lampa, Simone

    AU - Henle, Klaus

    AU - Klenke, Reinhard

    AU - Hoehn, Marion

    AU - GRUBER, Bernd

    PY - 2013

    Y1 - 2013

    N2 - The main goal of non-invasive genetic capture-mark-recapture (CMR) analysis is to gain an unbiased and reliable population size estimate of species that cannot be sampled directly. The method has become an important and widely used tool to research and manage wildlife populations. However, researchers have to struggle with low amplification success rates and genotyping errors, which substantially bias subsequent analysis. To receive reliable results and to minimize the time and costs required for non-invasive microsatellite genotyping, one must carefully choose a species-specific sampling design, methods that maximize the amount of template DNA, and methods that could overcome genotyping errors, especially when using low-quality samples. This article reviews the literature and the pros and cons of the main methods used along the process described above. The review is strengthened by a case study on Eurasian otters (Lutra lutra) using feces; we tested several methods for their appropriateness to accommodate for genotyping errors. Based on this method testing, we demonstrated that high genotyping error rates are the key problem in this process leading to a severely flawed dataset if no consensus genotype is formed. However, even if generating consensus genotypes minimizes errors dramatically, we show that it may not achieve a definite eradication of all errors, which results in overestimated population sizes if conventional estimators are used. In conjunction with these findings, we offer a step-by-step protocol for non-invasive genetic CMR studies to achieve a reliable estimate of population sizes in the presence of high genotyping error rates.

    AB - The main goal of non-invasive genetic capture-mark-recapture (CMR) analysis is to gain an unbiased and reliable population size estimate of species that cannot be sampled directly. The method has become an important and widely used tool to research and manage wildlife populations. However, researchers have to struggle with low amplification success rates and genotyping errors, which substantially bias subsequent analysis. To receive reliable results and to minimize the time and costs required for non-invasive microsatellite genotyping, one must carefully choose a species-specific sampling design, methods that maximize the amount of template DNA, and methods that could overcome genotyping errors, especially when using low-quality samples. This article reviews the literature and the pros and cons of the main methods used along the process described above. The review is strengthened by a case study on Eurasian otters (Lutra lutra) using feces; we tested several methods for their appropriateness to accommodate for genotyping errors. Based on this method testing, we demonstrated that high genotyping error rates are the key problem in this process leading to a severely flawed dataset if no consensus genotype is formed. However, even if generating consensus genotypes minimizes errors dramatically, we show that it may not achieve a definite eradication of all errors, which results in overestimated population sizes if conventional estimators are used. In conjunction with these findings, we offer a step-by-step protocol for non-invasive genetic CMR studies to achieve a reliable estimate of population sizes in the presence of high genotyping error rates.

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    KW - fecal DNA

    KW - microsatellites

    KW - screening approach.

    U2 - 10.1002/jwmg.604

    DO - 10.1002/jwmg.604

    M3 - Review article

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    JO - The Journal of Wildlife Management

    JF - The Journal of Wildlife Management

    SN - 0022-541X

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    ER -