Can Genetic Estimators Provide Robust Estimates of the Effective Number of Breeders in Small Populations?

Marion Hoehn, Bernd Gruber, Stephen Sarre, Rebecca Lange, Klaus Henle

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    Abstract

    The effective population size (Ne) is proportional to the loss of genetic diversity and the rate of inbreeding, and its accurate estimation is crucial for the monitoring of small populations. Here, we integrate temporal studies of the gecko Oedura reticulata, to compare genetic and demographic estimators of Ne. Because geckos have overlapping generations, our goal was to demographically estimate NbI, the inbreeding effective number of breeders and to calculate the NbI/Na ratio (Na = number of adults) for four populations. Demographically estimated NbI ranged from 1 to 65 individuals. The mean reduction in the effective number of breeders relative to census size (NbI/Na) was 0.1 to 1.1. We identified the variance in reproductive success as the most important variable contributing to reduction of this ratio. We used four methods to estimate the genetic based inbreeding effective number of breeders NbI(gen) and the variance effective populations size NeV(gen) estimates from the genotype data. Two of these methods - a temporal moment-based (MBT) and a likelihood-based approach (TM3) require at least two samples in time, while the other two were single-sample estimators - the linkage disequilibrium method with bias correction LDNe and the program ONeSAMP. The genetic based estimates were fairly similar across methods and also similar to the demographic estimates excluding those estimates, in which upper confidence interval boundaries were uninformative. For example, LDNe and ONeSAMP estimates ranged from 14â¿¿55 and 24â¿¿48 individuals, respectively. However, temporal methods suffered from a large variation in confidence intervals and concerns about the prior information. We conclude that the single-sample estimators are an acceptable short-cut to estimate NbI for species such as geckos and will be of great importance for the monitoring of species in fragmented landscapes.
    Original languageEnglish
    Pages (from-to)1-10
    Number of pages10
    JournalPLoS One
    Volume7
    Issue number11
    DOIs
    Publication statusPublished - 2012

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    Lizards
    Inbreeding
    Gekkonidae
    Monitoring
    inbreeding
    Population
    Population Density
    confidence interval
    population size
    demographic statistics
    Demography
    Confidence Intervals
    methodology
    Time and Motion Studies
    monitoring
    Linkage Disequilibrium
    Censuses
    linkage disequilibrium
    sampling
    Genotype

    Cite this

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    title = "Can Genetic Estimators Provide Robust Estimates of the Effective Number of Breeders in Small Populations?",
    abstract = "The effective population size (Ne) is proportional to the loss of genetic diversity and the rate of inbreeding, and its accurate estimation is crucial for the monitoring of small populations. Here, we integrate temporal studies of the gecko Oedura reticulata, to compare genetic and demographic estimators of Ne. Because geckos have overlapping generations, our goal was to demographically estimate NbI, the inbreeding effective number of breeders and to calculate the NbI/Na ratio (Na = number of adults) for four populations. Demographically estimated NbI ranged from 1 to 65 individuals. The mean reduction in the effective number of breeders relative to census size (NbI/Na) was 0.1 to 1.1. We identified the variance in reproductive success as the most important variable contributing to reduction of this ratio. We used four methods to estimate the genetic based inbreeding effective number of breeders NbI(gen) and the variance effective populations size NeV(gen) estimates from the genotype data. Two of these methods - a temporal moment-based (MBT) and a likelihood-based approach (TM3) require at least two samples in time, while the other two were single-sample estimators - the linkage disequilibrium method with bias correction LDNe and the program ONeSAMP. The genetic based estimates were fairly similar across methods and also similar to the demographic estimates excluding those estimates, in which upper confidence interval boundaries were uninformative. For example, LDNe and ONeSAMP estimates ranged from 14{\^a}¿¿55 and 24{\^a}¿¿48 individuals, respectively. However, temporal methods suffered from a large variation in confidence intervals and concerns about the prior information. We conclude that the single-sample estimators are an acceptable short-cut to estimate NbI for species such as geckos and will be of great importance for the monitoring of species in fragmented landscapes.",
    author = "Marion Hoehn and Bernd Gruber and Stephen Sarre and Rebecca Lange and Klaus Henle",
    year = "2012",
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    language = "English",
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    Can Genetic Estimators Provide Robust Estimates of the Effective Number of Breeders in Small Populations? / Hoehn, Marion; Gruber, Bernd; Sarre, Stephen; Lange, Rebecca; Henle, Klaus.

    In: PLoS One, Vol. 7, No. 11, 2012, p. 1-10.

    Research output: Contribution to journalArticle

    TY - JOUR

    T1 - Can Genetic Estimators Provide Robust Estimates of the Effective Number of Breeders in Small Populations?

    AU - Hoehn, Marion

    AU - Gruber, Bernd

    AU - Sarre, Stephen

    AU - Lange, Rebecca

    AU - Henle, Klaus

    PY - 2012

    Y1 - 2012

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    AB - The effective population size (Ne) is proportional to the loss of genetic diversity and the rate of inbreeding, and its accurate estimation is crucial for the monitoring of small populations. Here, we integrate temporal studies of the gecko Oedura reticulata, to compare genetic and demographic estimators of Ne. Because geckos have overlapping generations, our goal was to demographically estimate NbI, the inbreeding effective number of breeders and to calculate the NbI/Na ratio (Na = number of adults) for four populations. Demographically estimated NbI ranged from 1 to 65 individuals. The mean reduction in the effective number of breeders relative to census size (NbI/Na) was 0.1 to 1.1. We identified the variance in reproductive success as the most important variable contributing to reduction of this ratio. We used four methods to estimate the genetic based inbreeding effective number of breeders NbI(gen) and the variance effective populations size NeV(gen) estimates from the genotype data. Two of these methods - a temporal moment-based (MBT) and a likelihood-based approach (TM3) require at least two samples in time, while the other two were single-sample estimators - the linkage disequilibrium method with bias correction LDNe and the program ONeSAMP. The genetic based estimates were fairly similar across methods and also similar to the demographic estimates excluding those estimates, in which upper confidence interval boundaries were uninformative. For example, LDNe and ONeSAMP estimates ranged from 14â¿¿55 and 24â¿¿48 individuals, respectively. However, temporal methods suffered from a large variation in confidence intervals and concerns about the prior information. We conclude that the single-sample estimators are an acceptable short-cut to estimate NbI for species such as geckos and will be of great importance for the monitoring of species in fragmented landscapes.

    U2 - 10.1371/journal.pone.0048464

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    M3 - Article

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    JO - PLoS One

    JF - PLoS One

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