A model-derived short-term estimation method of effective size for small populations with overlapping generations

Annegret Grimm, Bernd GRUBER, Marion Hoehn, Katrin Enders, Klaus Henle

    Research output: Contribution to journalArticle

    2 Citations (Scopus)

    Abstract

    If not actively managed, small and isolated populations lose their genetic variability and the inbreeding rateincreases. Combined, these factors limit the ability of populations to adapt to environmental changes, increasingtheir risk of extinction. The effective population size (Ne) is proportional to the loss of genetic diversity and thereforeof considerable conservation relevance. However, estimators of Ne that account for demographic parametersin species with overlapping generations require sampling of populations across generations, which is oftennot feasible in long-lived species.2. We created an individual-based model that allows calculation of Ne based on demographic parameters thatcan be obtained in a time periodmuch shorter than a generation. It can be adapted to every life-history parametercombination. Themodel is freely available as an R-package NEff.3. The model was first used in a simulation experiment observing changes in Ne in response to different degreesof generational overlap. Results showed that increased generational overlap slowed annual rates of heterozygosityloss, resulting in higher annual effective sizes (Ny) but decreased Ne per generation. Adding the effect of differentrecruitment rates only affectedNe for populations with low generational overlap.4. The model was further tested using real population data of the Australian arboreal gecko Gehyra variegata.Simulation results were compared to genetic analyses andmatched estimates of the real population very well.5. Unlike other estimation methods of Ne, NEff neither requires long time series of population monitoring norgenetic analyses of changes in gene frequencies. Thus, it seems to be the first method for calculating Ne withinshort time periods and comparably low costs facilitating the use ofNe in applied conservation and management.
    Original languageEnglish
    Pages (from-to)734-743
    Number of pages10
    JournalMethods in Ecology and Evolution
    Volume7
    DOIs
    Publication statusPublished - 2016

    Fingerprint

    estimation method
    individual-based model
    effective population size
    isolated population
    inbreeding
    simulation
    environmental change
    life history
    extinction
    time series
    gene
    sampling
    monitoring
    methodology
    cost
    demographic statistics
    experiment
    genetic variation
    Gekkonidae
    rate

    Cite this

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    title = "A model-derived short-term estimation method of effective size for small populations with overlapping generations",
    abstract = "If not actively managed, small and isolated populations lose their genetic variability and the inbreeding rateincreases. Combined, these factors limit the ability of populations to adapt to environmental changes, increasingtheir risk of extinction. The effective population size (Ne) is proportional to the loss of genetic diversity and thereforeof considerable conservation relevance. However, estimators of Ne that account for demographic parametersin species with overlapping generations require sampling of populations across generations, which is oftennot feasible in long-lived species.2. We created an individual-based model that allows calculation of Ne based on demographic parameters thatcan be obtained in a time periodmuch shorter than a generation. It can be adapted to every life-history parametercombination. Themodel is freely available as an R-package NEff.3. The model was first used in a simulation experiment observing changes in Ne in response to different degreesof generational overlap. Results showed that increased generational overlap slowed annual rates of heterozygosityloss, resulting in higher annual effective sizes (Ny) but decreased Ne per generation. Adding the effect of differentrecruitment rates only affectedNe for populations with low generational overlap.4. The model was further tested using real population data of the Australian arboreal gecko Gehyra variegata.Simulation results were compared to genetic analyses andmatched estimates of the real population very well.5. Unlike other estimation methods of Ne, NEff neither requires long time series of population monitoring norgenetic analyses of changes in gene frequencies. Thus, it seems to be the first method for calculating Ne withinshort time periods and comparably low costs facilitating the use ofNe in applied conservation and management.",
    keywords = "annual effective size, Gehyra variegata, heterozygosity, individual-based modelling, life-history parameters, overlapping generations, population demography, R-package NEff",
    author = "Annegret Grimm and Bernd GRUBER and Marion Hoehn and Katrin Enders and Klaus Henle",
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    language = "English",
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    pages = "734--743",
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    publisher = "John Wiley & Sons",

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    A model-derived short-term estimation method of effective size for small populations with overlapping generations. / Grimm, Annegret; GRUBER, Bernd; Hoehn, Marion; Enders, Katrin; Henle, Klaus.

    In: Methods in Ecology and Evolution, Vol. 7, 2016, p. 734-743.

    Research output: Contribution to journalArticle

    TY - JOUR

    T1 - A model-derived short-term estimation method of effective size for small populations with overlapping generations

    AU - Grimm, Annegret

    AU - GRUBER, Bernd

    AU - Hoehn, Marion

    AU - Enders, Katrin

    AU - Henle, Klaus

    PY - 2016

    Y1 - 2016

    N2 - If not actively managed, small and isolated populations lose their genetic variability and the inbreeding rateincreases. Combined, these factors limit the ability of populations to adapt to environmental changes, increasingtheir risk of extinction. The effective population size (Ne) is proportional to the loss of genetic diversity and thereforeof considerable conservation relevance. However, estimators of Ne that account for demographic parametersin species with overlapping generations require sampling of populations across generations, which is oftennot feasible in long-lived species.2. We created an individual-based model that allows calculation of Ne based on demographic parameters thatcan be obtained in a time periodmuch shorter than a generation. It can be adapted to every life-history parametercombination. Themodel is freely available as an R-package NEff.3. The model was first used in a simulation experiment observing changes in Ne in response to different degreesof generational overlap. Results showed that increased generational overlap slowed annual rates of heterozygosityloss, resulting in higher annual effective sizes (Ny) but decreased Ne per generation. Adding the effect of differentrecruitment rates only affectedNe for populations with low generational overlap.4. The model was further tested using real population data of the Australian arboreal gecko Gehyra variegata.Simulation results were compared to genetic analyses andmatched estimates of the real population very well.5. Unlike other estimation methods of Ne, NEff neither requires long time series of population monitoring norgenetic analyses of changes in gene frequencies. Thus, it seems to be the first method for calculating Ne withinshort time periods and comparably low costs facilitating the use ofNe in applied conservation and management.

    AB - If not actively managed, small and isolated populations lose their genetic variability and the inbreeding rateincreases. Combined, these factors limit the ability of populations to adapt to environmental changes, increasingtheir risk of extinction. The effective population size (Ne) is proportional to the loss of genetic diversity and thereforeof considerable conservation relevance. However, estimators of Ne that account for demographic parametersin species with overlapping generations require sampling of populations across generations, which is oftennot feasible in long-lived species.2. We created an individual-based model that allows calculation of Ne based on demographic parameters thatcan be obtained in a time periodmuch shorter than a generation. It can be adapted to every life-history parametercombination. Themodel is freely available as an R-package NEff.3. The model was first used in a simulation experiment observing changes in Ne in response to different degreesof generational overlap. Results showed that increased generational overlap slowed annual rates of heterozygosityloss, resulting in higher annual effective sizes (Ny) but decreased Ne per generation. Adding the effect of differentrecruitment rates only affectedNe for populations with low generational overlap.4. The model was further tested using real population data of the Australian arboreal gecko Gehyra variegata.Simulation results were compared to genetic analyses andmatched estimates of the real population very well.5. Unlike other estimation methods of Ne, NEff neither requires long time series of population monitoring norgenetic analyses of changes in gene frequencies. Thus, it seems to be the first method for calculating Ne withinshort time periods and comparably low costs facilitating the use ofNe in applied conservation and management.

    KW - annual effective size

    KW - Gehyra variegata

    KW - heterozygosity

    KW - individual-based modelling

    KW - life-history parameters

    KW - overlapping generations

    KW - population demography

    KW - R-package NEff

    U2 - 10.1111/2041-210X.12530

    DO - 10.1111/2041-210X.12530

    M3 - Article

    VL - 7

    SP - 734

    EP - 743

    JO - Methods in Ecology and Evolution

    JF - Methods in Ecology and Evolution

    SN - 2041-210X

    ER -