Inferring demography and selection in organisms characterized by skewed offspring distributions

Andrew M. Sackman, Rebecca B. Harris, Jeffrey Jensen

    Research output: Contribution to journalArticle

    Abstract

    The recent increase in time-series population genomic data from experimental, natural, and ancient populations has been accompanied by a promising growth in methodologies for inferring demographic and selective parameters from such data. However, these methods have largely presumed that the populations of interest are well-described by the Kingman coalescent. In reality, many groups of organisms, including viruses, marine organisms, and some plants, protists, and fungi, typified by high variance in progeny number, may be best characterized by multiple-merger coalescent models. Estimation of population genetic parameters under Wright-Fisher assumptions for these organisms may thus be prone to serious mis-inference. We propose a novel method for the joint inference of demography and selection under the ψ-coalescent model, termed Multiple-Merger Coalescent Approximate Bayesian Computation, or MMC-ABC. We first demonstrate mis-inference under the Kingman, and then exhibit the superior performance of MMC-ABC under conditions of skewed offspring distributions. In order to highlight the utility of this approach, we reanalyzed previously published drug-selection lines of influenza A virus. We jointly inferred the extent of progeny-skew inherent to viral replication and identified putative drug-resistance mutations.

    Original languageEnglish (US)
    Pages (from-to)1019-1028
    Number of pages10
    JournalGenetics
    Volume211
    Issue number3
    DOIs
    StatePublished - Mar 1 2019

    Fingerprint

    Demography
    Metagenomics
    Aquatic Organisms
    Influenza A virus
    Population Genetics
    Drug Resistance
    Population
    Fungi
    Joints
    Viruses
    Mutation
    Growth
    Pharmaceutical Preparations

    Keywords

    • Coalescent theory
    • Population genetics
    • Selection
    • Sweepstakes reproduction
    • Time-sampled inference

    ASJC Scopus subject areas

    • Genetics

    Cite this

    Inferring demography and selection in organisms characterized by skewed offspring distributions. / Sackman, Andrew M.; Harris, Rebecca B.; Jensen, Jeffrey.

    In: Genetics, Vol. 211, No. 3, 01.03.2019, p. 1019-1028.

    Research output: Contribution to journalArticle

    Sackman, Andrew M. ; Harris, Rebecca B. ; Jensen, Jeffrey. / Inferring demography and selection in organisms characterized by skewed offspring distributions. In: Genetics. 2019 ; Vol. 211, No. 3. pp. 1019-1028.
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