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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