Computationally efficient composite likelihood statistics for demographic inference

Alec J. Coffman, Ping Hsun Hsieh, Simon Gravel, Ryan N Gutenkunst

Research output: Contribution to journalArticle

33 Scopus citations

Abstract

Many population genetics tools employ composite likelihoods, because fully modeling genomic linkage is challenging. But traditional approaches to estimating parameter uncertainties and performing model selection require full likelihoods, so these tools have relied on computationally expensive maximum-likelihood estimation (MLE) on bootstrapped data. Here, we demonstrate that statistical theory can be applied to adjust composite likelihoods and perform robust computationally efficient statistical inference in two demographic inference tools: ∂a∂i and TRACTS. On both simulated and real data, the adjustments perform comparably to MLE bootstrapping while using orders of magnitude less computational time.

Original languageEnglish (US)
Pages (from-to)591-593
Number of pages3
JournalMolecular Biology and Evolution
Volume33
Issue number2
DOIs
StatePublished - Feb 1 2016

Keywords

  • composite likelihood
  • demographic inference
  • likelihood ratio test
  • parameter uncertainties

ASJC Scopus subject areas

  • Medicine(all)
  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

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