The Phylogenetic Mixed Model

Elizabeth A. Housworth, Emília P. Martins, Michael Lynch

Research output: Contribution to journalArticlepeer-review

200 Scopus citations


The phylogenetic mixed model is an application of the quantitative-genetic mixed model to interspecific data. Although this statistical framework provides a potentially unifying approach to quantitative-genetic and phylogenetic analysis, the model has been applied infrequently because of technical difficulties with parameter estimation. We recommend a reparameterization of the model that eliminates some of these difficulties, and we develop a new estimation algorithm for both the original maximum likelihood and new restricted maximum likelihood estimators. The phylogenetic mixed model is particularly rich in terms of the evolutionary insight that might be drawn from model parameters, so we also illustrate and discuss the interpretation of the model parameters in a specific comparative analysis.

Original languageEnglish (US)
Pages (from-to)84-96
Number of pages13
JournalAmerican Naturalist
Issue number1
StatePublished - Jan 2004
Externally publishedYes


  • Comparative method
  • Mixed model
  • Phenotypic evolution
  • Phylogenetic analysis
  • Phylogenetic heritability
  • Quantitative genetics

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics


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