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Am Nat. 2004 Jan;163(1):84-96. Epub 2004 Jan 28.

The phylogenetic mixed model.

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  • 1Department of Mathematics, Indiana University, Bloomington, Indiana, 47405, USA.


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.

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