Phylogenetic comparative methods

Phylogenetic comparative methods are always an area of hot discussion and lots of methodological development. So I thought it would be useful to highlight some recent papers that have developed new methods in the past year. Please email me or leave a comment if there is anything I have omitted or if something new comes out.

Thomas Hansen and colleagues have introduced a new method for studying adaptation using comparative methods. Their approach is a generalisation of the Ornstein-Uhlenbeck model that allows for adaptive constraints and phylogenetic intertia. They have an R-package SLOUCH which can be used to fit the model.

In Evolution Liam Revell has developed a new approach for data reduction and size correction using phylogenetic approaches – this is often done wrongly as the transformation is commonly applied before phylogenetic analysis, however it should be correctly done at the same time.

A new method in Functional Ecology allows one to test for phylogenetic dependence in complex multivariate data that also incorporate measurement error.

What will prove, I think, to be a very popular method is a new approach for testing for phylogenetic signal and analysing correlates of binary traits, basically a phylogenetic logistic regression by Anthony Ives and Ted Garland. The approach will allow linear modelling of correlates of a binary traits, which has been difficult before.

In a related area, another very important development is in the analysis of speciation and extinction rates when these are affected by a binary trait. FitzJohn et al. have shown how the BiSSE model, developed to do this, can be applied when phylogenies are incompletely resolved.

Likely to be of interest to many using comparative methods is a paper by Richard Smith on the use and misuse of Reduced Major Axis line fitting. He discusses the assumptions of this method, which are not widely appreciated.

In the American Naturalist Marc Lajeunesse has developed methods linking comparative analysis and meta-analysis, basically allowing meta-analysis to be corrected for phylogenetic non-independence.

In Proc B a new method for integrating spatial and phylogenetic dependence has been presented, and in JEB there has been a review of the ‘deadly sins of comparative analysis’ (apologies for self-promotion!).

Just to end with here is another method for explaining adaptation.

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One thought on “Phylogenetic comparative methods

  1. Pingback: methods.blog « Lars Götzenberger

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