Evol Ecol Res 8: 975-995 (2006)     Full PDF if your library subscribes.

A method for calculating means and variances of comparative data for use in a phylogenetic analysis of variance

Patrik Lindenfors*

Department of Zoology, Stockholm University, SE-106 91 Stockholm, Sweden

e-mail: Patrik.Lindenfors@zoologi.su.se


Question: Is there a general method for applying an analysis of variance (ANOVA) to phylogenetic data sets that allows for the incorporation of any assumption of evolutionary model?

Mathematical method: I describe a method that enables the calculation of means and variances of the traits of monophyletically related species. These means and variances are calculated using evolutionary rates derived from estimated nodal values and can thus incorporate any assumption of evolutionary model. Furthermore, calculations of phylogenetically corrected mean squares are described through a worked example to show how these can be implemented into a complete-blocks ANOVA.

Key assumptions: The assumptions of this method are, as for all comparable methods, that the phylogeny is known without error and that estimated nodal values are correct. Since the method can utilize nodal values using any evolutionary model, the latter assumption can to a degree be circumvented.

Conclusions: I compare the presented method to alternative tests conceptually, but also using an idealized example and an example derived from the real world, to show the utility of the approach described herein.

Keywords: analysis of variance, comparative methods, independent contrasts, phylogenies.

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