MRE Symonds (2002) The effects of topological inaccuracy in evolutionary trees on the phylogenetic comparative method of independent contrasts. Systematic Biology 51: 541-553.
What is it about?
Independent contrasts was the primary method, for a number of years, of controlling for phylogeny in comparative analyses. What happens if the phylogeny you are controlling for is wrong? How will that screw up results of independent contrasts analysis? This paper uses computer simulation to test this (answer: it’s more of a problem if you’ve got tips wrong, rather than deeper branches: oh and don’t use random phylogenies or no phylogeny).
What’s the story behind it?
My PhD thesis was on “Phylogenetic accuracy and comparative studies of life histories” – so this paper was really at the core of my PhD. I had taken a couple of years out of science after my PhD to do something different (working as the Science Co-Ordinator for a scientific charity called The Charles Darwin Trust), but this paper represented my toe getting back into the water (actually written whilst still working in the above job). It also represented the only time I’ve written computer code in my career (I taught myself C++ to do this). The paper did, at the review stage, get one of the most withering comments I’ve ever received as an author: “With much revision, a small part of this paper may be worthy of publication as a note”.