Botany 2014 – Model checking, data cleaning, and phylogenies galore

Phylogenetics. It’s just one damned argument over which set of information is more important after another. Or something like that. Taken from the play/film by Alan Bennett.

Will Pearse

Will Pearse

I was lucky enough to be invited to speak at the colloquium on Phylogenetic Comparative Methods organised by John Schenk at Botany this year. I’m not really a botanist (shhh!), but I’m glad I attended: lots of cool talks, and lots of nice people.

Stephen Smith‘s talk really impressed me; he addressed the tendency for phylogenetics to become divorced from standard evolutionary questions by showcasing how next-gen processing can link them back together again. Everyone who’s been through Evo101 remembers that gene duplication and selection pressures can give dodgy phylogenetic inference. He showed that, if we’ve essentially sequenced everything, variation among gene trees lets us measure and quantify such processes, giving more questions phylogenetics can answer. Apparently this is all possible with variants of his graph method, but please don’t ask me to explain how!…

Erika Edwards launched a rather scathing attack on a recent paper examining angiosperm radiation. I’m not entirely sure I agreed with all of her points, but I was saddened that she didn’t have time to get onto her examples of how assuming the same process operates throughout the whole of a phylogeny isn’t reasonable. I think this is a very good point, and I think models that allow for variation across clades are often ignored, but desperately needed.

Outside of the symposium, there were a lot of talks dedicated to the phylogenetics of particular clades. In almost every case I saw, people were looking for lots of loci they could target, and I very rarely heard anyone use the term RADSeq or SNP at any point. People seemed very concerned about gene trees, and I was surprised to hear it discussed in terms that sounded an awful lot like the great morphology vs. genetic data debates I remember being forced to read about. Indeed, at one point someone actually uttered the phrase “those of you over the age of 40 will remember…” and then proceeded to talk about how to know when we have enough information to conduct an analysis. Maybe there is a chance for past battles to help us in the future!


About will.pearse
Ecology / evolutionary biologist

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