A recent paper in Nature Communications (Abadi et al. 2019) investigated model selection in phylogeny reconstruction. Selecting an appropriate model of nucleotide substitution is considered best practise in phylogenetics, and indeed many studies have show that accurate modelling of substitution processes can substantially improve phylogenetic estimates. The authors quite surprisingly find that this practise may not be necessary after all. From multiple datasets of diverse simulated sequences, they find that the models chosen by commonly used criteria do not perform better than the most complex model. They conclude that cases model selection can be skipped altogether, and all phylogenetic inferences be performed with a complex model.
There are other interesting aspects of this paper, but I here want to focus on the claim (and that data that's used to support it) that model selection does not improve phylogenetic inference. Below, I will argue that
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