Back in September, I complained that a PLoS ONE article purporting to provide “valuable insight into the evolution of eukaryotes” contained substantive problems that should have been caught during the peer review process (“A cautionary tale on reading phylogenetic trees“). The problems are so serious that, in my opinion, they render the bulk of the results invalid.
There were also numerous problems with the interpretation of those results, mainly stemming from misunderstandings about what kinds of information phylogenetic trees represent:
Some of these problems are just rhetorical, but some of them are substantive, and this is the real problem. A failure to understand that phylogenies represent sister group relationships has led to incorrect interpretations of evolutionary relationships, such as that the outgroup is more closely related to one ingroup clade than another, that the sister of one clade is a ‘link’ to another clade, and that a single branching event can have a bunch of different divergence times.
I later admitted, in response to criticism from a reader, that I may have been overly pedantic in pointing out some of the rhetorical problems (“A valid point“). In this post, though, I’m going to focus on the substantive problems and respond to a couple of comments to the original post.