Some responses to “A cautionary tale on reading phylogenetic trees”

PLoS ONE logo

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.

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Placozoan diversity and taxonomy

If I didn’t study Volvox, I would probably study placozoa. Placozoa are animals, but you wouldn’t know it to look at them. They look and behave very much like giant amoebae, big enough to be visible to the naked eye.

Trichoplax adhaerens

Trichoplax adhaerens. By Bernd Schierwater – Eitel M, Osigus H-J, DeSalle R, Schierwater B (2013) Global Diversity of the Placozoa. PLoS ONE 8(4): e57131. doi:10.1371/journal.pone.0057131, CC BY 4.0, Link

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A valid point

A reader commented by email about my criticism of the PLoS ONE article that inferred a multigene phylogeny of eukaryotes, with Chlamydomonas reinhardtii as the outgroup (“A cautionary tale on reading phylogenetic trees“).

Although you are of course correct to complain about nearly everything in the paper (esp. re “basal” and node rotations), and I am sure the tree is wrong in more ways than it is right, I think you might reconsider or put in context complaints about the “provides a link between”. My thought is simply that if one has a long branch between two nodes in a tree, if you add a taxon group that branches off in the middle of this long branch, then it does, in a sense, provide a “link” between these two nodes. A more proper way to put it is that it provides information concerning the ancestral state at the two original nodes (i.e., may substantially modify the posterior probability of the states at the two nodes). I doubt that the authors mean it in this sense, but in the general context of teaching people about trees, I would want students to understand this.

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A cautionary tale on reading phylogenetic trees

I have written before about the perils of naive interpretations of phylogenetic trees (“Extant taxa cannot be basal“). Others, notably Krell & Cranston and Crisp & Cook, have pointed out that this is not just a language issue; such misreadings can cause substantive problems in the way evolutionary history is understood.

A new paper in PLoS ONE, “A tree of life based on ninety-eight expressed genes conserved across diverse eukaryotic species,” contains several instructive examples. PLoS ONE is open access, so you can read the original paper without an institutional subscription. A tweet by Frederik Leliaert got this paper on my radar, and it piqued my interest because of the startling observation that the inferred phylogeny shows Chlamydomonas as sister to all other eukaryotes.

It made me frown, too.

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Volvox 2015: taxonomy, phylogeny & ecology

Volvox africanus

Volvox africanus (from Herron et al. 2010)

The worst-kept secret among Volvox researchers is that the current volvocine taxonomy is a train wreck. Within the largest family, the Volvocaceae, five nominal genera are polyphyletic (Pandorina, Volvulina, Eudorina, Pleodorina, and Volvox). Of the remaining three, two are monotypic (Platydorina and Yamagishiella). Only the newly described Colemanosphaera is monophyletic with more than one species. The extent of the problem was suspected long before it was confirmed by molecular phylogenetics, and ad hoc attempts to deal with it have led to the existence of such taxonomic abominations as ‘sections,’ ‘formas,’ and ‘syngens.’ An overhaul is called for, but it is complicated by the aforementioned loss of type cultures.

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