PLoS ONE retraction

PLoS ONE logo

A Senior Editor at PLoS ONE has notified me that the paper I first complained about back in September (“A cautionary tale on reading phylogenetic trees“) has been retracted. I still have lots of questions.

As a reminder, the paper, “A tree of life based on ninety-eight expressed genes conserved across diverse eukaryotic species,” inferred a phylogeny of eukaryotes using genes expressed in rice and conserved across 49 eukaryotic genomes, including animals, plants, fungi, and protists. Divergence time estimates among the included species were based on synonymous substitution rates.

The paper first came on my radar because the authors used one of my study organisms, the unicellular green alga Chlamydomonas reinhardtii, as an outgroup. This is weird, because the green algae are known to be closely related to the land plants, of which many were included in the ingroup. It’s a basic principle in phylogenetics that the outgroup cannot be more closely related to any members of the ingroup than the members of the ingroup are to each other. This is true by definition: the outgroup has to be outside of the ingroup.

As I read the paper, more problems became apparent. Some of these were just semantic; frequent readers will know that I’m picky about cladistic terminology. Many, though, were substantive. The outgroup choice simply invalidates everything downstream of that, meaning that every analysis based on the phylogenetic tree is useless. A good tree never grew from a bad seed.

I won’t rehash all of the problems with the paper here. I posted a summary on the PLoS ONE website, and more detailed analyses here and here. A couple of the highlights include a five-fold range of estimates for the same divergence, for example 110 million years to 549 million years for the divergence between plants and animals (none of which is remotely plausible, by the way), and divergence times badly at odds with the fossil record (for example, 124 million years for sea urchin vs. zebrafish, implying that chordates originated in the Cretaceous).

Two of the article’s authors responded to my criticisms with defenses that I found wholly inadequate (“Some responses to ‘A cautionary tale on reading phylogenetic trees‘”). The journal wouldn’t tell me very much, citing confidentiality, but they did confirm that they were “reviewing these concerns.” Which was clearly true, since the paper has now been retracted.

As I’ve said before, the journal failed these authors:

At some stage, the peer review process failed these authors. The problems I’ve identified here and in my previous post could have been fixed, and they should have been fixed as a condition of publication. The best-case scenario here is that the handling editor chose reviewers who were not qualified to evaluate phylogenetic and molecular clock analyses. Even that scenario leaves some blame for the reviewers; any biologist (any educated human, really) should have recognized the absurdity of a mid-Cretaceous divergence between plants and animals.

I would like to know why these problems weren’t fixed before publication. Either they weren’t identified by the reviewers or the handling editor didn’t require the authors to fix them.

The questions I sent to the Publications Manager, and for which I still don’t have answers, were

1. How many external reviewers reviewed the paper?
2. Do any of the external reviewers have expertise in eukaryotic phylogenetics/phylogenomics?
3. Did any of the external reviewers identify what I see as the major problems (outgroup choice, internal contradictions, absurd divergence time estimates, and misinterpretations of the inferred tree)?
4. If so, did the handling editor override the reviewers’ recommendations by not requiring these problems to be fixed?

I give the journal some credit for retracting the paper, and I do appreciate the Senior Editor alerting me of that. We all make mistakes, and what’s important is what we do to fix them. But there’s no reason it should have taken as long as it did, nearly nine months. That’s nine months with nothing from the editors to indicate a problem with the paper, nine months in which 4,000 people read the paper. Thankfully, no one has cited it yet, but who knows how many citing manuscripts are in review, their authors unaware that they’re about to propagate bad information?

PLoS ONE stats

The journal has been aware of the problems with the paper for almost all of that time:

It shouldn’t have taken a week to confirm that, yes, Chlamydomonas was an inappropriate choice of outgroup and, yes, the authors really did infer a mid-Cretaceous origin of chordates, and to post an expression of editorial concern. Just “Some concerns have been raised about this paper, and we’re looking into it” would have done.

I’m also not thrilled with the lack of transparency. I understand that the journal can’t (and shouldn’t) give out information that would identify who the reviewers were. None of my questions would have done that, though. “Confidentiality” is a lame excuse for keeping the number of reviewers secret.

I hope the authors will redo their analyses (with a more appropriate outgroup choice) and submit to a new journal, and I hope the new journal does a better job with it than PLoS ONE did.


  1. another stewart says

    There’s a comment on the Retraction Watch article which suggests how the peer review might have failed – allegedly an editorial assistant without domain knowledge might direct the article to the wrong academic editor, who then selects unqualified reviewers rather than sending it back to be sent to the right place.

  2. another stewart says

    Would it be feasible for a revised article to be submitted to PLoS One as a new article? PLoS One strikes me as a natural home for this paper.

    Functionally equivalent papers have been published, using a different (i.e. not rice) “anchor” species. Because of this I fear that journals focused on phylogeny might consider it insufficiently novel for publication. But replications are not to be sniffed at, so I’d want better for the study. properly analysed, than to end up in a journal of last resort. But as a layman I may not be aware of suitable mid-rank journals, so perhaps my worries are unwarranted.

  3. Matthew Herron says

    I doubt that PLoS ONE will take another look at it. The authors told me they were revising the paper in response to criticisms, and the retraction suggests to me that their revisions didn’t satisfy the editors. I hope they do find a home for (a revised version of) the paper, but I doubt it will be there.

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