Field of Science

Sexy paper just out in PLoS ONE

My lab has taken its initial journey on the PLoS ONE train.

Yesterday, our paper entitled "An Expanded Inventory of Conserved Meiotic Genes Provides Evidence for Sex in Trichomonas vaginalis" was published in PLoS ONE. It's a updated and detailed report on the ongoing work in my lab to generate and curate an "inventory" of genes involved in meiosis that are present across major eukaryotic lineages. This paper focuses on the protist, Trichomonas vaginalis, an organism not known to have a sexual phase in its life cycle.

Here is the Abstract:
Meiosis is a defining feature of eukaryotes but its phylogenetic distribution has not been broadly determined, especially among eukaryotic microorganisms (i.e. protists)—which represent the majority of eukaryotic ‘supergroups’. We surveyed genomes of animals, fungi, plants and protists for meiotic genes, focusing on the evolutionarily divergent parasitic protist Trichomonas vaginalis. We identified homologs of 29 components of the meiotic recombination machinery, as well as the synaptonemal and meiotic sister chromatid cohesion complexes. T. vaginalis has orthologs of 27 of 29 meiotic genes, including eight of nine genes that encode meiosis-specific proteins in model organisms. Although meiosis has not been observed in T. vaginalis, our findings suggest it is either currently sexual or a recent asexual, consistent with observed, albeit unusual, sexual cycles in their distant parabasalid relatives, the hypermastigotes. T. vaginalis may use meiotic gene homologs to mediate homologous recombination and genetic exchange. Overall, this expanded inventory of meiotic genes forms a useful “meiosis detection toolkit”. Our analyses indicate that these meiotic genes arose, or were already present, early in eukaryotic evolution; thus, the eukaryotic cenancestor contained most or all components of this set and was likely capable of performing meiotic recombination using near-universal meiotic machinery.
Here are my impressions of publishing in PLoS ONE (so far)...

  • It was fast. Submission to acceptance was less than a month. It took us longer to revise the final copy than to gain initial acceptance.
  • The PLoS editorial staff were very accommodating and helpful throughout the process. In particular, they quickly transferred our manuscript between other PLoS journals (where it was initially rejected).
  • The review process was great. In this case, only one reviewer was contacted. S/he liked the paper, and gave some suggestions for improvement that were left up to us to incorporate. We heeded some, but not all of the advice given.
  • It was (fairly) inexpensive. The "page charges" ($1125) were ~40% less than those levied for a similar non-OA journal that we have published in recently.
  • There was no opportunity given for making corrections to proofs. I have already identified an issue with one of the tables that would have been corrected in proof had there been an opportunity. There are always a few things that the author can notice that the copy editors (however talented they are) might miss. Why not add the author as a final checker?
  • The Journal Management System (for e-submission and tracking) is a bit too complicated for my taste. It takes quite a while (1+ hour) to get all of the information pasted into the form. I may just need to get to used to this level of front-end effort. However, as noted above, the journal staff helped me by moving all of the manuscript info from one journal to another. If not, it would have been painful to repeat.
  • As of this posting, our paper has not yet appeared in the listing of papers published yesterday. I assume (and hope) that this is a small and non-frequent oversight, but an annoying one when it's my paper!
I think that the PROS much outweigh the CONS in this case. Direct any comments on the paper itself to the PLoS ONE site.


  1. Congrats on getting the paper out, I look forward to reading it. BTW did you get a chance to look at Kong et al.. I would be interested in your opinion of whether the human RNF212 is a good putative ortholog of the ZHP-3 gene in C elegans. The association study is certainly pretty impressive.


  2. congratulations on getting the paper out. A paper of mine just came out in a BMC journal.

    I am a big fan of open access publishing of science but I am unhappy with parts of the BMC process. I agree that the pros outweighed the cons but I also had an issue with proofing. The BMC process did not have a copy editing step! There are typos in the published version of our paper that I and the other authors did not catch until it was tool late.

    Is having a competent copy editor look over the proofs really a particularly costly step in the process?

  3. I have a big CON about the paper "not yet appearing on the webpage" of currently released PLOS One articles: I contacted the production staff and they mistakenly gave it the citation year of "2007" not 2008. Thus, my first primary-authored paper will likely NEVER appear in anyone's eTOCs, PubCrawler or other notifications because these are all for CURRENT articles (not mistakenly year-old or even over-a-week-old articles) and now (8/13/08), a week after the paper was published (on 8/6/08) this still hasn't been fixed. Because of such a small mistake as the release year being wrong, the sequence citations in Genbank for the paper didn't get updated and I had to update these myself too. I also noticed misleading production-level changes in two tables that would have been rectified if there had really been a proof stage.

    Obviously you get what you pay for. Cheap production costs yielded some production oversights. I can appreciate how many hours and effort a copy editor and production staff spend on these seemingly small details now since I followed up on a few points myself. So many fewer people will see the paper since it's release date was mis-cited by the journal itself that it doesn't matter, right?

    PLOS One should charge more money for publication fees to pay for more detail-oriented production staff and to give authors a chance to proofread the production proofs. I've published in BMC Evolutionary Biology and didn't have these problems.

  4. Your cons are small change, really. Not to belittle your pain, but it sounds like an overall good experience (though I do totally agree that one more round of proofing with the authors should happen).

    So you submitted first to PLoS Biology and they bounced you down? We have two papers we want to send to PLoS, and I think one is appropriate for Biology and the other may be best for ONE. I wonder if we should send them both to Biology, or what.... I suppose I'll ask.

    I applaud your decision to pick PLoS and OpenAccess.

  5. You forgot one pro, and it's a big one. Those of us without access to paid journals will be able to read and learn from it. Thanks for choosing OpenSource and PLoS One.

  6. I didn't forget about or disagree with any of the PROs that John or anyone else listed! In fact I think it's very important that scientific literature be as broadly distributed as possible, as it is by open access journals. I'm also not sore (As Greg implies) about the paper bouncing down from PLoS Biology (by the editors, without review) to PLoS One. Our paper (S.B. Malik, A.W. Pightling, L.M. Stefaniak, A.M. Schurko & J.M. Logsdon Jr. 2008.
    received a thoughtful, constructive and thorough review at PLoS One.

    I do not know Greg or Mike but their comments would suggest that they may not have read the paper yet, and that they already have relatively secure faculty jobs and forgot what it's like to be a student or postdoc in need of good current exposure to help them get increasingly elusive fellowship support and eventually a faculty job.

    I'm very grateful that John -albeit aware of the PROs- didn't view the CONs as "small change" and is actively promoting his current and former mentees' work even if there is an oversight by the typesetters. If John and I don't complain about production/typesetting/editing problems in our own paper, then who will? (Trees falling in forest without being heard...)

    Also, my comment to the effect that PLoS One could charge more to ensure that pre-publication proofs are provided, read and fixed would just ensure that everyone gets to read higher-quality papers with fewer typos. The people whose grants pay publication fees would still pay them and the people whose fees get waived because they cannot pay would still have them waived, and anyone with internet access could still read the articles for free.

    Anyway, please just read our paper. I noticed that several of you are actively helping to promote evolution over creationism and ID. Please keep it up. It really bugs me that the ID gang uses meiosis as an example of something that is irreducibly complex and couldn't have evolved from anything else. Our paper shows that the meiosis-specific molecular machinery for meiotic recombination are related to general-function DNA recombination and repair machinery, and that core meiotic machinery most likely evolved once in eukaryotic evolution. These are important scientific findings for dissemination, even if you disagree with my criticism of our second experience with open-access publishing.

  7. Neat study. I am not into PLoS yet, but hope to be one day. By the way, I am an entomologist. I am new to this site. I love your posts here.


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