Monday, December 26, 2011

New Fossil Species of 2011 - A PLoS ONE Retrospective

What do sauropods, primates, crabs, cats, and crocodiles have in common? They're all animals in the fossil record that had new species named in PLoS ONE this year!

Chela (claw) of Geograpsus severnsi, from Paulay & Starmer, 2011

As 2011 winds down, I'm going to devote two posts to some navel-gazing at paleontology in the online, open access journal PLoS ONE. PLoS ONE really has been a ground-breaking publication, partly responsible for spawning the term "megajournal" as well as inspiring clones from the very publishers who invested some effort over the past few years in downplaying the worth of the PLoS ONE publishing model.

[Note before we continue: Although I do have an "official" volunteer role as one of the academic and section editors for the journal, any opinions in this post are entirely my own.]

Skull of Arenysuchus gascabadiolorum, from Puértolas et al., 2011

In any case, let's start our 2011 retrospective with a look at some of the new taxonomy that appeared this year. 17 new species of extinct organism were named on the "pages" of PLoS ONE this year, but these were not by any means distributed evenly across the tree of life.

Five out of 17 were mammals, only one was a non-vertebrate (a lonely, recently extinct land crab from Hawaii), and three - THREE!!! - were sauropodomorph dinosaurs. What kind of crazy world is this where sauropodomorph taxa outnumber crocodylimorphs, and arthropods? Dinosaurs as a whole did quite well, with seven new non-avian dinosaurs gracing the HTML code of PLoS ONE.

New Fossil Taxa Named in PLoS ONE - 2011
Arenysuchus gascabadiolorum (crocodyliform)
Boutakioutichnium atlasicus (theropod footprint)
Gaudeamus aslius (rodent)
Gaudeamus hylaeus (rodent)
Geograpsus severnsi (crab)
Kawichthys moodiei (chondrichthyan)
Khoratpithecus ayeyarwadyensis (primate)
Leonerasaurus taquetrensis (sauropodomorph)
Leyesaurus marayensis (sauropodomorph)
Linhevenator tani (troodontid)
Lycophocyon hutchisoni (carnivoramorph mammal)
Panthera zdanskyi (felid)
Paravipus didactyloides (theropod footprint)
Pissarrachampsa sera (crocodyliform)
Talos sampsoni (troodontid)
Tapuiasaurus macedoi (sauropod)
Tonsala buchanani (bird)

In 2012, I would love to see the following trends:
  • An expansion in the number of new taxa published in PLoS ONE (assuming that high scientific standards are maintained - no junk taxa, please).
  • Greater diversity in the taxonomic groups represented. Archosaurs are cool and all, but where are the plants? Where are the brachiopods? This will probably just take time, and perhaps a pioneer in each field of study to raise awareness of the journal. I first seriously considered publishing in PLoS ONE because a high-profile dinosaur worker published there, and I suspect other folks in other fields have similar thoughts.
  • More authors taking advantage of the format of PLoS ONE when submitting their new taxonomy. With few or no practical limits on figures (color, size, number) and text, every new description could potentially (and should, with few exceptions) get the monographic treatment. I am happy to say that most authors did just this, but there is always room for improvement!

Skull of Tapuiasaurus macedoi, from Zaher et al., 2011

In the next post: PLoS ONE is now a major force in paleontological publishing. What were the overall trends in 2011? What might the future bring?


Anonymous said...

I actually know a certain well-respected professor of Palaeobiology (microfossils, mainly) who refuses hands down to publish in PLOS, or even credit any material from it, as he thinks the peer-review process is poor. I wonder if others hold the same opinion, which might affect the three trends you mention..

Andy said...

That's unfortunate. . .I of course would argue the peer review process at the journal is pretty good (not perfect - but then this applies to every publishing venue). Of course, any specific examples of poor papers should get called out in the literature or other appropriate venues!

Donald Prothero said...

I was hoping you would list ALL new taxa of 2011--in which case, my Matthewlabis was published in JVP this year....and next year, I'll have a BUNCH of new fossil peccaries named...

Andy said...

Sorry, Don, had to keep it focused (only so many hours in the day)! Here's to 2012 being the year of the peccary!

Thomas Holtz said...

Actually, there is a much bigger topic related to PLoS that is related to the lack of non-vertebrate papers: it has basically nil Earth Science component. Paleobotanists, micropaleontologists, and invertebrate paleontologists are strongly in the sphere of Geology, not Biology; and PLoS has done near diddly squat to attract the Geosciences.

It still has the reputation among geoscientists as being a fly-by-night operation, unfortunately.

Bill Parker said...

I believe the paper I published with Jeff Martz in 2010 was and is the only geology paper published in PLoSONE. I thought it was a great venue for that type of paper. No size limits, color figures; we even published a geological map! Plus it is open access. Can't be beat.

Andy said...

I do agree that PLoS needs to pay more heed to geology. In fact, the physical sciences in general are pretty neglected in the journal, probably reflecting the biological bent of the organization's founders.

Joanne said...

This post is a great reminder of how Open Publishing is becoming more prevalent as scientists see it's value.

I am paying "blog calls" to each @scio12 attendee to say "Hi" and give your blog a shoutout on twitter (I'm @sciencegoddess). I look forward to meeting you in January!

John Bruno said...

Andy, PLoS One - like other broad science journals in general - doesn't "need to pay attention to - and specific discipline. If the scientists in a discipline want to be published in PLoS One, then all they have to do is submit there papers there! I used to be a PO editor and there isn't any devious plans to exclude Geos.

Be the first in your field to start utilizing the journal and reap the rewards! A lot of ecologists and coral reef biologists initially scoffed at PO, but now it is the go to place, especially in the latter field.

So what are ya waiting for?!


Jaime A. Headden said...

How does PLoS ONE broaden its appeal into the geo-centered sciences? Should, perhaps, people working or who have worked in the Open-Source Media centers and journals like this band together at places such as GSA and SVP and push for wider availability? Note that the works are becoming increasingly cited, recognized and that this raises the impact factor and such? The lack of paper seems a non-issue as I see it, but I think many people are hung up over it, desiring a physical copy in the sense of historical connection to journals of ye old era.

Heinrich Mallison said...

as much as I like PLoS ONE, I sometimes wonder where people get the money from - or if the majority of papers is published under the waiver.

There are other journals that are free of charge and open access, with unlimited figures etc. it is a bit surprising to see how PLoS ONE has managed to become THE archosaur OA journal so quickly.

Andy said...

@Heinrich - I suspect (but don't know for sure) that many folks have grants or get waivers.

Mike Taylor said...

"There are other journals that are free of charge and open access, with unlimited figures etc. it is a bit surprising to see how PLoS ONE has managed to become THE archosaur OA journal so quickly."

I feel your pain, Heinrich. Honestly, I think the PE made some bad decisions that meant it squandered a lot of its first-mover advantage. It's fixing a lot of those now (most notably, big figures and publish-when-ready), and that's going to help a lot.

(It may seem trivial, but for me the biggest strike against PE right now is the use of a sans-serif font. It just doesn't look like science without serifs.)

Mike Taylor said...

More generally, I agree that monocultures are bad, and that -- excellent though PLoS is -- we no more want it to have total control over scientific publishing than we want Elsevier to.

Anonymous said...

I know of at least one paleobiology related paper published in PLOS this past year that was rejected from more reputable paleo journals, basically in unmodified form.

Also, I recall some discussion by colleagues in other fields (ecology) about how lax the peer review process was.

Open access is great, but subpar peer review is not.

Ian said...

Could one issue with why Plos1 and not PalaeoElectronica is benefitting from an open access boom be that palaeo papers in Plos1 are 'piggybacking' to some degree on the impact factor of all the other bio-sciences papers that are published in Plos1? Need an open access journal AND something that looks good on your job search/tenure forms? Plos1 has a higher impact factor than all of the palaeo journals, and roughly comparable to general biology journals like Proceedings B, Evolution etc.

The following Plos1 paper on evolutionary biology suggested this was the case with evo papers that piggybacked high impact factor journals - "while the impact of evolutionary papers published in multidisciplinary journals is substantially overestimated by their overall impact factor, the impact of evolutionary papers in many of the more specialized, non-evolutionary journals is significantly underestimated."

It would be interesting to look at the citation rates of Plos1 paleo papers vs the average.

Now while all of this shouldn't matter, and I may be massively generalising here, I suspect that many of the people who are more open access friendly/aware may be a younger generation who coincidentally also have to consider things like impact as they battle a tough jobs market...

Andy said...

@Anonymous - If the paper you mention had genuine technical flaws, then this can be addressed in comments at PLoS ONE, or in the peer reviewed literature elsewhere. It is quite possible that the reviewers for the PLoS version were not the same as those at the other journals. It's not unheard of (at any journal) for authors to tweak the requested/blocked reviewer list to the editors to sidestep issues with a previous version of the manuscript. It's also possible that the paper was rejected from other journals for not being of "broad enough interest." I don't know the paper you are talking about (and don't need to know, although if it's one that I handled, I actually would appreciate some more background). This is not making excuses for a bad paper - simply giving some context.

On the other hand, if you feel that there were ethical failings involved, then you should report this to PLoS ONE (and any other relevant bodies) so that it can be addressed.

On your last point, I think the peer review process in the paleontology section is pretty good (at least as far as I know). Results may vary depending on the editors in the other topics, though. It's important to keep in mind that acceptance of PLoS ONE as a legitimate publishing outlet varies greatly between disciplines, research groups, etc.