Monday, 21 September 2015

Meet Mosaiceratops - the Mosaic ceratopsian

Although most of my posts are on pterosaurs, I did get my palaeontological start working on a ceratopsian dinosaur called Centrosaurus as an undergrad in Alberta. While I don't actively work on them anymore (other than trying to finish the manuscript!), they do still hold a special place in my heart, which is why I was very interested in a new species of ceratopsian named today. 

The evolution of ceratopsians (horned dinosaurs best known as animals like Triceratops and Centrosaurus) is not entirely understood. They are generally though of as being closely related to pachycephalosaurs (the dome-headed dinosaurs like Pachycephalosaurus), and are normally remembered for their large horns and bone frills, often well ornamented. The first ceratopsians com from the Upper Jurassic of China, while neoceratopsians first appear in the Lower Cretaceous, with most more derived species being found in the Upper Cretaceous. Although best known for the horns and frills, ceratopsians didn't always have crazy ornamentation. Basal ceratopsians and early neoceratopsians didn't have any horns and had only very little frills. A new species of basal neoceratopsian, Mosaiceratops azumai has been named from the Upper Cretaceous of China, by Zheng et al. (2015). 

Mosaiceratops is significant because of it's mosaic of features reflected in the name, meaning "mosaic horned-face", the mosaic made of a number of characters previously found only in some other groups. A single partial skeleton is known, including part of the skull and a large portion of the post-cranial skeleton. 
Mosaiceratops fossil (a), drawing (b), and skeletal reconstruction (c) from Zheng et al. 2015
The interesting part about Mosaiceratops is the mosaic of features. While it is still considered to be a basal neoceratopsian, it is found quite late, as most basal ceratopsians are found during the Lower Cretaceous. Despite this, it has several plesiomorphic ("ancestral") characters that are not found in other basal neoceratopsians. It also contains features that were previously only found in psittacosaurids, among the basal ceratopsians and basal neoceratopsians. Mosaiceratops is not a psittacosaurid, meaning these features are not diagnostic to that group. One of these features includes the lack of teeth on the premaxilla. This is something seen in more derived neoceratopsians, and psittacosaurids, but not in the rest of the basal neoceratopsians, suggesting that in ceratopsian evolution, there had to be reversals somewhere. Zheng et al. (2015) suggest that lack of premaxillary teeth is a diagnostic feature of the Psittacosauridae and Neoceratopsia, and the animals neoceratopsians that have premaxillary teeth actually underwent a reversal to the primitive condition found in basal ceratopsians. If this is the case, this is one of the few times there has been a major reversal like this in dinosaur evolution, although the authors recognise their analyses are not as well supported as they could be. Additionally, Mosaiceratops has features that are in-between psittacosaurids and more derived neoceratopsians, which places it in this position in a phylogenetic analysis. 
Phylogenetic position of Mosaiceratops from Zheng et al. 2015
Mosaiceratops is extremely important in helping us understand early ceratopsian evolution. We are slowly starting to fill the holes and figure out how this clade evolved. This is yet another case that shows that evolution does not happen in any specific order. Animals can have a mosaic of features that are shared with those more primitive AND those more derived than them, and there is no clear direction of traits or evolution. 

If you want to learn more about ceratopsians, and another fairly recently named basal neoceratopsian, Aquilops, check out this Palaeocast episode with Andy Farke. 


Wednesday, 9 September 2015

Pterosaur with 2 eggs?

Understanding reproduction in extinct animals can be extremely difficult as we lack the necessary information of soft tissues. However, there are certain things we can learn from fossils, and particularly well preserved fossils are even better.

3D preserved Hamipterus eggs with soft impressions
showing a soft pliable egg (Wang et al. [4]).
For example, we know that pterosaurs were egg-layers like other reptiles. In a phylogenetic context, pterosaurs are located in between crocodiles and birds in terms of modern animals, which both lay eggs, meaning it was most likely pterosaurs would have too. Thanks to fossils, we know that they did. While pterosaur egg fossils are rare, they do exist. The first pterosaur eggs were found in China[1-2], and Argentina[3] and come from Early Cretaceous pterodactyloids. The eggs have embryos preserved, and the material from Argentina can even be identified as Pterodaustro. Further pterosaur eggs have been found, and we know that pterosaur eggs were softer (much like those found in snakes) rather than hard calcareous shells like those seen in birds, thanks to one of the first finds that suggested pterosaur shells were leathery[2], and some 3D preserved eggs with impressions in them, from the Hamipterus bonebed in China[4].

Kunpengopterus counterslab and drawing showing 2 eggs
in black from Wang et al. [5]
This is a recent study that I saw presented at Flugsaurier 2 weeks ago, where Alex Kellner mentioned it in his talk on pterosaur reproduction. A pterosaur described a few years ago has been recently restudied, and is potentially teaching us a bit more about pterosaur reproduction in a paper published in July. Wang et al. [5] discovered some interesting features in the counterslab of the pterosaur Kunpengopterus. The counterslab is not fantastically preserved, in fact the images make it hard to see things, but what they have pointed out are not one but two eggs present with the individual. One egg is visible just below the pelvis, as if it had been expelled shortly before or after death, while the other is still visible within the body cavity. In close up images, you can see two rounded egg-shaped structures in these areas. The first egg, the one below the pelvis, was identified initially when this specimen was first described. The second one, however, is new. For the first time, it seems that pterosaurs could have 2 eggs in their body at once.
Outline of eggs from A) the pelvic region, and B) inside the body cavity from Wang et al. [5].
So what does that mean? Who cares if they have 2 eggs? Wang et al. [5] further go into the significance of this find. They suggest that this pterosaur was actually a pregnant female, pregnant with 2 eggs when it died. Having 2 eggs at once is a sign of having 2 functioning oviducts, which is interesting because while most extant reptiles have 2, birds have only 1 functioning oviduct. In birds, this has been thought of as relating to decreasing mass for the evolution of flight, especially as non-avian dinosaurs appear to have 2 functioning oviducts as well. The thought was that having only 1 functioning oviduct was essential to decrease mass in order to achieve flight. However, that seems not to be the case if pterosaurs were able to have 2 oviducts, while being the largest animals ever to achieve powered flight.

This new study provides a lot of interesting information about pterosaur reproduction that we previously didn't know, and of course for me, it's interesting when it comes to the evolution of flight. I'm always interested when people suggest that flight couldn't have evolved without things like the reduction of an oviduct. I think this study shows that mass reduction to achieve flight is not as straight forward or "black and white" as we may have previously thought. Different taxa do different things, and what may be valid in birds, is not valid in pterosaurs, and vice versa.

1. Wang and Zhou. 2004. Pterosaur embryo from the Early Cretaceous. Nature 429: 621. 
2. Ji et al. 2004. Pterosaur egg with a leathery shell. Nature 432: 572. 
3. Chiappe et al. 2004. Argentinean unhatched pterosaur fossil. Nature 432: 571-572.
4. Want et al. 2014. Sexually dimorphic tridimensional preserved pterosaurs and their eggs from China. Current Biology 24: 1323-1330.
5. Wang et al. 2015. Eggshell and histology provide insight on the life history of a pterosaur with two functional ovaries. Annals of the Brazilian Academy of Sciences.

Monday, 7 September 2015

Preprints in science

I've recently been having a discussion with a colleague on Twitter about preprints in science, and thought it would be good to open the discussion here. For those of you that don't know, preprints are where you publish your manuscript before it goes to peer review. The most common and well known means of doing this is by publishing a manuscript on the arXiv, where most physicists post their papers before submitting to a journal. Some journals don't allow this as they consider it to be previously published, but most permit this and in some cases even encourage it, as people can comment on it before going to peer review.

Despite it's prominence in physics, biology and other sciences (I'm thinking of palaeontology of course) have been particularly slow on the uptake of this, for reasons I've never fully understood, but my colleague shared these views and was not convinced by the preprint process. On one hand, I understand some of the hesitations he mentioned. Preprints are essentially the first submission to a journal, wrought with errors (mostly just typos, but sometimes some scientific errors as well), which could cause some miscommunications to the public or to other scientists when errors get propagated in the literature or media. Also, preprints are not peer reviewed. While I agree that peer review has it's issues, I do still believe that it has a place in academia and is important. Articles published in preprints have not been properly peer reviewed, which could lead to fringe ideas or studies that have not been properly scrutinised being read and cited. I understand both of these concerns, but I think that in the issue of preprints, they are not particularly valid for several reasons.

1. The arXiv has been working in physics for over 20 years, in fact longer than the World Wide Web. They've had a lot of time to make it work the way they want it to. Once an article is posted on the arXiv, that article has priority. This means that if two (or say 10) groups around the world are working on the same problem, whoever gets it onto the arXiv first gets priority and is recognised as being first, without having to wait for months for it to go through peer review. Of course there will be typos and errors, but the general theme of the paper and description of the experiment or study is still the same. If you're working in a field where other people are working on similar things, this is essential. Why should your work be held up and you be prevented from having priority just because the journal you submitted to is slower? Or a reviewer is away at a conference or on field work? Or a reviewer is one of the other people working on this and wants to slow you down, knowing they have a paper in review? It takes out those human aspects of the system that slow it down. Having gone through this before, I would much rather have had the uncorrected manuscript of my first paper published immediately, rather than waiting the excruciatingly stressful year from acceptance to publication (plus the 6 months before that that it was in review, etc.), waiting for someone else to publish something similar. Preprints allow you to get priority there and then.

2. We know that work in preprints is not peer-reviewed, or edited, and some people have concerns that any incorrect information will be propagated. First of all, we are scientists, we are not idiots. We know that preprints are not peer reviewed, and for this reason, when reading a preprint, you should not expect it to be perfect, and take that into account. When reading a preprint on the arXiv, readers are cautious. Papers from the arXiv can be cited, but physicists won't cite specific details or quote lines on a paper on the arXiv. They will, however, cite general ideas of the paper - "Smith et al. (2015) was the first to do an experiment using X, Y, and Z." - because regardless of peer review or not, they WERE first.

3. This point is related to the first two. I mentioned earlier that some journals (in physics) actually prefer and actively encourage publication on the arXiv before submitting to the journal. The reasons for this are simple - authors are essentially getting unsolicited peer review, and allowing for their paper to be publicly scrutinised long before publication. For a journal, this means that if they've received a paper to review, and find that it's already made it to the press, and been heavily scrutinised by the relevant parties in the world BEFORE even going to peer review, and all the talk is positive, it's a shoe-in for publication. Job done. Or, imagine getting a paper to peer review and finding that it has already been cited. Congrats, your paper gets a gold star. A recent example of this happened a few weeks ago when a big physics paper was posted on the arXiv. I won't go into details because I'm not a physicist (and probably most of you aren't either), but essentially it solved a massive problem in quantum photonics doing something that had never been managed before. It was such a big story, that within days of the preprint going up, it had been covered by New Scientist, Nature, PhysOrg, Science, etc., without even being officially peer-reviewed. And of course what did this mean? It meant that groups around the world who work on this field immediately bunkered down for the day, dissecting the paper and experiment, and coming to the conclusion that they had done it right. This paper is likely going to be published in Nature or something very similar, and it's already got a huge stamp of approval on it. We're talking Nature guys. It's not just small journals that take papers that have been on preprints - Nature actually prefers physics papers that have been on the arXiv. Less work for them!

4. Finally, for those interested in open access, this means that regardless of where your manuscript ends up in the end, your research is accessible to everyone. You don't need a university ID or have to pay for papers that are preprints. While you could publish your paper in Nature and have the joy of a big fancy Nature paper, anyone in the world can still read your research and see what you did from the preprint.

So what are the downsides? What are the concerns that people have?:

  • Someone could steal my work - well actually no, they couldn't, because the preprint would mean that you had priority. If it becomes a big thing in biology, everyone would see you posted it first. No one can take it from you
  • But what about all the mistakes? It's not peer reviewed - I think I've gone through this pretty well, but essentially, it's more about the big picture than the nitty gritty details. 
  • Why would a journal publish something already online? - because it gives them free, easy, and quick peer review, and a good idea of what the community thinks about the paper. 
  • How does it benefit me? Why not just wait for the final paper instead of an unformatted manuscript? - because this is fast. Peer review can be so slow. And is subject to people with agendas. Your paper shouldn't be delayed because someone doesn't like you or is doing something similar. You should still get priority if you did it first.
  • But how do I know what happened to the preprint afterwards? - on the arXiv, there is a system that authors can upload additional versions and updates. Once a paper is listed, you can upload additional versions when they come back from review, just as manuscript files. This way anyone can see exactly what has changed between versions throughout peer review, and then at the end, a link to the final published paper is given. It's an easy way to track exactly what they changed from one version to the next, so you know if it was a major experimental problem, or just some typos. 
  • If there are other concerns, please let me know!

This discussion actually started from my colleague being unhappy that his uncorrected, unformatted accepted manuscript had been posted by the journal, rather than waiting 2 weeks for the final to come out. Of course this is a bit different, because it had already been through peer review and was accepted, but I think that the general topic of speed is still relevant here. If you are 100% positive that no one in the world has looked at the same thing as you and won't come out with the same paper in the next 2 weeks, then that's fine. But imagine if someone else out there is working on it? Wouldn't you want it out there ASAP regardless of a few typos?

As far as I can see, there are no downsides to preprints, once the community accepts them. In biology, we are still woefully behind in this regard, that many journals do not accept manuscripts that have been put as preprints, and current nomenclature acts may prevent things like species being named in preprints. But this can change, and it is slowly starting to. PeerJ now offers a preprint server, which people are starting to submit to.

Please please please comment if you have anything related to this to discuss. I'm curious about what other people think about preprints. I know the view of physicists and some biologists, but I'm interested in other views. What do you think about preprints or uncorrected/unformatted proofs?

Thanks Josh - Obviously, I'm not a physicist, but my partner Josh is. Through years of him posting papers on the arXiv I've gained perhaps a better understanding of how it works than many non-physicists, and thanks to him for answering all my questions and pointing me to specific articles I would find useful in this discussion.

EDIT: Previously this post suggested that the journal Science did not allow for their papers to be published elsewhere as preprints. As you can see from the comments below, that was previously their policy, but is not anymore. Papers in Science can indeed appear as preprints elsewhere.

Saturday, 5 September 2015

Flugsaurier and SVPCA

The last 2 weeks have been crazy busy and stressful for me, and I'm glad that I can now sit down and relax, and get back to some blog posts! The reason for the stress has been that I attended, and was on the organising committees, of 2 separate conferences: Flugsaurier, a conference for pterosaur research held every 2-3 years; and the Symposium of Vertebrate Palaeontology and Comparative Anatomy, a yearly conference for mostly UK-based (but all are welcome) researchers.


Flugsaurier 2015 took place in Portsmouth, UK, and was an exceptional conference. For pterosaur researchers like me, this conference was just great. Typically when I go to conferences there are 3-4 talks on pterosaurs (if I'm lucky), and the rest of the conference is more indirectly relevant to my work. Flugsaurier meant that I had 2 full days of pterosaur talks to listen to, and a day with workshops. I have to say that the talks were great. As most of the research presented is not published, I won't describe the research in detail. If you're interested in finding out what was presented, the titles of the talks and posters can be found here. Talks included topics like functional morphology, muscular reconstruction, pterosaur trackways, new specimens (including a new 3D Triassic pterosaur!), limits of biomechanics, aerodynamics, and much much more. I quite enjoyed Rachel Frigot's talk on the pelvic musculature of a small pterosaur from the Isle of Wight, Vectidraco, mostly because I also happened to be talking about this specimen. We're looking at different aspects of the same specimen, and I think that we will be able to say some interesting things about it in the end, doing completely different things. But that's all I'll say as it's still very much in it's infancy (at least I know it is for me). I also was interested in Alex Kellner's talk on pterosaur reproduction, which was recently published and I will try to post about sometime soon. I somehow managed to get my name on 4 abstracts at the conference, including my talk on spinal nerve foramina in pterosaurs (using Vectidraco), a poster co-authored with Dave Hone and others on rhamphorhynchine bone thickness, a talk by Darren Naish on azhdarchids from Romania, and my former student Charlie Navarro's talk on pterosaur jaw evolution.

I think the highlight for many people came on the 3rd day in the workshops. The second workshop was put on by Colin Palmer and Mike Habib, two of my supervisors, on pterosaur aerodynamics and biomechanics. While it was scheduled for 1.5 hours, we had a marathon 4-hour session, with a few breaks in between. As workshop coordinator, and obviously interested in the topics, I thought this was fantastic, and apparently other people agreed. We worked through several problems or questions related to pterosaur flight, and what kind of tests or methods could be used to answer these questions. Thanks so much to Mike and Colin for this stellar performance.

As always, I was interested in the ratio between males and females at the conference, particularly because it seemed to not have so many speakers that were female. Turned out that I was right in suspecting that. Of 30 scheduled talks, only 28 were actually given, of which 5 were presented by women. That's just 18%. Seems quite sad really. Of total delegates, only 23% were female as well. It seems that pterosaur palaeontology needs more women! From what I can think of, the majority of women that work on pterosaurs were at the conference and presented, so it's not just because of missing people. So terrible... But well done to the 5 ladies who presented - Rachel Frigot, Taissa Rodrigues, Maria Leal, Fabiana Costa, and yours truly. Interestingly, 3/5 of the women are Brazilian... even more to ponder!

Anyways, I loved the conference. Most of the big pterosaur names were there and it was good to meet everyone. Can't wait for the next one, tentatively in LA!


This year's Symposium of Vertebrate Palaeontology and Comparative Anatomy was held at my home university, the University of Southampton, in the National Oceanography Centre. The 63rd annual SVPCA was extremely successful, breaking records of attendance (about 160 delegates), and the auction fundraising (over £1900 raised for the student fund). We had a team of awesome Southampton people on the committee, mostly run by Gareth Dyke, Jessica Lawrence Wujek, Aubrey Roberts, and I. We had more talks than ever, in a large number of topics from fish, to birds, to mammals, to dinosaurs, and everything in between. Unfortunately, I didn't make it to many talks, so I won't talk about them... but what I did see was great. If you want to see the programme, it can be found here.

Again, I was interested in the breakdown between males and females. SVPCA fared better than Flugsaurier in terms of equality, but it's still not great. Of 64 talks, 15 of them (24%) were presented by a woman. However, 35% of the total delegates were female. And interestingly enough, 34% of the posters were lead by women, which matches the total percentage. This follows what other people have said and reported before - women are not giving talks as much as men. I know that in this case it is not due to women's talks being rejected as SVPCA rejects very few (if any) abstracts. Therefore, women just aren't submitting abstracts for talks as much as they are for posters. While the general numbers are consistent with what was seen at my 2012 SVPCA, on the plus side, there were more female-lead posters this time than previously. Let's hope we can keep this trend on the up!

Next year, SVPCA will kindly be hosted by Peter Falkingham at Liverpool John Moore's University. Can't wait to hear what he plans for it!

Thanks again to everyone who came to both conferences and making them so awesome. See you all soon! Now I need to get back to my this thing called my PhD...