About protohedgehog

Palaeontologist, working on a PhD at Imperial College in vertebrate biodiversity and extinction. Digs science communication, science policy, and opening up the research process. Tweets vigorously as @protohedgehog.

‘Open’ is about equality

This was originally posted at: http://blogs.plos.org/paleocomm/?p=487

OpenCon 2014 was an epic milestone for the global research community. OpenCon 2015 was different. OpenCon 2015 was a storm. Never have I seen such energy, such drive, such raw creativity unleashed than on the few days we had in Brussels.

Designed to bring together students and early career researchers from all facets of research and from all corners of the globe, OpenCon 2015 is about empowering the research community to advance open data, open access, and open education.

Throughout the event, I began to wonder whether we might be using the wrong words to describe what we do. We talk about ‘open’ as in free to read, free to access, free to remix and re-use, etc. – some or all of these things depending on who you talk to. These words have also been hi-jacked by commercial publishers, to the extent that we now think of ‘open’ as an additional ‘service’ which we have to pay for.

But I think what the ‘Open Community’ is really championing is something much more fundamental here: freedom and equality; the removal of barriers. It’s not about ‘open access’, it’s about ‘equal access’ – open levels the playing field. What it provides is a new baseline, stating that every single person on this planet, if they choose to, has the freedom and the opportunity to access the outputs of research.

Mike Eisen, co-founder of PLOS, quizzes our panel!

Mike Eisen, co-founder of PLOS, quizzes our panel!

Continue reading

Down with the impact factor

The impact factor is one of the most mis-used metrics in the history of academia. Stephen Curry and others have written much about the ‘impact factor’ disease, stating that if you use it in almost any form then you’re “statistically illiterate”, something which I’m inclined to agree with.


Image by Hilda Bastian

But such conversations about the impact factor are designed for one-on-one combating of its use. We often talk about ‘changing the culture’ of research assessment, which addresses the bigger picture of research assessment. And that means getting those who pull the strings to listen and make the changes we all advocate for. To that end, I’ve drafted an Open Letter template for researchers (with help from the community). This letter is to send to people in positions of power at different institutions, co-signed by as many academics as possible who believe in fairer and evidence-based assessment. It can be re-mixed, shared, edited, whatever you want. It’s just a tool to help empower researchers make the change we advocate for against the prevalent mis-use of the impact factor.

In the UK, there are currently only two universities (Sussex and UCL) who have signed DORA, the San Francisco Declaration on Research Assessment. This Declaration recommends for Institutions:

1. Be explicit about the criteria used to reach hiring, tenure, and promotion decisions, clearly highlighting, especially for early-stage investigators, that the scientific content of a paper is much more important than publication metrics or the identity of the journal in which it was published.

2. For the purposes of research assessment, consider the value and impact of all research outputs (including datasets and software) in addition to research publications, and consider a broad range of impact measures including qualitative indicators of research impact, such as influence on policy and practice.

There is absolutely nothing to lose from employing these recommendations. All we gain is an enriched and informed process of evaluation, and one which does away with non-sensical, mis-used metrics that are more purchased than earned anyway.

So take this letter, sign it, share it, and become the change.

The Open Research Glossary

A few months ago, we published the crowd-sourced Open Research Glossary, details of which can be found here. We’ve taken this to the next level now, and published the updated and much prettier version of this resource on Figshare. This means it is now openly licensed for re-use, and can also be cited like any normal research article. We also popped it on Zenodo, because why not!

The original document can be edited here, and remains an open crowd-sourced initiative, which means anyone can add or change anything they want. We strongly encourage the academic community to contribute to and broadly share this resource, so that we can all be a little bit more informed about the vastly complex topic of ‘Open Scholarship’.

This latest change was thanks to the hard work of Joe McArthur of the Right to Research Coalition, who have been kind enough not only to assist with formatting and the generation of an xml version of this document (pending), but also hosting the resource on their website.

If anyone has any questions, comments, or suggestions, then I’d love to hear them! In the mean time, I hope you find this useful. Thanks again to everyone who has contributed to or shared this work.

New fossil croc on the block

This was originally posted on the PLOS Paleo blog

Crocodiles are freakin’ amazing animals. They’ve been around for about 250 million years, and throughout this time have survived two mass extinctions, and at least twice decided to hitch up and take to the seas. Their historical diversity, and general weirdness, was vast compared to what we see in modern crocs, which are on the face of it all fairly similar. Extinct forms included those that looked like armadillos and even ate plants, as well as some that became gigantic and streamlined for swimming out to sea. Others were up to 12 metres long, and snacked on dinosaurs!

Sarcosuchus 1A (c)Nicholls2015

The giant croc Sarcosuchus, by Bob Nicholls

All modern crocs, alligators, caimans, and gharials belong to a group known as Crocodylia. The origins of this group can be traced back to the Cretaceous, when many of these bizarre croc-cousins, known collectively as crocodyliforms, where still around. Trying to work out the evolutionary origins of modern crocs though has proven to be a bit confusing for palaeontologists. Part of this is simply due to the fact that the fossil record preserves incomplete remnants of the lineage leading to modern crocs, which in turn creates issues in our understanding the relationships and anatomical changes that led to the origin of Crocodylia.

One thing we do know is that a group known as Eusuchia are the direct ancestors of modern crocs – Crocodylia belongs to Eusuchia, but not all eusuchians are crocodylians, if that makes sense. That’s because some eusuchians went extinct during the Cretaceous, leaving just crocodylians (and a couple of other non-eusuchian groups like the now extinct marine dyrosaurids) around to take charge. One of the problems which croc workers have been trying to figure out is what defines Eusuchia, and therefore what croc species can be assigned to this group. If we know this, then we can look at the evolutionary changes that led to the origins of modern crocodilians, and why these chappies became so successful.

Eusuchians have been traditionally recognised based on a couple of really important modifications to the ‘standard’ crocodyliform skeleton that reflect major changes in their lifestyle. One of these involves the movement of the choanae, an opening in the top of the mouth that helped crocs to breathe more efficiently, from a position closer to the nostrils to a position further back in the skull. This was due to the development of what’s called the secondary palate, the bony surface in the roof the mouth which grew as the overall skull lengthened in crocs to form the snout. Another important development of eusuchians was to do with the vertebrae. Until eusuchians, crocodyliforms (remember, the ancestors of modern crocs) had vertebrae in which the articular surfaces were either flat or concave, which limited mobility of the vertebral column. In Eusuchia, the articular surface facing towards the tail became progressively more hemispherical-shaped, or convex outwards, to what we call a ‘procoelous condition’, forming a sort of ball and socket articulation. This would have allowed greater flexibility of the vertebral column, which is a pretty useful adaptation to have.


Those holes towards the back, labelled by I7, are the choanae. Source.

So why the confusion about what the origins of Eusuchia? Well, for starters, a lot of fossils that look like they could be a eusuchian are often preserved in a way that we can’t tell what the choanae and vertebral columns looked like, or these bits are just missing. This leads to quite a lot of uncertainty about what constitutes a ‘true’ eusuchian, and has complicated both the species that can be assigned to Eusuchia, and the pattern of acquisition of these important anatomical features. Recently, a couple of papers by Alan Turner overhauled Eusuchia, and he suggested that other groups, including Paralligatoridae and Atoposauridae could both be included within Eusuchia too (see here and here – both open access). However, I don’t think this is 100% correct, as few if any of the species from these groups can be conclusively shown to have the features that define Eusuchia as mentioned above, and it is possible that atoposaurids and paralligatorids lie outside of Eusuchia (disclosure: I have a paper in review discussing this a bit at the moment). So that’s a nice additional layer of confusion to add in!

The different types of joint between vertebrae. Source.

The different types of joint between vertebrae. Source.

So that’s a whole lot of background, and I think important to wrap our heads around for a couple of reasons. Firstly, it shows that trying to figure out the taxonomy and evolutionary relationships of extinct animals is complicated, and pretty dynamic as far as what constitutes science (evidence-based inference) goes. Secondly, it shows how complicated our current understanding of the origins of modern crocs is, and the reasons for this complexity. Thirdly, it highlights how important new fossil finds might be in helping to unravel some of this evolutionary mess, which provides us with a nice segue into…

New croc species klaxon! Well, actually, two new crocs! A new study in PLOS ONE has identified two new species of crocodyliform from the same genus, Loheucosuchus (Low-hay-kwo-soo-kus). The first of these new crocs comes from near the village of Fuentes, Cuenco, in Spain, from a fossil locality known as Lo Hueco. The fossils here come from a time right towards the end of the Cretaceous, in time intervals known as the Campanian and Maastrichtian. This new species was called Lohuecosuchus megadontos, and it’s probably pretty obvious where the genus name comes from. The species name means ‘big tooth’, and refers to the well, uniquely big teeth this new croc has! ‘suchus’ is Latinized from the Greek word souchos, and refers to an Egyptian crocodile-headed god!

The holotype of Lohuecosuchus megadontus in above (dorsal) and below (ventral) views

The holotype (specimen upon which a name is founded) of Lohuecosuchus megadontus in above (dorsal) and below (ventral) views

As well as this new genus and species, they named a second new species referred to the new genus, Lohuecosuchus mechinorum, from the Fox-Amphoux site from Department of Var in France, and based on extensive comparisons with previously known material referred to a different species. The species name ‘mechinorum’ in this case is from the Mechin Collection (in honour of Patrick and Annie Mechin) at the Muséee des Dinosaures in Espéraza, France, which houses the specimens.

Another couple of views of Lohuecosuchus megadontus specimens

Another couple of views of Lohuecosuchus megadontus specimens

These new findings seem to provide a bit of insight into how Late Cretaceous crocs from Europe are related. They all fit within a newly resolved group known as Allodaposuchidae, named after Allodaposuchus as is common when naming these types of group. Allodaposuchus has been known for quite a while from multiple localities referred to several species from the Late Cretaceous of Europe. It’s what we like to call in palaeontology a ‘taxonomic nightmare’.

Holotype specimen of Lohuecosuchus mechiorum

Holotype specimen of Lohuecosuchus mechinorum

Allodaposuchidae seems to be related to another group of fairly unusual crocs known as Hylaeochampsidae, named after (you guessed it) Hylaeochampsa, another croc known from the Early Cretaceous of the Isle of White in Europe. Now Hylaeochampsidae is a bit of a taxonomic mess. Previously, species from the Cretaceous of North America (known as Pachycheilosuchus) and another from Italy called Pietraroiasuchus (I can’t say it either..), where assigned to this group, along with others from Europe like Acynodon and Iharkutosuchus. But membership has always been in a bit of a state of flux, depending on which researchers you ask. This is important as historically, hylaeochampsids have been regarded as the earliest, or most basal, eusuchians. Solve Hylaeochampsidae, solve Eusuchia. Oh yeah, it’s all coming together now.

Importantly, this new study finds both Allodaposuchidae and Hylaeochampsidae together to be the sister group to Crocodylia. In non-phylogenetics speak, this means that these groups are the closest relatives to the group that includes all modern crocodiles, alligators, and gharials, with the three of them together sharing a common ancestor (i.e., common origin). Hylaeochampsidae is found to comprise just Hylaeochampsa, Acynodon, and Iharkutosuchus – three exclusively European crocs. This is important, as it pretty much cements the idea that Crocodylia originated in Europe from an exclusively European stock of eusuchian crocs. Or so it would seem..

However, I wouldn’t be a croc palaeontologist if I didn’t raise a few potential issues. Or at least, things that spring to mind. The way in which palaeontologists analyse the relationships of organisms is though what we call phylogenetic analysis. These produce ‘phylogenies’, commonly depicted as trees, which illustrate the hierarchical relationships of organisms. These analyses are based on data matrices that comprise the morphology of organisms reduced to numerical codes that describe different aspects of their anatomy, and the different conditions these can take across all animals considered. What this means is that often when designed, these character matrices are created to test very explicit hypotheses about organismal relationships, based on whatever it is you want at the time, such as the relationships of a group or the position of a particular animal (taxon). But what a lot of researchers do, I imagine mostly for convenience, is to take data matrices used to test previous hypotheses, and simply add a new species into that matrix to test what is by default a very different hypothesis. And that’s what happened here. The new study uses a matrix by Chris Brochu and Glenn Storrs, published back in 2012, designed to test the relationships of a new crocodylian species from the Pliocene-Pleistocene (the last few million years) of Kenya. So the question is, is that matrix adequate to test the relationships of a ‘basal eusuchian’ from the Late Cretaceous of Europe? As Chris was one of the co-authors on the new study, I’m sure they gave lots of thought to this. But by using a matrix designed to test the relationships of more advanced crocodylians, the character matrix will contain a lot more characters (anatomical features) that are found in more advanced crocodylians in order to resolve their relationships. By extension, this means that fewer of these characters will be appropriate to test ‘deeper’ crocodylian relationships back in the Cretaceous, and might explain why several species previously regarded as eusuchians are falling outside of this group in their analyses. If you think about the logic behind this, it’s like looking just at modern birds, and trying to figure out what the relationships of Archaeopteryx are from it. You have to sample much deeper from down in the tree at older forms more closely related to the target animal in order to adequately test its relationships. While I don’t think this is a major issue with the results and placement of Lohuecosuchus, and the resolution of the new group Allodaposuchidae, I think it would have been really good to test alternative relationships for it by using different and possibly more appropriate matrices.

Time-calibrated phylogeny based on the new analyses

Time-calibrated phylogeny based on the new analyses

As well as this, such potential inadequacy might help to explain a few of the oddities in their results. As well as just using the matrix of Brochu and Storrs, they added several taxa mentioned above to this matrix and ‘coded’ them for their morphology. These included Shamosuchus, Pietraroiasuchus, and Pachycheilosuchus, and which the new analysis found all to be outside of Eusuchia. Weird that. While perhaps not unexpected for anyone familiar with these crocs, it is probably due to the issues mentioned above, and not sampling other crocs from deeper down in the tree related to these. In addition, the use of the closely related Bernissartia as what we call an outgroup (the taxon used to define the sequence of morphological evolution by being the most ‘basal’ in the analyses) is probably not appropriate, as typically more distantly related taxa are needed in order to understand what the actual ‘basal’ features of a group are. This issue has been raised recently with crocs, which found a completely different placement for a major marine radiation known as Thalattosuchia to be in a different phylogenetic placement depending on what is used as an outgroup.

But, if the resolution of an allodaposuchid-hylaeochampsid only Eusuchia is true (along with Crocodylia), then it has some pretty important implications. Both of these groups went extinct at the end of the Cretaceous, in the mass extinction that also took out the pterosaurs, marine reptiles, and the non-avian dinosaurs. Could it be that this removed competition with early crocodylians, and allowed them to radiate in their absence? This supports recent studies which showed that crocs actually seemed to do pretty well after the end-Cretaceous mass extinction, and shows that while we might think of extinction as generally bad, it really depends on whether you’re one of the survivors or not..

So for now, I’d still say we still haven’t fully resolved Eusuchia, and the results of this new study should be taken with a pinch of salt. Still, a cool new croc, and I look forward to seeing future analyses including it to see where it fits within the broader scheme of croc evolution.

Spinosaurus sails on

Spinosaurus stormed into the public imagination when it was witnessed scrapping with T. rex in the wildlife documentary known as Jurassic Park III. It’s popularity subsequently boomed, as frankly, it is a totally bizarre dinosaur. It’s back is adorned with a large sail, it had long clawed arms for grappling, and a snout that resembles a crocodile more than a dinosaur, elongated and full of teeth for snatching up prey.

Last year, Spinosaurus hit the public eye again, based on new research showing that this dinosaur was an efficient swimmer, dwelling in the lakes and rivers of the Cretaceous of North Africa, where it would ambush unsuspecting fish (and any careless dinos!). Interestingly, reconstructions showed it as a knuckle-walking quadruped, with teeny tiny legs and a body longer than that of T. rex. The original article is totally paywalled here.

Image: Brian Engh

Image: Brian Engh

However, there was a huge amount of controversy over the study, largely revolving around the reconstruction of Spinosaurus – it couldn’t be demonstrated that a composite skeleton comprised the same single animal, the same age of animal (important for size estimates), the same species or even family of dinosaur! For a research study that got worldwide press coverage (including its own TV show!), you’d think that such pretty hefty issues would be ironed out before publication to avoid the possibility of any scientific miscommunication. You’d think..

Continue reading