Sunday, 29 November 2015

Dimetrodon is Bathygnathus? Or Bathygnathus is Dimetrodon?

While the west of Canada is known for Late Cretaceous dinosaur fossils, the east has a number of Paleozoic outcrops with some early terrestrial tetrapods. In 1845, before Canada was even a country, a fossil of an upper jaw and some teeth was found on Prince Edward Island, and was first described in 1854. As the second ever vertebrate fossil to be found in Canada, this specimen has had an interesting history.

It was first identified as an extinct 'saurian', then as a dinosaur, followed by a theriodont, and finally correctly identified as a sphenacodontid, a group of early synapsids (a group of tetrapods with no temporal fenestra, or holes, in their skulls, consisting of mammals today) which includes the famous extinct sail-backed reptile Dimetrodon grandis. It hails from the Lower Permian, 283-290 million years ago, and was called Bathygnathus borealis. The fragmentary nature of the fossil made it difficult to determine the exact affinities of this specimen. Over the years it has been studied by a number of people, and similarities have been identified with Dimetrodon, Sphenacodon, and Ctenospondylus, but the similarities have never been major enough to warrant an official change. That is, until now.
ANSP 9524 - type specimen of 'Bathygnathus' borealis (Brink et al. 2015)
Dr. Kristin Brink worked on Dimetrodon and similar animals during her PhD research at the University of Toronto (Mississauga) and studied the specimen which is now housed at the Academy of Natural Sciences in Philadelphia. Primarily working on tooth of these similar animals, she was able to study the specimen using CT scans and compare it to other sphenacodontids[1]. She re-described the specimen and underwent phylogenetic analysis and found some interesting results, including that dental characters appear to be extremely important in sphenacodontid taxonomy. Based on phylogenetic analysis of morphological characters, Dr. Brink found that 'Bathygnathus' borealis appeared as a sister taxa to Dimetrodon grandis, and nestled within 3 species of Dimetrodon.
Cladogram showing position of 'Bathygnathus' borealis (Brink et al. 2015)
'Bathygnathus' borealis has the same tooth count, denticles, and tooth roots as Dimetrodon grandis, characters only found  in D. grandis. Brink et al. (2015) concluded that 'Bathygnathus' borealis was actually Dimetrodon borealis, making this specimen the first and only Dimetrodon in Canada.

The interesting and very important thing about this paper is related to the the rules of taxonomic nomenclature and priority. Bathygnathus borealis was named 20 years before Dimetrodon, meaning that by the law of priority, Bathygnathus should have priority and replace Dimetrodon. However, Dimetrodon is a well known and very famous fossil and no one wants to lose that name. Exceptions are occasionally made when there is a strong reason to retain initial names, and they have started a case with the International Commission of Zoological Nomenclature (ICZN), the group responsible for taxonomic names and problems like this. If they succeed, we won't lose Dimetrodon, but gain a new species of 'Dimetrodon' borealis!

And don't forget to do the survey! I've teamed up with Science Borealis, Dr. Paige Jarreau from Louisiana State University and 20 other Canadian science bloggers, to conduct a broad survey of Canadian science blog readers. Together we are trying to find out who reads science blogs in Canada, where they come from, whether Canadian-specific content is important to them and where they go for trustworthy, accurate science news and information. Your feedback will also help me learn more about my own blog readers. If you complete the survey, you will be entered to win a prize, and be given a high resolution science photograph.

It only take 5 minutes to complete the survey. Begin here:

Brink KS, Maddin HC, Evans DC, and Reisz RR. 2015. Re-evaluation of the historic Canadian fossil Bathygnathus borealis from the Early Permian of Prince Edward Island. Canadian Journal of Earth Sciences 52: 1109-1120.

Wednesday, 25 November 2015

Survey time! Please take part :)

To my readers...

I've teamed up with Science Borealis, Dr. Paige Jarreau from Louisiana State University and 20 other Canadian science bloggers, to conduct a broad survey of Canadian science blog readers. Together we are trying to find out who reads science blogs in Canada, where they come from, whether Canadian-specific content is important to them and where they go for trustworthy, accurate science news and information. Your feedback will also help me learn more about my own blog readers.

It only take 5 minutes to complete the survey. Begin here:

If you complete the survey you will be entered to win one of eleven prizes! A $50 Chapters Gift Card, a $20 surprise gift card, 3 Science Borealis T-shirts and 6 Surprise Gifts! PLUS everyone who completes the survey will receive a free hi-resolution science photograph from Paige's Photography!  

It's a great chance for me to get feedback on who is reading my blog, and for Dr. Jarreau to get more detailed feedback about Canadian science blogs in general, but of course, you don't need to be Canadian to take part. Please take the time to fill out the survey, and you may even win a prize!

FYI I'm registered with Science Borealis as Liz Martin-Silverstone, so that is probably the name to use when they ask.

Thanks to all in advance!

Thursday, 19 November 2015

To self-fund a PhD or not? That is the question...

I am a (partially) self-funded PhD student. As such, prospective PhD students often ask me if I would recommend going into a PhD without secure funding, which is a bit of a complicated issue. Doing a PhD self-funded has it's ups and downs, and pros and cons, which I'm going to try to summarise here, as it's something I think a lot about.

To start, I'll explain my situation a bit. As many of you know, I'm a PhD student at the University of Southampton in the UK, however, I'm originally from Canada, which complicates things. I have just started my 3rd year of a 3-4 year PhD on pterosaur biomechanics. As I'm not from the UK, yet doing a PhD here in the UK, funding has always been difficult. Before starting at Southampton, I had intended on doing a PhD at the University of Bristol, where I did my MSc. Unfortunately, I was unable to secure any funding, and was looking at the prospect of ending up approximately £80000 in debt at the end, assuming I would be unsuccessful of finding any funding (which, indeed, was an unlikely event). With this daunting prospect, I decided to try for a PhD at the University of Southampton, where my now supervisor was confident I would secure something. After interviewing fairly well, I ended up being given an offer that was suggested to be quite good for an international student: the graduate school would cover half of my tuition, and I would receive a Research Training Support Grant (RTSG) of an unknown amount (at least £1100 per year), and I would be responsible for the rest. No stipend, still responsible for about £9000 a year of tuition, and a lower RTSG than students funded through research councils like NERC. 

Seeming like a much better offer than nothing, I accepted, confident I would eventually manage to find some more funding. At the end of my first year, I successfully was granted an NSERC award from the Canadian science funding agency, a hearty sum of $21000 CAD per year. My supervisor was also able to secure some additional research funding for me in order to cover my CT scans (of course I chose a project that isn't cheap), and I've since managed to get some funding from external sources to cover travel or research trips (thanks to the Palaeontological Association and Geological Society of London, and one of my supervisors - Mike Habib). However, I have applied for far more than that (nearly 20 if I counted correctly, since my MSc, and I'm not telling you how many were successful). In fact I don't know of any other PhD student that has applied to the same number of grants/scholarships/awards as I have, and while I have definitely improved over time, it's still just as depressing when you get that "sorry, you weren't selected" letter. The reality is that as an international student, even if the university covers half of my tuition, I'm still responsible for £9000 a year in fees, which is barely covered by my Canadian scholarship, and I have nothing to cover my living expenses. In fact, if it wasn't for my husband's PhD funding (and now job) and some help from both of our fathers (thanks Dad and dad-in-law!), we never would have been able to make it work. 

This sounds pretty unpleasant and unappealing, so what are the pros of doing it on your own? There aren't a lot of advantages, but I would argue that there are some major ones. First of all, you don't have the same kind of pressure to finish. In the UK, PhD's are funded for 3 years, with the possibility of extending it to 3.5, but rarely 4. As I've started my 3rd year, this means most of my friends are aiming to finish by the end of this year, or the middle of next year. I, however, don't have that rush. I've been surviving without my living expenses being covered for 2.5 years now, and an extra year isn't going to kill me. I am able to focus on the problem at hand without massively stressing over getting it done by this time next year. The other advantage is that I don't have a funding agency breathing down my neck, directing my research. Because I am self funded, the project is more-or-less up to me. Of course my supervisors give me suggestions and help, but what I do and where I go with it is more up to me than those who have been given funding for specific projects. These two major advantages of left me pretty happy with my PhD project and where I'm going.

However, would I recommend it? Not unless you have something to fall back and catch you if you can't find funding. Don't go into it expecting to find full funding in your first year, especially if you're not from the country you're doing your PhD in. So many funding bodies don't provide funding to people from outside the UK/EU, and they don't give funding for tuition or living expenses. It's pretty easy to find funding to cover conferences or research expenses, but a lot harder to help out with your dinner and to put a roof about your head. 

There are also a lot of problems that pop up and that you wouldn't expect, and I can think of 2 examples of things that have happened to me. First of all, it makes the possibility of extensions a bit terrifying. If something happens to you and you need to suspend your PhD, you can get an extension to go beyond the normal 4 year limit. It may seem like a good offer, but it's a bit of a trojan horse - if you don't have funding, and are barely living day-to-day, that extra few months may kill you financially, and there is no funding agency to ask for help, even if it would help your project. Another problem I've had is funding for Open Access. I am a big proponent of Open Access publications. However, did you know that in the UK universities will only cover the fees if you are funded by a UK research council? I didn't... I've been able to get fee waivers for both of my papers published with PLOS ONE, but it wasn't easy. And I don't have the money to throw around for a PeerJ subscription either. It makes it just that little bit harder to do than for people who can just ask their uni to pay.

So, my advice? Don't start a self-funded PhD unless you know that you can finance it yourself if need-be. Everyone assumes they'll find funding later on, but it's really hard to get once you start. You might get lucky and get some, or you might not, so be aware of that before you start. And to supervisors and academics: for the love of all of us self-funded students, don't promise money that you don't have! I've heard countless stories of people starting with the promise of funding from supervisors that just doesn't appear. If you want a student that badly, find money for them without lying or promising something you don't have, even if you're doing it out of the goodness of your heart and are positive you will find money. Sometimes, you don't, so don't say it until it's in your hands! It's much harder to realise a year into a PhD that you can't afford it when no funding appears than to just hold off in the first place and wait for secure funding. And finally, if you're going to do it, make sure it is something that you truly want to work on and that you are happy with. Don't pay to do a PhD that you will end up hating. It is absolutely not worth it.

After posting this, I realised that I should really add this: I am fortunate because I am not fully self funded, but I know a number of people that are, with varying degrees of support. While I have some tuition covered, I still pay more than anyone else I know for a PhD (with the exception of one other self-funded person I know). Other people have fees waived, but less RTSG, and some still pay fees, or have no RTSG, or both, but none with a stipend. There are varying branches to the self-funded tree. and I can only truly comment on the one I am on: I have a fairly large amount of funding, but not nearly enough to cover my fees or living costs.

Any other self-funded PhD's out there who have comments, please leave them! I'd love to hear other people's opinions.

Monday, 2 November 2015

Skeletal mass in birds

I've spent a lot of time on this blog rambling about estimating mass in extinct animals, including talking about the "lightweight" skeleton in birds, pterosaur bone mass, and the likelihood of giant pterosaurs weighing as low as 70 kg. Now I'm going to talk a bit more about this problem, specifically looking at the relationship between skeletal mass and total body mass in birds, the topic of my most recent paper.

In 1979, a paper came out looking at the relationship between skeletal mass and total body mass in birds, which was remarkably similar to that same relationship in mammals [1]. Since the two groups had such a similar relationship, the same was to estimate the total body mass in pterosaurs, after estimating the skeletal mass using simple geometric methods [2]. Because mammals and birds are so different and far apart in the evolutionary tree, it was thought that a similar relationship between the two meant that other animals like pterosaurs would share a similar relationship. Of course, I'm interested in pterosaur mass, so these methods are interesting to me.

During my MSc, my supervisor Colin Palmer and I looked at the original 1979 study a bit closer and found some slight problems with it. First of all, while they sampled a large number of bird taxa, each species average skeletal and body mass was determined from just 1-6 individuals, with most of them being just a single individual. How can they know this is a normal average weight? Additionally, the original data were presented in a log-log scale, showing a nice tight relationship with little variability. However, when the data were plotted on a linear scale, significant variability could be seen. This made us more interested in the topic.

When I started my PhD, my supervisor Gareth Dyke told me about a big dataset that his friend Gary Kaiser had meticulously collected on over 700 bird specimens from the Royal British Columbia Museum, which included total body mass and skeletal mass for over 400 individuals from 79 species. This dataset has more individuals than the original, but fewer species, meaning we had 1-30 individuals for each species, giving us a much better picture of average mass and variation within a species. With some help from an undergraduate student Ria McCann, and a lot of stats help from Orsi Vincze, we started to look at this dataset and saw some pretty interesting patterns, which we recently published in PLOS ONE [3]. First of all, our new dataset turned out to result in a pretty similar relationship to the original study, which was good news. We also found that there was even more variability within our dataset than the original study, which isn't surprising with a large number of individuals per species. For example within a single species, the rhinoceros auklet, total body mass varied from 0.4-0.6 kg (approximately 33%), while skeletal mass were varied by almost a factor of two. At a total body mass of about 470-490 g, the measured skeletons weighed in from 26 g to 34 g. This is a large range for a single species. Total body mass ranged from just 256 g, up to 616 g.
Variation in body mass and skeletal mass in the rhinoceros auklet.
Of course, that range could be due to age, and we thought it may be possible that age would affect these relationships. Unfortunately, it can be difficult to determine age of a bird if it is found dead (as most of these specimens were), so the only age classes we could determine was whether the bird was within it's hatchling year, or above that. However, we found no statistical difference between the two groups, suggesting that this feature does not change ontogenetically, which was a bit surprising. We also looked at males vs. females, as it was suggested that this could change things. We know that female birds regulate the amount of calcium in their bones depending on what cycle of egg-laying they are in, as they use the calcium from their eggs to make the hard shells. Again, however, we found no statistical differences between the two groups.
Sexual variation between male (blue) and female (red) birds
One thing I was most looking forward to testing was if there were any differences between different flight modes. Birds that fly in different ways having different body set ups with slightly different morphological adaptations, like longer, more slender wings for birds that soar. But are their skeletons built differently? For example, do birds that spend more time on ground, so-called 'burst-adapted' birds like pheasants and ptarmigans, have more robust skeletons that are maybe less 'light-weight' than traditional bird skeletons? Well at least between the 3 main flight modes we tested (soaring, continuous-flapping, and flap-gliding), they are not different. Unfortunately, we didn't have a large enough sample size of burst-adapted flyers to see if they were statistically different. I'd like to look at this more as my hunch is they will be different. I'd also be interested in seeing how passerines would be different, as passerines use a type of flying that is referred to as intermittent-bounding, where they kind of hop through the air with intermittent periods of flapping and not. Our new data set didn't have any passerines in it, which is fairly uncommon since they make up a large number of modern bird species.
Different flight modes - blue = soaring, red = flap-gliding, green = continuous flapping.
But why is this important? Well going back to the original question about mass estimation, we found that these results were correlated with phylogeny. This means that for a group of modern birds, like Neornithes, this relationship holds true. However, as you move further from this group, the relationship is going to be less and less supported. So moving into groups with no modern representatives like enantiornithine birds, which are significantly different from modern birds, or non-avian theropod dinosaurs, this relationship is going to be less accurate. Finally, moving all the way to pterosaurs, which are the sister group to dinosaurs, this relationship may not yield an accurate result, which is something that we hinted to in my first paper on pterosaur bone mass estimation [4].

I think that using the more traditional methods of volumetric mass estimation is likely to be more accurate for pterosaurs, for this reason, rather than using skeletal correlates as is becoming more common. Unfortunately, that requires more complete skeletons and a lot more work. Pterosaurs have no modern analogues or close relatives, suggesting that skeletal correlates are not going to work. Jon Tennant wrote a great post on this paper as well over at PLOS Paleo if you want to take a look!

Another thing I'd like to point it is the dataset we used. Gary Kaiser and Carl Jonsson collected a large amount of data on these specimens, including measurements of various skeletal elements, most of which we didn't use in this study. We know that a lot more information can be used from this dataset and many more interesting studies can use it, and we have posted the data up on the PLOS One website as supplementary material. We hope that someone can use the data for more in-depth studies like this! Please share if you know someone who could use it!

1. Prange HD et al. 1979. Scaling of skeletal mass to body mass in birds and mammals. American Naturalist 113: 103-122.
2. Witton MP. 2008. A new approach to determining pterosaur body mass an its implications for pterosaur flight. ZittelianaB 28: 143-158.
3. Martin-Silverstone E, Vincze O, McCann R, Jonsson CHW, Palmer C, Kaiser G, Dyke G. 2015. Exploring the relationship between skeletal mass and total body mass in birds. PLOS ONE 10: e0141794.
4. Martin EG and Palmer C. 2014. A novel method of estimating pterosaur skeletal mass using computed tomography scans. Journal of Vertebrate Paleontology 34: 1466-1469.