Thursday, 24 October 2013

Preprint For Accepted Papers

It has finally happened. My first paper has been accepted! Look forward to seeing "A novel method of estimating pterosaur bone mass using computed tomography scans" published in the Journal of Vertebrate Palaeontology sometime next year. *sigh* I was (perhaps naively) hoping for the paper to be published soon, but hey, it's now officially "In Press", which means I can put it on my CV! Super excited about that.

I'm thinking about putting it somewhere on a preprint server like PeerJ, or ArXiv. Does anyone have any advice about this? Or know anything about it? If a paper has been accepted, and copy edited, but isn't going to be officially published for a while, is it ok to put it somewhere like this? Do journals have policies against this? I'd appreciate any information or advice, because I'm not sure what I should do! I need to run any ideas past the other author as well, but I wanted to have all the info first.

EDIT: Since posting this, I have found out that preprint is not an option for JVP. Unfortunately, it looks like I'm just going to have to wait and get it out there the old fashioned way instead. I'm a bit annoyed that the journal says the average time from acceptance to publication is 3 months on their website, but since being accepted, I have been told it's more like 8 months. Gr.

BUT because I can, here it is:
Martin, E. G., and Palmer, C. In Press. A novel method of estimating pterosaur bone mass using computed tomography scans. Journal of Vertebrate Paleontology.

EDIT 2: Since I'm not allowed to put it online anywhere and it won't be published for a while, here is the abstract for a talk I gave on the same topic at SVPCA 2012. If anyone wants to know more about it, let me know!

A novel approach to estimating pterosaur bone mass using CT scans 
Elizabeth Martin & Colin Palmer 
University of Bristol 

Body mass estimation in extinct animals can provide information about ecology and biomechanics of the animal and is vital for flying animals as it determines its ability to take off, land, and indeed, fly. However, existing mass estimation methods for pterosaurs produce a wide range of values, especially in the larger animals. This hinders our understanding of their flight capabilities and indicates a need for a more accurate method for estimating body mass. A novel approach has been developed that uses CT scans of pterosaur wing bones to determine the volume of bone material and thus the bone mass. Results show much larger masses for some bones than previous methods, which indicates that a reassessment of methods for estimating total mass in pterosaurs is required. 

Sunday, 15 September 2013

The Amazing Galapagos

This is a little bit late, but life has taken over for the last month and a half and I haven't had a chance to write. So finally, here it is: my amazing trip to the Galapagos. 

First, some background and history on the Galapagos. The Galapagos Islands are a chain of volcanic islands about 1000 km off the coast of Ecuador, in the Pacific Ocean. The islands are part of Ecuador, and were made famous when Charles Darwin, the English naturalist travelled there. In 1831-1832, he joined a voyage on the HMS Beagle, which brought him to the Galapagos Islands, where his studies of the plants and animals, and especially the finches, led to his theory of natural selection in his 1859 book "On the Origin of Species".

Now, our amazing trip. The majority of the islands are uninhabited, and protected. This means that there are no cars, hotels, or anything on most of the islands; just nature. Each day, the cruise ship we were on was anchored at sea, and we took boats of 16 to the island we were seeing. We had a morning island visit, then back to the ship for lunch, then another excursion in the afternoon.
Map of the Galapagos Islands
Highlights: Espanola Island
What a cutie! Sleeping Galapagos sea lion (Image by Liz Martin)
Our first day on the islands was a truly amazing experience. We started at Gardner Bay, on Espanola Island, which is a very calm bay, with hundreds of sea lions. As there are no natural land predators on the islands, and the animals are well protected, they have little reason to fear people. As such, they are often very curious, especially the sea lions. When you get on the islands, you're supposed to stay far away from the animals, but this can be hard with the sea lions, especially the young ones, as they are extremely friendly and curious. They will walk right up to you, and chase you around, and as long as they aren't the bull males, they are relatively harmless. The Galapagos sea lion (Zalophus wollebaeki) breeds almost exclusively on the Galapagos Islands, but also on another single Ecuadorian island, and they are found throughout the Galapagos. We wandered around the bay for an hour or so, watching the sea lions, and also got our first view of marine iguanas. After walking, we got to go snorkelling for the first time, which was absolutely amazing. If I thought sea lions were friendly on land, I was in for a surprise for what happened in the water. The sea lions will swim right up to you, even at your face, and at the last minute they turn and swim underneath you. They have so much fun with people in the water, it was absolutely amazing. Definitely one of my favourite experiences on the trip.

The afternoon excursion was also a big highlight for me. We went on a long hike, and saw numerous animals. First, there were hundreds of marine iguanas, which I will talk about later. The main highlight of the afternoon for me was Punta Suarez, where many bird species nest. We saw the amazing blue-footed boobies (which are common throughout the Galapagos), Nazca boobies, Galapagos hawks, and my favourite, waved albatrosses. This was the only time we saw albatrosses, and they truly were magnificent. The waved albatross (Phoebastria irrorata) are basically endemic to the Galapagos, although there are a few pairs that nest on the Ecuadorian Island of Isla de la Plata. We were fortunate enough to witness their courtship behaviours, which consists of a bizarre dance where they repeat their movements over and over while they rock back and forth, stick their heads down to the ground, open their beaks wide, and more. When they finally choose a mate, waved albatrosses mate for life. We also got to see one albatross take off, which was a bit awkward, as these animals are fairly large, with a wingspan of about 2.3 m, and they do a kind of waddling/running take off. I sat for as long as I could watching them soar over the cliff. I spent a lot of time imagining them as pterosaurs (of course), and they were absolutely majestic. It was very hard to leave this place
Part of a waved albatross mating dance. Image by Liz Martin
Highlights: Floreana Island
A frigatebird with a baby turtle in its mouth. Photo by Liz Martin
The morning of Floreana Island started out with a walk to a bay. When we looked into the water, we realised that this bay was full of stingrays. We could stand at the end of the water and the waves would bring them towards us, as many as 10, just sitting in the water. The other interesting thing on this bay was that there was a green sea turtle nest. We weren't able to go up to the nesting site as it is off limits, but we could see the tracks from where the females had gone up and laid the eggs. Green sea turtles (Chelonia mydas) are known from both the Pacific and Atlantic oceans, and they lay clutches of 70-100 eggs. This nest had apparently recently hatched, as we knew there were many baby sea turtles, trying to get out of this nest. How did we know this if we couldn't see them? Well, we had the very fortunate/unfortunate (depending on who you ask) sight of a frigatebird swooping down and trying to eat these baby turtles. We watched several attempts, as it would swoop down, miss, and go back up, circling until it would try again. Finally, we watched as it managed to pick up one baby turtle, and fly away. As sad as it was for the turtle, it was a perfect example of "the circle of life", and just shows why they lay so many eggs. We were told that of 100 eggs, only 10 would successfully make it to the water, and of those 10, only 2-3 would survive until maturity. After that, we got to go snorkelling again, where we swam with a sea turtle!

Highlights: Isabela Island
Note the small vestigial wings on the flightless cormorant.
 Photo by Liz Martin
Isabela Island is the largest island in the Galapagos. It is formed from five separate volcanoes, all but one still active, and much of our walk was over old lava flows. Here we saw flamingoes, more blue-footed boobies, flightless cormorants, marine iguanas, and sea lions. No one really knows how the flamingoes on the Galapagos got there, as they are not strong flyers, and the islands are 1000 km from the mainland. There are only about  500 nesting pairs here. In a small in-land lagoon, we also saw some white-tipped reef sharks, which had come in through an underground system of cracks through the lava. The main highlight for me was the flightless cormorants, the only truly aquatic, flightless bird other than penguins. While penguins have evolved flipper-like wings to "fly" underwater, the flightless cormorant (Phalacrocorax harrisi) has extremely reduced wings and extensively webbed and powerful feet. These vestigial wings are used only to assist in balancing while they hop around rocks, while they propel through the water with their feet. This species is found only on the Galapagos Islands. We also got our first view of the Galapagos penguin (Spheniscus mendiculus), the northernmost species of penguin.
Galapagos penguin. Photo by Josh Silverstone
In the afternoon, we got to see our first glimpse of both the land iguanas, and giant tortoises. While marine iguanas are black, land iguanas (Conolophus subcristatus) are brightly coloured. Different islands have different subspecies with different sizes and colours, but they are primarily yellow, red, and orange.
A land iguana. Photo by Liz Martin
Highlights: Fernandina and Isabela Islands
One of the many "piles" of marine iguanas we encountered.
Photo by Liz Martin.
At Fernandina, we saw another large colony of marine iguanas. Marine iguanas are very interesting. The marine iguana (Amblyrhynchus cristatus) is endemic to the Galapagos, and is the only truly marine lizard in the world. They are black, in order to better take in the sunlight to allow them to warm up. They feed solely in the water on algae, and spend about half an hour a day diving into the water to feed, and the rest of the day basking in the sun to warm up from the cold water. To help with warming up, they are normally found in large clusters, sometimes with hundreds of iguanas in one place. We also stumbled upon several bones: a reconstructed whale skeleton with a dolphin skull, and some sea lion skulls, which of course I had great fun inspecting. After the walk, I got to partake in a deep water snorkel, where we saw some more sea turtles, fish, and numerous invertebrates along the coast.

Off the cost of Isabela for the first and only time, we saw a fur seal! Unfortunately, I don't have a great picture of it, but we watched a mother and young fur seal playing with the zodiac. The Galapagos fur seal (Arctocephalus galapagoensis) is endemic to the Galapagos, and is the smallest of the fur seals. They are currently endangered, as they were nearly hunted to extinction in the past.

Highlights: Santa Cruz Island
A dome-shaped giant tortoise in the wild. Photo by Liz Martin
On our last day, we spent time on the populated island of Santa Cruz. First, we went to the Charles Darwin Research Station, where they focus on breeding tortoises, and numerous other research projects to help protect the life in the Galapagos. We also got to go to the highlands, where we were able to see giant tortoises in the wild. The giant tortoise (Geochelone elephantopus) is found on a few tropical islands in the world, and as many as 11 subspecies exist in the Galapagos, with different subspecies on different islands or regions of islands. These subspecies and populations have little to no interaction with each other, and are morphologically distinct, with many people believing they are on their way to becoming separate species. Already, there are two distinct morphotypes: saddle-back, and dome-shaped shells. Unfortunately, many of the subspecies are in decline or have become extinct, which is why the Charles Darwin Research Station is focusing much of their efforts on tortoise conservation.
Lava lizard from Espanola island. Photo by Liz Martin

Other highlights
Being on the Galapagos in general was absolutely amazing, and there were a few things that I can't pick as being a specific highlight of a day or island. Mainly, these include some great examples of evolution and adaptation. There are seven species of endemic lava lizards in the Galapagos, with one species present on 10 islands, and the other 6 being restricted to single islands. They are generally very colourful, with females being more colourful than males, and differ morphologically from island to island.
Some of Darwin's finches. Photo by Liz Martin

Of course as a biologist, seeing Darwin's finches was always amazing. Unfortunately, I'm not able to identify them at all, but was able to see the slight differences in beaks that lead Darwin to his theory of natural selection. They are spread throughout the islands, with 13 species in total.

Swimming blue-footed booby. Photo by Liz Martin
And finally, although I won't talk about them in detail because there are discussed quite heavily in many aspects of biology, seeing blue-footed boobies was of course great. We were fortunate enough to see one of their famous mating dances, watch them fly, dive into the water to feed, and swim along the surface. These birds are truly magnificent, and their feet really are bright blue!

Blue-footed booby. Photo by Liz Martin
The biggest highlight of all was just being on these islands, barely touched and disturbed by humans, and seeing the nature first hand. Seeing the different populations of animals on different islands, and how these animals differ and adapt from island to island was amazing. Even the plants have adapted to different pressures, responding to birds that feed on their leaves. I would highly recommend to anyone, especially anyone interested in evolutionary biology to take advantage if they ever get a chance to go there. I hope you've enjoyed my account of my trip, and more importantly, that you've learned something you didn't know before!

Background info:
While some of the information in this post came from the book Galapagos Wildlife by David Horwell and Pete Oxford, most of it actually came from the brilliant guides we had along the way. The naturalists really know what they're talking about, and they were a never-ending source of information about the islands, the wildlife, and more! Thanks to them for teaching me what they knew.

Saturday, 18 May 2013

PhD at Southampton!

I have some great news! Just over a week ago, I went to Southampton for a PhD interview for a project on mass estimation in pterosaurs. That weekend, I was offered the project and some funding, which I officially accepted on Friday. I will start sometime at the beginning of October, and will be moving to Southampton probably in September. I'm really excited about it as I get to do some work that was directly related to some cool stuff I found in my Master's!

The project will be supervised by a combination of Bristol and Southampton supervisors, with Gareth Dyke being the main supervisor. As the project will rely heavily on CT scans, we're hoping to take advantage of the excellent CT scanner that Southampton has, and I've managed to secure access to a few specimens already for scanning. It will expand on what I did for my MSc with Colin Palmer (who will be involved in the PhD as well), which was developing a method of estimating bone mass using CT scans, which resulted in some pretty interesting finds. The masses for the bones we measured were about twice as heavy as what previous methods had found, which is very interesting. That paper is currently in review, and we are confident that it will be successful!

This PhD will expand on the MSc work by looking at more bones, and more importantly, more groups and taxa of pterosaurs. This way, we should be able to gain some insight into the bone mass of several different animals, but also how this may be related to phylogeny, and how bone and body mass may have evolved throughout the Pterosauria. Once bone mass has been determined, I am hoping to apply some modelling techniques to get an idea of soft tissue mass, using some of the muscular reconstructions in the literature.

All-in-all, I think I will be very busy for the next few years, learning all about pterosaur bones and mass. I'm really excited that I have finally sorted out a PhD, and that it's doing something that I am very interested in! Stay tuned for more details coming soon :)

Sunday, 21 April 2013

Projects Galore

Apparently it has been 2 months since I last wrote a post, so I figured I should give a bit of an update on what's going on with me. In short: a lot. I have been so busy in the last month and will continue to be until I head back to Canada in June. So, what is keeping me busy you ask?

1. I'm still in the process of trying to get my first publication. I've heard that the first publication is always the hardest (although I'm not sure any of them are "easy"), but I just want this thing done! I have just spent the weekend re-formatting it to submit to a different journal than we originally aimed for, and adding some things to make it better, and we should be submitting it sometime soon. I really want to get this thing out! Stay tuned!

2. With some help and encouragement from Matt Wedel, I've decided to try to do some Air-Space Proportion work on the pterosaur bones that I have scans for. On the plus side, I already have all the information that I need, and I just need to convert the numbers. I've now done this for all the bones I've already analysed, and I need to do it on a few more partial bones that I have scans from (thanks to my supervisor Colin Palmer) but not analysed. The preliminary work is showing some pretty interesting stuff with some things coming out as completely different from what you might expect. I'm also hoping to take a look at some pigeon CT scans to compare them to. My goal is to work on this as much as possible and present it at SVPCA in Edinburgh in August. Exciting stuff!

3. I'm also still working on a paper from my undergrad thesis on Centrosaurus, which I'm hoping will be getting there soon. I spent about a month working on a matrix on mainly centrosaurines, and have been waiting to hear back from my undergrad supervisor about it. I heard a few weeks ago that he was doing some unrelated analyses using my matrix, to see if it worked, which is exciting. In the meantime, I'm planning on presenting this work in a poster at the Progressive Palaeontology conference in Leeds next month. Finally something to show from this project!

4. And finally (project wise), the project that has been taking up most of my time is the one that I can say the least about. I'm currently doing some really interesting work on some tiny fissure fossils from Wales. It's pretty neat, but I can't really talk about it much yet. If we get enough done, I just might present this at PalAss in Zurich in December!

5. I'm also preparing for a PhD interview at Southampton which will take place next month. I'm extremely nervous about it, and I'm not sure what to do for preparation. Eek!

All-in-all, lots going on for me! I'm hoping that I'll be able to get a few papers out of these various projects, which will be really interesting and exciting!

Thursday, 14 February 2013

Making Data Public (and a small matrix-related rant)

In the world where there is a constant debate over the merits and disadvantages of Open Access journals and science, we are often bombarded with blogs and posts about it. I am generally a silent proponent of Open Access journals, agreeing that it is important, but not particularly versed in all of the politics so I tend to keep quiet. That being said, I have recently stumbled upon a related issue that has affected me in the last few weeks: the importance of making your data public.

Although my primary research interest is in pterosaurs, I am currently writing up a manuscript from my undergraduate thesis, which was on the ceratopsian dinosaur Centrosaurus. Much to my surprise, the most recent discussion with my former supervisor (and the senior/co-author) went in a different direction than I was expecting: he wanted me to develop a character matrix and do a phylogenetic analysis. Now I've never done this before, although I've taken several courses and have a good basic understanding of the concept, I've never actually developed a matrix and done my own analysis. Upon discussion with him, we decided that I would use several published matrices and merge them together, taking several characters from each matrix.

Looking through recently published matrices, I came across the Farke et al. (2011) paper in which Spinops sternbergorum was described. I sent him an email, and he was very happy to share the matrix, and character descriptions (although those are available from the supplementary information of the paper) and he sent along the .nex file. Super helpful, because then I had it already in a matrix that I could open, copy, paste, edit, etc. Thanks so much for that Andy! Then, I had to add some taxa that were published more recently, like Xenoceratops foremostensis (Ryan et al. 2012), and Pachyrhinosaurus perotorum (Fiorillo and Tykoski 2012). The Xenoceratops matrix was published directly in the paper as a table (not as easy to follow the correct character number, but available), while P. perotorum was found in the supplementary material (in a more easily viewable format). The best, however, came when I looked up a paper on Anchiceratops (Mallon et al. 2011). On the downside, the paper is published in a non-open access journal, which means not everyone can access it. On the BIG upside, included in the supplementary material is the actual .nex matrix file which allows you to see all the characters, states, and taxa, right in the format you want. It makes it soooo much easier to access and much quicker when these are available at your finger tips, without having to send many emails to people asking for it. There are several other (mainly older to be fair) phylogenetic papers that don't post the matrix, or characters used, which makes it really difficult to figure out how they've done things.

Unrelated to my story, and covered much in other places so I won't cover it in detail here, is a wonderful story of a recent publication that used previously published data in a huge analysis. Larson and Currie (2013) were able to study over 1000 small theropod teeth from southern Alberta, using data that had previously been published and new data. A study of this scale would clearly have taken a lot longer if they had to do sit down and do all the measurements on 1183 small teeth. Fortunately for them, (and us), they were able to spend their time analysing the data already available, rather than painstakingly measuring them. They determined that the number of small theropods present from this area has been greatly underestimated, and that many species are known only from teeth. Cool! For more information, you can check out this blog by Jon Tennant.

Take home message: make your data open to everyone! For the most part, I have dealt with people who are extremely open and willing to email me stuff if it isn't posted. But wouldn't it be better if you didn't have to email every time? If you could just go online and access it? It shouldn't be some top-secret information. Post it!

And finally, a small rant on matrices. I know that there are disagreements about characters, so not every published matrix is going to use exactly the same characters, but WHY do people insist on changing character states around in a way that just makes things difficult?? For example, there are several characters in Fiorillo and Tykoski (2012) that are just different enough from all other matrices I've looked at that you can't just directly copy the states. Why is it necessary to switch it from the postorbital horncore height being compared to the basal skull length (which every paper does) to comparing it to the length of the face? Or change numbers slightly so one one paper a character is considered to be long if it's 0.8 or more, while in another it's 0.75? Pretty sure that is unnecessary! Make it easy, people!

Farke, A.A. et al. 2011. A new centrosaurine from the Late Cretaceous of Alberta, Canada, and the evolution of parietal ornamentation in horned dinosaurs. Acta Palaeontologica Polonica 56: 691-702. Freely accessible here.
Fiorillo, A.R. and Tykoski, R.S. 2012. A new Maastrichtian species of the centrosaurine ceratopsid Pachyrhinosaurus from the North Slope of Alaska. Acta Palaeontologica Polonica 57: 561-573. Freely accessible here.
Larson, D.W., and Currie, P.J. 2013. Multivariate analyses of small theropod dinosaur teeth and implications of paleoecological turnover through time. PLoS ONE 8: e54329. Freely accessible here.
Mallon, J.C., et al. 2011. Variation in the skull of Anchiceratops (Dinosauria, Ceratopsidae) from the Horseshoe Canyon Formation (Upper Cretaceous) of Alberta. Journal of Vertebrate Paleontology 31: 1047-1071.
Ryan, M.J., et al. 2012. A new ceratopsid from the Foremost Formation (middle Campanian) of Alberta. Canadian Journal of Earth Sciences 49: 1251-1262.

Sunday, 3 February 2013

Moving up in the world!

I have news! I have now officially graduated from my Masters! I now have a Masters with Distinction! Hurrah! Since graduating, I've also submitted my PhD application for a PhD at the University of Southampton. I'm super excited about this, as the project will be a continuation of my project at Bristol looking at body mass of pterosaurs. Now I just have to wait to hear from them about an interview, which I've been told should be sometime in March. Now I will start preparing for my interview. I've never done an academic interview before, so any suggestions would be greatly appreciated!

Next on my list is to get some publications done. I have (again) sent my pterosaur manuscript to my MSc supervisor to edit. I'm really confident that it's nearly ready to submit. I think I've addressed the major issues that it had, and hopefully will be sending it in shortly. Unfortunately, in addressing these issues, it has gained too many words and it's now over the word limit. Now I'm not sure what to do! I'm also still working on a Centrosaurus paper that I've been working on since my undergrad. I just have to do a phylogenetic analysis and it'll be done. Oh ya, and re-write a bunch of stuff. In a couple of months though, I could have not one, but two publications! Just need to focus for the next few weeks!

Friday, 18 January 2013

Flying things that lived a long time ago

Inspired by an awesome XKCD comic, this is what I study using only the thousand most common English words. Well, it's more of a description of the animals, but it's still entertaining. I'll work on it and get a better one later, but this is the start: 

I study flying animals that died a really long time ago. They are cold blooded animals and had some hair-like covering but lots of skin. They flew using a really long finger and skin that went from the end of the finger to their legs. They moved their arms up and down to push against the air and fly. These animals were the biggest flying animals ever, some as big as a bus, but others were small. Some had lots of teeth that they used to catch food, but others had no teeth and ate animals that live in water whole. I look at pictures of their inside hard body parts to guess how heavy they were. This can tell us if they would have been too heavy to fly, and how they could fly. Did they use their power to fly? Or just put their arms out and let the air push them? We can look at animals that live today to better understand animals that lived a long time ago.

If anyone wants to give it a go, try it out here!