Year in review 2016

2016 was best described as a busy year. It started incredibly well with 4 publications in the first four months starting off in January with my first publication on a fossil I found:

Halliday TJD, Cuff AR, Prasad GVR, Thanglemmoi MS, Goswami A, 2016. New record of Egertonia (Phyllodontidae, Elopiformes) from the Late Cretaceous of South India. Papers in Palaeontology. DOI: 10.1002/spp2.1040. Paper link, blog.

The following month the PhD student on the project, Marcela Randau, published the first of her papers on the vertebral column of cats:

Randau M, Goswami A, Hutchinson JR, Cuff AR, Pierce SE. 2016. Cryptic complexity in felid vertebral evolution: shape differentiation and allometry of the axial skeleton. Biological Journal of Linnean Society. DOI: 10.1111/zoj.12403. Paper link, blog.

The early part of they year would also involve various efforts in the field with different cat species as a student and I attempted to gather force plate data (with varying levels of success).

March was a slow publishing month, but April was to be a double whammy with both the papers on cat muscle scaling across the postcrania:

Cuff AR, Sparkes EL, Randau M, Pierce SE, Kitchener AR, Gosawmi A, Hutchinson JR, 2016. The scaling of postcranial muscles in cats (Felidae) I: forelimb, cervical and thoracic muscles. Journal of Anatomy 229, 128-141. Paper link, blog

Cuff AR, Sparkes EL,Randau M, Pierce SE, Kitchener AR, Gosawmi A, Hutchinson JR, 2016. The scaling of postcranial muscles in cats (Felidae) II: hindlimb and lumbosacral muscles. Journal of Anatomy 229, 142-152. Paper link, blog

Also in April I joined Anjali (as well as Ryan and Carla from the lab) on another trip to Argentina where we joined up with our Argentinian colleagues for continued explorations of the Salta area looking for more fossils. It was a largely unproductive trip in terms of finding many new fossil locales, but we did rule out large areas, revisited the site I discovered previously and found another very promising site. Hopefully Anjali is successful with a large grant that would allow for a longer term exploration of the area with a bigger crew.

April was to be the final month of publishing for a while, but in May my blog passed the 10,000 view mark (or at least as far as blogger's tally count goes) so at least that publishing kept going strong. 

At the end of June and into early July I attended the International Congress of Vertebrate Mophology - ICVM. It was another fabulous conference with an abundance of cool science. It made up for not being able to make SVP this year, the first time I haven't attended in 6 years. In years gone by I've heard stories of the attendees who haven't missed on in 40+ years. Guess that won't be me!

The summer would lead to publishing my two most popular blog posts of all times, the first on why extraordinary claims need extraordinary evidence (still surprised there haven't been many comments on it), and the second on some of my favourite figures from palaeontological papers. Both posts got over a thousand hits in their first month which no other posts before or since have matched.

August was a particularly crazy month as I was expecting to be unemployed when September got around. Applications had gone into various places with a fair few rejections before interview, one failed interview (although a friend got the job so can't be too upset about it), and eventually an interview at RVC which was successful in getting me three more months employment as a technician whilst searching for something longer term.

In September I started my technician role, and whilst filling in the paperwork to start was invited to interview for postdoc on John's massive European Research Council (ERC) grant looking at the evolution of pseudosuchians (the crocodile line), and dinosaurs in the Triassic. After a tricky interview and encountering what I now think is a brilliant question on who I would invite to a symposium about the project (although hated it at the time as I blanked on names), I would eventually be offered the position which I gladly accepted. I would be returning to dinosaurs in December, learning some new techniques, and having a couple more years at the RVC.

After a six month hiatus, October would bring the next publication with Marcela again publishing on felid vertebral columns and her kindly writing a blog post for me becoming the first guest blogger on my site.

Randau M, Cuff AR, Hutchinson JR, Pierce SE, Goswami A. 2016. Regional differentiation of felid vertebral column evolution: a study of 3D shape trajectories.Organisms, Diversity & Evolution

DOI 10.1007/s13127-016-0304-4. Paper link, blog

November would result in my paper on felid brains (in combination with Anjali and our summer student/Imperial Uni undergrad) being accepted, and at present it has a DOI, but we are awaiting proofs before it gets published fully. I was hoping it would be fully online before the end of the year to count as published in 2016 and take my final total up to 6 for the year but it has not made it. At the start of the year I had hoped for 7-10 papers to be published this year. The 2 papers in review (one should be accepted after this round), a few failed projects (like digital image correlation on cat bones) and collaborations that are completed from my end, but not submitted are where I fell short. All of these should add to the expectation of at least 5 more by the end of 2017.

Ultimately December would bring the start of my second postdoctorate on the ERC project (expect many, many posts over the next few years on it), as well as leaving the UK for a much needed 3 week break having not had time off since Easter and feeling exhausted from work.

Across the year I have been practicing what I preach in regards to reviewing papers, with 12 reviews completed for 5 papers across 6 journals (one I got for 2 different journals when it wasn't deemed suitable for the first journal). Somewhat crazily, I have accepted another review across the Christmas holidays, so will be reviewing another one early in 2017.

It has been another good year for me, although maybe not so much politically for science in the UK with Brexit threatening large amounts of funding and collaborations. It shall be interesting to see where things go and I live in the optimistic (and probably vain) hope that it is not the doom and gloom we all fear,

A final amazing figure for the year from an undergraduate research project at Leicester (and a great example of how to get students thinking about science at all levels). I have to say I have nothing to do with the research, but it is a fun studying into whether the satellite phone swallowed by the Spinosaurus in Jurassic Park 3 could really have been heard by the main characters.

Childs et al., 2016. Dinosaur in-dial-gestion. Journal of Physics Special Topics.
Fig 1. A rough model of the path travelled by the sound, with Z-values from the literature.

Happy New Years and best wishes to all for 2017!

The cat's backs - a guest post

Two papers recently have come out that I have been involved in, and am thankful to Marcela Randau (the primary author) for giving up time between finishing a PhD, postdoc hunting and preparing for lecturing to write this post. If anyone reads whatsinjohnsfreezer.com regularly, you will see an identical post there as Marcela, understandably, didn't have time to write two similar but different posts for us both as we clambered for her expertise in felid vertebral columns.

The cat’s back.

by Marcela Randau (m.randau@ucl.ac.uk)

It is often said that all cats are very similar in terms of their skeletal morphology (“a cat is a cat is a cat”). But is this really the case? It may be if only gross, qualitative anatomy is taken into consideration, i.e., if you just eyeball the skeletons of tigers and lions you might find yourself not knowing which one is which. But with huge advances in technology that allows for extracting detailed shape information off a structure (e.g., a skull) and for analysing this information (‘Geometric Morphometrics’), it has become more and more possible to distinguish between relatively similar forms – which may be from distinct species, separate sexes, or even just different populations of the same taxon.

And it is reasonable to think that cat skeletons might be a lot more different than what meets the eye, as for a lineage of apparently similarly built animals, with not that much variation in diet (all cats are hypercarnivores) there is substantial variation in body mass (over 300-fold just in living species!) and in ecology across cat species. From the cursorial cheetah to the arboreal clouded leopard, felids present a wide range of locomotory adaptations. Yes, all cats can climb, but some do it better than others: think lion versus margay (yes, they do descend trees head-first). As hypercarnivores, all cats are meat specialists, but they also change with regards to how big their prey is, with a general and sometimes-not-so-black-and-white three-tier classification into small, mixed and large prey specialists. The rule of thumb is ‘if you are lighter than ~20-25kg, hunt small stuff. If you are heavier than that, hunt BIG BIG things, much bigger than yourself. And if you are in the middle ground, hunt some small-ish things, some big-ish things, and things about your size. Well, -ish’ – their prey size preference has a lot to do with energetic constraints (have a look at Carbone et al. 1999; and Carbone et al. 2007, if you're interested in this). But the fun bit here is that form sometimes correlates quite strongly with function, so we should be able to find differences in some of their bones that carry this ecological signal.

Indeed, for a while now, we have known that the shape of the skull and limbs of felids can tell us a lot about how they move and how big their prey is (Meachen-Samuels and Van Valkenburgh 2009, 2009), but a large proportion of their skeleton has been largely ignored: we don’t know half as much about ecomorphology and evolution of the vertebral column. Well, it was time we changed this a bit! As the PhD student in the Leverhulme-funded ‘Walking the cat back’ (or more informally, “Team Cat”) project, I’ve spend a big chunk of my first two years travelling around the world (well, ok, mainly to several locations in the USA) carrying a heavy pellet case containing my working tool, a Microscribe, to collect 3-D landmarks (Fig. 1) across the presacral vertebral column of several cat species. And some of first results are just out! Check them out by reading our latest paper, “Regional differentiation of felid vertebral column evolution: a study of 3D shape trajectories” in the Organisms Diversity and Evolution journal (Randau, Cuff, et al. 2016).

Fig. 1: Different vertebral morphologies and their respective three-dimensional landmarks. Vertebral images are from CT scans of Acinonyx jubatus (Cheetah, USNM 520539).

Building from results based on our linear vertebral data from the beginning of the year (Randau, Goswami, et al. 2016), the 3-D vertebral coordinates carry a lot more information and we were able to describe how this complex shape-function relationship takes place throughout the axial skeleton (in cats at least) in much better detail than our prior study did. One of the difficulties in studying serial structures such as the vertebral column is that some clades present variation in vertebral count which makes it less straightforward to compare individual vertebrae or regions across species. However, mammals are relatively strongly constrained in vertebral count, and Felidae (cats; living and known fossils) show no variation at all, having 27 presacral vertebrae. So adaptation of the axial skeleton in mammals has been suggested to happen by modification of shape rather than changes in vertebral number.

Using a variety of geometric morphometric analyses, under a phylogenetically informative methodology, we have shown that there is clear shape and functional regionalisation across the vertebral column, with vertebrae forming clusters that share similar signal. Most interestingly, the big picture of these results is a neck region which is either very conservative in shape, or is under much stronger constraints preventing it from responding to direct evolutionary pressures, contrasting with the ‘posteriormost’ post-diaphragmatic tenth thoracic (T10) to last lumbar (L7) vertebral region, which show the strongest ecological correlations.

We were able to analyse shape change through functional vertebral regions, rather than individual vertebrae alone, by making a novel application of a technique called the ‘Phenotypic Trajectory Analysis’, and demonstrated that the direction of vertebral shape trajectories in the morphospace changes considerably between both prey size and locomotory ecomorphs in cats, but that the amount of change in each group was the same. It was again in this T10-L7 region that ecological groups differed the most in vertebral shape trajectories (Fig. 2)

Figure 2: Phenotypic trajectory analysis (PTA) of vertebrae in the T10 – L7 region grouped by prey size (A) and locomotory (B) categories.

So in the postcranial morphology of cats can be distinguished, changing its anatomy in order to accommodate the different lifestyles we see across species. But the distinct parts of this structure respond to selection differently. The next step is figuring out how that might happen and we are working on it.

While Team Cat continues to investigate other biomechanical and evolutionary aspects of postcranial morphology in this interesting family, we’ve been able to discuss some of these and other results in a recent outreach event organised by the University College of London Grant Museum of Zoology and The Royal Veterinary College. We called it “Wild Cats Uncovered: movement evolves”. Check how it went here: (https://blogs.ucl.ac.uk/museums/2016/11/17/cheetah-post-mortem/) and here (http://www.rvc.ac.uk/research/research-centres-and-facilities/structure-and-motion/news/wild-cats-uncovered), with even more pics here (https://www.flickr.com/photos/144824896@N07/sets/72157676695634065/ ).

References used here:

Carbone, C., Mace, G. M., Roberts, S. C., and Macdonald, D. W. 1999. Energetic constaints on the diet of terrestrial carnivores. Nature 402:286-288.

Carbone, C., Teacher, A., and Rowcliffe, J. M. 2007. The costs of carnivory. PLoS biology 5 (2):e22.

Meachen-Samuels, J. and Van Valkenburgh, B. 2009. Craniodental indicators of prey size preference in the Felidae. Biol J Linn Soc 96 (4):784-799.

———. 2009. Forelimb indicators of prey-size preference in the Felidae. Journal of morphology 270 (6):729-744.

Randau, M., Cuff, A. R., Hutchinson, J. R., Pierce, S. E., and Goswami, A. 2016. Regional differentiation of felid vertebral column evolution: a study of 3D shape trajectories. Organisms Diversity and Evolution Online First.

Randau, M., Goswami, A., Hutchinson, J. R., Cuff, A. R., and Pierce, S. E. 2016. Cryptic complexity in felid vertebral evolution: shape differentiation and allometry of the axial skeleton. Zoological Journal of the Linnean Society 178 (1):183-202.

11/11/2016

This post has a cryptic date as a title, but it signifies that two years from the blog's inception, I am still here and people are still reading it. I've never really gone into why the blog started and credit/blame goes to John Hutchinson at the RVC who, at one of his weekly team meetings, was talking about our online presence and encouraged us to get a researchgate and academia profile, as well as twitter and consider starting a blog. I have always enjoyed outreach so the blog was an obvious step, although I haven't always enjoyed writing and it is the one thing I struggle with most when it comes to my own research.

My blog started with a simple post on a SVP conference I had just attended in Berlin and it was a simple starting point for me. I enjoy conferences to meet and mingle with people and talk science, and I was expecting the Berlin SVP to be the last one I attended for a while as my work was looking mainly at modern species. That turned out to not be the case as I attended last year having managed to work on scaling of extinct cats. This year I didn't make SVP as I was finishing my contract with UCL and starting a short-term technician role at the RVC and there were no travel funds, but I managed to attend the very amazing ICVM in July instead. It is still a bit weird for me going to conferences and people knowing your name from work you've done.

The blog has developed covering topics such as my postdoc research, and stuff on ornithomimosaurs - the group of dinosaurs I did my PhD on. I even ventured out of my comfort zone of the strictly scientific into a bit of historical things on how cats and human interactions have evolved and changed through time. It was an eclectic mix of topics as I was finding a direction for the blog. To be honest, the blog remains an eclectic mix of topics as it covers things I am interested in and working on.

I've also spent a lot of time talking about my publications. It helps that I had a productive few years in my first postdoctorate in terms of publications with 8 papers in the last 2 years, 2 in review, 1 about to be submitted, and about 5 more in the works across various collaborations. However, I make a particular effort with the blogs on the papers as I know many of my friends and family aren't experts and can only understand one in every 3-5 words (apparently in some papers, my parents get even fewer) due to the specialist nature of some of our research. I'm still trying to get my first guest blog post from one of my colleagues who was the lead author on two of the most recent papers looking at felid vertebral columns. If anyone does ever want a copy of a paper, just give me a shout and I'll get you a .pdf as soon as I can.

I've particularly enjoyed getting to show off some of the field work I've been lucky enough to work on, whether it was digging for fossils in India or Argentina, or the postdoc work on cats (1 or 2). A lot of my work is done in labs/my office but I cannot ever fail to emphasise how much I think field work is vitally important for palaeontologists for collecting fossils, or actually getting hands on animals to see how they actually work.

One of the Cat Survival Trust leopards having a yawn

There are some bloggers who are very active in showing the human side of the science in terms of their emotions and feelings, and to that end I've tried hard to show myself in my writing, but have kept a lot of my personal life out of my blog (although kind of got close discussing the job hunt). That aspect is not likely to change even though work and personal life are sometimes tough to tell apart right now. I am hopeful that some of the things I publish are helpful particularly to others in terms of advice and guidance whether that is for people interested in getting involved in palaeontology or young career researchers going through similar things in their academic careers.

I like numbers so there has been a change from how I monitor visitors from just using the blogger details (about 18,250 page views in the last 2 years), and got Google analytics. It's only been active since mid-June but allows me to see better who is reading and what is being read. Each post still has a variable number of reads, but I did have two since June hit 1000 reads already. Unsurprisingly, dinosaurs do better than job search chat. In that time, I've had readers from 79 countries (I have regular readership from about 30 countries each month), with the USA being the largest readership and all 50 states and DC have had people read the blog.

Readership of the blog since June from Google Analytics. Darker colours are higher numbers of views.

I'd like to thank everyone who has been reading, and particularly those who keep widely sharing my blog and the posts so widely. I know with my Twitter and personal Facebook I don't reach more than about 700 people with a high overlap across the two so getting as many viewers as I have is largely thanks to them.

What changes can people expect in the next 2 years? There will be a general winding down of cat chat as I move away from the project (although there is probably a year or so worth of research that I am involved in). That being said there may be one shortly about the outreach event we did on the evening 9 November where we carried out a postmortem on a cheetah that was donated to us via a museum for science and outreach. The animal had passed away at a UK zoo and we were lucky enough to be able to use its unfortunate death for science and teaching the general public.

Picture preview of the postmortem. Myself in the middle working on the forelimb. Photo from the RVC link above, Photo credit: Oliver Siddons

What comes next for me? Well, I've been offered and accepted a job at the RVC as a postdoc in John's lab for another 2 years and I will be returning to dinosaurs and crocodiles looking at the evolution of the two groups' locomotion. Expect lots of posts showing "Team Dawn Dino" at work with live crocodiles and tinamous (fairly primitive birds from Central and South America), as well as work on fossils. I am hoping to still sneak out on field work from time to time to get dirty in the field. The quest for a new species is ongoing! If anyone has any digs upcoming and are looking for volunteers, do give me a shout.

The blog is never going to become a massive thing like IFLS (which became click baity and designed to make money). I am going to keep posting my research and things that interest me. I am hopeful to get a few colleagues who I have worked with share their knowledge, particularly on collaborations where I am not the first author. I will do my best to make sure everything I publish is accurate and up-to-date, but feel free to call me out on mistakes or missed citations as I will happily update the blog accordingly.

Thanks again to everyone reading and do let me know in the comments if there are things you like/dislike or think I could do differently.