Tuesday, 15 August 2017

A quick career biography - a case study in swimming though the system


Following a series of interesting discussions on Twitter, which set out the problems and perils faced by early career researchers, I thought it might be somewhat therapeutic (for me at least) to sit down and think about the pathway that’s led me to my current position. This isn’t intended to be preachy, to trivialise the problems faced by others, or to brag, but I thought it might be of interest to the broader discussion about careers in academia and how they might progress.

During my PhD, in the Earth Sciences Department at the University of Cambridge, I had a blast. I was lucky enough to be a member of large cohort of friends, all of whom were really into what they were doing and who knew how to have a great time while doing it. I had the funding to do what I needed, opportunities to earn extra cash through teaching, was at a university were life was made pretty easy in general, had a terrific social life and a strong mutual support network. As the end of my PhD loomed closer and the spectre of unemployment appeared I started applying for jobs – in total, I applied for something like 20 positions in a relatively short space of time. Of those applications, I only got long-shortlisted for one (which was ultimately unsuccessful) and on the day my funding ran out I had only a couple more irons in the fire and went to sign-on for unemployment benefit. Luckily, the last decision I was waiting for struck gold and I got a fully-funded four-year fellowship at Trinity College. So, two weeks after I signed-on, I went back to the job centre and signed-off as the job started almost immediately. This gave me a financial cushion and also the freedom to do what I wanted to academically – I had no ‘boss’ as such, just my own research proposal to work with. The first 6 months of my fellowship were spent completing my thesis and the rest of the time pursuing various other projects. In many ways this was a great time – I had a salary, no other responsibilities, could set my own agenda and continued to work in a place with established linkages and friends – the ideal first job.

It wasn’t all roses, however – during the second year of my fellowship (a few months after submitting my PhD) I suffered from a lengthy bout of clinical depression and had a period of around 9 months where I simply wasn’t able to function properly. I couldn’t work and could barely bring myself to interact with anyone else – a large portion of this time was spent lying on a sofa staring blankly ahead, with periods of intense, unresolvable restlessness in between. Thanks to support from my partner, friends, family, GP and Trinity I got through it, though I was on medication for around 18 months, and had regular counselling during the first (and worst) few months of this illness. Trinity responded well, allowing me as much time as I needed to recover and offering to add time to the fellowship to account for the period where I was too ill to work (a generous offer, which in the end I didn’t need to take up due to getting another job after the fellowship). They didn’t offer any other formal help, aside from general moral support, but they did give me reassurance and space to recover. The depression wasn’t due to the fact that my future beyond the length of the job was unclear, nor to any stresses involved in the job, but to a combination of other personal reasons, related to the fact that my cohort of friends gradually departed (while I remained), a certain amount of PhD post-partum anxiety, and two other coincident minor, but worrying, illnesses, which got blown out of proportion. Apart from this, the majority of my postdoc period was, on balance, pretty enjoyable. Other than the eventual stress about where the next job might come from as the fellowship ticked down, I was able to set my own agenda and was treated as a grown-up by my colleagues in permanent positions. I was given opportunities to shoulder some collective responsibility ­– I, along with all of the other junior fellows participated in a minor way in the running of the College and had the same voting rights and privileges as the other fellows – and I never felt marginalised. Luckily for me, I applied for a got another job while still in the tenure of my fellowship, so went straight into this, without an extended period of failed applications or unemployment.

My next job was as a lecturer at Oxford University. It involved a move to a department that I found much more challenging, not only due to the change in role – which involved more formal teaching as well as the associated administrative demands it made, and the need to increase my research profile (not to mention some pressure to get that first grant) – but also due to the different set of personalities I encountered. It was a much less enjoyable place to work than my old Department and if it hadn’t been for a handful of friendly staff that took me under their wing, I’m not sure how long I would have lasted (although I eventually built up a small research group of my own, which helped buffer me from the isolation I’d felt on arrival). In addition to not liking my new department, I took a quick dislike to Oxford ­– a city too large to retain the charm of the university precinct, but too small to have the diversity and distractions of a bigger city. It was isolating socially and much more hierarchical academically than anything I’d witnessed in Cambridge: although I was a full member of faculty, most decisions in my department were made by a small group of senior professors who rarely consulted more widely. In addition, there were few people who had any inkling or interest in the sorts of things I worked on. My partner was still a PhD student at the time, and still based in Cambridge, so we also had the added strain of maintaining a long-distance relationship while neither of us had any money (his grant was on fumes and eventually ended – I was on a low salary). Although I lived in Oxford for a while (in temporary accommodation that was provided for new staff, which remains the worst place I ever lived in) I found that I had no social life, nor much in the way of an intellectual life either, and when my partner got a job in London and moved there I soon followed. For the next two and a half years I commuted back and forth from London to Oxford: this was physically exhausting and financially burdensome, but at least meant I had a social life again. To be fair to my boss, he was happy to support my decision to move and enabled me to work in London one day each week out of term time. I became a visitor at the Natural History Museum (NHM), with Fridays becoming a research day in the collections.

The Oxford job was a 4 year fixed-term post and as the end drew near there were relatively few other opportunities available. This led to another period of anxiety and I spent time applying for the few relevant academic jobs that arose and for individual fellowships (with zero success at making a shortlist) and I began to have serious discussions about alternative career paths (I still think I’d have had potential as a Foreign Office diplomat or savage management consultant). At this time, the NHM dinosaur researcher job came up and I was lucky enough to be shortlisted. Following the interviews I wasn’t the first choice candidate (that honour went to a colleague and close friend who went on to head up another major dinosaur collection instead), but when this candidate declined I found myself offered the job. In many ways the NHM has been exceptionally kind to me – I find myself in constant awe of the collections, the building, the sense of history and also my colleagues who are hardworking, brilliant to hang out with and dedicated. As with all permanent jobs, however, there still loomed the prospect of passing my probationary period – and this isn’t just a rubber-stamping exercise (and least three of my close contemporaries failed their probation and either left or transitioned to other non-research roles). Nevertheless, I was able to cross the Rubicon and the stability that this now permanent job gave me boosted my productivity, which has been recognised by my subsequent climbing of the greasy pole within the museum’s ranks. Even now there are still anxieties – we’re a public institution and in times of austerity permanent jobs get cut, and I’ve seen good, productive colleagues lost to these purges. Although the days of worrying about changing jobs are to some extent behind me, and I’m financially stable, I now have different burdens of expectation in terms of getting consistent grant funding, contributing to managerial and corporate roles, and in maintaining a research profile, despite having less and less research time. There were not stress factors when I was younger and the jobs were less pressured and more research oriented. In addition, when you reach middle age other burdens come into play - your own health can be more of a concern and parents, and if you have them kids, take more of a toll on your personal time in terms of finding that work/life balance.

Many of the career-related problems that academics face are not unique to academia. My friends who work in other sectors have also had to change job frequently, including changes of town or city, often with young families in tow, and difficult decisions regarding relationships, children and other life choices have to be made. They also face periods of uncertainly and unemployment and a few work in industries where there isn’t much support to deal with these issues. I’m sorry to say that the pressures don’t go away or lessen as you transition into a permanent job – they just change. Moreover, although I think that things are genuinely tougher for postdocs now than they were in my day (which should be the subject of another post), to some extent those in my generation been there too – facing the same uncertainties over the next job, where it will be, and how this will affect our lives outside of the workplace. I’ve had two particular lows in my career (my period of depression and my first year in Oxford) and in neither case were they associated with career worries, but with other factors. Career worries were real also, but I found mechanisms to manage them, which involved keeping a dialogue going and being realistic about the next stage when things didn’t look like they were going to work out the way I wanted.

As I said at the outset, it’s not my intention to preach. I just wanted to set out my own experiences as a case study, so those going through the early stages of their career can see how things might pan out. Some of you might recognise some of this, others might think I’ve been fantastically lucky (with no cause to pontificate), and others might be disappointed that the challenges they face now are tougher than those I had to overcome.

Thursday, 23 March 2017

Shaking the tree ...

Evolutionary biologists are constantly striving to improve our knowledge of the tree of life. Although this may seem like an esoteric exercise, of interest to a select few, understanding the pattern of evolution is fundamental to everything else that we might want to know regarding evolutionary history. Schemes of relationships offer a framework for understanding rates of evolution, the geographical history of a group, the ways in which different anatomical, physiological and behavioural features develop and change, and provide insights into the dynamics of adaptive radiations and extinctions. Given the foundational nature of this work, it should be unsurprising that scientists are forever revisiting the relationships of even the most familar of animal groups, in order to check and double-check that they've got things right. An impressive recent example of this comes from work on the interrelationships of the major mammalian groups, where new analyses of primarily molecular data were able to solve many features of the mammalian tree that were previously mysterious and that created a number of new, previously unsuspected groupings, such as Afrotheria, that paved the way for a different understanding of mammal evolution.

In 1887, Harry Govier Seeley, then a Professor at Kings College London, proposed a new classification for a group of extinct reptiles whose remains were being unearthed in Europe and North America. These animals, dinosaurs, were known to share a number of features in common, but there had been little consensus over their relationships and how they should be classified. He noticed several features that differed consistently between the various animals that had been assigned to this group and proposed that they could be divided to into two great tribes - Saurischia (the 'lizard-hipped' dinosaurs) and Ornithischia (the 'bird-hipped' dinosaurs). Unsurprisingly, the most obvious feature he used was hip structure, but Seeley also noted other features that supported these groupings and that distinguished them from each other. Seeley considered that his two groups were probably not particularly closely related and that they arose from different ancestors. Indeed, his arguments were so persuasive that his scheme held sway unchallenged for almost 100 years. The first challenge came in the early 1970s when Robert Bakker and Peter Galton (1974) argued that Saurischia and Ornithischia were each descended from the same common ancestor, making Dinosauria a natural, or monophyletic, group, rather than distant relatives as Seeley and others had advocated. This challenge was debated by the scientific community and upheld by analyses of expanded datasets (and new computational methods for assessing relationships) during the 1980s. Since the late 1980s, the palaeontological community has accepted dinosaur monophyly as dogma (and expanded this dogma to include birds firmly within the dinosaurian radiation), in comparison with the previous 100+ years where dinosaur polyphyly was the accepted model. However, in spite of this radical change, Seeley's dichotomous division of dinosaurs into Saurischia, composed of Theropoda and Sauropodomorpha, and Ornithischia survived (e.g. Gauthier 1986; Sereno 1999).

Since the 1980s, various dinosaur experts have looked at these fundamental splits in the dinosaur tree and their work upheld Seeley's model, with most of the debate concentraing on the exact positions within the tree of a few early, controversial species, such as Eoraptor and Herrerasaurus (e.g. Langer & Benton 2006). However, although these analyses often examined numerous detailed features they relied on only a handful of animals to inform the shape of the dinosaur tree. The past 20 years have witnessed a rush of discoveries of early dinosaurs, from all major lineages and from many parts of the world, and have also seen the recognition of a whole new group of close dinosaur relatives, the silesaurs (e.g. Nesbitt et al. 2010). This new information was incorporated into a variety of analyses, but all of these were focused primarily on the particular relationships of these new animals rather than the overall structure of the dinosaur evolutionary tree - probably because of the broad consensus that surrounded Seeley's neat and logical scheme.

The vast amount of new data now available, in combination with new software packages that allow huge datasets to be analysed rigorously and rapidly, seemed to offer an opportunity to take another look at dinosaur relationships with fresh eyes. With this in mind, my PhD student Matt Baron together with my former PhD advisor (and Matt's other advisor) David Norman, and I decided to see if this new information might affect our knowledge of the dinosaur tree. Matt built a data matrix containing 74 species of early dinosaurs and their close relatives, using specimens from all over the world and concentrated in the Middle Triassic–Early Jurassic, the time at which these major splits took place. Over 450 separate anatomical features were checked for each of these species and the resulting data analysed. It's worth bearing in mind that all other recent analyses of this problem included no more than 12–15 examples of early dinosaurs, on which to base the entire early evolutionary history of the group. Analysis of these data resulted in the recovery of an unexpected and radical tree topology that offers a challenge to Seeley's 130 year old hypothesis. This tree found that theropods were more closely related to ornithischians than either group was to sauropods, thus removing much of the content from Seeley's Saurischia (the carnivorous herrerasaurs remained with the sauropodomorphs, however). This new grouping of Theropoda + Ornithischia has been dubbed Ornithoscelida in a paper published in Nature that presents our new hypothesis (Baron et al. 2017). Ornithoscelida is a name originally proposed by 'Darwin's bulldog' Thomas Henry Huxley in 1870 in a classification that preceded Seeley's, but that was largely ignored. The name means 'bird-limbed' and refers to the hollow, gracile and elongate leg and arm bones found in theropods and ornithishians. In our analysis this new grouping receives strong support, with 21 features that seem to unite these animals to the exclusion of the sauropodomorph dinosaurs.

Given previous definitions of various dinosaur groups, this new tree requires some new definitions for commonly used names if we are to keep all dinosaurs as dinosaurs. For example, the most common definition (the common ancestor of sparrows and Triceratops and all of its descendants), would now exclude Diplodocus and other sauropods from Dinosauria. This was a step too far for us and so we proposed a new scheme of definitions to help stabilise the use and definition of some of these names, not only to account for if the new tree is potentially right, but also that would allow the tree to change if we were wrong without altering the meaning of these names.

In addition to giving us a new dinosaur tree, if our results stand up to detailed scrutiny by other palaeontologists, then they might be used to provide many new insights into dinosaur evolution. This would include looking again at the timing and pace of dinosaur origins, the evolution of various key characters, such as feathers and carnivory, and into the areas where dinosaurs might have first appeared. As with anything in science, our tree is a hypothesis - it is there to be stretched and tested to see if it is stronger than those that have come before and if it has the power to explain more about dinosaur evolution than other competing schemes. If we're wrong and there are better alternative explanations for the patterns we see then we'll have to accept that evidence and move on - that's how science works. In the meantime we hope that people will look at this with an open mind rather than rejecting it in a knee-jerk fashion due to its challenge to a well established and embedded dogma. While Huxley might be cheering us from the shades, we're also aware that Seeley would be shaking his head. Time will tell which one of them was closer to the truth.

References


Bakker, R. T. & Galton, P. M. Dinosaur monophyly and a new class of vertebrates. Nature 248, 168–172 (1974). 
Baron, M. G., Norman, D. B. & Barrett, P. M. A new hypothesis of dinosaur relationships and early dinosaur evolution. Nature (2017).
Gauthier, J. Saurischian monophyly and the origin of birds. In The origin of Birds and the Evolution of Flight (ed. K.Padian). Memoir of the California Academy of Science 8 1–55 (1986).
Huxley, T. H. On the Classification of the Dinosauria with observations on the Dinosauria of the Trias. Quarterly Journal of the Geological Society 26, 32–51 (1870).
Langer, M. C. & Benton, M. J. Early dinosaurs: a phylogenetic study. Journal of Systematic Palaeontology 4, 309–358 (2006).
Nesbitt, S. J., Sidor, C. A., Irmis, R. B., Angielczyk, K. D., Smith, R. M. H & Tsuji, L. A. Ecologically distinct dinosaurian sister group shows early diversification of Ornithodira. Nature 464 (7285): 95–98 (2010).
Seeley, H. G. On the classification of the fossil animals commonly named Dinosauria. Proceedings of the Royal Society of London 43, 165–171 (1887).
Sereno, P. C. The evolution of dinosaurs. Science 284, 2137–2147 (1999). 

Friday, 17 March 2017

Lake Kariba dinosaur expedition: Part 3, finale

On reaching island 126/127 we began our search for the original Vulcanodon site. A thick lava flow forms the top of the cliffs, capping a series of bright orange and red mudstones and sandstones that comprise the Lower Jurassic Forest Sandstone Formation. Some of these layers were swarming with the burrows of animals that had lived in the sediment, suggesting that at times this ancient environment was a little wetter than generally thought. The island is small, so we were able to narrow down our search fairly quickly. Although we're confident that we did find the area that yielded Vulcanodon, were weren't lucky enough to find any other material on this occasion. The vertical cliffs didn't offer many opportunities to prospect for fossils and we were left wondering how the original team, lead by Prof. Michael Bond in the 1960s, had accomplished the back-breaking work of getting the huge bones out of the site. The foreshore was more promising, however, and were lucky enough to find isolated fossil bones in several places, all of which were attributable to more primitive sauropodomorph dinosaurs than Vulcanodon, which were probably from a more Massospondylus-like animal. While at the site we took the opportunity to learn more about its geology, measuring detailed sections and noting the lithology and structures present. This turned out to be a valuable exercise as it helped to form a basis for correlating the Vulcanodon site with other dinosaur-bearing sites around the lake shore and it also offered us some new clues on the geological age of Vulcanodon and on some of the other sites nearby, which will be the subject of a paper that the team is currently writing.

Cervical vertebra of a Massospondylus-like dinosaur found close to the Vulcanodon type locality on island 126/127 (photo: Pia Viglietti)
The nearby islands had very similar geology and we prospected several of these hoping to find new material. All were marked by the same characteristic dark basaltic lava flows and orange-red Forest Sandstone sediments and some showed evidence of major faults. These faults created some confusion when we were trying to work out where we were in each section, but after visiting lots of sites we began to work out how all of these features were related. We found bone on most of the islands, but they were usually small, isolated pieces, rather than associated or complete specimens. Nevertheless, in those cases where we could identify the bones, they were all of sauropodomorph dinosaurs and we identified many new potential sites that we hope to revisit in the future.

After several days of prospecting the islands around 126/127, we decided to move to sites closer to Kariba town. Our captain moved Musankwa eastward to moor off of Musango Island, where Steve Edwards runs his safari camp. Steve has been prospecting the area for many years and has amassed an important collection of material. Some of these specimens, including more evidence of sauropodomorph dinosaurs, come from the Forest Sandstone, but the majority of them come from an older unit that is probably of Late Triassic age, called the Tashinga Formation. The Tashinga Formation also consists of mudstones and sandstones, but parts of it were deposited under much wetter conditions than the Forest Sandstone. This is shown by the abundance of fossil wood on Musango Island and the nearby shore - fragments of wood are scattered everywhere in the soil and some spots has masses of large tree trunks that showed the region had been densely wooded at this time. In addition, other fossils also suggest the presence of water bodies (at least on a seasonal basis) as shown by finds of numerous large lungfish tooth plates.

Some huge Late Triassic tree trunks with palaeontologists for scale (photo: Lucy Broderick)
Among Steve's collection, and among the fossils we spotted while walking, we found some sauropodomorphs , but the remains of lungfish and other reptiles were much more common. Some of these fossils represent an interesting reptile that is the first of its kind to be reported from this area of Africa and the team is currently working on a description of these specimens. Over the next few days we walked though some of the areas around the island so that we could also study the geology, with the aim of trying to pin down a narrower age estimate and to work out how the different fossil-bearing units of the area were related to each other.

 The team poring over some of Steve Edward's fossils while at Musango Safari Camp (photo: Pia Viglietti)
After long hot days of walking through the bush, usually with at least one eye peeled for nearby elephants or hippos, our evenings around Musango were spent trying to supplement dinner with the excellent fish that could be caught in the lake (with varying amounts of success), as well as spotting some of the abundant bird life. While at Musango we also witnessed brutal tropical thunderstorms, which would come rolling in during the early hours of the morning while we were asleep. As many of us slept on deck (where it was nice and cool), we'd often be awoken by the crack of thunder, some amazing celestial pyrotechnics, and the drip of cold rain onto our faces through the mosquito nets as it found a way through the canopy.

A rare example of fishing success, with a triumphant Pia showing off her skills (photo: Lucy Broderick)
Following several pleasant and productive days at Musango, the final part of the trip involved another move to the east, closer yet to Kariba town, and a stay moored off of Spurwing Island, where we walked the shorelines looking for more places that might yield fossils. Again, assisted by the local rangers, we were lucky to find sites that yielded large sauropodomorph bones. Although none of these were particularly complete, they were of high quality, well preserved and some were partially articulated, suggesting that exploratory excavations in these areas might reveal interesting new material.

Steve Edwards checking out some of the sauropodomorph bones on Spurwing Island (photo: Lucy Broderick)
By the end of our trip we'd prospected a transect over 50 km in length and had visited numerous outcrops of both Late Triassic and Early Jurassic age. Our specimens have been deposited in the National Museum in Bulawayo and the information we've obtained on new sites, many of which were previously unknown, and on the geology of the area, is currently being compiled for publication. Our trip back down the lake was marked by more interesting weather, notably an amazing waterspout that we watched cross the lake surface followed by a torrential downpour that dampened our spirits somewhat as we unloaded Musankwa back in harbour. Nevertheless, the amazing scenery of Lake Kariba, its stunning natural beauty, and the new material we'd seen all combined to make this an exceptional and productive trip. The team is already planning to return to some of the more promising locations in the hope of finding some really spectacular material in future.

Friday, 17 February 2017

The science behind the movie: what we really know about dinosaurs and how


This is an article that I wrote to accompany a lecture I gave at the Royal Albert Hall, back in November 2016, in conjunction with some screenings of Jurassic Park that were accompanied by a live orchestra. For various reasons, this didn't get published and I just found it again and thought I might as well pop it on here ...

The premise underlying the Jurassic Park franchise is an elegant one: that dinosaur DNA, preserved in the guts of ancient mosquitoes trapped in amber, could be used to clone these animals, bringing them back to life using the latest genetic technology. A terrific idea, but, sadly, one that remains deeply within the realms of science fiction as - to date - no-one has discovered even a fragment of dinosaur DNA, nor do we currently have the means to clone a dinosaur even if we were lucky enough it’s original genetic material. More hopefully, some scientists are attempting to bring back other famous animals from extinction, including the iconic woolly mammoth. Mammoths are lot younger than dinosaurs, having gone extinct only a few thousand, rather than millions, of years ago, and this means that many of their remains, frozen in Siberian permafrost, can yield large amounts of viable DNA for scientists to work with. However, even in this case a cloned mammoth is still a long way off. In addition to the numerous ethical problems that would surround the resurrection of an extinct species (the world has changed significantly since the last mammoth drew breath), there are still numerous scientific obstacles to mammoth cloning, not the least of which is that we have yet to learn enough about the reproduction of those animals that would be the best hosts for implanted mammoth embryos – elephants. So, given that we’re unlikely to see dinosaurs roaming our zoos and safari parks anytime soon, how do scientists determine how these amazing animals fed, ran, bred and died?

Palaeontologists, the scientists that study extinct life, have a surprising array of tools with which they can examine the fossilized remains of animals and plants to determine how they might have appeared and behaved when alive. In the case of dinosaurs we have their skeletons, but we also have other evidence that can give deep insights into their daily lives, including preserved gut contents, eggs, nests, footprints, skin impressions and even dinosaur poo. Detailed examination of skeletons provides information on the shapes of the bones and how they fit together. Comparisons with living animals are also key, as if we can identify similar features in these living animals, whose biology we can study in real time, we can then infer similar functions for those same features in extinct animals. Rough patches and flanges on bone can be used to reconstruct the positions of muscles, cartilage and ligaments, and studying the scratches and wear patterns on teeth reveals vital information on diet and feeding. This type of work has been carried out since dinosaurs were first discovered, in the early eighteenth century, and continues to provide new results today. However, this classical approach has been expanded thanks to the advent of an array of modern technologies, pioneered in fields as disparate as medicine and engineering, which are now being applied to fossils on an almost routine basis.

Perhaps the most significant of these advances has been the application of computed tomographic (CT) scanning. CT scanning uses rotating X-rays to build up a three-dimensional model of both the internal and external anatomy of an object and has diverse applications ranging from diagnostic use in medicine to checking car or airplane parts for flaws before they leave the factory floor. CT can be used to peer inside dinosaur bones and reveal features of the skeleton that were previously difficult to access, including the shapes of the brain and the air-filled sacs that ran through many dinosaur bones. The CT scans produce perfect virtual models of the bones that can then be subjected to testing in ways that would be impossible with a fragile or cumbersome fossil. By importing these virtual models into different computer programmes, dinosaur skeletons can be clothed in muscle, subjected to forces generated by walking, running and feeding, and tested to destruction in ways that no worthy museum curator would permit on the original bones themselves.

By carefully cutting thin sections through dinosaur bones and putting them under the microscope, we can age dinosaurs and work out how fast they grew to adulthood. This is done by counting the growth lines in the bone walls, which were laid down each year in a tree-ring like fashion. Dinosaurs grew really fast, with even the largest species reaching full size in no more than 30 years – and like humans dinosaurs had a teenage growth spurt. Some dinosaur fossils are so spectacularly preserved they include evidence of soft tissues like skin, muscle and internal organs, which give vital clues on dinosaur biology and appearance. For example, some spectacular fossils from China show that many meat-eating dinosaurs were covered in thick coats of feathers, helping to cement the idea that birds are nothing more than small, meat-eating dinosaurs that gained feathers and learnt how to fly. The recognition that birds are dinosaurs is an idea that has been proven beyond reasonable doubt in the last 20 years and also gives us new clues on what extinct dinosaurs might have been like. As living dinosaurs they can be used to test some of the ideas that palaeontologists have proposed based on bones alone. Moreover, they carry a direct genetic legacy of their dinosaurian ancestry, which means that bird genes are dinosaur genes, even though birds represent only one specialized branch of the dinosaur family tree. Some scientists are currently attempting to switch on long dormant genes in living birds that might have been responsible for producing the teeth, characteristic skull shapes and long tails of their dinosaur ancestors. These efforts are already producing impressive results, with genes being found that can transform bird beaks back into more dinosaur-like snouts and those that can stimulate hens to form teeth. Surprisingly, this work is not only interesting in its own right, but it has implications for human health as some of the key genes are also important in regulating various strains of human cancer, so this pure science project on dinosaur genes is providing insights that could improve human health too. Moreover, this type of genetic manipulation, based on the DNA of living dinosaurs, is probably the closest we will ever get in reality to a Jurassic Park scenario.


Saturday, 11 February 2017

Lake Kariba dinosaur expedition: Part 2


On arrival in Harare we were met by one of our local hosts, Dave Glynn, who whisked us to his house in the suburbs where were to meet the other team members. Dave and his wife Julie run a tourism business in Zimbabwe and organised most of the logistics for our trip, as well as hosting us before and after the fieldwork. They also provided our accommodation at Kariba, placing their houseboat on Kariba, Musankwa, at our disposal. As the day wore on, we were joined by Darlington Munyikwa, the Deputy Director of National Museums and Monuments, and Michael Zondo, from the Bulawayo Museum, both of whom have extensive fieldwork experience within Zimbabwe and had been on many trips to look for dinosaur material all over the country. All of us were to stay with Dave and Julie, to allow an early start on the road to Kariba. That night we were joined by more of the crew, namely the Broderick family, Tim, Patricia and Lucy. Tim was a geologist with the Zimbabwean Geological Survey and had spent many days walking and mapping our study area and his wife Patricia and daughter Lucy were veterans of many fossil hunting trips. Lucy is a professional photographer and was to prove invaluable in documenting our sites and finds. Over dinner we discussed our hopes for the trip and a strategy for making the most of our time around the shores of Lake Kariba.

After a short night and an early start, we packed our vehicles with field kit, 10 days worth of fresh food and other supplies, hitting the road at 4:30 am in order to reach Kariba by early afternoon. It was still dark as we left Harare, but as the sun rose it revealed a beautiful country. Most of the region between Harare and Kariba is farmland and the rains had left the landscape lush and green. After one minor breakdown, which was quickly repaired, we reached Kariba at lunchtime. The Broderick family caught up with us en route, bringing with them another team member, Rowan MacNiven, a fossil-mad restaurateur from San Francisco, whose loud and frequent shouts of “BONE!!!” would become a hallmark of the trip. 

Loading up the speedboats at Kariba and getting ready to cross the lake (photo: Pia Viglietti)

On arrival at Kariba we were met by the final member of our party, Steve Edwards, whose lodge, Musango Safari Camp, was based on the shores of the lake, in prime fossil-hunting territory. This is the point at which our work really began and the whole group was needed to transfer our supplies to the two speedboats that were to take us across the lake to rendezvous with Musankwa. We’d have these speedboats, and two other pontoon boats, with us for the entire trip to allow us to explore the convoluted coastline. With everything safely stowed we boarded and began the 90-minute journey westwards to meet Musankwa, which was lying moored off of the island that was to be the site of our first prospecting trip. The houseboat was essential as camping in the area is potentially hazardous, with lion, elephant, hippo and other game in the areas we wanted to prospect. In addition, it allowed easier transport of stores and was an excellent mobile base for moving from island-to-island and from lake-to-shore.

Some days the commute to work is a lot more pleasant than others (photo: Pia Viglietti)

During our journey across the lake we got our first real flavour of the region. Lake Kariba is one of the largest artificial lakes in the world and is 140 miles (~220 km) long, up to 20 miles (~32 km) wide and has a maximum depth of just under 100 m (although most of it is significantly shallower). It was formed by damming the eastern end of the Kariba Gorge, which forms part of the Zambezi river valley, close to Kariba town, which took place in 1955–59. It forms the international boundary between Zambia and Zimbabwe and was created by the colonial government for the region, prior to the independence of both countries. The lake filled between 1958­–63 and a hydroelectric plant at the dam supplies most of the electricity for both nations, while the lake is used for commercial fishing and tourism. The fringes of the lake are dotted with numerous small islands (which were large hills before the flooding of the valley) and the southern (Zimbabwean) border of the lake is occupied by Matusadonha National Park. The area is densely vegetated, with mopane forest and grassland running down to the shores, and has prolific birdlife and game. During our transfer we were entertained by white-winged terns fishing, African sea eagles flying overhead, and sightings of elephant on the shore and hippo bobbing along the the lake margins. 

Elephant and hippo were frequent visitors to our fieldsites (photo: Pia Viglietti)

The houseboat Musankwa, which was to be our home during our time on Kariba (photo: Jonah Choiniere)

The geology in the area is complex, with much faulting, and the southern shore of the lake is composed mostly of ‘Karoo-aged’ rocks thought to be equivalents to those found in South Africa, which range from Permian to Early Jurassic in age. The area has suffered some drought over the past few years, exposing more shoreline than usual, increasing the amount of land that we were able to prospect. Some of the islands are named, but many are known only by a formal numbering system. Our destination, and base for the next few days, was to be island 126/127. This was chosen as it is the type locality for the earliest known sauropod, Vulcanodon karibaensis, literally ‘the volcano tooth from Kariba’. Vulcanodon, which is known from incomplete remains, is one of the most important animals for understanding the origin of sauropods and all of the available material comes from this island. These bones are now stored in Bulawayo, but one of our aims was to find out more about this site and, hopefully, to find new material … 

The bright orange cliffs that yielded Vulcanodon on islands 126/127, capped by a dark layer of basalt (photo: Pia Viglietti)

Sunday, 5 February 2017

Lake Kariba dinosaur expedition: Part 1


Our knowledge of dinosaur evolution is based on a series of snapshots provided by the fossil record, with a handful of key regions providing the lion’s share of information for any particular time period. This relies on serendipity – rocks of the right age and type need to be preserved in a way where they are accessible for collection – and the distribution of these deposits is essentially random, due to numerous geological processes acting to different extents in different areas at different times. For example, our most detailed insights on the last dinosaurs currently come from the western USA and Canada, whereas presently our information on the earliest dinosaurs is confined to Argentina and Brazil.

Southern Africa provides an important piece in this puzzle, with a series of sandstone and mudstone deposits laid down on broad river floodplains, that were laid down at a time when dinosaurs were first starting their rise to numerical and ecological dominance. These environments became more arid through time, culminating in vast dune seas, where dinosaur fossils could still be found. This series of rocks is referred to as the Stormberg Group in South Africa and reveals not only the dinosaurs but also the other members of a series of terrestrial faunas that lived during the Late Triassic and Early Jurassic, spanning a period when several pulses of extinction rocked the world at the Triassic/Jurassic boundary. The Stormberg Group has been (and continues to be) the focus of much attention and has yielded some of the best-known African dinosaurs, which are often known from abundant and beautiful material. These include the ornithischians Heterodontosaurus and Lesothosaurus, the theropods Dracovenator and Coelophysis, and (most abundantly) the sauropodomorphs, including Antetonitrus, Massospondylus, Pulanesaura and many others.

Adjacent regions of southern Africa, including Botswana, Lesotho, Zambia and Zimbabwe, have similar sedimentary series that are thought to correlate with those in South Africa, but for various reasons these deposits are have been less thoroughly explored. Nevertheless, some important material is known from these areas, with rich localities in Lesotho (which have supplied beautiful early mammal and Lesothosaurus material, as well as dinosaur footprints) and Zimbabwe. Many sites are known in Zimbabwe, with well-known taxa such as Coelophysis and Massospondylus known from the south of the country, while the early sauropod Vulcanodon was found on the shores of Lake Kariba on its northern border. Several field crews have worked on sites in the south of Zimbabwe more recently, finding new and important material, but the potentially rich dinosaur sites around the shores of Lake Kariba have not been prospected by palaeontologsts since the time of Vulcanodon’s discovery in 1969.

More recently, a small band of dedicated amateur palaeontologists and geologists, including local safari camp owner Steve Edwards and geologist Tim Broderick, have had their eyes to the ground along the shores of Lake Kariba and have found interesting new material of their own. Steve and Tim mentioned this material to various dinosaur specialists around the world, including my colleague Jonah Choiniere (based at the Evolutionary Studies Institute in Johannesburg) and I. The presence of Vulcanodon, and other Early Jurassic dinosaurs elsewhere in Zimbabwe, as well as the exciting news that new material was being found, suggested to Jonah and I that a trip to area would be fruitful and exciting. After months of background research, building new contacts with colleagues in Zimbabwe, and raising the money, Jonah was able to organise an expedition to the Lake Kariba area, in which I was lucky enough to participate, along with several other Zimbabwean and South African colleagues. So, on the 5th January 2017 Jonah, his postdoc Pia Viglietti, our joint PhD student Kimi Chapelle and I left Johannesburg, bound for Harare …

Tuesday, 24 May 2016

'Unspecialised' dinosaur herbivores: not so boring after all


One of the central tenets of palaeobiology is that similar looking skeletal structures in different taxa convey similar functions in life. Hence, the presence of serrated teeth, like those of extant carnivorous varanid lizards, imply carnivory in theropods, and the convergent acquisition of long, graceful lower legs in gazelles and ornithopods suggests cursoriality in the latter. While some of these form/function relationships have proved relatively robust to quantitative, experimental testing, the generality of several classical form/function comparisons has been questioned by recent work. For example, experimental studies on living teleost fish have shown that skeletal morphology alone does not predict jaw movements: predictions made on bones alone fail and real jaw movements could only be deduced when soft tissues and nervous control mechanisms were factored in (e.g. Lauder 1995). These, and other similar studies, have shown that we should no longer rely uncritically on simple form/function correlations, but should test these assumptions through experiment or modelling. This will allow us to avoid erroneous functional predications that would otherwise resonate through ecological reconstructions and discussions of homology, as well as influencing other functional work.


Thanks to the development of new and refined experimental methods, as well as sophisticated computer modelling techniques, we are now in a position where we can test at least some of the mechanical properties of fossil skeletons (and of living tissues) in ways far more rigorous than the early comparative anatomists could have imagined. With this in mind, my colleagues Stephan Lautenschlager, Charlotte Brassey, David Button and I decided to look at the skull function of three different herbivorous dinosaurs to investigate some aspects of the form/function question.

We selected skulls of the Late Cretaceous therizinosaurian theropod Erlikosaurus (the subject of Stephan’s PhD), the Late Triassic sauropodomorph Plateosaurus (from David’s PhD thesis), and the Late Jurassic thyreophoran Stegosaurus (based on the complete, but disarticulated skull of ‘Sophie’ the NHM’s new specimen, which was CT scanned and reconstructed virtually by Charlotte). Although these taxa are widely separated in time and space, and are phylogenetically distant from each other, we chose them as their skulls are superficially similar in several respects, due to many of the features classically associated with a herbivorous diet. Many of these features were acquired convergently, though some are due to their shared deep phylogenetic heritage. All three taxa have skulls that are relatively elongate and narrow, with low snouts, and the snouts are relatively long in comparison to overall skull length. The external openings are large, the mandibles are slender with slightly depressed jaw joints, there is no evidence for substantial kinesis within the skull, and the teeth are coarsely denticulate, relatively small, numerous and did not occlude. Traditionally these features have been associated with ‘weak’, fast bites, a lack of sophisticated chewing mechanisms, or indeed of any real specialisation (e.g. Norman & Weishampel 1991). As a result, it’s generally been thought that these skulls would have functioned similarly in life, with corresponding ideas about probable food plants and ecological roles (e.g. reliance on ‘soft’ vegetation, lack of oral processing).

From left to right, skulls of Erlikosaurus, Stegosaurus and Plateosaurus (Image courtesy of Stephan Lautenschlager/University of Bristol)
            
However, when we subjected models of these skulls to multibody dynamic and finite element analyses, what we found surprised us (Lautenschlager et al. 2016). Instead of behaving similarly, each of the skulls has its own unique function. Stegosaurus had a higher than expected bite force, in the range of 166–321 N, which overlaps with that of some living mammalian herbivores. By contrast, those of Erlikosaurus and Plateosaurus were much lower and similar to each other (50–121 N and 46­–123 N, respectively). These differences in bite force were accompanied by differences in stress patterns within the skulls. Plateosaurus seems have experienced the lowest and most evenly distributed stress patterns (implying a skull adapted to deal with a variety of different forces), whereas overall peak stresses were much higher in Erlikosaurus and Stegosaurus. In Stegosaurus, stresses were concentrated in the snout, whereas in Erlikosaurus they seem to have been highest in the posterior part of the skull. In addition, the skull of Erlikosaurus experienced the greatest amount of deformation during biting, but those of both Stegosaurus and Plateosaurus experienced very little shape change. 

Finite element models of 'Sophie' the NHM Stegosaurus, the image at the rear grossly exaggerated to look at possible deformation patterns (image courtesy of Stephan Lautenschlager/University of Bristol)


These results imply that each taxon had quite different feeding strategies, a conclusion that differs from previous ideas about these ‘unspecialised’ herbivores. For example, the differences in maximum bite force suggest that these taxa might have been feeding on diverse sorts of vegetation, with the higher bite force of Stegosaurus implying that it was able to feed on a broader, or tougher, range of plant parts/types than either the ‘prosauropod’ or therizinosaur. This higher bite force was enabled by a larger jaw muscle mass in Stegosaurus and/or an arrangement of the jaw muscles that allowed more efficient conversion of muscle force into bite force. The lower bite forces of Plateosaurus in combination with its high cranial robustness are consistent with low fibre herbivory, dealing with soft vegetation that required little chewing, and/or omnivory (the skull could have withstood dealing with struggling small prey, for example). Erlikosaurus appears to have been specialised to use the tip of its snout in plucking vegetation, as the skull performs exceptionally badly when biting food at the back of the mouth. Nipping soft vegetation with the tips of the jaw is also consistent with its low bite forces.

            Previously, these three taxa were all thought to be relatively ‘boring’ herbivores that simply nipped and swallowed soft plants. It now seems that one was eating much tougher vegetation, another was a generalist that could exploit different food sources, and the third was a specialist with a rather delicate way of feeding itself. This work shows that first appearances based on simple application of the form/function paradigm can be misleading. Novel functions have now been revealed that would have gone unnoticed if it were not for detailed biomechanical modelling of each skull. This leads me to wonder what other functional surprises might be lurking in dinosaur skulls, especially as so few have been really thoroughly studied in this way.



References

Lauder, G.V. 1995. On the inference of function from structure. In Functional Morphology in Vertebrate Paleontology (ed. J.J. Thomason), pp. 1–9. Cambridge: Cambridge University Press.

Lautenschlager, S., Brassey, C., Button, D. J. & Barrett, P.M. 2016. Decoupled form and function in disparate herbivorous dinosaur clades. Scientific Reports 6: 26495. doi:10.1038/srep26495

Norman, D.B. & Weishampel, D.B. 1991. Feeding mechanisms in some small herbivorous dinosaurs: processes and patterns. In Biomechanics in Evolution (eds J.M.V. Rayner & R.J. Wootton, pp. 161–81. Cambridge: Cambridge University Press.