I submitted my PhD thesis in September 2016, and got word back a few weeks before Christmas that it had been accepted by the university for the award of my degree! Barring a few changes, of course. Technically, my thesis has been 'accepted with changes'.

For those who don't know how the process works:

1. 1. You submit your thesis to the university graduate school, along with a list of people who you think are expert enough to read and peer review it.
2. 2. The university sends the thesis to two of these experts.
3. 3. The experts read the thesis, note down edits they would like you to make, and then send it back to the graduate school along with a recommendation to 'accept with changes', 'accept with changes and review', 'revise and resubmit', or 'no changes required'.
4. 4. The university then sends their recommendation and edits (if required) to you.
5. 5. In my case, which is 'accept with changes', you have 3 months to make these edits and upload the revised thesis for the graduate school to examine.
6. 6. Then, if the graduate school is happy with the revisions, you upload a THIRD and final version of the thesis.
7. 7. Now you can breathe!

It would have been lovely to recieve it back with 'no changes required', but hey, it would be wonderful to submit perfectly written papers for peer review and not need changes to them too, but we aren't all perfect! 

I'll add one more reason to the list: because there's a photoshoot and you can't convince the photographer that science does indeed happen in the absence of labcoats.

I use Mendeley as my reference manager, and will sing its praises to anyone I meet asking what citation software they should use for writing research manuscripts. It's super easy to import article PDFs into your virtual library, ask it to 'watch folders' for new PDFs you've downloaded, has a pretty good stab at labelling articles in your library by looking at the metadata, and cites-while-you-write with its MS Word plug-in.

​You can even highlight passages and jot down notes within each PDF in the form of floating sticky notes, called 'annotations'.

​​But I wish that those annotations were more accessible in their own right.

You might, for example, read a paper in Mendeley about the taphonomy of mammal carcasses. There's an interesting line about teeth: that while they are more resistant to weathering than bones, they can still crack and split in hot and dry environments. You highlight this sentence and add an annotation with your thoughts. 

But how do you find that annotation at a later date? Until you read that paper again, you might not remember that it even exists.

Mendeley does not allow you to view all annotations you've ever created, or even indicate which PDFs either do or don't have annotations. If you remember reading something interesting and writing something about it, you better hope that you remember what you wrote, as you can find annotations by searching for key words within them. And if you're like me and just want to review your past notes, good luck trying to remember all the papers you've added annotations to over the last 6 months.

​There are, of course, work-arounds for this: you could tag all papers you add annotations to with a key word such as 'Annotations' or mark each paper with the 'favourite' star symbol, but this relies on you never forgetting to include this step.

You could copy the contents of each annotation in to an Excel spreadsheet or mind map, and group them by theme. That way you can review your database or mindmap and find your way back to the original paper. But this feels like double handling - why not just write the annotation in the mind map in the first place? What I would LOVE is a mind-mapping tool within Mendeley, where you could click and drag annotations on to nodes/branches, but I realise this could be nightmarish to code and implement.

I can't say I've come up with a solid solution for this problem yet. Has anyone else figured out a better annotation workflow for Mendeley, or do you use other software and reference manager combinations to keep track of your research notes?

Geology is an important component of any taphonomic investigation. This helps to 'set the scene' when considering potential taphonomic pathways: what environment did these ancient creatures live in? What happened to their bodies after they died? What environment were they buried in, and how quickly were they buried?

To this end, my colleagues and I have just published a paper about the ancient environment of the Winton Formation at Isisford to better understand the taphonomic history of crocodyliforms, osteichthyan fish, and dinosaur fossils uncovered there. We propose that around 100 million years ago, Isisford lay in the middle of a river delta that flowed into the nearby Eromanga Sea. 

We came to this conclusion by studying the sandstone concretions that encase each of the fossils found at Isisford. These concretions formed when sand grains were cemented together with calcium carbonate (calcite) from calcium-rich groundwater. The majority of fossils appear not to be distorted or warped in any way, and as fossilisation occurs under high temperature and high pressure, it seems the concretions surrounding the buried bones and afforded them some protection. If this calcite cement, and therefore the concretions formed before fossilisation, then information about groundwater quality where the bones were buried would be locked away in the calcite minerals themselves - specifically, isotopes of carbon and oxygen. 

​We tested the carbon and oxygen stable isotopic values of the calcite cement, and by comparing our results to what is ‘typical’ for fresh water and sea water, found that it formed in a brackish water environment. This wasn’t terribly surprising: the regional geology indicates that the Eromanga Sea was nearby Isisford at this time, but until now we hadn't known whether it affected the environment at Isisford or not. When we examined geological core logs from near Isisford, and compared it to the types of rocks we found at the site, we concluded that these animals were buried in a river delta that flowed into the sea, with fresh river water mixing with salty ocean water. Unfortunately, there aren’t large exposures of Winton Formation at the site that would allow for typical facies analysis, but we worked with the material we had and came up with some pretty solid conclusions.

Our next question is: if these animal's carcasses were buried in a river delta, did they die there or were their bodies washed in from far away? Did they even live nearby at all? That is the subject of future papers that we will be publishing mid to late next year.

References
Syme, C., Welsh, K., Roberts, E., and Salisbury, S. 2016. Depositional environment of the Lower Cretaceous (upper Albian) Winton Formation at Isisford, central-western Queensland, inferred from sandstone concretions. Journal of Sedimentary Research, 86: 1067-1082. DOI: 10.2110/jsr.2016.67

Let's compare the sizes of these two dinosaurs: a hummingbird versus a Tyrannosaurus rex tooth. T. rex was only, oh, about 2 million times heavier than a hummingbird! Just look at the variation the vertebrate bauplan can achieve, just within theropoda! Brilliant!

​The powerful bite of a crocodile can cut through flesh and bone. Their teeth puncture, scratch, scrape and crush the skeletons of their prey. They leave behind tooth marks etched into bone, taphonomic traces which have been identified in the fossil record, and can tell us about the feeding behaviours and morphologies of ancient crocodylians. Or so we thought.

A new study by Drumheller et al. (2016) found that crocodile bite marks on bones do not seem to differ between crocodiles young and old, or male and female, or long-snouted and short-snouted. They collected bones bitten by 21 species of modern crocodylians and studied the types of bite marks left on bones surfaces – whether they were pits, punctures, scores, or furrows, and whether these marks were bisected (with extra notches or scoring from serrated teeth) or hooked (marks that changed direction). They compared the types and shapes of these bite marks to the snout shape, size, sex, age, feeding behaviour (the famous ‘death roll’), and captive or wild status of each individual crocodylian that created them. They found no significant difference between the shape of the bite marks and the individual who made them – even for crocodylians of different ages, with different snout shapes, or different feeding behaviours!

However, they did determine that bisected bite marks – those showing extra notches or scoring – were indicative of the teeth of crown Crocodylia. And as bisected bite marks have been found on fossil bones, the culprits can be successfully identified as a crocodylian (or perhaps a non-crocodylian crocodyliform – that is, animals not related to modern crocodylians, but instead an ancient offshoot of crocodyliforms that are now extinct). But not every individual crocodylian creates bisected bite-marks every time they feed, depending on whether their teeth are freshly erupted and sharply serrated, or old and worn down.
​
So, it seems you might be able to identify a crown Crocodylian as the culprit of a bone bite-mark, but cannot predict its age, sex, snout shape, or which method it chose to dispatch of its prey.  

References
​
Drumheller, Stephanie K., and Brochu, Chris A. 2016. Phylogenetic taphonomy: a statistical and phylogenetic approach for exploring taphonomic patterns in the fossil record using crocodylians. PALAIOS, 31: 463-478. [Paywalled]

I have finally handed in my PhD thesis!

I've included the title and thesis abstract below, for anyone so inclined to read it.

So what's the next step? Can I call myself Dr. Syme yet? Not quite. Over the next 3-4 months, two qualified taphonomists will examine the thesis, and note whether any changes to the text or figures need to be made. Once those changes have been incorporated, the thesis can then be formally accepted by UQ!

​Now for the waiting game...

Life by the Eromanga Sea: Taphonomy of crocodyliform and osteichthyan fossils from the Lower Cretaceous (upper Albian) portion of the Winton Formation at Isisford central-west Queensland.

ABSTRACT
In 1995, the articulated and semi-articulated fossilised remains of two small crocodyliforms and a large predatory fish were discovered in the Lower Cretaceous (upper Albian) portion of the Winton Formation near the town of Isisford, central-west Queensland (hereafter referred to as ‘Isisford’). Subsequent expeditions yielded further crocodyliform and osteichthyan fossils, as well as those of non-avian dinosaurs. The crocodyliforms were described as a new genus and species, Isisfordia duncani Salisbury et al., 2006. Phylogenetic analysis found that Isisfordia was a basal eusuchian, indicating that modern crocodyliforms may have originated in the Australian part of Gondwana. A partially complete and articulated osteichthyan fossil discovered in 2005 was described as a new species of the ichthyodectiform Cladocyclus, C. geddesi Berrell et al., 2014, expanding the geographic range of this genus outside of Brazil and Morocco. As deposition of the Winton Formation is thought to have occurred in fluvial and lacustrine settings, these taxa are considered to have inhabited freshwater environments.

The preservation and composition of the Isisford vertebrate assemblage is in sharp contrast to that of other vertebrate-bearing localities of the Winton Formation, the best known of which occur near the town of Winton, 240 km north-west of Isisford. The Isisford fossils are found encased in fine-grained sandstone concretions, often ex-situ and laying in Cenozoic and recent alluvium. In contrast, vertebrate fossils found nearer to Winton are typically preserved as disarticulated elements in siltstone hosted ‘bone-beds’. Additionally, taxa found nearer to Winton include sauropod and theropod dinosaurs, freshwater turtles, and lungfish, none of which has been recovered from Isisford. Furthermore, a detrital zircon dating study of the fossil-bearing Winton Formation localities indicates that Isisford is 6–8 million years older than localities nearer Winton. It is not clear if these differences in fossil preservation and faunal composition are temporal, or due to dissimilar environmental or taphonomic processes. It is also not known whether the Isisford fossils are autochthonous or allochthonous, which has bearing on the interpretation of their preferred habitats in life, and in clarifying the nature of the depositional environment in which their remains were interred. With this in mind, the primary aim of this study was to record decay sequences in modern crocodyliforms (C. porosus) to better understand the taphonomy of I. duncani fossils, examine the sedimentology of the Winton Formation at Isisford to identify the depositional setting, and elucidate the taphonomic history of the I. duncani and C. geddesi specimens.

An aquatic actualistic decay experiment using juvenile Indo-Pacific crocodiles (Crocodylus porosus) revealed that on average, carcasses ‘bloat and float’ five days post-mortem then remain at the water’s surface for approximately one month. The majority of disarticulation occurs not during bloat and float, but after the carcass sinks. Excluding rapid burial, it appears that high degrees of articulation and completeness can only occur if the bloat and float phase is either inhibited or eliminated.

Sedimentological analysis indicates that the Isisford concretions consist of feldspathic litharenites cemented with calcite. Given the cement-supported nature of the concretions, along with minimal fossil deformation, this suggests that the concretions formed during early diagenesis prior to sediment compaction. Stable isotopic analysis of calcite 18O/16O and 13C/12C ratios versus Vienna Pee Dee Belemnite (delta 18O VPDB and delta 13C VPDB) indicates that this cement precipitated from brackish pore waters during sulphate reduction and methanogenesis. Given the location of Isisford during the late Albian near the regressing Eromanga Sea, along with the presence of mud rip-up clasts and fossil plant debris, it appears that the concretions formed in a lower deltaic plain or estuarine setting.

The Isisford fossils range in preservation style from fully articulated through to disarticulated skeletal elements, and show minimal signs of abrasion or weathering. The close association of discrete articulated skeletal segments suggests that prolonged bloating and floating did not occur. Additionally, the lack of tetany in these specimens suggests they did not suffer any toxic shock pre- or peri-mortem. I propose that the majority of the fossils are autochthonous or parautochthonous, and that I. duncani and C. geddesi lived and died in a delta or estuary connected to the Eromanga Sea.

The fossil taxa of Isisford should be analysed in the context of more contemporaneous taxa of the late Albian Eromanga Sea – namely those from the Toolebuc Formation, Allaru Mudstone, and Mackunda Formation – rather than taxa from the relatively younger portions of the Winton Formation. Furthermore, studies focussing on the J/K mass extinction event and radiation of crocodyliforms should list the preferred habitat of I. duncani as deltaic or estuarine brackish waters, not freshwater. And no longer do palaeobiogeographical studies involving C. geddesi need to invoke mechanisms for freshwater adaptation, as it appears it was brackish water tolerant, which has already been proposed for other Cladocyclus spp. from South America and Morocco.

Corkboard of Curiosities have done it again! Click on the image below to read a lovely explainer on what taphonomy is.

... would we mammals be 'scurrying' at the feet of our dinosaurian masters?

Prof. Jonathan Losos recently gave a talk (summarised in this article by Cameron Hill) and stated that it is arrogant to assume that humanity is the pinnacle of evolution, and somehow inevitable over a long enough evolutionary time scale. Which I completely agree with.

But the assertion that, if the Cretaceous-Paleogene (K-Pg) mass extinction hadn't happened, meaning that non-avian dinosaurs weren't wiped out 65 million years ago, that they would still be ruling today? I'm not so sure.

What if certain groups of mammals had opportunities to out-compete non-avian dinosaurs? (Yes, those opportunities usually come around when mass extinctions occur and niches open up for the taking). However, there is evidence that non-avian dinosaurs were already on the decline before the K-Pg mass extinction event (see here, here, here, and here). Perhaps new niches would have opened up for mammal groups even without an asteroid crashing landing in the Yucatán Peninsula. Or any other group of animals, for that matter. New research proposes that it was the avian dinosaurs (birds) ability to eat seeds that allowed them to survive the K-Pg extinction. If the non-avian dinosaurs were declining anyway, would avian dinosaurs still have taken this seed-y niche?

It comes down to how we identify faunal turnover in the fossil record, and how we understand the causes for changes in the 'dominant' clade. Mass extinctions are commonly invoked to mark the end of one clade's reign and the start of another - from synapsids (often known as 'mammal-like reptiles') dominating the Permian then suffering mass extinction at the Permian-Triassic boundary, after which pseudosuchian diversity increased throughout the Triassic until the Triassic-Jurassic extinction event. Then, dinosauria took over newly created niches and ruled the rest of the Mesozoic until the K-Pg event, where synapsids (in the form of mammals) once again took the reins.

If non-avian dinosaurs had survived the K-Pg extinction event, how sure can we be that they would still be around today? I don't think we can say for certain that another extinction event wouldn't have happened between 65 million years and now. Perhaps the pseudosuchians (in the form of crocodiles) would have taken over once again. I think it's reasonable to propose that continental drift and ice ages would have inevitably occurred as they did, regardless of what animals were alive. Physics (and geography) will do what it wants to do, after all. Would non-avian dinosaurs, even with their proto-feathery fluff, have survived ice ages or 'ice house' conditions? They had survived a period of global cooling at the Jurassic-Cretaceous boundary, but it was not technically an ice age. What about the pseudosuchians? Furry mammals didn't appear to do too badly in our evolutionary history, but they were already in dominant niches prior to various ice ages.

One thing is for sure: I one-hundred percent agree with Prof. Losos that humanity, or even bipedalism in any animal, is not inevitable in Earth's evolutionary history.

They've done it again! The fabulous creators at Corkboard of Curiosities has a very clear and succinct run down of cladistics - how we determine which groups of animals are more closely related to one another. Head over there to find out how!