How to destroy generations of childhood memories in an instant: Yutyrannus huali

Childhood memories of dinosaurs have received another shattering blow today. The latest culprit is Yutyrannus huali, a large basal tyrannosauroid from the lower Cretaceous of China, complete with elongate integumental filament structures, or ‘protofeathers’. The etymology is quite special, says lead author Xing Xu, translating into a blend of Mandarin and Latin as ‘beautiful feathered tyrant’. This species is the latest wonder to be exhumed from the fossil treasure trove known as the Yixian Formation, a series of volcanogenic and lacustrine deposits that are currently guiding and re-working our understanding of dinosaur evolution. Of course, being such prominent study, Nature saw fit to pop it behind a $32 paywall.

One small step for digital Palaeontology

The time of digital technology is upon us. No scientific domain is embracing it’s fast-paced and dynamic progression more so than Palaeontology. One such realm that is exploding with new studies and enrapturing the minds of people and the global media is the increasing possibility to digitise and manipulate three-dimensional fossils. Surface laser-scanning, C-T scanning and mechanical digitizers are all commonplace now in palaeontological studies. The implications of such techniques are far-reaching, from reconstructing robotic dinosaurs (see video), to understanding vertebrate biomechanics at an intricate level. Other palaeontologists digitally reconstruct the internal anatomy of various organisms; for example, in the Herefordshire deposits in the UK, digital models are recreated from exquisitely preserved fossils within nodules to look at the evolution of the internal structures  that were pivotal in the evolution of extant hyperdiverse invertebrate groups, such as arthropods.

It is pretty well established that the fossil record is fraught with completeness issues. I covered the problem of this in a previous post in terms of understanding biodiversity patterns in deep geological time, in the context of lineage completeness. Another problem however is individual specimen completeness. Several authors have attempted to compensate for this secondary level of ‘bias’, using various quantitative metrics, and use these to guide assessments of biodiversity through time in specific lineages (e.g., sauropod dinosaurs). Another problem is that often, fossils have been ‘squished’ and distorted by the weight of successive layers of rock over the thousands or millions of years they have been buried for. This is a problem which is typically found in dinosaur skulls, making them somewhat resemble Imhotep in The Mummy (this may be fictional).

Ugly beyond all reason, possibly as a result of post-mortem decay. "You talking to me?!"

Geometric morphometrics is something that I’ve mentioned in previous posts. It sounds awful, the  very mention of it usually enough to put people off or smash a keyboard upside your head. But thanks to several review papers, the basic concepts are now much easier to grasp and apply to a variety of scientific hypotheses. Statistics are quantitative, easy to record, less subjective than qualitative statements, and available for repeated manipulation through a wide variety of methods. The integration of geometry-based analysis is now commonplace in almost every aspect of Palaeontology, intimately coupled with an increase in the availability of digital techniques. The fact that you don’t have to damage unique specimens during the processes (usually) is a bonus too!

The latest analysis, and a critical study for palaeontologists and museum curators around the world, uses geometry-based reconstruction of a poorly-preserved fossil to digitally reconstruct missing or distorted parts. And the best part about it, is that it’s fully open access (including all supplementary videos); the comment that “this method does not require specialised software or artistic expertise” is perhaps a bit misleading, as you firstly need a fossil and a CT scanner (or a previous scan), a pretty beasty PC, and the software mentioned is hardly cheap (Rhinoceros is €195 for a student license, and for Geomagic the cheapest price I could find was $8000). The actual software used (Mimics) appears to be free, but I’m still awaiting confirmation for downloading. Additional software, such as MeshLab and Autodesk Maya are freeware, at least for trial versions.

Clack et al. set out to build a method of digital reconstruction that builds upon previous methods, giving greater geometric accuracy. The methods revolve around using a digital mesh obtained through laser or C-T scanning as a model for a landmark-based geometric reconstruction. The sample specimen is a vertebra from the infamous tetrapod fossil Acanthostega. Only one half of the vertebra is actually preserved, therefore this was digitally reconstructed and attached to its mirror image, creating a bilaterally symmetrical three-dimensional element.

Landmark selection involved a mixture of Type 1 and Type 2 landmarks; that is topographically homologous points, mixed with sites of geometric significance, such as local maxima or minima of curvature. These were used as the basis for constructing a surficial grid of contour lines describing the medial and lateral geometry of the neural spine. Videos of the processes involved are actually available online, embedded within the article, a really awesome and useful addition, making the whole methodology more transparent and easier to replicate, should you wish. There’s not really much else to say about the methodology; the processes, such as modelling and surface extrapolation are laid out systematically and reasonably easy to understand for anyone with an understanding of the concepts of geometry and fossils.

The resultant reconstructions are high quality, smooth and geometrically faithful in representing the original vertebra in three dimensions, free of any taphonomic deformation or distortion, and with missing parts accurately reproduced. The groups of models created are validated using Procrustes superimposition and principal components analysis, two standard statistical techniques. The first two principal components do appear to have a low explanatory power however (PC-1 = 24.3%), which may be an issue relating to the complexity in the form of the vertebra. The authors are right to discount the use of the thin-plate spline technique, as this is known to be misleading in that the deformation patterns it produces are homogeneous with respect to the landmark configuration, leading to potentially false morphological variation in areas of no data, something which is largely overlooked.

Acanthostega model reconstruction, half-fish half-muppet; Copyright - Eliot Goldfinger

The advantages of the techniques explored here are in the handling style of the models, and their statistical power and accuracy. Furthermore, anyone can conduct or replicate these methods, providing they have access to an initial CT scan. The potential applications are numerous too: digital models of reconstructed elements can give more accurate parameters for biomechanics where data may have been previously extrapolated in a subjective or qualitative manner; it may yield hitherto unknown data for character construction, which may in turn increase the validity of phylogenetic analysis. The landmark mapping procedure may need refinement in terms of increasing the number of points, such as by using semi-landmarks, which will more accurately reconstruct the surface geometry and open the way for other statistical procedures.

The study represents a great step forward though in accurate specimen reconstruction, and reveals another field in which the power of geometric morphometric techniques is unparalleled. A limitation could be that to reconstruct missing parts, you have to have an idea of what the gross geometry is, meaning at least one half of a bilaterally symmetrical element must be present. This means that if you wanted to reconstruct the neural spine for example, it would be impossible if the whole part was absent, even if the entire centrum was preserved. This is something that could be integrated in future using close relatives of the species that are being reconstructed.

Did Archaeopteryx Really Have Black Plumage?

Not surprisingly, the latest Archaeopteryx study has kicked up quite a stir within the media and scientific realms, considering the iconic status it has attained since discovery some 150 years past. This latest paper by Carney et al. and published in the journal Nature Communications claims to have resolved the plumage colour of a feather possibly from  Archaeopteryx, a pretty neat little addition to the reconstruction of this critical species. They use methods employed during previous studies, namely the morphological or structural analysis of melanin-bearing organelles within feathers called melanosomes to infer that Archaeopteryx possessed an entirely black plumage.

The notorious black feather (Image Copyright: WitmerLab at Ohio University)

There is no doubt that the structures are in fact melanosomes, and no doubt that melanosomes contribute to plumage colour. But the question is, how much do they contribute to the plumage colour..? Well, I don’t know. In fact, no-one knows, at least in extinct avian theropods. The authors don’t discuss this either. It has however been discussed elsewhere in similar studies, albeit only qualitatively and in passing.

One comment is from Zhang et al. 2010: “Melanosomes are lyosome-related organelles of pigment cells in which melanins are stored and are responsible in part for the colours exhibited by modern birds.”

And Li et al. 2010: “Other molecular pigments such as carotenoids and porphyrins also produce plumage colours but are not preserved morphologically, thus we cannot address their possible effects here.”

That seems like a pretty big caveat. It’s like saying if you mix green, yellow and red paint in unknown quantities, you get red every time. Or something similar, I suck at analogies. The point is, if in modern birds, there are other significant structures that dictate or contribute towards plumage colour, does it make sense to try and predict colour when these are absent?

UPDATE: Ryan has been kind enough to clarify this point in a comment below.

Furthermore, the 95% confidence intervals the authors use are practically useless. Look at the ordination provided in Figure 4 (not sure if I can copy it here, so won’t..).  These 95% confidence ellipses mean nothing in the slightest, or at least nothing meaningful. What they should have shown is an envelope includes 95% of all points within a sample, so that when you insert data ‘blind’, if it falls within a completely discriminated envelope, you can be 95% certain that it belongs to that group (i.e., 95 times out of 100, a blind data point will be correct). The envelopes shown in figure 4 clearly do not show this (if you don’t have access to the paper, ask me for a copy, or take my word for it). As a result, the points calculated for the particular Archaeopteryx feather analysed could really be grey or black, or maybe brown at a push (the number of colour choices is simply overwhelming..).

So was Archaeopteryx lithographica black?

Probably, probably not.

Carney et al. (2012) New evidence on the colour and nature of the isolated Archaeopteryx feather, Nature, DOI: 10.1038/ncomms1642

Li et al. (2010) Plumage patterns of an extinct dinosaur, Science, 327, 1369-1372

Negro et al. (2009) Porphyrins and pheomelanins contribute to the reddish juvenal plumage of black-shouldered kites, Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology, 153(3), 296-299

Zhang et al. (2010) Fossilized melanosomes and the colour of Cretaceous dinosaurs and birds, Nature, 463, 1075-1078

An Introduction to Fossil Preservation

Recently, the UKAFH invited me to write an article for them on fossil preservation. What kind of palaeontologist would possibly decline! [excluding inverts - they don't count]

This is just a nice basic guide to taphonomic processes, designed for people with limited knowledge of geology or palaeontology. Feedback, as always, is welcome!

 

 

Introduction

The fossil record is our one and only key to a physical understanding of ancient or extinct life. Over the years a wealth of fossil remains have been uncovered, ranging from the earliest microbial life to the largest eukaryotic animals, and from isotopic signatures to fragments of DNA. These remains of dead organisms are found in two major divisions: as body fossils, where an actual specimen is preserved in some form or as trace fossils, where a particular aspect of an organism’s life is preserved, typically as trackways or burrows.

Processes

The process of preservation is termed taphonomy, and can be broken down into three main stages: necrosis, biostratinomy and diagenesis. The death of an organism, necrosis, is the initial stage in preservation, and is related to either trauma or physiology. Biostratinomy refers to the processes from death to post-mortem burial, such as transportation, bacterial decay and potential scavenging. The time taken during this stage is a critical aspect of preservation likelihood. Finally, diagenesis refers to the processes relating to the transformation of sediments into rock, and organisms into fossils. The mode of preservation leading to what we see in rocks is determined at this point, through the interaction of the surrounding sediment chemistry and the recalcitrance of various tissues. During these three stages, numerous factors act to destroy fossils, including microbial decay, predation, and a multitude of biogeochemical processes. In order for a fossil to be preserved, at some point in the taphonomic cycle, one or more of these processes must be arrested. The degree to which taphonomic breakdown is prevented is directly proportional to the degree of preservation attained.

Modes of Preservation

Permineralisation or Petrifaction

This is the most common style whereby soluble minerals in the surrounding sediments and fluids are deposited within interstitial organic pore spaces, leading to a variety of styles of preservation. This is the most common preservation in most invertebrates, organic-walled microfossils and bones. Directly observable using various microscopic methods, this needs to be distinguished from recrystallization and dissolution processes to reconstruct the initial tissue structure.

Desiccation

The most infamous recent occurrence of desiccation-based preservation is the “dinosaur mummy” from Dakota, the aptly named, Dakota. This Upper Cretaceous hadrosaur preserves actual recrystallized tissue remains, including tendons and ligaments and the epidermal microstructure, in amazing detail. The carcass is thought to have undergone rapid burial on the periphery of a sandy river channel, enclosing it in an anoxic environment and significantly enhancing its preservation.

Tar

The La Brea Tar Pits in Los Angeles, California are renowned for the immaculate presence of a multitude of Pleistocene-age mammals. They are the products of crude oil seepage, with lighter hydrocarbon phases being siphoned off via fractionation until just sticky tar remains. The predominant hypothesis for the mass accumulations of fossils is that, once an animal was mired, it became the target for packs of predators, who ultimately met the same sticky fate as their intended prey. Little soft tissue is preserved, but the concentration of bones more than compensates. The bones are actually infused by the tar, turning them a dark brown colour. Smaller invertebrates as well as plant macro- and microfossils are also abundant here. The tar creates a completely anoxic environment in which little to no decay can occur.

Amber

Amber is the solidified remains of ancient tree sap. Organisms that are unlucky (or lucky?) enough to be preserved in amber create the most intricate and beautifully preserved fossils of all. Featuring prominently as John Hammond’s cane top in Jurassic Park, they deserve pride of place due to the exquisite detail typically preserved. The most famous deposit is the Eocene-age Baltic Amber, which has produced perfectly preserved plants, insects and even small vertebrates. Amber, like tar, entombs organisms within a completely anoxic environment, ceasing all decompositional processes.

Carbonisation

This process involves the conversion of organic tissues into a carbonaceous film or residue through either pyrolysis (i.e., thermochemical decomposition) or destructive distillation (anaerobic decomposition), usually as a result of low-grade regional metamorphism. It is the process that converts woody material into coal seams. Typical fossils found preserved like this are graptolites in shales, typically associated with scavenger-free deep-water anoxic environments, as well as marine vertebrate integument (e.g., in the Holzmaden Shale).

Permafrost

Infamous for the occasional Woolly mammoth occurrence in Alaska and Siberia. The conditions lock organisms, complete with integument and flesh, in time. DNA has even been extracted from several specimens and is incredibly useful in accurately retracing pachyderm lineages.

Volcanogenic

Classic examples where volcanic interaction has led to sites of exceptional taphonomy include the Mistaken Point Biota (Ediacaran, Newfoundland), and the Jehol Biota (Lower Cretaceous, China). The advantages of volcanogenic interaction are two-fold; firstly, they create toxic, anoxic environments, and are typically rapidly deposited creating the perfect preservational scenario. Secondly, they contain radioactive elements which can be used for high-precision radiometric dating, which can be applied by association to intercalated fossiliferous horizons. At the two mentioned sites, episodic ash falls capture and smother local fauna and flora. These are typically found interbedded with thin mudstones and shales, suggestion that they are lakeside communities mixed in with autochthonous benthic fauna. Fauna preserved associated with these ash deposits have a diagnostic opisthotonic neck posture, infamously depicted in the birds and avian theropods of the Jehol fauna, in the classic ‘angel pose’. This is possibly indicative of hypersaline or toxic waters as a cause of death.

Traces

The study of trace fossils is known as Ichnology. Trace fossils are the direct result of biological activity and have their own independent taxonomic system. This makes them extremely useful in reconstructing the behavioural palaeoecology of extinct organisms. They can represent anything from nesting sites, to anastomosing series of trackways, and can be preserved as either exogenic (on the surface of a fabric) or endogenic (made within sediments). The preservation potential for trace fossils is typically a function of grain size and depositional facies.

Geological Biases

The fossil record is an incredibly biased sample of ancient ecosystems. Scientists estimate that only 15% of the composite species in an ecosystem are typically preserved, and of these, most are those with ‘hard parts’ (e.g., shells, cuticle, bone). There are also biases reflecting the depositional environment (e.g., fluvial, lacustrine, marine, aeolian, volcanogenic), and amount of rock sampled, amongst others, which recently scientists have begun to unravel in the hopes of better determining the controls on preservation through deep geological time, and the effect this has on our understanding of the fossil record and diversity dynamics.

Lagerstätte

Occasionally, palaeontologists are fortunate enough to come across sites of exceptional preservation known as Lagerstätten (German for ‘storage place’). These represent snapshots in time, and come into two flavours: Konservat-Lagerstätten and Konzentrat-Lagerstätten. The former represents an accumulation of fossils where the detail preserved is on an incredibly intricate level, such that ‘soft parts’ are visible, even to the molecular level. The best known examples of these include the Burgess Shale (Cambrian, Canadian Rockies), and the Jehol Biota (Lower Cretaceous, China). Here, preservation of articulated elements, original labile soft tissues, unaltered mineral compositions and orientations, and even intracellular structure can be preserved, indicating the early termination of diagenetic processes or that early mineralisation sufficiently outpaced degradation. Konzentrat-Lagerstätte, on the other hand, represent unusually high concentrations of fossils, typically representing an in situ community. A classic example of this is the Morrison Formation bone bed (Late Jurassic, North America). Deposits like these typically represent mass mortality events such as flooding.

Recent Advances

Until recently, most fossils were interpreted in terms of their macroscopic preservation features. However, with technological advances such as the increasingly commonly used computed-tomography (CT) scanning and scanning-electron microscopy (SEM), sophisticated details about micro-scale preservation in numerous fossils are being recovered. Accordingly, palaeontologists are uncovering more about macro- and micro-scale physical features, as well as physiological, cellular and even sub-cellular processes.

Further Reading

Allison, P. A. and Bottjer, D. J. (2011) Taphonomy: process and bias through time, second edition, New York: Springer

Nudds, J. and Selden, P. (2008) Fossil-Lagerstätten, Geology Today, 24(4), 153-158

Schweitzer, M. H., Avci, R., Collier, T. and Goodwin, M. B. (2008) Microscopic, chemical and molecular methods for examining fossil preservation, Comptes Rendus Palevol, 7, 159-184

Upchurch, P., Mannion, P. D., Benson, R. B. J., Butler, R. J. & Carrano, M. T. (2011, in press). Geological and anthropogenic controls on the sampling of the terrestrial fossil record: a case study from the Dinosauria. In: Comparing the Geological and Fossil Records: Implications for Biodiversity Studies, McGowan, A. J. and Smith, A. B. (eds). Geological Society, London, Special Publication 358: 209-240

Anomalocaris, I choose you!

The origin of life began in our oceans. Complex life, with some forms somewhat resembling what we see today and others too bizarre to even imagine arose over half a billion years ago. This is a time way before the rule of the dinosaurs, and even older than your great great grandparents. Life in the seas is teeming with experimental forms. Perhaps one of the more famous ancient critturs, is Anomalocaris. It was the apex predator of the primordial Cambrian seas, sizing up at over 3 feet in length, which is a pretty terrifying prospect for any contemporaneous organisms!

Copyright of someone else

 

A new study by a research time led by John R. Patterson and published in Nature reports on the visionary system of these ancient predators. Soft-bodied preservation in fossils is incredibly rare, as any palaeontologist will tell you. They are typically confined to Konservat-Lagerstätten, the most famous of which is undoubtedly the Burgess Shale of British Columbia. The authors of this latest study describe exceptional fossils from the Cambrian aged Emu Bay Shale of South Australia, including the notorious Anomalocaris preserved in exquisite detail.

The preservation of structural detail is so pristine, that 16,000 hexagonally packed lenses are visible (using scanning-electron microscopy) in a single compound eye. This would have granted Anomalocaris supreme hunting vision, rivalling the sharpest vision of any extant insects! The authors speculate that this ‘key innovation’ (aspects of organismal phenotype that promote diversification) could have been a catalyst for the largely accepted Cambrian ‘arms race’.

This seems to be another case, where fossil species that have previously been considered as ‘evolutionary dead-ends’, have actually proven to be exceptionally morphologically ‘advanced’, even compared to modern organisms. Just because a particular species is extant today, it does not in any way imply that they are more evolutionarily ‘advanced’ than a species that is extinct. Species go extinct for numerous reasons; environmental, climatic, and trophic factors, to name a few, all play a part in the likelihood of a species’ success. For example, pandas may be an evolutionary dead-end, as they are largely unable to adapt to their local environment (to quote a palaeontologists’ favourite case). Conversely, theropod dinosaurs were some of the most successful predators to ever live on Earth, but the [non-avian] lineages went extinct due to extrinsic casual factors that had little to do with their intrinsic biology. Needless to say, if a meteorite hit the Earth right now *touch wood*, and our species was wiped out, would we be historically remembered as evolutionary successes or failures?

As a final thought, what would it be like if Anomalocaris was still around today..?

 

Maybe I should take up artistry instead..

A man can dream, a man can dream..