Wednesday 7 November 2018

The Calm Before The Storm

Hello there after a year of silence. I intended to post on some of my misdeeds over the summer, but this unfortunately slipped my mind. Perhaps this was for the best, as I can directly follow on from my previous post. As a quick precis of that post, I am redirecting this blog to provide a personal account of applying for PhDs. I was inspired to do this by two sources: 1) a blog by a colleague of mine abut what actual PhD life is like; 2) a blog post about a researcher's personal experience of the trials and triumphs of post doctoral life. Both gave me insight into my future career path that I was unaware of and could not have hoped to have obtained from a workshop on how to apply for this, that and the other. I hope to provide the same resource for the antecedant step in the academic pipeline so that the reader might have a better idea about what application is like and whether a PhD is for them.

As a brief prelude, I'll give a brief picture of my position prior to application. I have wanted to pursue a career in academia since I started my integrated master's course in palaeontology and evolution at the University of Bristol. My vague understanding of PhDs at that time was that they were competitive. To that end, I decided to start building a portfolio of research and CV candy that I could use as ammunition for future PhD applications. These were derived primarily from research projects which have given me a record of publication and a range of practical skills (coding, CT data segmentation, statistical methods ect), and attendance of scientific conferences. While I undertook these endevours with the endgoal of PhDs in mind, I also genuinely wanted to conduct research for research's sake and had a great time doing so. Indeed, they helped confirm for me that academia was what I wanted to do. In my experience, it was hugely worthwhile to dip a toe into research before taking the plunge.

So why am I writing now? Because I have now had 'the talk'. In a meeting with my personal tutor and MSc supervisor Professor Michael Benton, he asked the dreaded question of 'so what next after uni?'. My answer: 'PhD'. Mike's first bit of advice was to apply for everything that interests you. There is no point doing a PhD that you are not going to enjoy, but equally it is perhaps too risky to apply for just that 'perfect project'. I had that perfect project lined up, incidentally with Mike as a supervisor, and so was a little surprised when he said this. Mike's next point made sense of the need to apply for multiple projects, a point that I had failed to fully appreciate - PhD's are not just competitive; they are BLOODY competitive.

Funding, at least for sciences in the UK, is part of what drives this competition. While the UK government now offers PhD loans, I was not keen on the idea of another £50,000 debt on top of my undergraduate loans. Instead, most science PhDs are funded by grants from a number of different bodies. The Royal Society or the Leverhulme Foundation offer grants to support research projects, which in turn are then undertaken by a PhD fellow. The largest UK funding body, however, is the National Environmental Research Council (NERC). NERC was another PhD-related entity that I was vaguely aware of, but have only recently begun to get to grips with, again with surprises in store. Note: every funding-related point in this post relates to NERC and NERC funded PhDs specifically.

NERC has a number of different subgroups which award PhD funds depending on the location of the hosting university. I will be applying for a number of projects at the University of Bristol and so NERC funding for these projects comes under the long-winded acronym of NERC GW4+ DTP2. GW4+ refers to the four West Country (Great Western - GW) universities of Bristol, Bath, Exeter, Cardiff plus (+) non-university institutions like the British Geological Survey or British Antarctic Survey). DTP is simply the doctoral training partnership. I have no idea what the 2 refers to.

I previously thought that I would apply for a funded PhD position in competition with other applicants, and  that the PhD supervisor(s) would make their choice. Not so. Instead I will be in competition with all other applicants applying to GW4+ hosted PhDs, for around 30 NERC funding awards. This changed the way I viewed the process of the PhD application and just how competitive it is. What I did not realise is that the project and the candidate are somewhat separate elements. A supervisor submits a PhD for funding consideration and NERC accepts it if it will further NERC's overarching research goals (detailed on their website). NERC then awards funding to a PhD candidate applying for a project under consideration for funding, regardless of what the project is, based on the strength of that candidate. Effectively, NERC chooses which projects are bound to advance their research goals, then makes a calculated investment in a candidate who is likely to make them a return on that investment by completing any of those projects, and in their potential future career as a post-doctoral researcher. Of course, your worthiness is still partly contingent on your choice of PhD project. It would be a poor investment on the part of NERC to fund a student with a stunning track record in isotope geochemistry for a considered project on elateroid beetle parasitology, despite the individual academic viabilities of the candidate and the project. Consequently, Mike's initial advice about applying for multiple PhD projects at a variety of institutions is not just to increase your chances of getting a PhD outright, but to increase the chances that a research council will consider you to be a worthy candidate for funding.

Next came a point about interviews. I will be able to provide a much more personal account of this part of the process down the line, but for now I will focus again on what I gained from my conversation with Mike. As I thought that the supervisor selected the candidate, I thought that the interview panel would include the supervisor, or be conducted solely by the supervisor themself. Not so. As NERC is assessing potential for investment, the panel consists of NERC-selected individuals who have nothing to do with the project. According to Mike, the interval will then proceed through three main phases: past (your previous academic track record - credentials), present (why this PhD - show your passion) and future (what will you do after your PhD - future return on the investment). Finally, Mike mentioned that during the interview it may be of use to have physical records of your achievements to hand - handing the panel the first page of your published scientific paper will have a powerful impact.

At this point I am feeling quite confident about application. There are several projects which would be a good fit for me and the experiences gained throughout my undergraduate degree, both research-wise and module-wise give me the credentials to back this up on my applications. While it has meant fewer family holidays during the summer than I would have liked, I feel that my investment in this academic ammunition will pay off. The proof, however, will be in the pudding.

Friday 5 January 2018

Awful Changes

Awful Changes (1830) by Henry de la Beche. Here, de la Beche
encapsulated the growing public and scientific concern posed by
the fossil record about the possibility of extinction.
The discovery of ichthyosaurs by the world-famous fossil hunter Mary Anning in 1811 marked the beginning of a revolution in both biology and geology. 15 years previously, the great naturalist Georges Cuvier documented fossil elephants which had no living representatives, determining that the species must be extinct. The revelation that animals could vanish from the face of an Earth created by a benevolent, loving God was concerning, but it was tempered by the herds of living elephants which roamed the African savannah and Indian jungles. Perhaps a few primitive tribes might become extinct every now and again but surely entire groups of organisms, products of divine thought, would persist? Yet ichthyosaurs, with their dolphin-shaped body, but distinctly reptilian anatomy, were unlike anything that still existed. They proved that life on Earth was not only fragile, but truly vulnerable unto the point of total extinction. Along with the burgeoning science of geology, ichthyosaurs became part of an unsettling enlightenment which illuminated deep time, lost worlds and cataclysmic revolutions that changed the face of the Earth itself. Thought turned to mankind's place in this world. Were we really God's chosen race to keep dominion over the Earth or were we just like any another species, lost in a seemingly endless expanse of geological time and just as susceptible to its ravages as the ichthyosaurs? This fear was encapsulated by Henry de la Beche in his 1830 cartoon Awful Changes, depicting the extinction of humanity and the return of ichthyosaurs in an entirely new age on Earth.

I draw your attention to Awful Changes for three reasons. Firstly it is a great cartoon, secondly advertisement with a spot of shameless self promotion. Dinosaurs have dominated the palaeontological spotlight in the media, but ichthyosaurs have finally been given their own documentary, presented by Sir David Attenborough! Attenborough and the Sea Dragon, due to air this coming Sunday at 20:00 on BBC1 will document the discovery of a new species of ichthyosaur, using cutting edge analytical techniques to reconstruct everything from its skeleton to the colour of its skin. I had the privilege of working on the former, digitally extracting the bones from CT scan data and putting the complete skeleton back together. This will be featured on the program, along with about three seconds of my left ear and right hand. I had the chance to meet the great man as well as see some of the filming on site at the University of Bristol and I can promise it will be an excellent show.

Ben (bottom right) entertains us with tales of the Jurassic
seas. I am third from the left, wearing the dark blue shirt
The third reason is change itself. The last year has kept me too busy to be able to regularly update this blog. While reading papers from the forefront of palaeontological research should theoretically give me still more to blog about, the time taken to read and digest those papers is substantial. Additionally, a greater appreciation for the controversies and caveats surrounding cutting edge research makes it difficult to write popular science blog articles without getting bogged down in the technical details and internally quibbling about how accurate my article really is. I will only become busier over the coming months, particularly this time next year when I will apply for PhDs in palaeontology. This may present an opportunity for rebranding and rejuvenating my blog, however. Two other blogs have inspired this change. Dr Ben Moon's excellent blog on ichthyosaurs also provides a record of his deeds and doings during his own PhD. Ben was my supervisor on reconstructing the ichthyosaur for the BBC and features for much longer than three seconds on the BBC program, highlighting the key features of the skeleton and its scientific importance. You can check out his blog here:

My other source of inspiration comes from a blog post written by Dr Paul Barrett, a dinosaur palaeontologist at London's Natural History Museum. Dr Barret's article focuses not on his work, but rather what the life of a post doctoral researcher is like, from its greatest moments to the trials and tribulations it can also bring. After my PhD I intend to continue palaeontological research and Dr Barret's article gave me a perspective on my chosen career path that I had neither considered or was even previously aware of. You can check out his article here:

As Dr Barrett details at the end of his article, he does not preach about how to be a post doctoral researcher. Rather, he provides a case study of what it can be like; I found this far more personal and useful than other more practically focused online resources about PhDs - the NERC postgraduate application guidelines are terribly specific and terribly dry! Thus, inspired by both Drs, I will aim to provide a case study of what it is like to be a PhD student. What I record here will hopefully be of use not just to fossil fondlers like myself, but to any undergraduate or even secondary school student considering the career path I am pursuing. By making this change now, I will not only be able to provide a case study of my PhD, but also of the application process. I will likely begin posting in earnest next December. I may occasionally indulge in some self promotion about my ongoing research or publications. As these will likely be an important aspect of my PhD application, it may be useful to have a brief record of them here. Blogging about palaeontological news stories has been great fun, but it is time for a (not so awful) change. More anon...

Tuesday 31 January 2017

A Tail Of Two Histories

The basic vertebrate body plan is a tube with a head at one end and a tail at the other. Over millions of years it has been ornamented with all manner of adaptations, including limbs, fins, spines, teeth, eyes and even secondary loss of such features, yet the basic plan has persisted. Heads are crucial to the body, providing the bulk of sensory information and neurological processing, and adaptations for specific modes of feeding. Tails are similarly important. In virtually all marine vertebrates it is the primary means of propulsion. In many species of primate it serves as a fifth limb for rapid maneuvering in tree tops, while in several big cats it is used to balance the forces acting on the body during a chase. Clearly the tail is a vital element of vertebrate evolutionary history.

The evolutionary progression of tails in primitive and derived
fish, showing the place of Aetheretmon valentiacum
The largest group of fish alive today are the teleosts. The embryos of these fish have an asymmetrical 'dual tail' consisting of an upper scaly branch containing the vertebral column and a lower fleshy lobe, the caudal fin. The growth of this upper tail is stunted during early development, becoming part of the body, while the caudal fin grows into a symmetrical tail in the adult form.

Primitive relatives of teleosts, the chrondrosteans, carry a dual tail structure into adulthood. What this suggests is that the loss of the upper tail during teleost development was an example of ontogeny (embryological development) recapitulating phylogeny (evolutionary development). Yet without fossils of a primitive two-tailed ancestor this theory is somewhat weakened.

Now a recent study of 350 million year old fish fossils from Scotland has provided conclusive proof that the theory is incorrect, providing a more suprising view of vertebrate evolutionary history. Lauren Sallan, an assistant professor in the School of Arts & Science's Department of Earth and Environmental Science, studied fossils of an extinct teleost relative Aetheretmon valentiacum which had resided, largely unstudied, in fossil collections across Scotland. The smallest specimens, barely over an inch in length, were of juveniles at an intermediate stage of development. If ontogeny had recapitulated phylogeny, then these juveniles should have been similar in form to adults. Yet the juveniles had a tail like that of modern teleost juveniles, while the adults had asymmetrical tails more like chondrosteans.

The asymmetric tail of Aetheretmon valentiacum (front)
versus the symmetrical tail of modern teleosts (back)
'What this shows is that ancient fish and modern fish had the same developmental starting point that has been shared over 350 million years,' said Sallan. 'It's not the ancestral tail showing up in modern teleost larvae; it's that all fish have two different structures to their tail that have been adjusted over time based on function and ecology for all of these species.'

This argument extends to tetrapods which are descended from the same class of fish as the teleosts. As such, the tails of tetrapods and modern fish are not truly the same structure adapted for different purposes; instead in the former the lower caudal tail is lost and the vertebral tail enlarged, while in the latter the upper tail is reduced and the caudal fin enlarged.

'It tells us why we have all this diversity in fins and limbs in past and present,' added Sallan. 'There might have been some lineages that favored one form over another for functional or ecological reasons. If a fish couldn't adapt this trait, which is so vital for swimming, they might have gone extinct.'

The next step in studying this quirk of evolution would be to confirm the molecular pathways underlying the dual tail development in tetrapods and fish.

Saturday 19 November 2016

The First Invasion Of The Land

In most accounts of evolutionary history, the first invasion of the land was by plants, closely followed by animals. Yet it is becoming increasingly clear that the first true invasion actually occurred many hundreds of millions years earlier. Even before the first slimy, leafless plants basked on some rocky shore of Gondwana or Laurentia, a thin microbial scum spanned the otherwise barren waterways of these continents. How far back the terrestrial fossil record extends, however, has been less clear. Microbes are certainly hardy, yet the Earth's continents were a much harsher place billions of years ago; virtually devoid of nutrients and blasted by radiation.

The Barberton Mountains contain some of the most ancient rocks on Earth
Recently, however, evidence has shown that in spite of these hostile conditions, there were living organisms on Earth an incredible 3.22 billion years ago. Some of the oldest rocks on Earth can be found in the Barberton Belt in South Africa.

In 2013, fieldwork conducted by an international team of researchers recovered rock samples from an ancient braided river system and the surrounding soils - palaeosols. Contained within these samples were microscopic grains of iron sulphide which showed a layered structure. By examining the ratio of sulphur isotopes in the mineral, the researchers found that exterior rim ratio matched that found in modern environments inhabited by sulphur bacteria. In addition the cores of the grains bore a different ratio.

This suggested that the fluctuating braided rivers periodically exposed the grains to either dry or wet conditions. During the latter, sulphur bacteria colonised the grains, leading to the different composition of the rims. At 3.22 billion years, the rocks constitute the oldest evidence for terrestrial life. The conditions the sulphur bacteria endured were undoubtedly harsh, including periodic desiccation and constant exposure to ultraviolet radiation. The fact that they were able to colonise such an environment, shows that they must have developed already the genes required to make them the hardy survivors they are today.

Three billion year old rocks from Pilbara
which preserve an ancient microbiome
A second study, this time by researchers from the University of Oregon, has shown that not only was there life on the land during the late Archaean eon, 3 billion years ago, but that complex ecosystems also formed.

Using advanced imaging techniques and isotopic analysis on three billion year old palaeosols from Pilbara, Australia, they found a microbiome consisting of five distinct species. The largest were the spindle-shaped actinobacteria, which are an important component of soils. Smaller spherical forms were similar to purple sulphur bacteria, whose metabolic activities were likely responsible for the sulphate minerals detected within the soil.

'With cell densities of over 1,000 per square millimetre and a diversity of producers and consumers, these microfossils represent a functioning terrestrial ecosystem, not just a few stray cells,' said Gregory Retallack, a professor in the Department of Earth Sciences and director of paleontology collections at the Museum of Natural and Cultural History, University of Oregon. 'They are evidence that life in soils was critical to the cycles of carbon, phosphorus, sulphur and nitrogen very early in the history of the planet.'

The researchers went on to say that these palaeosols may be a useful guide for the search of life on other planets. When we peer further back in time, the degree of difference between the rocky planets in our solar system regresses significantly. As such, to look at the earliest ecosystems is not just a view into the past, but possibly one across space as well.

On The Origin Of Coral Symbiosis

The beautiful colours of corals come from dinoflagellate
algae living within their tissues in a symbiotic relationship
Ever since the advent of cameras capable of filming underwater, there have been a surfeit of nature documentaries full of beautiful, vibrant images of coral reefs. Not only are corals morphologically diverse, they often display an extraordinary range of colours. This results from algae which live within the coral tissue and form symbiotic relationships with the animals. Ecological studies have shown that these symbioses have proved critical to the success of corals in recent geological history, hence why the phenomenon of coral bleaching - the loss of the algae under stressful conditions - is a worrying prospect for future biodiversity. It has been less clear, however, when this relationship first arose and how it may have contributed to the success of corals in the past.

The algae, specifically dinoflagellates, have little in the way of a fossil record, let alone one which can be conclusively linked to corals. Instead an international team of researchers looked at the ratios of isotopes of nitrogen, carbon and oxygen, as dinoflagellates have a significant impact on ammonium uptake and carbonate deposition in the coral tissue. Studying modern corals, they found that symbiosis correlated with a low ratio of 14N to 15N. Polished sections of corals from 210 million year old rocks from Antayla, Turkey, were then examined in the same fashion.

'Although algae were not present in the fossils, they left behind chemical signatures,' said Xingchen Wang from Princeton University. 'We found strong evidence that the fossilized coral were symbiotic and that they lived in a nutrient-poor environment. We were able to link the environmental conditions from 200 million years ago to the evolution of corals.'

Polished sections of 210 million year old, well
preserved corals from Antayla, Turkey
Corals are generally assumed to indicate shallow, sunlit marine conditions, although deep water, darker forms are known. This study helps confirm that the Antayla corals did hail from such an environment, and provides a methodological framework for investigations of dinoflagellate symbiosis in other coral fossils.

Corals suffered a catastrophic decline during the PT mass extinction 250 million years ago, along with virtually all other marine clades. In the wake of this event, modern scleractinian corals evolved. This clade expanded rapidly 205 million years ago, suggesting that symbiosis may have driven their rise. This highlights the importance of preventing coral bleaching in order to help preserve the biodiversity of not just corals, but the reef habitats they form, habitats which are increasingly under threat from human activity.

Thursday 10 November 2016

A Preserved Dinosaur Brain (Yep You Read It Right)

From nervous systems and skin to DNA and proteins, recent advances in technology combined with new discoveries and analyses of old specimens have rapidly broadened the parameters of what we know the fossil record is capable of preserving. Yet sometimes the fossil record throws up specimens which seem like they are straight out a science fiction story. The idea of finding a fossilised dinosaur brain sounds like a plot element from an outlandish B movie, but against all expectations that is exactly what has been uncovered. What is more, this brain is not from an exciting new site in China or Brazil, both famous for the remarkable quality of many of their fossils, but from the UK - the home of dinosaur palaeontology and palaeontology itself.

The brain endocast and a tomographic rendering of it. Scale bar is one centimetre
The specimen was found in 2004 by an amateur fossil hunter near Bexhill, Surrey. To the untrained eye it is just a small brown pebble, but distinctive features show it to be an endocast of a dinosaur skull.

Endocasts form when sediment infills a skull and preserves an internal mould of the brain case. These are typically simple objects which record topography. This specimen, however, is one of those rare examples where the internal microstructure of the brain is also preserved.

133 million years ago Sussex was a swampy floodplain environment interspersed with forests. Anoxic, acidic conditions in the swamps prevented bacterial decay while fine sediment allowed for faithful preservation of the microstructure. In this case this is the first instance it has been recorded from a dinosaur.

The chances of preserving brain tissue are incredibly small, so the discovery of this specimen is astonishing," said co-author Dr Alex Liu from Cambridge's Department of Earth Sciences.

Using a mix of SEM and CT scanning, an international team of researchers were able to reconstruct networks of blood vessels and collagen strands within the outer neural tissues of the meninges. The shape of the endocast showed that it likely came from a close relative of Iguanodon, one of the first dinosaurs to be named. The structure of these meninges was neurologically closest to crocodiles and birds. This makes sense as phylogenetically crocodiles are their closest living relatives while birds are nested within the dinosaur clade.

'As we can't see the lobes of the brain itself, we can't say for sure how big this dinosaur's brain was,' said Norman. 'Of course, it's entirely possible that dinosaurs had bigger brains than we give them credit for, but we can't tell from this specimen alone. What's truly remarkable is that conditions were just right in order to allow preservation of the brain tissue. Hopefully this is the first of many such discoveries.'

The discovery of a dinosaur brain is a crucial step in palaeontology being able to study dinosaur physiology as if these creatures were alive today.

Wednesday 12 October 2016

A Devonian Nursery

A cluster of mantid hatchlings on the underside of a leaf
Some animal parents devote little care to their young. Many mantids will simply glue their clutch of eggs to the underside of a leaf and leave them to it. Hatchlings have to fend for themselves, and not just from predators, cannibalism amongst siblings is common.

Other animals are rather more attentive to their broods' needs. African bullfrog males will watch over pools containing developing tadpoles, even going so far as to dig canals to larger bodies of water if the nursery pool is in danger of drying up. Nursery-type behaviours have also been observed in the fossil record from a diverse array of organisms ranging from dinosaurs to sharks.

Recently one such nursing site has been uncovered in 360 million year old rocks in a quarry in Belgium. It is special as it is the oldest known instance of multiple species, specifically of placoderms, using a common nursery. Placoderms were an ancient lineage of fish which flourished during the Silurian and Devonian. They were the first vertebrates to develop jaws, which encouraged a wide range of feeding possibilities and ecological niches. While their skeletons were composed of cartilage, they were covered in plates of body armour.

A reconstruction of the immative placoderms and the
Strud nursery. Order of species is same as in the text
'These sorts of juvenile-only assemblages are rare in the fossil record,' said Dr Ted Daeschler from the Academy of Natural Sciences of Drexel University, 'We are quite sure that the juvenile-only placoderm assemblage is not the result of sorting of small material by water currents because there are larger skeletal elements of other kinds of fish. We believe this points to a nursery.'

Discovered near Strud, the site consisted of a multitude of largely complete skeletons of immature fish species Turrisaspis strudensis, Grossilepis rikiki and Phyllolepis undulata alongside the elements of the adults. The paucity of adults suggests that the site was only used for egg laying and/or live birth as opposed to parental care, yet was well protected from predators. It was shallow and contained slow-moving, sheltered water and was further protected by large, spiny plants, fossils of which were found alongside the placoderms.

'By studying the past, with the ability to see a moment in time and changes through time, we are better able to understand ecosystems and the organisms that live in them today,' said Sebastien Olive also from Drexel University. 'Geologists say that the present is the key to understanding the past. But we can also say that the past is the key to understanding the future.'

Today many mating, nesting and nursery sites in multiple ecosystems are threatened by human activities. An understanding of their mechanics in response to past conditions is key to effective direction for current and future conservation schemes.

Sunday 4 September 2016

A New Contender For The Earliest Known Fossils

The identity of the oldest fossil is hotly contested. As palaeontology is the science which concerns itself with the remains of past life on the planet, the oldest definite traces of life are perhaps its most important pursuit. For decades the focus has been the rocks of the Pilbara craton in Western Australia. Ranging from 3 to 3.5 billion years old they are among the more ancient records of the early planet, and as they are largely sedimentary, have excellent fossil preservation.

New discoveries are always contentious, however. Recently the Apex Chert fossils, dated at 3.43 billion years old and hailed for years as the oldest fossils on earth, were shown to be no more than hydrothermal artefacts which happened to look like bacterial filaments.

The site in Isua where the fossils were identified
Since then, fossils from Pilbara have buffeted this title back and forth by a few tens of millions of years, most recently settling on 3.48-billion-year-old stromatolites from the Dresser Formation.

Yet a new discovery led by Professor Allen Nutman from the University of Wollongong, Australia, may push back the definitive record of life on earth by an incredible 220 million years.

Rocks older than those of the Pilbara craton are rare, but a significant amount exists in the Isua Supracrustal Belt in Greenland. The older sediments in the Belt have been largely metamorphosed and so have offered little opportunity for palaeontological study. The likely presence of stromatolites, however, has been identified in sediments dated to 3.7 billion years old.

A and B: the 3.7 billion year old Isua stromatolites. C and D:
younger, indisputable Australian stromatolites for comparison
The rocks were recently exposed by snowmelt and consist of dolomites and storm-wave generated breccias. Rare earth element signatures in the rocks suggest a marine setting. This image of a shallow sea fits with younger, uncontested stromatolite assemblages. The macroscopic nature of the stromatolites is a good start, but there are many processes which can create similarly shaped, layered structures.

Their biogenicity, however, is supported by four lines of evidence. The specimens are internally laminated in a way which could not have been generated by post-depositional processes; an isotopic and rare earth element signature which precludes a hydrothermal origin; the presence of an originally low temperature dolomite which requires a microbial origin; and on lapping of the dolomite matrix with the stromatolites, indication growth above the boundary of the sediment and the water, a non-sedimentary phenomenon.

The age of the stromatolites is the same as the most parsimonious estimates for the origin of life. Their complexity therefore indicates that the origin of life is older still. How much older is difficult to say. Preserved carbon isotope ratios indicate biological processes at 3.8 billion years old. Isotopic evidence by itself is not the strongest case, but these newly discovered stromatolites suggest that the signature may be genuine. Geological evidence shows that the early planet was much more hospitable than previously suspected and so the origin of life may well be over four billion years old. Such an age also has intriguing implications for how life may have affected early geochemical cycles on the planet to make it more hospitable, thus paving the way for later, more complex developments in evolutionary history.

Friday 2 September 2016

On The Origin of Tethys

Faulted basalts at the mid Atlantic ridge
Alfred Wegener proposed the theory of continental drift in 1915, but it would take several decades before key evidence to support the theory came to light.

Amongst the breakthroughs which vindicated Wegener was the discovery of the liquid mantle on which the crust floated and the identification of fossil assemblages which hinted at successive reconfigurations of ancient continents.

Yet the biggest breakthrough was the discovery of seafloor spreading. Sampling of the Atlantic seabed had shown that it was composed of basalt and the volcanic source of the rock to be a linear extrusion zone in the middle of the ocean – the mid ocean ridge. Magnetic surveys revealed on either side of this ridge stripes of basalt which had been polarised in alternating directions by the reversals of the Earth’s magnetic field. Today this mirrored magnetic ‘bar code’ is the classic signature of a spreading centre and of the formation of new ocean seafloor.

The Atlantic was the first place where this bar code was identified and since then it has been identified in the Pacific. As new ocean floor is generated on one side of a tectonic plate, however, it is destroyed by subduction on the opposite, As such the oldest identified oceanic crust was from the mid Jurassic at just 180 million years old. Recently, however, a far older bar code was found in the Mediterranean. Collection of tectonic data about the Mediterranean basin has been limited by the thick sedimentary layers covering its bottom. Magnetic surveying by a team led by Roi Granot from the Ben-Gurion University of the Negev, Israel, found a bar code signature dated at 340 million years old – early Carboniferous.

The red tracks show anomalous magnetic data, indicative
of the ancient bar code pattern of the Tethys seafloor
Its position within the Mediterranean Sea suggests that it was once part of Tethys – the ocean which preceded the Atlantic and oversaw over 200 million years of evolutionary history.

This interpretation is intriguing as Tethys was thought to have formed during the breakup of Pangaea 300 million years ago. This new piece of evidence, suggests that the ocean was much older than previously thought.

‘With the new geophysical data, we could make a big step forward in our geological understanding of the area,’ said Granot.

In addition to its impact on regional geology, the opening of Tethys had a major impact on the biosphere due to the new epeiric ocean ecosystems that began to form. The earlier origin of the ocean therefore has important implications for the evolution of the new marine taxa during the Carboniferous.

Sunday 28 August 2016

Putting Up Roots, Laying Down Soil

The stems of marram grass anchor coastal dunes to a great depth
Smooth white sand is the look of an ideal beach holiday. Yet such perfect stretches bordering coastal dunes are restricted to a narrow band practically on the water line.

Move just a little further in-land and the sand becomes hummocky and dotted with thin stems of marram grass - a dune environment.

As Dunes are continually in flux, the grasses are often buried. They grow back rapidly towards the light and flourish until the next deluge. Yet tug on one of these grasses and you may end up pulling several metres of buried stem from the dune. Their presence plays a key role in stabilizing the dunes. In most environments roots anchor soils together, in coastal dunes it is the long stems of grasses. 

Recent evidence, however, has shown that a similar process may have also played a role in the geoengineering of the Earth during the invasion of the land by plants. Around 390 years ago, the first trees with long, deep-reaching roots evolved. These roots enhanced the weathering of rock which in turn promoted the formation of thick, nutrient rich soils. The soils themselves were then bound together by the roots of other, smaller plants.

This was the end of the geoengineering process, occurring tens of millions of years after plants made the move onto land. The earliest forms did not possess roots and so had no geoengineering impact. The intermediate stages are less well documented, but a recent discovery has shed light on the role stems played as well as the roots.

The 410 million year old rhizomes in floodplain sediments, with modern
plant roots hanging from the cliff face and breaking through the rock
Researchers, led by Jinzhuang Xue from Peking University, examined early Devonian sediments near Qujing City in Yunnan Province, China. Cliff exposures in one formation showed that the original floodplain sands and silts were interspersed with fossil rhizomes - stems - of the plant Drepanophycus.

These had not grown down through the sediment, but upwards to counter their burial by floodplain sediments, leaving behind an incredible 15 metres of rhizomes. Only the surface plant would have been alive, yet the dead rhizomes would have played a crucial role in stabilising the floodplain sediments into a primitive type of soil. This soil was not of the kinds which exist today.

'It’s a spectacular sequence of sediments,' said Paul Kenrick from the Natural History Museum. London. 'It’s not creating a structured soil profile, more of a stabilised sediment. It's important in that respect.' Soils form the basis of virtually all terrestrial ecosystems, allowing a wide variety of plants to develop and in turn support more complex ecosystems. Understanding their origin is therefore a key step in understanding the colonization of the land, as well as giving a different viewpoint on the problems facing soils today, including leaching and deforestation.

Saturday 20 August 2016

Through The Lamprey's Eye

Lampreys and hagfish are not the most attractive creatures. Eel-like in form, living unsavoury lifestyles as carcass scavengers or parasites, they are not creatures you would wish to keep as pets. Yet they are prized by scientists. Hagfish slime has remarkable hydroscopic properties, and immensely strong for its weight, is a potential source for new synthetic polymers.

These creatures are also useful to evolutionary biologists looking to examine the early phases of vertebrate evolution. Sitting at the base of the vertebrate family tree, they are the most primitive members of the group and so offer insight into the life and morphology of the extinct and truly basal vertebrate species. One thing which marks out lampreys and hagfish is their simplicity.

Their bodies are little more than a tube with a circular, jawless mouth at one end and a rod of cartilage down the back. Their eyes are similarly primitive - little more than light sensitive spots - suggesting that eyes in vertebrates were a gradual acquisition and that the lamprey-like early group members had little more than a basic construct. A recent fossil discovery, however, has overturned this classic view of vertebrate evolution.

The 300 million year old specimen of Mayomyzon, showing the
preserved lens and retina, and the coloured banding along its back
The Mazon Creek fossil locality in Illinois has yielded remarkably well preserved specimens of lampreys and hagfish, showing soft tissue preservation. Just this year, an enigmatic species known as Tullimonstrum gregarium was identified as the former after decades of confusion over its true identity.

By examining preserved eyes within 300 million year old fossils of Mayomyzon (lamprey) and Myxinikela (hagfish) an international team of researchers, led by Professor Sarah Gabott from the University of Leicester, were able to show that eyes were much more complex in ancestral members of both groups, rather than primitive as was once suspected. The fossils showed in beautiful detail that the eyes were not mere photosensitive patches, but similar to sophisticated camera eyes of other vertebrates, complete with lenses and retinas.

'Sight is perhaps our most cherished sense but its evolution in vertebrates is enigmatic and a cause célèbre for creationists,' said Professor Gabott. 'We bring new fossil evidence to bear on an iconic evolutionary problem: the early evolution of the vertebrate eye. We will now scrutinize the eyes of other ancient vertebrate fossils to see if we can finally build a picture of the sequence of events that took place in early vertebrate eye evolution.'

Sight is important not just in and of itself. It opens up investigations into new behavioural possibilities, including camouflage, mating displays and warning colouration; analysis of the fossils revealed the presence of striped bands along the animals' lengths. Combined with newfound evidence of the complexity of nervous systems in stem group members of the animal phyla during the Cambrian, it suggests the possibility that organisms on the budding branches of the tree of animal life possessed similarly complex behaviours.

Wednesday 20 July 2016

Cretaceous Birds From The Amber Time Machine

The phrase amber time machine, first used in an eponymous documentary presented by David Attenborough, perfectly captures the palaeontological importance of preserved tree resin. The views into the past offered by amber are perhaps the most detailed in existence and certainly some of the most extraordinary. From intricate predatory battles to intimate mating embraces, the amber time machine has presented a rich variety of snapshots of the past. Discarded vertebrate fragments, such as shed bird feathers or reptile skins, have been found in amber. Larger fragments and organisms on the other hand are rare as most vertebrate species are typically too large to be trapped in blobs of resin or are at least large enough to wriggle free.

MicroCT scan data of the two specimens, showing
the remarkable preservation of the skeletal anatomy
Small lizards have been recorded on a number of occasions, but recently two bird wings were discovered in Burmese amber from the Angbamo site in the Katchin Province of the country. One pair probably came from a dismembered individual, discarded by a predator or scavenger trying to avoid consuming the larger wing weathers. Claw marks in the amber and evidence of decay projects in the other specimen, however, suggest that the individual was engulfed while still living.

The bird was most likely a hatchling - a theory backed by the osteology of the specimens. The digit proportions and arrangement themselves indicate that these hatchlings belonged to a now extinct group of birds known as the enantiornithes. At 98 million years old, these specimens were not primitive enantiornithes, but their juvenile anatomy makes precise placement within the group's phylogeny difficult. The association of the three dimensional preserved feathers with the skeletal remains - something never seen before in the fossil record - offered the researchers other angles of analysis.

The remarkable association of the feathers with skeletal remains in three dimensions.
The red arrows indicate the position of the claws. The scale bar is 2.5 millimetres
The profiles of the rachis (the central supporting quill of the feather), the degree of interlocking of the barbules to confer rigidity, and the asymmetry of the overall feathers suggests that they were used for powered flight.

In turn the angles between the rachis and the barbs of the feathers are consistent with advanced flying birds, making it likely that these hatchlings were more advanced enantiornithes.

Intriguingly, the developmental characteristics of the feathers were closer to those of adults than those of juveniles, suggesting that feather development in enantiornithes skipped the downy juvenile stage seen in modern birds. Most incredibly, the original colour patterns are preserved in fantastic detail without the need to resort to the SEM analysis of melanosomes, used in previous studies of feather colouration in fossilised birds and dinosaurs.

While not paradigm-changing, these bird wings preserved in amber are truly remarkable due to the wealth of information they contain. Rarely do fossils give us such a complete view of vertebrate anatomy and morphology, and in virtually all cases, such fossils are preserved as flat films, like the spectacular theropods and avians from the Liaoning fossil beds. 3D preservation of such detail, however, is known only from amber and even amongst amber, these specimens are unique. This particular view through the amber time machine is nothing short of astonishing.

Ancient African Agriculture

Words like agriculture and cultivation are strongly associated with humans. 10,000 years ago agriculture revolutionized everything from our societies to our genetics. Yet the phenomenon is not just restricted to our species. Other, often overlooked species of farmer, are ants and termites. Certain species will allow the growth of fungus within their colonies which serve to break down plant matter into digestible material. These farms are complex with the worker ants carefully maintaining conditions suitable for growth, removing competitive species of fungus, and repelling others which might eat the crop. Now recent evidence has shown that this practice of fungal agriculture is far older than our own 10,000 year-old origin date.

A comparison of the fossil burrows and
fungus (left) with modern examples (right)
Previously, genetic studies suggested that fungal farming in termites originated at least 31 million years ago. Yet fossil evidence confirms the existence of farming behaviours just 6 million years after this proposed origin; in-situ gardens of fungus, within termite colonies, from the Rukwa rift basin in the Tanzanian portion of the Great African Rift Valley.

Volcanic ash in-filling the colony galleries, as well as preserving the delicate internal structures, allowed for accurate dating of the specimens to 25 million years old. Some of the in-filling material, however, was composed of grains with a spherical texture and composition consistent with mylospheres - pellets of fecal matter, plant material and fungal spores which act as the starting material for fungal gardens. A smaller number of specimens preserved sections of the developed fungus combs themselves.

Preserved mylospheres within the burrows
Apart from confirming the antiquity of the symbiotic relationship between termites and fungus, the discovery has interesting implications for the origin of the practice itself. 25 million years ago, Africa was covered by tropical rainforests. As time progressed, drier climates resulted in the development of grasslands until a final climatic shift just a few million years ago resulted in the spread of deserts across much of the continent.

Arid climates developed much earlier in Tanzania, however, due to the opening of the Great African Rift. Fungal farming dramatically increased the range of habitats available to termites, allowing them to adapt to newly arid niches, as well as a generally harsher climate. While not worth the tens of billions that human agriculture generates today, termite agriculture has had a vital influence on the planet's characteristics for far longer.

New Research Highlights the Gradual Nature Of The Eukaryote Endosymbiosis Event

The position of the lokiarchaeota within the tree of life
The evolutionary transition from prokaryote endosymbiote to true eukaryote is a puzzle which we are only just beginning to understand in detail.

Recent advances in molecular technologies have allowed us to pinpoint the origins of eukaryotic genes and cell components within the antecedant bacterial and archaeal cells. Similarly, recent advances in our understanding of the tree of life have given us new insight into the transition.

Alphaproteobacteria and cyanobacteria have been known to be the ancestors of mitochondria and chloroplasts respectively for a while, but the nature of the archaeal host cell was only vaguely understood until the discovery of the lokiarchaeota. Discovered just last year around a deep sea hydrothermal vent, the lokiarchaeota have been identified as the closest relatives of the eukaryotes and the group from which the archaeal host cell prevailed.

Despite having the start and end points of the transition, the lack of true intermediates has nevertheless hindered our understanding of the difficulties involved. Previously it was assumed that the endosymbiotic event was rapid and harmonious. It has become ever more apparent, however, that it was a much more laboured process. Nick Lane's The Vital Question is particularly good at highlighting the issues involved, such as genetic parasitism on the host genome and intracellular competition between endosymbionts.

Now, a paper published just a few weeks ago, focusing on the genomes of bacteria and the lokiarchaeota, has further demonstrated that the origin of the eukaryotes was likely to be 'the result of a long, slow dance between kingdoms, and not a quick tryst.'

One major difference between eukaryotic and prokaryotic cell is their size and corresponding degree of organisation. Prokaryotes are small enough for diffusion to act as a sufficient means of transporting substances around their cells. As such they require very little in the way of internal organisation. By contrast the massive cells of eukaryotes are divided into multiple compartments linked by elaborate molecular transport systems.

Analysis of the genomes of the lokiarchaeota showed that they contain a greater number of eukaryotic signature proteins (ESPs) than any other prokaryote group, hence the placement of the lokiarchaeota next to the eukaryotes in the tree of life.

A diagram demonstrating the gradual acquisition of key elements
of the eukaryotic cell from antecedant prokaryotes
Crucially, however, a number of these proteins (small Raf and Arf-type GTPases), are critical components of eukaryotic intracellular transport systems. They are unlikely to perform a similar function in the lokiarchaeota, however, as they lack the enzymes required for the association of GTPases with membranes or components of membrane transport systems. Yet the genes and membrane lipids required to make these associations possible can be found in bacteria.

'The (archaeal) genome can be seen as 'primed' for eukaryogenesis,' said Buzz Baum from University College London. 'With the acquisition of a number of key genes and lipids from a bacterial symbiont, it would be possible for loki-type cells to evolve a primitive membrane trafficking machinery and compartmentalization.'

Subsequently, the gradual transfer of genes from bacterial symbiont to archaeal host would have led to the development of a eukaryotic transport system.

'We believe it will be very difficult to crack the mysteries of eukaryogenesis without first understanding the archaeal cell biology,' said Gautam Dey, also from University College London.

The researchers say that their next step will be to study the cell cycle and cellular morphology of the related archaeon Sulfolobus acidocaldarius (loki type cells have yet to be cultured in the laboratory) to better determine just how close the structure of such archaea is to true eukaryotic cells.

Tuesday 28 June 2016

New Evidence For Hair And Whiskers In Therapsids

Hairs perform a variety of sensory and protective roles in mammals
While not a defining feature of the group, hair plays a vital role in the lives of most mammals alive today. It functions as a means of insulation and camouflage, but in many cases, it has been adapted for additional purposes.

Cats and dogs will raise their hackles in a show of aggression while in hedgehogs, porcupines, echidnas and tenrecs they have been heavily keratinised into defensive spines. Similarly, whiskers are highly derived hairs adapted to sensory function by the placement of nerve endings at their base.

Well preserved fossils of early mammals show the presence of hair. It seemed likely that the reptilian ancestors of the first mammals, the therapsids, also had hair, yet their fossils did not preserve any such structures, leaving its temporal origin unclear. A recent discovery, however, has shown that some therapsids did indeed have hair. In mammals with whiskers, the trigeminal nerve is responsible for sensory transmission. It is housed within a bony tube called the maxillary canal, which is shortened in mammals to allow the end of the trigeminal nerve to innervate the soft tissue of the face.

'This leaves the trigeminal nerve free to follow the movements of a flexible snout,' said Dr Julien Benoit from the University of the Witwatersrand. 'In reptiles this canal is long and the nerve is enclosed in the maxilla all along its length, which prevents any movement of the nose and lips.'

By using a technique based on x-ray micro CT scanning, the researchers found that the maxillary canal in members of the prozostrodont group of therapsids was shorter compared to those of reptiles. Pits on the snout also pointed strongly to the presence of whiskers in the group and therefore hairs from which the whiskers must have evolved. Genetic research by the team showed that the development of body hair is controlled by the gene MSX2. It is also involved, however, in the development of mammary glands. It is effectively the gene that makes us mammals.

CT scans of ancestral therapsids, showing
the shortening of the maxillary canal (green)
The prozostrodonts are the direct ancestors of mammals and are a derived subgroup of the probainognathian clade of cynodont therapsids. In reptiles the parietal foramen in the roof of the skull houses an organ known as the third eye which is photosensitive and involved in Circadian rhythms and thermoreception.

In the probainognathians, the parietal foramen was lost by the ossification of the roof of the skull. This loss also trended with the enlargement of the cerebellum; both are mammalian traits.

Based on the anatomical changes within the prozostrodont probainognathians, the researchers suggest that changes in expression of the MSX2 gene 240 to 246 million years ago triggered the evolution of hair and whiskers, the enlargement of the cerebellum, complete ossification of the skull roof, and the development of the mammary glands - all classic mammalian features.

'Our research has shown that these features of mammals were already present in advanced therapsids, prior to the appearance of mammals,' said Benoit. 'It also has implications for understanding how mammals survived the domination of dinosaurs during the Mesozoic period and the subsequent evolutionary success of mammals.'

Sunday 26 June 2016

New Research Highlights Mammal Extinction During The KT Boundary

The classic image of the KT extinction: plucky mammals
emerging from burrows amidst a wasteland of dead dinosaurs
The classic image of the KT extinction event is the dinosaurs dropping like flies in a landscape filled with tree stumps and charred vegetation. The herbivorous species declined quickly while the carnivorous species clung on for a little longer, initially on the dwindling populations of prey and then as ever more desperate scavengers, until their final demise. Yet when the dust settled, the humble yet triumphant mammals emerged from their burrows to claim the new world, scampering through the skulls of their reptilian predecessors. Mammals are the dominant terrestrial vertebrate group today. Most of their diversity evolved soon after the KT extinction, but it was assumed that they had survived the extinction itself with little decline in their species numbers compared to the more unfortunate dinosaurs.

A recent study, however, has shown that they actually suffered extremely heavy losses. Analysis of the mammalian fossil record was conducted in western North America on a window from 2 million years prior to, to 300,000 years after the asteroid collision with Earth which marks the KT boundary. 'The species that are most vulnerable to extinction are the rare ones, and because they are rare, their fossils are less likely to be found,' said Dr Nick Longrich from the University of Bath. The species that tend to survive are more common, so we tend to find them. The fossil record is biased in favour of the species that survived. As bad as things looked before, including more data shows the extinction was more severe than previously believed.'

The red line marks the KT extinction. The rapid
recovery of the modern mammal groups is apparent
The analysis showed that an astonishing 93% of mammal species went extinct across the KT boundary. Intriguingly this is in excess of other groups which successfully traversed the extinction boundary also, such as birds, crocodiles and amphibians. This begs the question of why mammals then managed to become the dominant terrestrial vertebrate group. The answer, however, was also made apparent by the study. While mammals were hit hard, they recovery time was much faster compared to other surviving groups, doubling the number of species prior to the extinction in just 300,000 years.

'It wasn't low extinction rates, but the ability to recover and adapt in the aftermath that led the mammals to take over,' said Longrich. 'You might expect to see the same few survivors all across the continent. But that's not what we found. After this extinction event, there was an explosion of diversity, and it was driven by having different evolutionary experiments going on simultaneously in different locations.. This may have helped drive the recovery. With so many different species evolving in different directions in different parts of the world, evolution was more likely to stumble across new evolutionary paths.'

North America was closer to the epicentre of the impact event than other continents and so may have suffered a slightly higher rate of extinction than say Asia. The study, however, is based on a much larger data set than previous ones and so is certainly a more faithful representation of the change in mammal diversity across the KT boundary. Future studies may well confirm similarly high magnitudes of mammal extinction around the globe along with their phenomenally rapid recovery and subsequent ecological expansion

Sunday 29 May 2016

An Intriguing Development in Evolutionary Theory

A simplified version of the difference between allopatry and sympatry
The branching of lineages produces the tree of life. In order for branching to occur, an ancestral population must be split in such a way that the resultant daughter populations cannot interbreed and exchange genes.

Subsequent differences in mutation and selection between those two populations drives them apart to the point that they can be considered new species - an ancestral branch splits into two. There are two broad mechanisms for how this splitting occurs.

The first, allopatry, involves a geographical mating barrier such as a mountain range or a river which cannot be physically traversed and so is an effective means of preventing gene flow. The second, sympatry, is more contentious.

In sympatric speciation there is no geographical barrier. Instead a population becomes divided from within by a pre-mating barrier. This is any biological mechanism which ensures that groups of individuals within the population breed at different times. A common argument is that small variations in the microhabitat result in allopatric divisions, creating an illusion of sympatry when the habitat and its population is viewed as a whole. If sympatry is considered as a spatial rather than a biological variable, however, then preferences between microhabitats cannot be classed as sympatric effects, but as examples of niche displacement. True sympatry must therefore be another kind of phenomenon entirely.

A problem exists between the nature of sympatry - two genetically distinct populations occupying the same area and so its resources - and the basic ecological principle of competition. Interspecific competition between meta-populations (distinct groups within an over-arching population) and true species, and competitive exclusion (the better adapted meta-population or species will out-compete the other and either force it out of the area or to extinction) should mean that two meta-populations or species should not be able to sympatrically coexist. The logical conclusion of nature is read as being 'red in tooth and claw.'

A solution to the problem of the functional nature of sympatry has been proposed by Roberto Cazzolla Gatti from Tomsk State University, Russia; a solution which would add a profound twist into the nature of evolutionary theory.

'My model predicts that the coexistence of two species in a sympatric way can happen only if there is low competition or weak competitive exclusion between them and a kind of avoidance of competition that leads to a slight shift of the niche of a meta-population, which accumulated a series phenotypic difference due to genomic inclusions coming from other sources of genes. Thus, eventually, it's the avoidance of competition that drives the expansion of the diversity of living beings' said Gatti in his 2016 paper.

Gatti has proposed that this process of avoidance should be called endogenosymbiosis after the idea of endosymbiosis proposed by Lynn Margulis in 1960, as it relies on cooperation rather than conflict. In this new model, cooperation by the avoidance of conflict is responsible for the generation of biological diversity. Meanwhile the classical drives of natural selection, mutation and competition, become responsible for preserving and adapting lineages after their sympatric creation. Gatti proposed this model in 2015 but it is only recently that empirical evidence to support it has been found.

An example of a stickleback species
Researchers from the University of Bern, Switzerland, led by Dr David Marques, found that a population of stickleback fish, which were introduced and therefore isolated in Lake Constance 150 years ago, were splitting into two separate species at a rapid rate even when its two meta-populations bred in the same streams at the same time of year. Despite gene flow between the meta-populations, they split into two genetically and physically different types.

'We cannot know for sure that the Lake Constance sticklebacks will continue evolving until they become two non-interbreeding species' said Marques. 'But evidence for sympatric speciation is growing, from mole rats in Israel to palms on Lord Howe Island, Australia, and apple maggots evolved from hawthorn maggots in North America, leading some evolutionary biologists to think it could be surprisingly common.'

This example of sympatry clearly does not fit with the previous requirement of a pre-mating barrier, but as it does not involve a geographical mating barrier, neither can it be considered allopatric. Yet it fits with Gatti's conceptualization of sympatry within his cooperative model of evolution. This model will likely spark considerable debate. It may well be able to stand alone as an explanation for the functional mechanism behind sympatry. The potential for integration with other ideas in evolution, such as punctuated equilibrium or hierarchies of selection, on the other hand, remains unclear and is ripe for further study.

Macroscopic Eukaryotes From The Boring Billion

1.56 billion year old eukaryotic body 
fossils from the Gaoyuzhuang Formation
Fossil and genetic evidence pushes the origin of eukaryotes close to two billion years ago. This allows the event to be reliably linked to the increase in atmospheric oxygen and the swathe of environmental changes accompanying it.

Single celled and microscopic multicellular forms are well documented from 1.5 billion years onwards. Macroscopic eukaryotes, however, have only been found in rocks several hundred million years younger still. The reasons for this delay are somewhat unclear, but can be correlated to a billion year period of geochemical stagnation following the Great Oxidation Event. 

Now a recent fossil discovery in China, from the Gaoyuzhuang Formation has pushed back the record of macroscopic eukaryotes much closer to the origin of complex cells themselves. Previous reports of macroscopic eukaryotes of comparable ages were dismissed as inorganic artifacts of preservation or as colonies of prokaryotes with complex morphologies. The 1.56 billion year old Chinese discoveries, however, are undeniably eukaryotic. Microscopic sheets of cells with an organised, complex eukaryotic character were found in the same beds as carbonaceous impressions, a third of which fell into four discrete morphological categories. At 30 centimetres long and 8 centimetres wide, the largest specimen was far larger than any of the previously reported (and debunked) oldest macroscopic eukaryotes.

'Our discovery pushes back nearly one billion years the appearance of macroscopic, multicellular eukaryotes compared to previous research,' said Maoyan Zhu from the Nanjing Institute of Geology and Palaeontology.

The 1.56 billion year old microscopic cell
fragments from the Gaoyuzhuang Formation
The researchers characterised the fossils as similar in form to thalli, the singular form is thallus. A thallus is a sheet of cellular material which does not display differentiation into specific structures. Thalli are found in plants, fungi and a multitude of algal groups.

The fossils lack enough detail to be tied to any one of these groups. The base of the structures possessed holdfasts, suggesting at least a primitive form of differentiation in some of the cells in these creatures - further evidence of their eukaryotic nature.

The specimens have already attracted controversy, with a number of researchers suggesting that they are simply bacterial mats. Until conclusive evidence of this is put forward, however, they remain the oldest macroscopic eukaryotes in existence. 

Friday 13 May 2016

A Fossil Heart In An Ancient FIsh

Organ preservation is now a well documented phenomenon in the fossil record. From the nervous systems of primitive arthropods to the reproductive tracts of a number of exceptionally well preserved dinosaurs, a combination of new technologies and remarkable fossil discoveries, have enabled us to reconstruct the anatomies of long extinct species. In 2000 a fossilised heart was reported from a species of dinosaur known as Thescelosaurus. This was the first time such a structure had been reported from vertebrate remains. The discovery was quickly debunked, however, as an iron rich concretion - a quirk of the geological record. 

The 3D reconstruction of Rhacolepis. The heart is shown
in blue and the position of the valves with white arrows
In 2005, a series of organic traces representative of the heart was reported from fish from the Devonian in Scotland. These were flat films, however, which preserved little detail.

In contrast, the 113 to 119 million year old Santana formation is famous for its beautifully preserved 3D fish fossils which occasionally preserve traces of soft tissues, such as muscle blocks.

A specimen of one well- documented species, Rhacolepis, has been found to contain a heart preserved in 3 dimensions.

A phylogeny showing the placement of Rhacolepis in the actinopterygians
By taking x-ray scans using a synchrotron at 6 micrometre intervals, an international team of researchers were able to make a 3D digital reconstruction of the fossil, including the heart.

The scans clearly showed the conus arteriosus, a bulk-shaped portion of the apex of the heart which contained five valves for directing blood flow. Dissection of the heart of a modern tarpon allowed the researchers to determine the evolutionary complexity of the fossil heart using comparative anatomy.

Actinopterygians, or ray-finned fish, have highly varied heart structures. Primitive forms, such as chondrosteans, have up to nine valves controlling outflow, while the most advanced forms, the teleosts, have just one valve - the bulbus arteriosus.

The five valves of Rhacolepis show that its placement was intermediate within the actinopterygians close to the base of the teleost family itself. Comparative anatomy has been the primary means of identifying a fossil's place within the tree of life, since palaeontology was founded as a science. Comparison, however, has focused almost entirely on a creature's morphology and endoskeleton or exoskeleton. The ability to use elements of physiology within the comparative anatomy of fossils will prove to be an invaluable tool in future examinations of extinct branches of the tree of life.

Friday 29 April 2016

A Scorpion Mating Couple From The Permian

The fighting dinosaurs is one of the most remarkable and evocative fossils ever discovered. Consisting of a small theropod locked in combat with a Protoceratops mother desperately guarding a clutch of eggs, the pair were buried by the collapse of a nearby sand dune in their desert home. Rarely does in situ preservation capture such poignant and momentary glimpses of past worlds, particularly when it comes to actual body fossils. Trace fossils can be similarly evocative, but lack the tangible connection that a body fossil provides. As such, fossils like the fighting dinosaurs are priceless for the insight they give into the ecology and ethology of prehistoric creatures.

Recently, however, such a specimen has been uncovered from the Permian of Germany. As deserts spread across Pangaea, the lush Carboniferous forests began to fragment into isolated pockets and oases in the midst of a much harsher landscape. These green islands were points of rich biodiversity. The remains of one such island can be found under the city of Chemnitz, Germany. The ecosystem contained a wide variety of plants and arthropods which were buried 291 million years ago by ash from a nearby volcano, leading to the remarkable in situ preservation of its flora and fauna - a geological equivalent of Pompeii. Everything from tree trunks to leaf litter are in the same positions now as 291 million years ago, along with evidence of seasonality, articulated skeletons of amphibians and the impressions of reptile skin.

Birgit preserved within her burrow and surrounded
by fragments of moulted exoskeleton
In addition to the plant and vertebrate fossils, a small, hand dug excavation within the city itself uncovered two specimens of a new scorpion species, Opsieobuthus tungeri. The specimens were well preserved enough not just for species level identification, but their sex.

Scorpions possess a comb-like structure on the underside of their bodies which is used for prey and mate detection and general olfactory orientation. In males, these combs have more and longer teeth. The Chemnitz specimens were male and female, nicknamed Jogi and Birgit respectively. As well as being preserved within just two metres of one another, Birgit was found within a burrow and surrounded by fragments of a moulted exoskeleton.

An artist's impression of Jogi guarding the entrance to Birgit's burrow
The distance between the two is typical of a mating pair of scorpions of their size (12 centimetres) and the differing locations suggests that Jogi may have been guarding Birgit, a behaviour observable in modern day scorpions. The fragments of exoskeleton may also help explain why Birgit was in the burrow.

Scorpions, like all other arthropods, moult their exoskeletons in order to grow. This leaves them temporarily vulnerable to attack as their newly exposed cuticle takes time to mineralise and harden. Moulting within a burrow would have proffered some defence, along with Jogi. The nearby volcano, however, had other ideas.

Jogi and Birgit belonged to a primitive and now extinct group of scorpions. Other fossil evidence, however, shows that their temporal range overlapped with early representatives of the extant clade of scorpions as well as sharing similar behaviours in terms of mate guarding and moulting within burrows. This mating pair is a wonderful glimpse into life in the Permian period, along with the wider palaeontological setting of the Chemnitz lagerstatten. 

Friday 25 March 2016

Solving The Mystery Of Mazon Creek

An ironstone nodule containing
a fossil of the Tully Monster
Mazon Creek is one the most famous Carboniferous fossil localities in the world. Formed in a system of deltas on the Pangaea coast, the Mazon Creek shales contain nodules of iron stone. When split, these can be found to contain the exceptionally well preserved remains of a plethora of extinct species.

Plants are common, but vertebrates can also be found along with arthropods. Such creatures have mineralised body parts and so are easily preserved. Yet the preservation of soft tissues means that a host of soft-bodied creatures can be found at Mazon Creek, giving profound insight into the ancient ecosystem. Some species, however, have defied classification.

One such species is the Tully Monster, Tullimonstrum gregaricum. Bearing an odd blend of features, it has been banded between groups as diverse and distantly related as the molluscs, arthropods and conodonts. A recent study, however, lays the matter to rest.

Discovered more than 60 years ago, the type-specimen is still the most complete discovery. 1000s of other specimens, however, exist in the collections of the Field Museum in Chicago. This gave researchers, led by Victoria McCoy from the University of Leicester, enough material to make a detailed reconstruction of its anatomy, and in turn, its placement in the tree of life.

A reconstruction of Tullimonstrum, based on the new data from the study
Many specimens show a light coloured band running from snout to tail. This was previously interpreted as a gut. The apparent lack of a backbone, but distinct digestive system, made palaeontologists think that it had affinities with worm, mollusc or arthropod clades.

Closer examination of the structure, however, showed that it had a notochord - the defining feature of chordates. Its presence in the adult form helps narrow it down to the non-vertebrate chordates, namely the hagfish and lampreys. Several other features, including the structure of its teeth and a crescent-shaped pore in its mid-section, show that it belonged to the latter. As a stem group lamprey, the morphology of Tullimonstrum was highly unusual, with stalked eyes and a proboscis-like claw mouth.

'It would be fascinating to watch it swim around,' said Paul Mayer from the Field Museum. 'How does a Tully Monster make its living? We don’t know.' The next step for the researchers is to determine its lifestyle and ecology. Despite its bizarre morphology, the rich nature of the fossil locality will help to reconstruct its interactions with other organisms in its habitat.