Australian lungfish wins gold (for genome size)

There’s been some big lungfish news this week! A project led by Axel Meyer, Siegfried Schloissnig, Paolo Franchini, Kang Du, Joost Woltering and almost 15 others in their team, have published the full genome* for the Australian lungfish (Neoceratodus forsteri) in the high profile journal, Nature.

*A ‘genome’ is all of the genetic material of an organism and consists of DNA, while ‘genetics’ is concerned with the study of particular ‘genes’ and not necessarily the entire genome.

The genome of the Australian lungfish is absolutely huge at roughly 14 times the size of the human version, and is now the largest known in any animal. Previously the African lungfish, Protopterus, and then more recently the axolotl (salamander Ambystoma mexicanum), have been considered the record holders for this grand title.

This work by Meyer and team confirms the hypothesis that lungfish are the closest living lineage to the tetrapods (all amphibians, reptiles, birds and mammals), rather than the other group of living “lobe-finned fish”, the coelacanths. I like to say that in this way we can consider lungfish as our distant fishy cousins.

Figure 1 from the paper by Meyer et al. (2021) published in Nature showing the position of the lungfish (Neoceratodus) to tetrapods (https://www.nature.com/articles/s41586-021-03198-8)

For a time, the advent of molecular biology failed to definitively clarify this (known as the phylogenetic relationship) despite research on it spanning almost 30 years. The main issue was that the coelacanth, lungfish and tetrapod lineages are thought to have diverged from each other so long ago (about 420 million years ago!) which made piecing together their independent evolutionary molecular histories incredibly problematic. This is where palaeontology is absolutely invaluable for elucidating the relationships even between living animals when molecular methods may have their own limitations. Naturally I believe the best approach is to combine data from both lines of evidence to help us properly understand all life on earth today.

It was found that the lungfish had genes related to limb-like development in their fins, as well as some involved in air-breathing (lung surfactants and odour receptors) which were likely ‘preadaptations’ to living on land. The authors consider than these novelties found in lungfish -but not other fishes-, must have predisposed this group (sarcopterygians, the “lobe-fins”) to have been able to make that first foray onto land all those millions of years ago.

My photograph of a live animal, and 3D model of the Australian lungfish

These are just some of the reasons that I study lungfish in my own research, they are absolutely fascinating and hold the unique position as our closest fishy relatives (lungfish are more closely related to us than they are to a salmon or shark, for example). They are one of the best living representatives for helping us to understand what obstacles our distant tetrapod ancestors had to overcome to make their way from the water onto land almost 400 million years ago.

My own work researching lungfish has covered their air-breathing (Clement et al. 2016b; Clement & Long 2010a), muscles (Ziermann et al. 2017), brains (Challands et al. 2020; Clement et al. 2016a; Clement et al. 2016c; Clement et al. 2015; Clement & Ahlberg 2014), as well as fossils and the early evolution of the group (Gess & Clement 2019; Clement 2012; Clement & Long 2010b; Clement 2009; Long & Clement 2009). If you ever want to talk about lungfish, about these topics or otherwise, and specifically the Australian lungfish, then please get in touch! I have several ongoing projects also on these fabulous fishies.

Always excited to see these adorable fish at the Melbourne Museum

Parlez-vous français?

Nope, me neither! I speak some very rusty Japanese and a little Swedish, but can not claim to “parle français” myself. Despite this, I was a co-author on a French language article published last week by the journal Médecine/Sciences.

The article, L’origine phylogénétique des doigts, can be translated as “The phylogenetic origin of fingers”, and covers our work on the fish with fingers, Elpistostege. Our first article was published in Nature earlier this year, and you can read my original blog post about it too.

This new article was co-authored with Prof. Richard Cloutier and Prof. John Long and details our discovery of the first occurrence of digits in a fish, even though the pectoral fin of Elpistostege still retains primitive features, such as the presence of rays. The specimen is just the fourth Elpistostege fossil known. It was discovered by Richard and his team in 2010 in Miguasha, Quebec, Canada, and is about 375 million years old.

So if you’re a Francophile, Gallophile, or just love fish fingers, get reading about good ol’ Elpistostege!

Artist’s impression of Elpistostege by the very talented Chase Stone, image originally published in Scientific American

*** EDIT: more Elpi! This week a popular science article (in English) was published by The Science Breaker, a website that publish short lay-summaries (“breaks“) of scientific research. Our article “Elpistostege: a fish with legs or a tetrapod with fins?“, was again written by Richard, John and myself.

Alice, John and Richard in Adelaide during 2019

A million times brighter than the sun?

Have you heard of something called a synchrotron? Did you know they can produce light more than a million times brighter than the sun? Did you know we have one here in Australia?

A synchrotron is a very large machine – so large it needs its own purpose built building (about the size of a footy oval) to house it! It accelerates electrons around a ring super, super fast (almost to the speed of light) before shooting them off down “beamlines” to produce extremely powerful light. (Sharks with freaking laser beams, anyone?)

In my research I harness this powerful light like a supercharged X-ray machine to look inside ancient fossils. I’ve used the synchrotron in Melbourne, run by the Australian Nuclear Science and Technology Organisation (ANSTO) a few times now, as well as ESRF in Grenoble, France.

This machine creates a series of scans (tomograms) of an object based on the density of the various materials contained within (this is similar but distinct from neutron tomography). We can then create a 3D dataset from the resultant stack of images, and make 3D computer models from these scans for use in our research to look inside bone, virtually reconstruct a skeleton or run biomechanical analyses, for example.

Together with some of my colleagues, including visiting researcher Dr Tom Challands, I was due to visit the synchrotron in April this year. However, we all know COVID wreaked havoc with all the best laid plans… so our beamtime had been rescheduled for December… but alas, we were still not allowed to travel interstate to attend our experiment!

Thankfully, an incredibly generous colleague and collaborator, Dr Joseph Bevitt, came to our rescue. He drove one of our specimens from Sydney to Melbourne, collected some specimens on loan from the Melbourne Museum, and then scanned our material for us with the ANSTO beamline scientist, Anton Maksimenko.

Dr Joseph Bevitt at the Australian Synchrotron (Dec 2020)

Access to the ANSTO beamtime is absolutely invaluable for my research. It’s incredibly exciting to be able to use its state-of-the-art scanning technology to look inside rare and ancient fossils that are hundreds of millions of years old. I can’t wait to see the results from the scans made during this most recent visit…. watch this space!

Brains ‘primed’ for life on land

There’s been a small flurry of media activity this week about our recent paper on the brains and jaw muscles of some salamanders and lobe-finned fish (my favourites, remember). The original paper was published by the journal Royal Society Open Science and co-authored by myself with Tom Challands (University of Edinburgh) and Jason Pardo (University of Calgary).

The paper, “Mandibular musculature constrains brain–endocast disparity between sarcopterygians”, looked at the size and shape of the brains in the axolotl (Ambystoma), the fire belly newt (Cynops), lungfish (Neoceratodus and Protopterus) and the coelacanth (Latimeria).

We studied this to provide insight into what the brains of the first ‘tetrapods’ (the first fish that crawled onto land millions of years ago are relatives of the lobe-finned fishes) might have looked like. Living lungfish and amphibians such as salamanders are the closest extant (living) relatives of those first fossil tetrapods.

We found that lungfish and salamanders have brains that are actually quite large and fill their skulls to a much higher degree compared to the coelacanth. Furthermore, it seems that there might be an interplay between the skull architecture and size of the jaw muscles and the overall size or “fullness” of the brain in these animals.

You can read more about it here from:

BLiSS*Adelaide 2020

Last week I “attended” another virtual conference, this time a Science & Innovation meeting held by EMCR’s for EMCR’s (Early/Mid-Career Researchers) with a strong focus on multidisciplinary collaboration across local institutions, called BLiSS*Adelaide.

The organisers did a great job pivoting and adapting to an online format, with sessions spread over four mornings throughout the week. This was some well-thought through scheduling to avoid Zoom-fatigue! The opening keynote was delivered by Dr Cathy Foley, Chief Scientist at CSIRO, and there was an engaging program of speakers each day as well as networking opportunities via “breakout rooms”.

Delegates were able to present their research via short 3-minute pre-recorded “Science Bites” and my contribution was called “Powerful Imaging Techniques for Palaeontology”. I am pleased to announce that I was awarded the Best Science Bites Presentation (People’s Choice – Lights, Camera, Action!) at the BLiSS*Adelaide 2020 Virtual Conference!

Many thanks to all who voted for my presentation, and thanks to the organisers and sponsors of the event which enabled such a great event to go ahead.

SVP goes virtual

The Society of Vertebrate Paleontology (SVP) is an educational and scientific society that holds an annual meeting each year (you may remember my visit to SVP in Brisbane last year). The SVP conference is usually the largest collection (accumulation?) of vertebrate palaeontologists and was due to be held in Cincinnati this year for it’s 80th iteration. Alas, as we well know, 2020 has not gone to anyone’s plan and so for the first time in it’s history, SVP went fully virtual!

I was honoured to be invited to participate in a special symposium “Frontiers in Paleoneurology and Neurosensory Evolution” convened by Alan Turner & Amy Balanoff. My talk was entitled “Brain-braincase relationships across the fish-tetrapod transition” and provided me with a great opportunity to show some recent work myself and colleagues have been doing on the brains of living fish and salamanders, as well as some braincases of ~340-375 million year old tetrapod-like fossil fish.

For those “attending” the conference, you can access my presentation via this direct link.

The conference organisers have done an amazing job adapting to the virtual format and accommodating scientists from across the globe in almost every conceivable time zone. We were able to watch pre-recorded presentations in our own time, but then there were live Q&A sessions attached to each theme.

It’s been really wonderful to be able to participate in this meeting during a year when large gatherings and overseas travel seem but a distant memory, but sharing our work and speaking with other scientists remains vital for continued sharing of knowledge and the overall advancement of our field.

Brains, brains, brains! (New paper out today)

Our latest paper was published yesterday in the journal Royal Society Open Science. This work was co-authored by myself with Tom Challands (University of Edinburgh) and Jason Pardo (University of Calgary), and has the title: “Mandibular musculature constrains brain–endocast disparity between sarcopterygians.”

In this work we applied a method developed in a previous paper to quantify and visualise the spatial relationship between the brain and its surrounding braincase in several animals. We investigated the living lobe-finned fishes (the coelacanth, Australian and African lungfish), as well as two salamanders (the axolotl and a newt).

Why did we do this? Firstly, brains are soft organs and so rarely fossilise and instead we are often only left with the hard, bony remains of an animal. This means that we must rely on the shape of the internal mould of the skull (an ‘endocast’) as a proxy for brain size and shape.

However, while birds and mammals typically have brains that nearly completely fill their brain cavities, those in fish, amphibians and reptiles are usually not so tightly constrained. This means that when we try to interpret the endocasts of fossils of extinct fish and early tetrapods (backboned animals with four limbs bearing fingers and toes) we don’t know with how much confidence we can infer how large certain brain regions were.

We found that the coelacanth is doing something very strange and has an absolutely tiny brain contained within a huge braincase (similar findings have recently been reported elsewhere). However, the lungfish and salamanders have brains that are filling their braincases to a higher degree than previously thought. We suggest that these patterns may potentially be related to the reinforcement in the skull from large jaw muscles, but we do need to examine some other basal tetrapods, such as frogs and caecilians, before we can be completely sure.

Left figures show overlap relationship between brain (grey) and endocast (red).
Right side images show the same information using a “heat-map” approach.
a-c, axolotl; d-f, newt; g-l, African lungfish; m-o, Australian lungfish; p-r, coelacanth.
(Silhouettes from http://phylopic.org/)

By investigating the brain-braincase spatial relationship in these living animals spanning the fish-tetrapod transition, we can use this information to better interpret fossils spanning the same critical juncture.

This approach is guided by something called the Principle of Proper Mass (Jerison 1973) which proposes that the larger a brain region, the more likely it is to be processing more information (remember that growing and maintaining large brains is energetically costly). Thus, if an animal has particularly large optic lobes compared to the olfactory region for example, we can reasonably assume that that animal relied more on its vision that its sense of smell.

It is my hope that this work will help us to pinpoint the origins of new behaviours as fish moved out of the water and began to colonise land over 385 million years ago.

YTP 2020

It was a great honour to receive my Young Tall Poppy award last night from His Excellency the Honourable Hieu Van Le AC in the Eclipse Room at the University of Adelaide.

Dr Alice Clement with her 2020 Young Tall Poppy Award.

“The Tall Poppy Campaign was created in 1998 by the Australian Institute of Policy and Science (AIPS) to recognise and celebrate Australian intellectual and scientific excellence and to encourage younger Australians to follow in the footsteps of our outstanding achievers.”

The award night was held in collaboration with Inspiring South Australia and National Science Week to celebrate both the Young Tall Poppy crop of 2020, but also the Unsung Hero Awards of South Australian science.

In particular, I wish to congratulate Graham Medlin from the South Australian Museum, citizen scientists Robert and Rosalie Lawrence for ‘Wild Orchid Watch’, and Dr Kylie Dunning (ARC Centre of Excellence for Nanoscale BioPhotonics) for their awards.

I feel very lucky to have been nominated by my mentor, Prof. John Long, and it was great to be able to celebrate in person on the night and hear about the varied research and outreach happening here in South Australia.

Dr Alice Clement with Prof. John Long at the 2020 SA Young Tall Poppy & Unsung Hero Science Award night.

Young Tall Poppy

I’m really excited to announce that I’ve been named one of the 2020 SA Young Tall Poppies by the Australian Institute of Policy and Science (AIPS).

The prestigious annual Young Tall Poppy Science Awards aim to recognise the achievements of Australia’s outstanding young scientific researchers and communicators. In particular, the ‘Tall Poppies’ are awarded to those who promote interest in science among school students and teachers, as well as an understanding and appreciation of science in the broader community.

I was one of three researchers from Flinders University recognised for our research and communication efforts, and I feel honoured to be in the company of hydrogeologist Dr Margaret Shanafield and archaeologist Dr Ian Moffat in this year’s cohort.

YTPx3
Photo credit: Tania Bawden, Flinders University

Congratulations to all other awardees, and many thanks to my supporter and nominator, Prof. John Long. There will be an official award ceremony in September held in the Reading Room of the Barr Smith Library with South Australia’s Governor, His Excellency Honourable Hieu Van Le.

Impact Seed Funding

I was fortunate enough to receive Impact Seed Funding from Flinders University in 2018. While in the grand scheme of things it was a relatively small amount of money, for an Early or Mid-Career Researcher (EMCR), awards like this can go a long way.

This funding enabled me to pursue my own line of research into palaeoneurology (fossil brains) and supported a visit to the Berlin Museum für Naturkunde (Natural History Museum) and a trip to the famous Institute of Vertebrate Paleontology & Paleoanthropology (IVPP) in Beijing, China.

Having museum visits funded in this way help me to research how brains evolved in our early fish ancestors, and enable me to try to understand the adaptations and novelties acquired in the brains of the first tetrapods (terrestrial vertebrates). Studies such as these go on to form “pilot studies” for larger funding schemes and projects, and provide me with the opportunity to lead and manage my own projects whilst forming new international collaborative partnerships.

I’m ever so grateful to the donor community and Flinders University for the Impact Seed Funding for Early Career Researchers. Being awarded these funds greatly supports my ongoing development into becoming an independent and competitive researcher.

Thank you.