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Learning from a ‘living fossil’
As we live and breathe, ancient-looking fish known as bowfin are guarding genetic secrets that that can help unravel humanity’s evolutionary history and better understand its health.
“For the first time, we have what’s called a chromosome-level genome assembly for the bowfin,” said Braasch, an assistant professor of integrative biology in the College of Natural Science. “If you think of the genome like a book, what we had in the past was like having all the pages ripped out in pieces. Now, we’ve put them back in the book.”
“And in order,” added Thompson, a postdoctoral researcher in Braasch’s lab and the first author of the new research report, published Aug. 30 in the journal Nature Genetics.
This is really important information for a few reasons, the duo said, and it starts with the bowfin being what Charles Darwin referred to as a “living fossil.” The bowfin, or dogfish, looks like an ancient fish.
This doesn’t mean that the bowfin hasn’t evolved since ancient times, but it has evolved more slowly than most fishes. This means that the bowfin has more in common with the last ancestor shared by fish and humans, hundreds of millions of years ago, than, say, today’s zebrafish.
Zebrafish — which are modern, so-called teleost fishes — are a notable example because they’re widely used by scientists as a model to test and develop theories about human health. Having more genetic information about the bowfin helps make the zebrafish a better model.
“A lot of research on human health and disease is done on model organisms, like mice and zebrafish,” Thompson said. “But once you identify important genes and the elements that regulate those genes in zebrafish, it can be hard to find their equivalents in humans. It’s easier to go from zebrafish to bowfin to human.”
For example, one particularly interesting gene is one that’s used in developing the bowfin’s gas bladder, an organ the fish uses to breathe and store air. Scientists believe that the last common ancestor shared by fish and humans had air-filled organs like these that were evolutionary predecessors to human lungs.
In their new study, the Spartan researchers could see that a certain genetic process in the bowfin’s gas bladder development bore striking similarities to what’s known about human lung development. A similar process is also present in the modern teleost fishes, but it’s been obscured by eons of evolution.
“When you looked for the human genetic elements of this organ development in zebrafish, you couldn’t find it because teleost fishes have higher rates of evolution,” Thompson said. “It’s there in modern fishes, but it’s hidden from view until you see it in bowfin and gar.”
The gar is another air-breathing fish with “living fossil” status that’s studied by Braasch and his team. With both the gar and bowfin genomes, the team was able to show where these genetic elements linked to gas bladder and lung formation were hiding out in the modern teleost fishes. The ancient fish enable researchers to build a better bridge between the established modern fish model organisms and human biology.
“You don’t want to base that bridge on one species,” said Braasch, who added this finding also strengthens the implications for evolutionary history. “This is another piece of the puzzle that suggests the common ancestor of fish and humans had an air-filled organ and used it for breathing at the water surface, quite similar to what you see in bowfin and gar.”
Although these findings have insights that are pertinent to all of humanity, Spartans might feel a special affinity for the bowfin. For starters, male fish turn their fins and throats a bright shade of green during spawning season. Also, famed biologist William Ballard of Dartmouth College studied bowfin development from eggs to larval fish at Michigan State’s W.K. Kellogg Biological Station during the 1980s. This was what he called his “Odyssey of Strange Fish,” and Braasch’s team now uses his work to guide their genomic analyses of bowfin development.
Bowfins are native to Michigan. They could be in the Red Cedar River on MSU’s campus now, according to Thompson, but they also can be quite elusive and, sometimes, very aggressive. This made collaborations essential for securing specimens. With colleagues at Nicholls State University in Louisiana, the team caught bowfins for genome sequencing. Amy McCune, a collaborator and professor at Cornell University, knew where to find bowfin eggs in upstate New York and had a graduate student gifted at securing these unique samples for investigating bowfin development.
The Spartans also had connections at other universities and institutions with experts in bowfin biology, chromosome evolution and more. All told, the team included researchers from six states as well as France, Japan and Switzerland. Back in East Lansing, graduate students Mauricio Losilla and Olivia Fitch, research technologist Brett Racicot, and Kevin Childs, director of the MSU Genomics Core facility, also contributed to the study, which comes with an interesting twist at the end.
Almost all vertebrate creatures that grow paired limbs or fins share a common gene.
“Humans use it, mice use it. All fishes that have been studied so far use it,” Braasch said. “The naïve expectation would be that bowfin do, too.”
But that’s not what the team found. The bowfin, the “living fossil,” has evolved a different way of growing its paired fins.
“For whatever reason, it changed its genetic programming. Even ‘living fossils’ keep evolving. They’re not frozen in time,” Braasch said. “It’s sort of a cautionary tale that we shouldn’t take these things for granted. You have to look trait by trait, gene by gene and across many different species to paint the complete picture.”
Recent strides in interdisciplinary archaeological research in Arabia have unveiled new insights into the evolution and historical development of regional human populations, as well as the dynamic patterns of cultural change, migration, and adaptation to environmental fluctuations.
One such breakthrough led by Griffith University’s Australian Research Centre for Human Evolution (ARCHE), in collaboration with international partners, comes from the exploration of underground settings, including caves and lava tubes, which have remained largely untapped reservoirs of archaeological abundance in Arabia.
Through meticulous excavation and analysis, researchers have uncovered a wealth of evidence at Umm Jirsan, spanning from the Neolithic to the Chalcolithic/Bronze Age periods (~10,000-3,500 years ago).
“Our findings at Umm Jirsan provide a rare glimpse into the lives of ancient peoples in Arabia, revealing repeated phases of human occupation and shedding light on the pastoralist activities that once thrived in this landscape,” said Dr Mathew Stewart, the lead researcher and a Research Fellow at ARCHE.
“This site likely served as a crucial waypoint along pastoral routes, linking key oases and facilitating cultural exchange and trade.”
Rock art and faunal records attest to the pastoralist use of the lava tube and surrounding areas, painting a vivid picture of ancient lifeways.
Depictions of cattle, sheep, goat and dogs corroborate the prehistoric livestock practices and herd composition of the region.
Isotopic analysis of animal remains indicates that livestock primarily grazed on wild grasses and shrubs, while humans maintained a diet rich in protein, with a notable increase in the consumption of C3 plants over time, suggesting the emergence of oasis agriculture.
“While underground localities are globally significant in archaeology and Quaternary science, our research represents the first comprehensive study of its kind in Saudi Arabia,” added Professor Michael Petraglia, Director of ARCHE.
“These findings underscore the immense potential for interdisciplinary investigations in caves and lava tubes, offering a unique window into Arabia’s ancient past.”
The research at Umm Jirsan underscores the importance of collaborative, multidisciplinary approaches to archaeological inquiry and highlights the significance of Arabia’s archaeological heritage on the global stage.
Researchers involved in this study work in close partnership with the Heritage Commission, Saudi Ministry of Culture, and the Saudi Geological Survey. Additional partners include King Saud University and key institutions in the UK, the USA, and Germany.
The fossilised remains of a second gigantic jawbone measuring more than two metres long has been found on a beach in Somerset, UK.
Father and daughter, Justin and Ruby Reynolds from Braunton, Devon, found the first pieces of the second jawbone to be found in May 2020, while searching for fossils on the beach at Blue Anchor, Somerset. Ruby, then aged 11, found the first chunk of giant bone before searching together for additional pieces.
Realising they had discovered something significant, they contacted leading ichthyosaur expert, Dr Dean Lomax, a palaeontologist at The University of Manchester. Dr Lomax, who is also a 1851 Research Fellow at the University of Bristol, contacted Paul de la Salle, a seasoned fossil collector who had found the first giant jawbone in May 2016 from further along the coast at Lilstock.
Dr Dean Lomax said: “I was amazed by the find. In 2018, my team (including Paul de la Salle) studied and described Paul’s giant jawbone and we had hoped that one day another would come to light. This new specimen is more complete, better preserved, and shows that we now have two of these giant bones — called a surangular — that have a unique shape and structure. I became very excited, to say the least.”
Justin and Ruby, together with Paul, Dr Lomax, and several family members, visited the site to hunt for more pieces of this rare discovery. Over time, the team found additional pieces of the same jaw which fit together perfectly, like a multimillion-year-old jigsaw.
Justin said: “When Ruby and I found the first two pieces we were very excited as we realised that this was something important and unusual. When I found the back part of the jaw, I was thrilled because that is one of the defining parts of Paul’s earlier discovery.”
The last piece of bone was recovered in October 2022.
The research team, led by Dr Lomax, revealed that the jaw bones belong to a new species of giant ichthyosaur that would have been about the size of a blue whale. Comparing the two examples of the same bone with the same unique features from the same geologic time zone supports their identifications.
The team have called the new genus and species Ichthyotitan severnensis, meaning “giant fish lizard of the Severn.”
The bones are around 202 million years old, dating to the end of the Triassic Period in a time known as the Rhaetian. During this time, the gigantic ichthyosaurs swam the seas while the dinosaurs walked on land. It was the titans’ final chapter, however — as the story told in the rocks above these fossils record a cataclysm known as the Late Triassic global mass extinction event. After this time, giant ichthyosaurs from the family known as Shastasauridae go extinct. Today, these bones represent the very last of their kind.
Ichthyotitan is not the world’s first giant ichthyosaur, but de la Salles’ and Reynolds’ discoveries are unique among those known to science. These two bones appear roughly 13 million years after their latest geologic relatives, including Shonisaurus sikanniensis from British Columbia, Canada, and Himalayasaurus tibetensis from Tibet, China.
Dr Lomax added: “I was highly impressed that Ruby and Justin correctly identified the discovery as another enormous jawbone from an ichthyosaur. They recognised that it matched the one we described in 2018. I asked them whether they would like to join my team to study and describe this fossil, including naming it. They jumped at the chance. For Ruby, especially, she is now a published scientist who not only found but also helped to name a type of gigantic prehistoric reptile. There are probably not many 15-year-olds who can say that! A Mary Anning in the making, perhaps.”
Ruby said: “It was so cool to discover part of this gigantic ichthyosaur. I am very proud to have played a part in a scientific discovery like this.”
Further examinations of the bones’ internal structures have been carried out by master’s student, Marcello Perillo, from the University of Bonn, Germany. His work confirmed the ichthyosaur origin of the bones and revealed that the animal was still growing at the time of death.
He said: “We could confirm the unique set of histological characters typical of giant ichthyosaur lower jaws: the anomalous periosteal growth of these bones hints at yet to be understood bone developmental strategies, now lost in the deep time, that likely allowed late Triassic ichthyosaurs to reach the known biological limits of vertebrates in terms of size. So much about these giants is still shrouded by mystery, but one fossil at a time we will be able to unravel their secret.”
Concluding the work, Paul de la Salle added: “To think that my discovery in 2016 would spark so much interest in these enormous creatures fills me with joy. When I found the first jawbone, I knew it was something special. To have a second that confirms our findings is incredible. I am overjoyed.”
The new research has been published today in the open access journal PLOS ONE.
Ruby, Justin and Paul’s discoveries will soon go on display at the Bristol Museum and Art Gallery.
Lomax said: “This research has been ongoing for almost eight years. It is quite remarkable to think that gigantic, blue whale-sized ichthyosaurs were swimming in the oceans around what was the UK during the Triassic Period. These jawbones provide tantalising evidence that perhaps one day a complete skull or skeleton of one of these giants might be found. You never know.”
The warming climate shifts the dynamics of tundra environments and makes them release trapped carbon, according to a new study published in Nature. These changes could transform tundras from carbon sinks into a carbon source, exacerbating the effects of climate change.
The warming experiments led to a 1.4 degrees Celsius increase in air temperature and a 0.4 degrees increase in soil temperature, along with a 1.6 percent drop in soil moisture. These changes boosted ecosystem respiration by 30 percent during the growing season, causing more carbon to be released because of increased metabolic activity in soil and plants. The changes persisted for at least 25 years after the start of the experimental warming — which earlier studies hadn’t revealed.
“We knew from earlier studies that we were likely to find an increase in respiration with warming, but we found a remarkable increase — nearly four times greater than previously estimated, though it varied with time and location,” says Sybryn Maes of Umeå University, the study’s lead author.
The increase in ecosystem respiration also varied with local soil conditions, such as nitrogen and pH levels. This means that differences in soil conditions and other factors lead to geographic differences in the response — some regions will see more carbon release than others. Understanding the links between soil conditions and respiration in response to warming is important for creating better climate models.
“Our work represents the first assessment of ecosystem respiration response to experimental warming across such a broad environmental gradient in the tundra, incorporating a comprehensive set of environmental drivers,” says Associate Professor Ellen Dorrepaal of Umeå University.
The study also offers a broader perspective on Arctic and alpine regions by predicting increases in respiration across the whole tundra area together with more detailed information about variation in the sensitivity of the response.
“We see that some areas, particularly parts of Siberia and Canada, exhibit greater sensitivity to warming,” says Professor Matti Kummu of Aalto University. “We anticipate an increase in respiration across the whole Arctic and alpine tundra, but more in situ data, particularly on the local soil conditions, is key to addressing the outstanding uncertainties and refining our predictions.”
Understanding how ecosystems shift in response to climate change and how these changes feed back into the climate is vital to get an accurate picture of how our world will change. These findings serve as an important baseline for improved climate models, but the researchers plan to refine them further by analyzing how the experimental sites change over time and expand the experiment’s scope to include new sites.
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