Wednesday, June 18, 2025

 

Earthworms reveal an evolutionary mechanism which could defy Darwin



A comparative genome study of earthworms and their marine relatives could challenge Darwin’s theory of evolution by showing that worms colonized land in evolutionary jumps



Spanish National Research Council (CSIC)





In 1859, Darwin imagined evolution as a slow, gradual progress, with species accumulating small changes over time. But even he was surprised to find the fossil record offered no missing links: the intermediate forms which should have told this story step by step were simply not there. His explanation was as uncomfortable as it was unavoidable: basically, the fossil record is an archive where most of the pages have been torn out.

In 1972, the scarcity of intermediate forms led the palaeontologists Stephen Jay Gould and Niles Eldredge to propose a provocative idea: punctuated equilibrium. According to this theory, rather than changing slowly, species remain stable for millions of years and then suddenly make rapid, radical evolutionary jumps. This model would explain why the fossil record seems so silent between species: large changes would happen suddenly and in small, isolated populations, well off the palaeontological radar. Although some fossils support this pattern, the scientific community remains divided: is this a rule of evolution, or an eye-catching exception?

Now a research team led by the Institute of Evolutionary Biology (IBE), a mixed research centre belonging to the Spanish National Research Council (CSIC) and Pompeu Fabra University (UPF), points for the first time to a mechanism of rapid, massive genomic reorganisation which could have played a part in the transition of marine to land animals 200 million years ago. The team has shown that marine annelids (worms) reorganised their genome from top to bottom, leaving it unrecognisable, when they left the oceans.  Their observations are consistent with a punctuated equilibrium model, and could indicate that not only gradual but sudden changes in the genome could have occurred as these animals adapted to terrestrial settings. The genetic mechanism identified could transform our concept of animal evolution and revolutionise the established laws of genome evolution.

An unprecedented invertebrate genomic library

The team sequenced for the first time the high-quality genome of various earthworms, and compared to them to other closely related annelid species (leeches and bristle worms or polychaetes). The level of precision was the same as for sequencing human genomes, although in this case starting from scratch, with no existing references for the studied species. Until now, the lack of complete genomes had prevented the study of chromosomal-level patterns and characteristics for many species, limiting research to smaller-scale phenomena – population studies of a handful of genes, rather than macroevolutionary changes at the full-genome level.

After putting together each of the genomic jigsaw puzzles, the team was able to travel back in time with great precision more than 200 million years, to when the ancestors of the sequenced species were alive. “This is an essential episode in the evolution of life on our planet, given that many species, such as worms and vertebrates, which had been living in the ocean, now ventured onto land for the first time,” comments Rosa Fernández, lead researcher of the IBE’s Metazoa Phylogenomics and Genome Evolution Lab.

The analysis of these genomes has revealed an unexpected result: the annelids’ genomes were not transformed gradually, as Neo-Darwinian theory would predict, but in isolated explosions of deep genetic remodelling. “The enormous reorganisation of the genomes we observed in the worms as they moved from the ocean to land cannot be explained with the parsimonious mechanism Darwin proposed; our observations chime much more with Gould and Eldredge’s theory of punctuated equilibrium,” Fernández adds.

A radical genetic mechanism which could provide evolutionary responses

The team has discovered that marine worms broke their genome into a thousand pieces only to reconstruct it and continue their evolutionary path on land. This phenomenon challenges the models of genome evolution known to date, given that if we observe almost any species, whether a sponge, a coral, or a mammal, many of their genomic structures are almost perfectly conserved. "The entire genome of the marine worms was broken down and then reorganised in a completely random way, in a very short period on the evolutionary scale,” Fernández says. “I made my team repeat the analysis again and again, because I just couldn’t believe it.”

The reason why this drastic deconstruction did not lead to extinction could be in the 3D structure of the genome. Fernández’s team has discovered that the chromosomes of these modern worms are much more flexible than those of vertebrates and other model organisms. Thanks to this flexibility, it is possible that genes in different parts of the genome could change places and continue working together. 

Major changes in their DNA could have helped the worms adapt quickly to life on land, reorganising their genes to respond better to new challenges such as breathing air or being exposed to sunlight. The study suggests that these adjustments not only moved genes around, but also joined fragments that had been separated, creating new “genetic chimeras” which would have driven their evolution. “You could think that this chaos would mean the lineage would die out, but it’s possible that some species’ evolutionary success is based on that superpower,” comments Fernández.

The observations in the study are consistent with a punctuated equilibrium model, where we observe an explosion of genomic changes after a long period of stability. However, the lack of experimental data for or against - in this case, 200-million-year-old fossils - makes it difficult to validate this theory.

Chromosomal chaos: problem or solution?

It seems from this study that conserving the genomic structure at the linear level - i.e., where the genes are more or less in the same place in different species - may not be as essential as had been thought. “In fact, stability could be the exception and not the rule in animals, which could benefit from a more fluid genome,” Fernández says.

This phenomenon of extreme genetic reorganisation had previously been observed in the progression of cancer in humans. The term chromoanagenesis covers several mechanisms which break down and reorganise chromosomes in cancerous cells, where we see similar changes to those observed in the earthworms. The only difference is that while these genomic breakdowns and reorganisations are tolerated by the worms, in humans they lead to diseases. The results of this study open the door to a better understanding of the potency of this radical genomic mechanism, with implications for human health.

The study has also reawakened one of the liveliest scientific debates of our time. “Both visions, Darwin’s and Gould’s, are compatible and complementary. While Neo-Darwinism can explain the evolution of populations perfectly, it has not yet been able to explain some exceptional and crucial episodes in the history of life on Earth, such as the initial explosion of animal life in the oceans over 500 million years ago, or the transition from the sea to land 200 million years ago in the case of earthworms,” Fernández notes. “This is where the punctuated equilibrium theory could offer some answers.”

In the future, a larger investigation of the genomic architecture of less-studied invertebrates could shed light on the genomic mechanisms shaping the evolution of the species. “There is a great diversity we know nothing about, hidden in the invertebrates, and studying them could bring new discoveries about the diversity and plasticity of genomic organisation, and challenge dogmas on how we think genomes are organised,” Fernández concludes.

The study involved the collaboration of research staff from the Universitat Autònoma de Barcelona, Trinity College, the Universidad Complutense de Madrid, the University of Köln, and the Université Libre de Bruxelles.

The study received support from SEA2LAND (Starting Grant funded by the European Research Council), and from the Catalan Biogenome Project, which funded the sequencing of one of the worm genomes.

CSIC Communication

comunicacion@csic.es 

 

ETSU fossil discovery reveals giant ancient salamander





East Tennessee State University
Rendering 

image: 

A rendering of the newly discovered salamander. 

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Credit: Matthew Inabinett/ETSU





A giant, strong-jawed salamander once tunneled through ancient Tennessee soil. 
 
And thanks to a fossil unearthed near East Tennessee State University, scientists now better understand how it helped shape Appalachian amphibian diversity. 
 
The giant plethodontid salamander now joins the remarkable roster of fossils from the Gray Fossil Site & Museum.  
 
The findings appeared in the journal Historical Biology, authored by a team of researchers from the Gray Fossil Site & Museum and ETSU: Assistant Collections Manager Davis Gunnin, Director and Professor of Geosciences Dr. Blaine Schubert, Head Curator and Associate Professor of Geosciences Dr. Joshua Samuels, Museum Specialist Keila Bredehoeft and Assistant Collections Manager Shay Maden.  

“Our researchers are not only uncovering ancient life, they are modeling the kind of collaboration and curiosity that define ETSU,” said Dr. Joe Bidwell, dean of the College of Arts and Sciences. “This exciting find underscores the vital role our university plays in preserving and exploring Appalachia’s deep natural history.”
 
Today, Southern Appalachian forests are renowned for their diversity and abundance of salamander species, especially lungless salamanders of the family Plethodontidae. Tennessee alone is home to more than 50 different salamanders – one in eight of all living salamander species.  
 
Dusky salamanders, common in Appalachian Mountain streams, likely evolved from burrowing ancestors, relatives of Alabama’s Red Hills salamander, a large, underground-dwelling species with a worm-like body and small limbs. Their explosive diversification began around 12 million years ago, shaping much of the region’s salamander diversity today. 
 
Dynamognathus robertsoni, the powerful, long-extinct salamander recently discovered at the site, had a bite to match its name. Roughly 16 inches long, it ranked among the largest salamanders ever to crawl across the region’s ancient forests. 
 
“Finding something that looks like a Red Hills salamander here in East Tennessee was a bit of a surprise,” Gunnin said. “Today they’re only found in a few counties in southern Alabama, and researchers thought of them as a highly specialized dead-end lineage not particularly relevant to the evolution of the dusky salamanders. Discovery of Dynamognathus robertsoni here in Southern Appalachia shows that these types of relatively large, burrowing salamanders were once more widespread in eastern North America and may have had a profound impact on the evolution of Appalachian salamander communities.”  
 
Dynamognathus robertsoni is “the largest plethodontid salamander and one of the largest terrestrial salamanders in the world,” Gunnin said. Dusky salamanders in the Appalachians today reach only seven inches long at their largest. 
 
Researchers believe predators like this one may have driven the rapid evolution of Appalachian stream-dwelling salamanders, highlighting the region’s key role in salamander diversification. 
 
“The warmer climate in Tennessee 5 million years ago, followed by cooling during the Pleistocene Ice Ages, may have restricted large, burrowing salamanders to lower latitudes, like southern Alabama, where the Red Hills salamander lives today,” said Samuels.  
 
Maden explained the naming of this new salamander. 
 
“This group of salamanders has unusual cranial anatomy that gives them a strong bite force, so the genus name – Dynamognathus – Greek for ‘powerful jaw,’ is given to highlight the great size and power of the salamander compared to its living relatives,” said Maden.  
 
The species name robertsoni honors longtime Gray Fossil Site volunteer Wayne Robertson, who discovered the first specimen of the new salamander and has personally sifted through more than 50 tons of fossil-bearing sediment since 2000. 
 
From volunteers and students to staff to faculty, the ETSU Gray Fossil Site & Museum is represented by a dynamic team of lifelong learners and is one of the many reasons ETSU is the flagship institution of Appalachia.   
 
“The latest salamander publication is a testament to this teamwork and search for answers,” said Schubert. “When Davis Gunnin, the lead author, began volunteering at the museum as a teenager with an interest in fossil salamanders, I was thrilled, because this region is known for its salamander diversity today, and we know so little about their fossil record. Thus, the possibility of finding something exciting seemed imminent.”

 

Research reveals that fish biofluorescence evolved more than 100 times in 112 million years



Two new studies on marine fish biofluorescence find a close link to coral reefs and a wide range of dazzling colors



American Museum of Natural History

Ochre-banded goatfish 

image: 

An ochre-banded goatfish (Upeneus sundaicus)

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Credit: © John Sparks and David Gruber





New research led by scientists at the American Museum of Natural History sheds light on the ancient origins of biofluorescence in fishes and the range of brilliant colors involved in this biological phenomenon. Detailed in two complementary studies recently published in Nature Communications and PLOS One, the findings suggest that biofluorescence dates back at least 112 million years and, since then, has evolved independently more than 100 times, with the majority of that activity happening among fish that live on coral reefs.

The new work also reveals that in marine fishes, biofluorescence—which occurs when an organism absorbs light, transforms it, and emits it as a different color—involves a greater variety of colors than previously reported, spanning multiple wavelengths of green, yellow, orange, and red.

“Researchers have known for a while that biofluorescence is quite widespread in marine animals, from sea turtles to corals, and especially among fishes,” said Emily Carr, a Ph.D. student in the Museum’s Richard Gilder Graduate School and the lead author on the two new studies. “But to really get to the root of why and how these species use this unique adaptation—whether for camouflage, predation, or reproduction—we need to understand the underlying evolutionary story as well as the scope of biofluorescence as it currently exists.”

For the Nature Communications study, Carr led a comprehensive survey of all known biofluorescent teleosts—a type of bony fish that make up by far the largest group of vertebrates alive today. This resulted in a list of 459 biofluorescent species, including 48 species that were previously unknown to be biofluorescent. The researchers found that biofluorescence evolved more than 100 times in marine teleosts and is estimated to date back about 112 million years, with the first instance occurring in eels.

The team also found that fish species that live in or around coral reefs evolve biofluorescence at about 10 times the rate of non-reef species, with an increase in the number of fluorescent species following the Cretaceous-Paleogene (K-Pg) extinction about 66 million years ago, when all of the non-avian dinosaurs died off.

“This trend coincides with the rise of modern coral-dominated reefs and the rapid colonization of reefs by fishes, which occurred following a significant loss of coral diversity in the K-Pg extinction,” Carr said. “These correlations suggest that the emergence of modern coral reefs could have facilitated the diversification of fluorescence in reef-associated teleost fishes.”

Of the 459 known biofluorescent teleosts reported in this study, the majority are associated with coral reefs.

For the PLOS One study, Carr and colleagues used a specialized photography setup with ultraviolet and blue excitation lights and emission filters to look at the wavelengths of light emitted by fishes in the Museum’s Ichthyology collection. Collected over the last decade and a half on Museum expeditions to the Solomon Islands, Greenland, and Thailand, the specimens in the study were previously observed fluorescing, but the full range of their biofluorescent emissions was unknown.

The new work reveals far more diversity in colors emitted by teleosts—some families of which exhibit at least six distinct fluorescent emission peaks, which correspond with wavelengths across multiple colors—than had previously been reported.

“The remarkable variation we observed across a wide array of these fluorescent fishes could mean that these animals use incredibly diverse and elaborate signaling systems based on species-specific fluorescent emission patterns,” said Museum Curator John Sparks, an author on the new studies and Carr’s advisor. “As these studies show, biofluorescence is both pervasive and incredibly phenotypically variable among marine fishes. What we would really like to understand better is how fluorescence functions in these highly variable marine lineages, as well as its role in diversification.”

The researchers also note that the numerous wavelengths of fluorescent emissions found in this study could have implications for identifying novel fluorescent molecules, which are routinely used in biomedical applications, including fluorescence-guided disease diagnosis and therapy.

Other authors involved in this work include Rene Martin, from the Museum and the University of Nebraska-Lincoln; Mason Thurman, from Clemson University; Karly Cohen, from California State University; Jonathan Huie, from George Washington University; David Gruber, from Baruch College and The Graduate Center, City University of New York; and Tate Sparks, Rutgers University.

 

Research in the Solomon Islands was supported by the National Science Foundation under Grant Number DEB-1257555.

The Museum greatly acknowledges the Dalio Foundation for its generous support of the inaugural Explore21 Expedition.

The Museum's Exlopre21 initiative is generously supported by the leadership contributions of Katheryn P. and Thomas L. Kempner, Jr. 

The 2019 Constantine S. Niarchos Expedition to Greenland was generously supported by the Stavros Niarchos Foundation. 

Research in Thailand was funded by the Museum and the National Science Foundation Graduate Research Fellowship Program under Grant Number DEB-1938103.

Additional funding for this work was provided by the National Science Foundation under Grant Number DGE-1746914.


Study DOIs:

Nature Communications: 0.1038/s41467-025-59843-7

PLOS One: 10.1371/journal.pone.0316789

 

ABOUT THE AMERICAN MUSEUM OF NATURAL HISTORY (AMNH)

The American Museum of Natural History, founded in 1869 with a dual mission of scientific research and science education, is one of the world’s preeminent scientific, educational, and cultural institutions. The Museum encompasses more than 40 permanent exhibition halls, galleries for temporary exhibitions, the Rose Center for Earth and Space including the Hayden Planetarium, and the Richard Gilder Center for Science, Education, and Innovation. The Museum’s scientists draw on a world-class permanent collection of more than 30 million specimens and objects, some of which are billions of years old, and on one of the largest natural history libraries in the world. Through its Richard Gilder Graduate School, the Museum offers two of the only free-standing, degree-granting programs of their kind at any museum in the U.S.: the Ph.D. program in Comparative Biology and the Master of Arts in Teaching (MAT) Earth Science residency program. Visit amnh.org for more information.

 

First ancient flying reptiles were winners of increasing Triassic humid environments



Changing climate conditions set the stage for pterosaurs to take to the skies ~220 million years ago




University of Birmingham





Pterosaurs which dominated the skies of the Triassic, Jurassic and Cretaceous periods first evolved to take to the air in warm and humid conditions during the Late Triassic, a new study suggests.

 

In a paper published in Nature Ecology and Evolution today (Wednesday 18 June), a research team including academics from the University of Birmingham, University College London and Friedrich-Alexander-Universität Erlangen-Nürnberg in Germany combined data on the distribution of fossils in the Triassic period with information on the ancient climate in the same areas.

 

The team focused on the distribution of two closely related groups, pterosaurs and lagerpetids. Living approximately 240 -201 million years ago, lagerpetids were a group of relatively small (rat-to-dog-sized) land- and tree-dwelling active reptiles. These small land-based reptiles are now considered the closest relatives to pterosaurs and, the study reveals, were able to tolerate a wider range of climate conditions than their close flying kin, including the arid areas of the ancient landmass Pangea. This broad tolerance resulted in a widespread distribution of this group.

 

Pterosaurs meanwhile appear to have been at first confined to the more humid conditions found in smaller areas of the ancient world, based on fossils found in modern day Italy and Austria, and southwestern U.S.A., all regions that at the time were close to the equator.

 

During the Late Triassic, climatic conditions changed across the globe, leading to a general increase in warm and humid conditions outside the equatorial belt. This became an opportunity that allowed the flying reptiles to rapidly spread across the globe including to high latitude areas such as what is now Greenland and South America.

 

Dr Davide Foffa from the University of Birmingham and corresponding author of the paper said:

 

“Pterosaurs capture the imagination, with the idea of terrifying reptiles dominating the airs at the time while dinosaurs were roaming the world. However, pterosaur origins are still wrapped in mystery. Our study adds new information to this puzzle, suggesting that their early evolution during the Triassic period into a dominant group may have been favoured by changing climates and environments.

 

Dr Emma Dunne from Friedrich-Alexander-Universität Erlangen-Nürnberg and a co-author of the paper said:

 

“Climate change is a leading cause of biodiversity change, both in the present day and the geological past. However, it is only in the last few years [with advances in modelling methods] that palaeontologists are getting to grips with how climate change impacted the biodiversity of prominent fossil groups like the pterosaurs."

 

Dr Alessandro Chiarenza from the University College London and co-leading author of the paper said: “Taken together, ecological models and fossil data paint a coherent picture of pterosaur early evolution.”

”Lagerpetids thrived as generalists, while pterosaurs, initially confined to humid-tropical niches and perhaps limited flight performance, occupied equatorial treetops.” adds Chiarenza.

 

When global climates shifted and forested corridors opened, those same wings catapulted them into every corner of the planet and ultimately carried them through one of Earth’s greatest extinctions. What began as a tale of missing fossils is becoming a textbook example of how palaeoclimate, palaeoecology and evolutionary innovation intertwine to illuminate a patchy history that has intrigued palaeontologists for two centuries.’

 

Gut microbiome composition and food insecurity linked to risk of cognitive impairment in adults



Findings suggest that gut microbes and access to nutritious food may jointly influence brain function




The Mount Sinai Hospital / Mount Sinai School of Medicine





New York, NY — [June 18, 2025] — A new study led in part by Mount Sinai researchers has found a compelling link between the composition of the gut microbiome and the risk of cognitive impairment (RCI) in adults, underscoring the complex role that both biology and social determinants—such as food insecurity—play in brain health. This is the first epidemiologic study to assess the modifying role that food insecurity may play on the relationship between the gut microbiome and RCI.

Published in NPJ Aging, this study investigated the role of food insecurity as an effect modifier between specific groups of microbes in the gut microbiome and RCI. The research shows that adults with lower microbial diversity and specific imbalances in gut bacteria were significantly more likely to experience cognitive impairment. The analysis also found that food insecurity—limited or uncertain access to adequate food—was independently associated with both poorer gut health and diminished cognitive performance.

“More than 12 percent (17.0 million) of U.S. households in 2022 experienced food insecurity at some point throughout the year, showing an increase from the 10.2 percent (13.5 million) prevalence in 2021,” said Shoshannah Eggers, Assistant Professor, Epidemiology, University of Iowa College of Public Health, and corresponding author on this study. Dr. Eggers began working on this study while a Postdoctoral Fellow at the Icahn School of Medicine at Mount Sinai.

“Food insecurity is consistently linked to adverse health outcomes such as poorer overall health and adverse neurological health outcomes. Understanding how gut health and social conditions interact gives us a fuller picture of what puts people at risk for cognitive decline,” said Dr. Eggers, who also serves as co-director of the Microbial Exposomics Lab and an associate member of the Environmental Health Sciences Research Center at the University of Iowa College of Public Health.

The study included 360 adult participants from the Survey of the Health of Wisconsin with complete data on food insecurity, RCI, and 16S rRNA sequencing—a test to figure out which bacteria are present in a stool sample.

Small groups of closely connected microbes (known as microbial cliques) associated with RCI were identified using an interpretable machine-learning-based algorithm—a type of machine learning model that not only makes predictions or decisions but also lets researchers understand how and why it made those predictions. All analyses were stratified by food insecurity level and adjusted for relevant confounders, like age, body mass index, and smoking.

The researchers identified two cliques whose associations with RCI were modified by food insecurity status. The presence of the clique with either Eisenbergiella or Eubacterium was more strongly associated with RCI for the food-insecure group. A clique representing the presence of Ruminococcus torques, Bacteroides, CAG-352F, and/or Eubacterium had a stronger association with RCI for the food-secure group.

The contrasting results between food-secure and food-insecure groups may be particularly important while devising microbial interventions for cognitive impairment, as food security status may alter the effectiveness of such interventions.

“These findings suggest that food insecurity is not just a socioeconomic issue—it may be a biological one too, influencing brain health via changes to the gut microbiome,” said Vishal Midya, PhD, MStat, Assistant Professor of Environmental Medicine at the Icahn School of Medicine at Mount Sinai and senior author of the study. “Cognitive impairment, including mild cognitive impairment and dementia, is increasing, particularly among older adults, and is primarily driven by an aging population. Future studies investigating why cognitive problems develop in people should consider food insecurity as one possible contributing factor.”

The study calls for more integrated public health approaches that address both nutritional access and gut health. It also opens the door for future interventions combining dietary support and microbiome-targeted therapies to reduce the risk of dementia, particularly in vulnerable populations.

This research was supported by grant funding by the National Institute of Environmental Health Sciences. DOI: 10.1038/s41514-025-00241-0. View the paper here.

###

About the Mount Sinai Health System

Mount Sinai Health System is one of the largest academic medical systems in the New York metro area, with 48,000 employees working across seven hospitals, more than 400 outpatient practices, more than 600 research and clinical labs, a school of nursing, and a leading school of medicine and graduate education. Mount Sinai advances health for all people, everywhere, by taking on the most complex health care challenges of our time—discovering and applying new scientific learning and knowledge; developing safer, more effective treatments; educating the next generation of medical leaders and innovators; and supporting local communities by delivering high-quality care to all who need it.

Through the integration of its hospitals, labs, and schools, Mount Sinai offers comprehensive health care solutions from birth through geriatrics, leveraging innovative approaches such as artificial intelligence and informatics while keeping patients’ medical and emotional needs at the center of all treatment. The Health System includes approximately 9,000 primary and specialty care physicians and 11 free-standing joint-venture centers throughout the five boroughs of New York City, Westchester, Long Island, and Florida. Hospitals within the System are consistently ranked by Newsweek’s® “The World’s Best Smart Hospitals, Best in State Hospitals, World Best Hospitals and Best Specialty Hospitals” and by U.S. News & World Report's® “Best Hospitals” and “Best Children’s Hospitals.” The Mount Sinai Hospital is on the U.S. News & World Report® “Best Hospitals” Honor Roll for 2024-2025. 

For more information, visit https://www.mountsinai.org or find Mount Sinai on FacebookInstagramLinkedInX, and YouTube.

 

About The University of Iowa
The University of Iowa is among the top public research institutions in the nation — offering a world-class education in over 200 areas of study to more than 32,000 students. From the most prestigious creative writing program in the United States, to a nationally recognized academic medical center, our balanced excellence in the arts and sciences encourages innovation and exploration across the disciplines.