KRAKEN STUDIES
Novel “digital fossil-mining” approach uncovers hidden fossils, revealing squids’ ancient origins
Summary author: Walter Beckwith
Using an innovative “digital fossil-mining” approach, researchers have uncovered hundreds of previously hidden fossil squid beaks, revealing a record that squids originated and became ecologically dominant roughly 100 million years ago – well before the end-Cretaceous extinction. Squids are the most diverse and globally distributed group of marine cephalopods in the modern ocean, where they play a vital role in ocean ecosystems as both predators and prey. Their evolutionary success is widely considered to be related to the loss of a rigid external shell, which was a key trait of their cephalopod ancestors. However, their evolutionary origins remain obscure due to the rarity of fossils from soft-bodied organisms. The fossil record of squids begins only around 45 million years ago, with most specimens consisting of just fossilized statoliths – tiny calcium carbonite structures involved in balance. The lack of early fossils has led to speculation that squids diversified after the end-Cretaceous mass extinction 66 million years ago. While molecular analyses of living species have offered estimates of squid divergence times, the absence of earlier fossils has made these estimates highly uncertain.
Here, Shin Ikegami and colleagues address these gaps using a novel approach – “digital fossil-mining” – which uses high-resolution grinding tomography and advanced image processing to digitally scan entire rocks as stacked cross-sectional images to reveal hidden fossils as detailed 3D models. Ikegami et al. applied this technique to Cretaceous-age carbonate rocks from Japan, uncovering 263 fossilized squid beaks, with specimens spanning 40 species across 23 genera and five families. The findings show that squids originated roughly 100 million years ago, near the boundary between the Early and Late Cretaceous, and rapidly diversified thereafter. According to the authors, the previously hidden fossil record greatly extends the known origins of both major squid groups – Oegopsida by ~15 million years and Myopsida by ~55 million years. Early Oegopsids displayed distinct anatomical traits that disappeared in later species, suggesting swift morphological evolution, while Myopsids already resembled modern forms. What’s more, the study suggests that Late Cretaceous squids were more abundant and often larger than coexisting ammonites and bony fishes, an ecological dominance that predates the radiation of bony fishes and marine mammals by over 30 million years, making them among the first intelligent, fast swimmers to shape modern ocean ecosystems.
For reporters interested in research integrity issues co-author Yasuhiro Iba notes, “accessibility and reproducibility in fossil-based studies have been strongly restricted by the fixation on studying physical specimens. In contrast, we performed all processes from fossil hunting to analysis in cyberspace and digitally released all specimens to the public. I believe that this breakthrough is critical to ensuring research integrity and will facilitate groundbreaking discoveries worldwide.”
Summary author: Walter Beckwith
Using an innovative “digital fossil-mining” approach, researchers have uncovered hundreds of previously hidden fossil squid beaks, revealing a record that squids originated and became ecologically dominant roughly 100 million years ago – well before the end-Cretaceous extinction. Squids are the most diverse and globally distributed group of marine cephalopods in the modern ocean, where they play a vital role in ocean ecosystems as both predators and prey. Their evolutionary success is widely considered to be related to the loss of a rigid external shell, which was a key trait of their cephalopod ancestors. However, their evolutionary origins remain obscure due to the rarity of fossils from soft-bodied organisms. The fossil record of squids begins only around 45 million years ago, with most specimens consisting of just fossilized statoliths – tiny calcium carbonite structures involved in balance. The lack of early fossils has led to speculation that squids diversified after the end-Cretaceous mass extinction 66 million years ago. While molecular analyses of living species have offered estimates of squid divergence times, the absence of earlier fossils has made these estimates highly uncertain.
Here, Shin Ikegami and colleagues address these gaps using a novel approach – “digital fossil-mining” – which uses high-resolution grinding tomography and advanced image processing to digitally scan entire rocks as stacked cross-sectional images to reveal hidden fossils as detailed 3D models. Ikegami et al. applied this technique to Cretaceous-age carbonate rocks from Japan, uncovering 263 fossilized squid beaks, with specimens spanning 40 species across 23 genera and five families. The findings show that squids originated roughly 100 million years ago, near the boundary between the Early and Late Cretaceous, and rapidly diversified thereafter. According to the authors, the previously hidden fossil record greatly extends the known origins of both major squid groups – Oegopsida by ~15 million years and Myopsida by ~55 million years. Early Oegopsids displayed distinct anatomical traits that disappeared in later species, suggesting swift morphological evolution, while Myopsids already resembled modern forms. What’s more, the study suggests that Late Cretaceous squids were more abundant and often larger than coexisting ammonites and bony fishes, an ecological dominance that predates the radiation of bony fishes and marine mammals by over 30 million years, making them among the first intelligent, fast swimmers to shape modern ocean ecosystems.
For reporters interested in research integrity issues co-author Yasuhiro Iba notes, “accessibility and reproducibility in fossil-based studies have been strongly restricted by the fixation on studying physical specimens. In contrast, we performed all processes from fossil hunting to analysis in cyberspace and digitally released all specimens to the public. I believe that this breakthrough is critical to ensuring research integrity and will facilitate groundbreaking discoveries worldwide.”
Journal
Science
Science
DOI
Article Title
Origin and radiation of squids revealed by digital fossil-mining
Origin and radiation of squids revealed by digital fossil-mining
Article Publication Date
26-Jun-2025
26-Jun-2025
Ancient squids dominated the ocean 100 million years ago
A new fossil discovery technique reveals that squids originated and rapidly became abundant, diverse, and dominant in the oceans 100 million years ago, reshaping our understanding of ancient marine ecosystems.
image:
An example of grinding tomography images
view moreCredit: Ikegami et al., Science, June 26, 2025
Squids first appeared about 100 million years ago and quickly rose to become dominant predators in the ancient oceans, according to a new study published in the journal Science. A team of researchers from Hokkaido University developed an advanced fossil discovery technique that completely digitizes rocks with all embedded fossils in complete 3D form. It allowed them to identify one thousand fossilized cephalopod beaks hidden inside Late Cretaceous rocks from Japan. Among these small and fragile beaks were 263 squid specimens including about 40 different species that had never been seen before.
Squids are rarely preserved as fossils because they don’t have hard shells. Their origin and early evolution are the biggest questions in the 500 million-year history of cephalopods, which have been model animals for long-term evolution. Squid beaks, hard mouthparts that have a high fossilization potential, are therefore important clues for studying how squids evolved.
One of the study’s most striking discoveries was how common squids were in ancient oceans. The team found that squid fossils far outnumbered those of ammonites and bony fishes. Ammonites are extinct shelled relatives of squids and have been considered among the most successful swimmers of the Mesozoic era.
“In both number and size, these ancient squids clearly prevailed the seas,” said Dr. Shin Ikegami of the Department of Earth and Planetary Sciences at Hokkaido University, the study’s first author. “Their body sizes were as large as fish and even bigger than the ammonites we found alongside them. This shows us that squids were thriving as the most abundant swimmers in the ancient ocean.”
The research also revealed that the two main groups of modern squids, Myopsida, which live near the shore, and Oegopsida, found in the open sea, were already present around 100 million years ago. Until now, scientists believed that squids only began to flourish after the mass extinction event that ended the age of dinosaurs about 65 million years ago. The new study shows that squids had already originated and explosively diversified long before then.
“These findings change everything we thought we knew about marine ecosystems in the past,” said Associate Professor Yasuhiro Iba of the Department of Earth and Planetary Sciences at Hokkaido University, who led the study. “Squids were probably the pioneers of fast and intelligent swimmers that dominate the modern ocean.”
Journal
Science
Method of Research
Imaging analysis
Subject of Research
Not applicable
Article Title
Origin and radiation of squids revealed by digital fossil-mining
Article Publication Date
26-Jun-2025
Examples of fossil lower beaks of squids from the Late Cretaceous discovered in this study. Scalebar: 1mm.
The digital fossil-mining method utilizes grinding tomography to create digitized rocks and reveal hidden fossils within them.
Credit
Digital fossil-mining of squid beaks
https://doi.org/10.6084/m9.figshare.29336441
Comparison between X-ray CT (left) and grinding tomography (right).
https://doi.org/10.6084/m9.figshare.29336525
Comparison between X-ray CT (left) and grinding tomography (right).
https://doi.org/10.6084/m9.figshare.29336525
Credit
Shin Ikegami, et al.
Shin Ikegami, et al.
UC Irvine-led team uncovers cell structures that squids use to change their appearance
Inspired by new knowledge, researchers develop tunable, multispectral composite material
University of California - Irvine
image:
Digital camera images of the entire body (top left) and dorsal mantle (top right) of a squid show the splotches’ blue, green, yellow, orange and red iridescent (angle-dependent) colors. An individual splotch (bottom, from left) transitions from transparent to red to orange to green at 0, 60, 90 and 120 seconds, respectively, when subjected to chemical and neurophysiological stimuli.
view moreCredit: Alon Gorodetsky Lab, UC Irvine
Irvine, Calif., June 26, 2025 – By examining squid skin cells three-dimensionally, a University of California, Irvine-led team has unveiled the structures responsible for the creatures’ ability to dynamically change their appearance from transparent to arbitrarily colored states.
The group of scientists, which included collaborators from the Marine Biological Laboratory at Woods Hole, Massachusetts, found that in vibrantly colored squid mantle tissues, light-manipulating cells called iridophores or iridocytes contain stacked and winding columns of platelets from a protein called reflectin, with the columns functioning as Bragg reflectors that selectively transmit and reflect light at specific wavelengths.
In a paper published today in Science, the researchers discussed how they took inspiration from the cells and their internal columnar structures to develop a multispectral composite material with adjustable visible and infrared properties.
“In nature, many animals use Bragg reflectors for structural coloration,” said co-author Alon Gorodetsky, UC Irvine associate professor of chemical and biomolecular engineering. “A squid’s ability to rapidly and reversibly transition from transparent to colored is remarkable, and we found that cells containing specialized subcellular columnar structures with sinusoidal refractive index distributions enable the squid to achieve such feats.”
Co-author Roger Hanlon, a senior scientist with the Marine Biological Laboratory, provided Gorodetsky’s UC Irvine team with access to squids, and his laboratory helped unravel the coloration and anatomy of the iridophore-containing tissues.
“These are longfin inshore squids – Doryteuthis pealeii – that are native to the Atlantic Ocean,” said Gorodetsky. “Marine Biological Laboratory has been famous for studying this squid and other cephalopods for more than a century, so we were fortunate to be able to leverage their world-class expertise with properly collecting, handling and studying these biological specimens.”
The team used holotomography, a microscopy technique that combines low-intensity light with quantitative phase imaging to create 3D images of clustered and individual cells. The instrument directly measures subtle shifts in light as it passes through the tissue and constructs a refractive index map of the sample, revealing structural and biochemical features.
“Holotomography used the high refractive index of reflectin proteins to reveal the presence of sinusoidal refractive index distributions within squid iridophore cells,” said co-lead author Georgii Bogdanov, a UC Irvine postdoctoral researcher in chemical and biomolecular engineering. “Platelets composed of the protein reflectin form winding platelet columns that fill the interiors of the iridophores. This complex system drives cephalopod mantle optics, with the cells and their internal structures regulating light transmission and reflection.”
Gorodetsky said the process of exploring and discovering the mechanisms underpinning the squids’ color-manipulation abilities inspired his team to develop flexible and stretchable visible appearance-changing composite materials from nanocolumnar sinusoidal Bragg reflectors and to then further augment these materials with infrared appearance-modifying capabilities by incorporating nanostructured metal films.
Using a suite of microscopy and spectroscopy instruments, the team verified that the modular and multifunctional composites could perform a variety of multispectral functions, including as camouflage, signaling, and sensing.
“These bioinspired materials go beyond simple static color control, as they can dynamically adjust both their appearances in the visible and infrared wavelengths in response to environmental or mechanical stimuli,” said co-lead author Aleksandra Strzelecka, Ph.D. candidate in chemical and biomolecular engineering. “Part of what makes this technology truly exciting is its inherent scalability. We have demonstrated large-area and arrayed composites that mimic and even go beyond the squid’s natural optical capabilities, opening the door to many applications ranging from adaptive camouflage to responsive fabrics to multispectral displays to advanced sensors.”
Gorodetsky said that the underlying fundamental insights gained from studying squid skin can be potentially broadly leveraged for improving a wide range of other optical technologies, such as lasers, fiber optics, photovoltaics, and sensors.
“This study is an exciting demonstration of the power of coupling basic and applied research,” he said. “We have likely just started to scratch the surface of what is possible for cephalopod-inspired tunable optical materials in our laboratory.”
Other team members were Sanghoon Lee, a UC Irvine postdoctoral scholar in chemical and biomolecular engineering; Nikhil Kaimal, a UC Irvine Ph.D. candidate in chemical and biomolecular engineering; and Stephen Senft, a research associate at the Marine Biological Laboratory.
The research was funded by the Defense Advanced Research Projects Agency and the Air Force Office of Scientific Research.
About the University of California, Irvine: Founded in 1965, UC Irvine is a member of the prestigious Association of American Universities and is ranked among the nation’s top 10 public universities by U.S. News & World Report. The campus has produced five Nobel laureates and is known for its academic achievement, premier research, innovation and anteater mascot. Led by Chancellor Howard Gillman, UC Irvine has more than 36,000 students and offers 224 degree programs. It’s located in one of the world’s safest and most economically vibrant communities and is Orange County’s second-largest employer, contributing $7 billion annually to the local economy and $8 billion statewide. For more on UC Irvine, visit www.uci.edu.
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Journal
Science
Method of Research
Observational study
Subject of Research
Cells
Article Title
Gradient refractive indices enable squid structural color and inspire multispectral materials
Article Publication Date
26-Jun-2025
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