Category: 7. Science

Fossils uncovered in northeastern Ethiopia, dating to between 2.6 and 2.8 million years ago, provide new insights into the course of human evolution.

An international team of researchers has uncovered new fossils in Africa showing that Australopithecus and the earliest known members of Homo lived in the same region at the same time, between 2.6 and 2.8 million years ago. Among the finds was a previously unknown species of Australopithecus, unlike any identified before.

The discoveries come from the Ledi-Geraru Research Project, led by scientists at Arizona State University. This site has already produced the world’s oldest known Homo specimen, as well as the earliest examples of Oldowan stone tools.

Detailed study of the newly recovered Australopithecus teeth confirmed that they represent a distinct species rather than belonging to Australopithecus afarensis, the species of the famous fossil “Lucy.” This finding reinforces that no remains of Lucy’s lineage are known to be younger than 2.95 million years.

“This new research shows that the image many of us have in our minds of an ape to a Neanderthal to a modern human is not correct — evolution doesn’t work like that,” said ASU paleoecologist Kaye Reed. “Here we have two hominin species that are together. And human evolution is not linear, it’s a bushy tree, there are life forms that go extinct.”

A research effort spanning decades

Reed serves as a Research Scientist at the Institute of Human Origins and is a President’s Professor Emerita in the School of Human Evolution and Social Change at Arizona State University. She has also co-directed the Ledi-Geraru Research Project since 2002.

So what fossils helped shape these new conclusions? The team uncovered 13 teeth in total.

The Ledi-Geraru site has drawn attention before. In 2013, Reed and her colleagues reported the discovery of the earliest known Homo fossil—a jaw dating to 2.8 million years ago. The new study builds on that legacy, describing additional teeth from the site that belong to both the genus Homo and a newly identified species of Australopithecus.

“The new finds of Homo teeth from 2.6 – 2.8 million-year-old sediments, reported in this paper, confirm the antiquity of our lineage,” said Brian Villmoare, lead author and ASU alumnus.

“We know what the teeth and mandible of the earliest Homo look like, but that’s it. This emphasizes the critical importance of finding additional fossils to understand the differences between Australopithecus and Homo, and potentially how they were able to overlap in the fossil record at the same location.”

The team cannot name the species yet based on the teeth alone; more fossils are needed before that can happen.

How do scientists know these fossil teeth are millions of years old?

Volcanoes.

The Afar region remains an active rift zone, marked by frequent volcanic and tectonic activity. When these volcanoes erupted, they released ash containing crystals known as feldspars, which provide scientists with a way to determine their age, explained Christopher Campisano, a geologist at ASU.

“We can date the eruptions that were happening on the landscape when they’re deposited,” said Campisano, a Research Scientist at the Institute of Human Origins and Associate Professor at the School of Human Evolution and Social Change.

“And we know that these fossils are interbed between those eruptions, so we can date units above and below the fossils. We are dating the volcanic ash of the eruptions that were happening while they were on the landscape.”

Ledi-Geraru’s ancient landscape

Finding fossils and dating the landscape not only helps scientists understand the species, but it also helps them recreate the environment millions of years ago. The modern faulted badlands of Ledi-Geraru, where the fossils were found, are a stark contrast to the landscape these hominins traversed 2.6 – 2.8 million years ago. Back then, rivers migrated across a vegetated landscape into shallow lakes that expanded and contracted over time.

Ramon Arrowsmith, a geologist at ASU, has been working with the Ledi-Geraru Research Project since 2002. He explained the area has an interpretable geologic record with good age control for the geologic time range of 2.3 to 2.95 million years ago.

“It is a critical time period for human evolution as this new paper shows,” said Arrowsmith, professor at the School of Earth and Space Exploration. “The geology gives us the age and characteristics of the sedimentary deposits containing the fossils. It is essential for age control.”

Reed said the team is examining tooth enamel now to find out what they can about what these species were eating. There are still remaining questions the team will continue to work on.

Were the early Homo and this unidentified species of Australopithecus eating the same things? Were they fighting for or sharing resources? Did they pass each other daily? Who were the ancestors of these species?

No one knows – yet.

“Whenever you have an exciting discovery, if you’re a paleontologist, you always know that you need more information,” said Reed. “You need more fossils. That’s why it’s an important field to train people in and for people to go out and find their own sites and find places that we haven’t found fossils yet.”

“More fossils will help us tell the story of what happened to our ancestors a long time ago — but because we’re the survivors, we know that it happened to us.”

Reference: “New discoveries of Australopithecus and Homo from Ledi-Geraru, Ethiopia” by Brian Villmoare, Lucas K. Delezene, Amy L. Rector, Erin N. DiMaggio, Christopher J. Campisano, David A. Feary, Baro’o Mohammed Ali, Daniel Chupik, Alan L. Deino, Dominique I. Garello, Mohammed Ahmeddin Hayidara, Ellis M. Locke, Omar Abdulla Omar, Joshua R. Robinson, Eric Scott, Irene E. Smail, Kebede Geleta Terefe, Lars Werdelin, William H. Kimbel, J. Ramón Arrowsmith and Kaye E. Reed, 13 August 2025, Nature.
DOI: 10.1038/s41586-025-09390-4

Funding: U.S. National Science Foundation

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Roughly 390 million years ago, the ancient seas witnessed a dramatic change. Marine animals began moving into deeper waters that had long been uninhabitable. New research suggests this expansion was fueled by a lasting rise in deep-ocean oxygen.

The source of that oxygen traces back to the spread of woody plants on land, the earliest forests on Earth. This environmental shift coincided with an explosion of new species, especially jawed fish.

These fish became the ancestors of nearly all vertebrates alive today. The link between oxygen levels and evolutionary diversification offers fresh insight into how life reshaped the oceans.

Oxygen rise shaped evolution

“It’s known that oxygen is a necessary condition for animal evolution, but the extent to which it is the sufficient condition that can explain trends in animal diversification has been difficult to pin down,” said co-lead author Michael Kipp, assistant professor at Duke University.

“This study gives a strong vote that oxygen dictated the timing of early animal evolution, at least for the appearance of jawed vertebrates in deep-ocean habitats.”

For decades, scientists believed deep-ocean oxygenation occurred only once, at the start of the Paleozoic Era about 540 million years ago.

Later evidence pointed instead to multiple phases. First, shallower waters became livable for breathing organisms, and only later did oxygen reach deeper environments.

Rocks reveal ocean oxygen history

Kipp and his colleagues focused on timing by studying sedimentary rocks once buried beneath ancient oceans.

They measured levels of selenium, an element that records traces of oxygen in the environment. Selenium occurs in different isotopes, and their ratios reveal whether oxygen levels were high enough to support animal life.

The team collected 97 rock samples dating from 252 to 541 million years ago, gathered from five continents.

At the time, these sites lay along outer continental shelves, the zones where land tapered into the ocean before plunging steeply downward. By analyzing isotope ratios in the samples, the researchers tracked oxygen’s reach through time.

Two deep-sea oxygen waves

Results showed two distinct deep-ocean oxygenation events. One brief episode occurred during the Cambrian period, about 540 million years ago.

The second began during the Middle Devonian, around 393 to 382 million years ago, and continues today. Between these events, oxygen dropped to inhospitable levels for most animals.

“The selenium data tell us that the second oxygenation event was permanent. It began in the Middle Devonian and persisted in our younger rock samples,” said co-lead author Kunmanee “Mac” Bubphamanee, a Ph.D. candidate at the University of Washington.

Vertebrates thrived with more oxygen

The Middle Devonian oxygen rise triggered what scientists call the “mid-Paleozoic marine revolution.” With oxygen now plentiful, jawed fish and other animals expanded into deeper waters and diversified.

Fossil evidence also shows that many species grew larger, likely supported by the richer oxygen supply. One example is shown in the featured image of this article – a prehistoric jawed fish from the Late Devonian called Dunkleosteus.

This geological shift aligned with another event on land: the spread of woody plants.

“Our thinking is that, as these woody plants increased in number, they released more oxygen into the air, which led to more oxygen in deeper ocean environments,” Kipp said.

First oxygen wave faded fast

The earlier Cambrian oxygen surge remains puzzling. Its decline likely prevented animals from permanently establishing themselves in deeper waters at that time.

“What seems clear is that the drop in oxygen after that initial pulse hindered the spread and diversification of marine animals into those deeper environments of the outer continental shelves,” Kipp noted.

Oxygen history warns about today’s oceans

Although the study looks far into the past, its message carries urgency now.

“Today, there’s abundant ocean oxygen in equilibrium with the atmosphere,” said Kipp. “But in some locations, ocean oxygen can drop to undetectable levels.”

“Some of these zones occur through natural processes. But in many cases, they’re driven by nutrients draining off continents from fertilizers and industrial activity that fuel plankton blooms that suck up oxygen when they decay.”

“This work shows very clearly the link between oxygen and animal life in the ocean. This was a balance struck about 400 million years ago, and it would be a shame to disrupt it today in a matter of decades.”

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Featured image: An artist’s rendering of a prehistoric jawed fish from the Late Devonian called Dunkleosteus. These sorts of large, active vertebrates evolved shortly after the deep ocean became well-oxygenated. Credit: 2008 N. Tamura/CC-BY-SA

The study is published in the journal Proceedings of the National Academy of Sciences.

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Small, colorless, and blind, amblyopsid cavefishes inhabit subterranean waters throughout the eastern United States. In a new study, Yale researchers reveal insights into just how these distinctive cave dwellers evolved — and provide a unique method for dating the underground ecosystems where they reside.

In an analysis of the genomes of all known amblyopsid species, the researchers found that the different species colonized caves systems independently of each other and separately evolved similar traits — such as the loss of eyes and pigment — as they adapted to their dark cave environments.

Their findings are published in the journal Molecular Biology and Evolution.

By studying the genetic mutations that caused the fishes’ eyes to degenerate, the researchers developed a sort of mutational clock that allowed them to estimate when each species began losing their eyes. They found that vision-related genes of the oldest cavefish species, the Ozark cavefish (Troglichthys rosae), began degenerating up to 11 million years ago. 

The technique provides a minimum age for the caves that the fishes colonized since the cavefish must have been inhabiting subterranean waters when their eyesight began devolving, the researchers said.

“The ancient subterranean ecosystems of eastern North America are very challenging to date using traditional geochronological cave-dating techniques, which are unreliable beyond an upper limit of about 3 to 5 million years,” said Chase Brownstein, a student in Yale’s Graduate School of Arts and Sciences, in the Department of Ecology & Evolutionary Biology, and the study’s co-lead author. “Determining the ages of cave-adapted fish lineages allows us to infer the minimum age of the caves they inhabit because the fishes wouldn’t have started losing their eyes while living in broad daylight. In this case we estimate a minimum age of some caves of over 11 million years.”

Maxime Policarpo of the Max Planck Institute for Biological Intelligence and the University of Basel is the co-lead author.

For the study, the researchers reconstructed a time-calibrated evolutionary tree for amblyopsids, which belong to an ancient, species-poor order of freshwater fishes called Percopsiformes, using the fossil record as well as genomic data and high-resolution scans of all living relevant species. 

All the cavefish species have similar anatomies, including elongated bodies and flattened skulls, and their pelvic fins have either been lost or severely reduced. Swampfish (Chologaster cornuta), a sister to cavefish lineage that inhabits murky surface waters, also has a flattened skull, elongated body, and no pelvic fin. While it maintains sight and pigment, there is softening of the bones around its eyes, which disappear in cavefishes. This suggests that cavefishes evolved from a common ancestor that was already equipped to inhabit low-light environments, Brownstein said. 

To understand when the cavefish began populating caves — something impossible to discern from the branches of an evolutionary tree — the researchers studied the fishes’ genomes, examining 88 vision-related genes for mutations. The analysis revealed that the various cavefish lineages had completely different sets of genetic mutations involved in the loss of vision. This, they said, suggests that separate species colonized caves and adapted to those subterranean ecosystems independently of each other. 

From there, the researchers developed a method for calculating the number of generations that have passed since cavefish species began adapting to life in caves by losing the functional copies of vision-related genes. 

Their analysis suggests that cave adaptations occurred between 2.25 and 11.3 million years ago in Ozark cavefish and between 342,000 to 1.70 million years ago (at minimum) and 1.7 to 8.7 million years ago (at maximum) for other cavefish lineages. The findings support the conclusion that at least four amblyopsid lineages independently colonized caves after evolving from surface-dwelling ancestors, the researchers said. 

The maximum ages exceed the ranges of traditional cave-dating methods, which includes isotope analysis of cosmogenic nuclides that are produced within rocks and soils by cosmic rays, the researchers noted.

The findings also suggest potential implications for human health, said Thomas Near, professor of ecology and evolutionary biology in Yale’s Faculty of Arts and Sciences (FAS), and senior author of the study. 

“A number of the mutations we see in the cavefish genomes that lead to degeneration of the eyes are similar to mutations that cause ocular diseases in humans,” said Near, who is also the Bingham Oceanographic Curator of Ichthyology at the Yale Peabody Museum. “There is the possibility for translational medicine through which by studying this natural system in cavefishes, we can glean insights into the genomic mechanisms of eye diseases in humans.”

Reference: Brownstein CD, Policarpo M, Harrington RC, et al. Convergent evolution in amblyopsid cavefishes and the age of eastern north american subterranean ecosystems. Mol Biol Evol. 2025;42(8):msaf185. doi: 10.1093/molbev/msaf185

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Our cells produce a variety of proteins, each with a specific role that, in many cases, means that they need to be in a particular part of the cell where that role is needed. One of the ways that cells ensure certain proteins end up in the right location at the right time is through localized translation, a process that ensures that proteins are made — or translated — close to where they will be needed. MIT professor of biology and Whitehead Institute for Biomedical Research member Jonathan Weissman and colleagues have studied localized translation in order to understand how it affects cell functions and allows cells to quickly respond to changing conditions.

Now, Weissman, who is also a Howard Hughes Medical Institute Investigator, and postdoc in his lab Jingchuan Luo have expanded our knowledge of localized translation at mitochondria, structures that generate energy for the cell. In an open-access paper published today in Cell, they share a new tool, LOCL-TL, for studying localized translation in close detail, and describe the discoveries it enabled about two classes of proteins that are locally translated at mitochondria.

The importance of localized translation at mitochondria relates to their unusual origin. Mitochondria were once bacteria that lived within our ancestors’ cells. Over time, the bacteria lost their autonomy and became part of the larger cells, which included migrating most of their genes into the larger cell’s genome in the nucleus. Cells evolved processes to ensure that proteins needed by mitochondria that are encoded in genes in the larger cell’s genome get transported to the mitochondria. Mitochondria retain a few genes in their own genome, so production of proteins from the mitochondrial genome and that of the larger cell’s genome must be coordinated to avoid mismatched production of mitochondrial parts. Localized translation may help cells to manage the interplay between mitochondrial and nuclear protein production — among other purposes.

How to detect local protein production

For a protein to be made, genetic code stored in DNA is read into RNA, and then the RNA is read or translated by a ribosome, a cellular machine that builds a protein according to the RNA code. Weissman’s lab previously developed a method to study localized translation by tagging ribosomes near a structure of interest, and then capturing the tagged ribosomes in action and observing the proteins they are making. This approach, called proximity-specific ribosome profiling, allows researchers to see what proteins are being made where in the cell. The challenge that Luo faced was how to tweak this method to capture only ribosomes at work near mitochondria.

Ribosomes work quickly, so a ribosome that gets tagged while making a protein at the mitochondria can move on to making other proteins elsewhere in the cell in a matter of minutes. The only way researchers can guarantee that the ribosomes they capture are still working on proteins made near the mitochondria is if the experiment happens very quickly.

Weissman and colleagues had previously solved this time sensitivity problem in yeast cells with a ribosome-tagging tool called BirA that is activated by the presence of the molecule biotin. BirA is fused to the cellular structure of interest, and tags ribosomes it can touch — but only once activated. Researchers keep the cell depleted of biotin until they are ready to capture the ribosomes, to limit the time when tagging occurs. However, this approach does not work with mitochondria in mammalian cells because they need biotin to function normally, so it cannot be depleted.

Luo and Weissman adapted the existing tool to respond to blue light instead of biotin. The new tool, LOV-BirA, is fused to the mitochondrion’s outer membrane. Cells are kept in the dark until the researchers are ready. Then they expose the cells to blue light, activating LOV-BirA to tag ribosomes. They give it a few minutes and then quickly extract the ribosomes. This approach proved very accurate at capturing only ribosomes working at mitochondria.

The researchers then used a method originally developed by the Weissman lab to extract the sections of RNA inside of the ribosomes. This allows them to see exactly how far along in the process of making a protein the ribosome is when captured, which can reveal whether the entire protein is made at the mitochondria, or whether it is partly produced elsewhere and only gets completed at the mitochondria.

“One advantage of our tool is the granularity it provides,” Luo says. “Being able to see what section of the protein is locally translated helps us understand more about how localized translation is regulated, which can then allow us to understand its dysregulation in disease and to control localized translation in future studies.”

Two protein groups are made at mitochondria

Using these approaches, the researchers found that about 20 percent of the genes needed in mitochondria that are located in the main cellular genome are locally translated at mitochondria. These proteins can be divided into two distinct groups with different evolutionary histories and mechanisms for localized translation.

One group consists of relatively long proteins, each containing more than 400 amino acids or protein building blocks. These proteins tend to be of bacterial origin — present in the ancestor of mitochondria — and they are locally translated in both mammalian and yeast cells, suggesting that their localized translation has been maintained through a long evolutionary history.

Like many mitochondrial proteins encoded in the nucleus, these proteins contain a mitochondrial targeting sequence (MTS), a ZIP code that tells the cell where to bring them. The researchers discovered that most proteins containing an MTS also contain a nearby inhibitory sequence that prevents transportation until they are done being made. This group of locally translated proteins lacks the inhibitory sequence, so they are brought to the mitochondria during their production.

Production of these longer proteins begins anywhere in the cell, and then after approximately the first 250 amino acids are made, they get transported to the mitochondria. While the rest of the protein gets made, it is simultaneously fed into a channel that brings it inside the mitochondrion. This ties up the channel for a long time, limiting import of other proteins, so cells can only afford to do this simultaneous production and import for select proteins. The researchers hypothesize that these bacterial-origin proteins are given priority as an ancient mechanism to ensure that they are accurately produced and placed within mitochondria.

The second locally translated group consists of short proteins, each less than 200 amino acids long. These proteins are more recently evolved, and correspondingly, the researchers found that the mechanism for their localized translation is not shared by yeast. Their mitochondrial recruitment happens at the RNA level. Two sequences within regulatory sections of each RNA molecule that do not encode the final protein instead code for the cell’s machinery to recruit the RNAs to the mitochondria.

The researchers searched for molecules that might be involved in this recruitment, and identified the RNA binding protein AKAP1, which exists at mitochondria. When they eliminated AKAP1, the short proteins were translated indiscriminately around the cell. This provided an opportunity to learn more about the effects of localized translation, by seeing what happens in its absence. When the short proteins were not locally translated, this led to the loss of various mitochondrial proteins, including those involved in oxidative phosphorylation, our cells’ main energy generation pathway.

In future research, Weissman and Luo will delve deeper into how localized translation affects mitochondrial function and dysfunction in disease. The researchers also intend to use LOCL-TL to study localized translation in other cellular processes, including in relation to embryonic development, neural plasticity, and disease.

“This approach should be broadly applicable to different cellular structures and cell types, providing many opportunities to understand how localized translation contributes to biological processes,” Weissman says. “We’re particularly interested in what we can learn about the roles it may play in diseases including neurodegeneration, cardiovascular diseases, and cancers.”

Reference: Luo J, Khandwala S, Hu J, et al. Proximity-specific ribosome profiling reveals the logic of localized mitochondrial translation. Cell. 2025. doi: 10.1016/j.cell.2025.08.002

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