extinction

Bringing the “functionally extinct” American chestnut back from the dead

American chestnut, Biology, extinction, genetic engineering, Genetics, Genomics, Invasive species, pathogens, plants, Science, trees / Beth Washington / February 12, 2026

Wiped out in its native range by invasive pathogens, the trees may make a comeback.

Very few people alive today have seen the Appalachian forests as they existed a century ago. Even as state and national parks preserved ever more of the ecosystem, fungal pathogens from Asia nearly wiped out one of the dominant species of these forests, the American chestnut, killing an estimated 3 billion trees. While new saplings continue to sprout from the stumps of the former trees, the fungus persists, killing them before they can seed a new generation.

But thanks in part to trees planted in areas where the two fungi don’t grow well, the American chestnut isn’t extinct. And efforts to revive it in its native range have continued, despite the long generation times needed to breed resistant trees. In Thursday’s issue of Science, researchers describe their efforts to apply modern genomic techniques and exhaustive testing to identify the best route to restoring chestnuts to their native range.

Multiple paths to restoration

While the American chestnut is functionally extinct—it’s no longer a participant in the ecosystems it once dominated—it’s most certainly not extinct. Two Asian fungi that have killed it off in its native range; one causes chestnut blight, while a less common pathogen causes a root rot disease. Both prefer warmer, humid environments and persist there because they can grow asymptomatically on distantly related trees, such as oaks. Still, chestnuts planted outside the species’ original range—primarily in drier areas of western North America—have continued to thrive.

There is also a virus that attacks the chestnut blight fungus, allowing a few trees to survive in areas where that virus is common. Finally, a handful of trees have grown to maturity in the American chestnut’s original range. These trees, which the paper refers to as LSACs (large surviving American chestnuts), suggest that there might have been some low level of natural resistance within the now-vanished population.

Those trees are central to one of the efforts to restore the American chestnut. If enough of them have distinct means of resisting the fungi, interbreeding them might produce a strain that not only survives the fungi but can also thrive in the Appalachians.

A related approach took advantage of the fact that the American chestnut can produce fertile hybrids with the Chinese chestnut, which had co-evolved with the introduced fungi and were thus resistant to lethal infections. The hope was that continued back-breeding of these hybrids with American chestnuts would result in trees that were very similar to American chestnuts yet retained the fungal resistance of their Asian cousins.

Both efforts suffered from the same problem that faces any biologist working on trees: They are slow-growing and can take years to reach a size at which they produce seeds. The situation was further complicated by the fact that the American chestnut can’t pollinate itself, so you need at least two trees before any breeding is possible.

Concerned about what this might mean for the potential reintroduction of the chestnut into the Appalachians, a third project turned to biotechnology. Research had identified oxalic acid as a key factor in the blight’s virulence. Wheat naturally produces an enzyme that degrades oxalic acid, and researchers inserted the gene that encodes that enzyme into the American chestnut genome, creating a genetically modified tree that can potentially disarm the fungus’ attack.

Without understanding the nature of resistance or the effectiveness of the transgenic gene, there’s no way to know which method would be most effective. So researchers from the American Chestnut Foundation assembled a massive collaboration to examine all these options and determine what would be needed to reintroduce blight-resistant chestnuts into the wild.

Tracking resistance

The scale of the effort is immense. All told, the team infected over 4,000 individual trees with the blight fungus and tracked their growth in Appalachian nurseries for an average of over 14 years. The trees were scored for resistance on a zero-to-100 scale based on the damage caused by the infection. This data was combined with some serious lab work; the team produced the highest-quality chestnut genomes yet (of both American and Chinese species) and gathered biochemical data on how the trees respond to infection.

It quickly became apparent that there were significant differences in the growth rates of some of the resistant trees. When planted at sites where viruses kept the blight in check, the Chinese chestnuts grew more slowly than native trees, while hybrids grew at an intermediate rate. That could make a big difference, as rapid growth may have enabled the chestnut to reach its former dominance of the canopy.

Somewhat surprisingly, this slow growth turned out to be a problem for the genetically modified American chestnuts as well. By chance, the wheat gene ended up being inserted into a gene known to be important for the growth of other plants. It seems to be important in the chestnut as well; plants with two copies of the inserted genes survived at 16 percent of their expected rate, and those with a single copy grew 22 percent slower than unmodified trees.

That said, there was a lot of variability among the genetically modified trees, with 4 percent of the tested trees showing both high blight resistance and growth comparable to that of unmodified American chestnuts. It will be important to determine whether this collection of traits remains consistent in ensuing generations.

In a bit of good news, the progeny from surviving American chestnuts grew like American chestnuts. In less good news, among 143 of these trees, only seven had resistance levels of above 50 on the team’s 100-point scale. It’s possible that interbreeding these trees could further boost resistance, but it also poses the risk of creating a population that’s too inbred to thrive after reintroduction.

Root causes

The research team decided to use their testing to investigate the genetic basis of resistance. There’s a very practical reason for this: If resistance is mediated by just a handful of genes that each have large impacts, it should be possible to continue breeding resistant strains back to regular American chestnuts and selecting for resistance. But if there are many factors with relatively small impacts, it will require directed interbreeding of hybrids to maximize both resistance and DNA originating from the American chestnut.

The team completed the highest-quality chestnut genomes for both the American and Chinese species, identifying about 25,000 to 30,000 genes in the different assemblies. They then used this information for two types of genetic analysis: quantitative trait locus identification and genome-wide association. Both approaches aim to identify regions of the genome associated with specific properties and estimate their impact.

The work suggested that resistance arises from a relatively large number of sites, each with relatively minor effects. For example, the sites in the genome identified by quantitative trait analysis typically boosted resistance by about 10 points on the researchers’ 100-point scale. In the genome-wide analysis, 17 individual genetic differences were associated with about a quarter of the heritable resistance traits. All of this suggests that, for the hybrids (and likely for the weaker blight resistance found in surviving American chestnuts), directed breeding among surviving trees will be needed.

For the root rot fungus, in contrast, it looks like there are a limited number of important alleles with a large impact.

The researchers also took an alternative approach to identify resistance factors, comparing 100 chemicals produced by resistant and susceptible strains. Among the 41 chemicals detected at higher levels in the Chinese chestnut, the researchers found a metabolite, lupeol, that completely suppressed the growth of the fungal pathogen. Another, erythrodiol, limited its growth. If we can identify the genes involved in producing those chemicals, we could use that knowledge to guide directed breeding programs—or even engage in gene editing to increase their production.

The team’s current plan is to use genomic predictions to select hybrid seedlings for planting in test orchards, aiming to identify plants with high growth and resistance. From there, the process can be repeated. But even after the exhaustive exploration of resistance traits, the researchers seem to believe that all three approaches—selecting resistant American chestnuts, breeding hybrids derived from Chinese chestnuts, and directed genetic modification—can help bring the American chestnut back.

The researchers warn, though, that as environmental disturbances and invasive species continue to push some key species to the brink of extinction, we need to get better at this kind of species rescue operation.

Science, 2026. DOI: 10.1126/science.adw3225 (About DOIs).

John is Ars Technica’s science editor. He has a Bachelor of Arts in Biochemistry from Columbia University, and a Ph.D. in Molecular and Cell Biology from the University of California, Berkeley. When physically separated from his keyboard, he tends to seek out a bicycle, or a scenic location for communing with his hiking boots.

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Corals survived past climate changes by retreating to the deeps

Biology, climate change, corals, evolution, extinction, Florida, mass extinction, Science / DJ Henderson / November 12, 2025

A recent die-off in Florida puts the spotlight on corals’ survival strategies.

Scientists have found that the 2023 marine heat wave caused “functional extinction” of two Acropora reef-building coral species living in the Florida Reef, which stretches from the Dry Tortugas National Park to Miami.

“At this point, we do not think there’s much of a chance for natural recovery—their numbers are so low that successful reproduction is incredibly unlikely,” said Ross Cunning, a coral biologist at the John G. Shedd Aquarium.

This isn’t the first time corals have faced the borderline of extinction over the last 460 million years, and they have always managed to bounce back and recolonize habitats lost during severe climate changes. The problem is that we won’t live long enough to see them doing that again.

Killer heat waves

Marine heat waves kill corals by messing with the photosynthetic machinery of symbiotic microalgae that live in the corals’ tissues. When the temperature of water goes up too much, the microalgae start producing reactive oxygen species instead of nutritious sugars. The reactive oxygen is toxic to corals, which respond by expelling the microalgae. This solves the toxicity problem, but it also starves the corals and causes them to bleach (the algae are the source of their yellowish color).

The 2023 marine heat wave was not the first to hit the Florida Reef—it was the ninth on record. “Those eight previous heat waves also had major negative effects on coral reefs, causing widespread mortality,” Cunning told Ars. “But the 2023 heat wave blew all other heat waves out of the water. It was 2.2 to four times greater in magnitude than anything that came before it.”

Cunning’s team monitored two Acropora coral species: the staghorn and elkhorn. “They are both branching corals,” Cunning explained. “The staghorn has pointy branches that form dense thickets, whereas elkhorn produces arm-like branches that reach up and grow toward the surface, producing highly complex three dimensionality, like a canopy in the forest.”

He and his colleagues chose those two species because they essentially built the Florida Reef. They also grow the fastest among all Florida Reef corals, which means they are essential for its ability to recover from damage. “Acropora corals were the primary reef builders for the last ten thousand years,” Cunning said. Unfortunately, they also showed the highest levels of mortality due to heat waves.

Coral apocalypse

Cunning’s team found the mortality rate among Acropora corals reached 100 percent in the Dry Tortugas National Park, which is at the southernmost end of the Florida Reef. Moving north to Lower Keys, Middle Keys, and most of the Upper Keys, the mortality stayed at between 98 and 100 percent.

“Once you start moving a little bit further north, there’s the Biscayne National Park, where mortality rates were at 90 percent,” Cunning said. “It wasn’t until the furthest northern extent of the reef in Miami and Broward counties where mortality dropped to just 38 percent thanks to cooler temperatures that occurred there.”

Still, the mortality rate was exceptionally high throughout most of Acropora colonies across the Florida Reef. “What we’re facing is a functional extinction,” Cunning said.

But corals have been around for about 460 million years, and they have survived multiple mass extinction events, including the one that wiped out the dinosaurs. As vulnerable as they appear, corals seemingly have some get-out-of-death card they always pull when things turn really bad for them. This card, most likely, is buried deep in their genome.

Ancestral strength

“There have been studies looking into the evolutionary history of corals, but the difference between those and our work lies in technology,” said Claudia Francesca Vaga, a marine biologist at the Smithsonian Institution.

Her team looked at ultra conserved elements, stretches of DNA that are nearly identical across even distantly related species. These elements were used to build the most extensive phylogenetic tree of corals to date. Based on the genomic data and fossil evidence, Vaga’s team analyzed how 274 stony coral species are related to one another to retrace their common ancestor and reconstruct how they evolved from it.

“We managed to confirm that the first common ancestor of stony corals was most likely solitary—it didn’t live in colonies, and it didn’t have symbionts,” Vaga said.

The very first coral most likely did not rely on algae to produce its nutrients, which means it was immune to bleaching. It was also not attached to a substrate, so it could move from one habitat to another. Another advantage the first corals had was that they were not particularly picky—they could live just as well in the shallow waters as in the deep sea, since they didn’t get most of their nutrients from their photosynthetic symbionts.

Descending from these incredibly resilient ancestors, corals started to specialize. “We learned that symbiosis and coloniality can be acquired independently by stony coral linages and that it happened multiple times,” Vaga said.

Based on her team’s research, past mass extinction events usually wiped out 90 percent of the species living in shallow waters—the ones that were colonial and reliant on symbionts. “But each such extinction triggered a process of retaking the shallows by the more resilient deep-sea corals, which in time evolved symbiosis and coloniality again,” Vaga said.

Thanks to corals’ deep-sea cousins, even the most extreme environmental changes—global warming or sudden, severe variations in the oceans’ acidity or oxygen levels—could not kill them for good. Each mass extinction event they’ve been through just reverted them to factory settings and made them start over from scratch.

The only catch here is time. “We’re talking about four to five million years before coral populations recover,” Vaga said.

Long way back

According to Cunning, the consequence of Acropora corals’ extinction in the Florida Reef is a lower overall reef-building rate, which will lead to reduced biodiversity in the reef’s ecosystem. “There are going to be cascading effects, and humans will be impacted as well. Reefs protect our coastlines by buffering over 90 percent of wave energy,” Cunning said.

In Florida, where coastlines are heavily urbanized, this may translate into hundreds of millions of dollars per year in damages.

But Cunning said we still have means at our disposal to save Acropora corals. “We’re not going to give up on them,” he said.

One option for improving the resilience of corals could be to crossbreed them with species from outside of Florida Reef, ideally ones that live in warmer places and are better adapted to heat. “The first tests of this approach are underway right now in Florida; elkhorn corals were cross bred between Florida parents and Honduran parents,” Cunning said. He hopes this will help produce a new generation of corals that has a better shot at surviving the next heat wave.

Other interventions include manipulating corals’ algal symbionts. “There are many different species of algae with different levels of heat tolerance,” Cunning said. To him, a possible way forward would be to pair the Acropora corals with more heat-tolerant symbionts. “This should alter the bleaching threshold in these corals,” he explained.

Still, even interventions like these will take a very long time to make a difference. “But if four or five million years is the benchmark to beat, then yeah, it’s hopefully going to happen faster than that,” Cunning said.

The upside is that corals will likely pull off their de-extinction trick once again, even if we do absolutely nothing to help them. “In a few million years, they will redevelop coloniality, redevelop symbiosis, and rebuild something similar to the coral reefs we have today,” Vaga said. “This is good news for them. Not necessarily for us.”

Science, 2025. DOI: 10.1126/science.adx7825

Nature, 2025. DOI: 10.1038/s41586-025-09615-6

Jacek Krywko is a freelance science and technology writer who covers space exploration, artificial intelligence research, computer science, and all sorts of engineering wizardry.

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Giant salamander species found in what was thought to be an icy ecosystem

Biology, Ecology, evolution, extinction, paleontology, salamander, Science, tetrapods / Kelly Newman / July 11, 2024

Feeding time —

Found after its kind were thought extinct, and where it was thought to be too cold.

Jacek Krywko – Jul 11, 2024 8: 00 pm UTC

A black background with a brown fossil at the center, consisting of the head and a portion of the vertebral column. — C. Marsicano

Gaiasia jennyae, a newly discovered freshwater apex predator with a body length reaching 4.5 meters, lurked in the swamps and lakes around 280 million years ago. Its wide, flattened head had powerful jaws full of huge fangs, ready to capture any prey unlucky enough to swim past.

The problem is, to the best of our knowledge, it shouldn’t have been that large, should have been extinct tens of millions of years before the time it apparently lived, and shouldn’t have been found in northern Namibia. “Gaiasia is the first really good look we have at an entirely different ecosystem we didn’t expect to find,” says Jason Pardo, a postdoctoral fellow at Field Museum of Natural History in Chicago. Pardo is co-author of a study on the Gaiasia jennyae discovery recently published in Nature.

Common ancestry

“Tetrapods were the animals that crawled out of the water around 380 million years ago, maybe a little earlier,” Pardo explains. These ancient creatures, also known as stem tetrapods, were the common ancestors of modern reptiles, amphibians, mammals, and birds. “Those animals lived up to what we call the end of Carboniferous, about 370–300 million years ago. Few made it through, and they lasted longer, but they mostly went extinct around 370 million ago,” he adds.

This is why the discovery of Gaiasia jennyae in the 280 million-year-old rocks of Namibia was so surprising. Not only wasn’t it extinct when the rocks it was found in were laid down, but it was dominating its ecosystem as an apex predator. By today’s standards, it was like stumbling upon a secluded island hosting animals that should have been dead for 70 million years, like a living, breathing T-rex.

“The skull of gaiasia we have found is about 67 centimeters long. We also have a front end of her upper body. We know she was at minimum 2.5 meters long, probably 3.5, 4.5 meters—big head and a long, salamander-like body,” says Pardo. He told Ars that gaiasia was a suction feeder: she opened her jaws under water, which created a vacuum that sucked her prey right in. But the large, interlocked fangs reveal that a powerful bite was also one of her weapons, probably used to hunt bigger animals. “We suspect gaiasia fed on bony fish, freshwater sharks, and maybe even other, smaller gaiasia,” says Pardo, suggesting it was a rather slow, ambush-based predator.

But considering where it was found, the fact that it had enough prey to ambush is perhaps even more of a shocker than the animal itself.

Location, location, location

“Continents were organized differently 270–280 million years ago,” says Pardo. Back then, one megacontinent called Pangea had already broken into two supercontinents. The northern supercontinent called Laurasia included parts of modern North America, Russia, and China. The southern supercontinent, the home of gaiasia, was called Gondwana, which consisted of today’s India, Africa, South America, Australia, and Antarctica. And Gondwana back then was pretty cold.

“Some researchers hypothesize that the entire continent was covered in glacial ice, much like we saw in North America and Europe during the ice ages 10,000 years ago,” says Pardo. “Others claim that it was more patchy—there were those patches where ice was not present,” he adds. Still, 280 million years ago, northern Namibia was around 60 degrees southern latitude—roughly where the northernmost reaches of Antarctica are today.

“Historically, we thought tetrapods [of that time] were living much like modern crocodiles. They were cold-blooded, and if you are cold-blooded the only way to get large and maintain activity would be to be in a very hot environment. We believed such animals couldn’t live in colder environments. Gaiasia shows that it is absolutely not the case,” Pardo claims. And this turned upside-down lots of what we knew about life on Earth back in gaiasia’s time.

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Searching for a female partner for the world’s “loneliest” plant

extinction, Science, syndication / Kelly Newman / June 16, 2024

getting no help from dating apps —

AI assists in the pursuit for one threatened plant species.

Laura Cinti, The Conversation – Jun 16, 2024 11: 11 am UTC

Enlarge / Map from drone mission search for the Encephalartos Woodii in the Ngoye Forest in South Africa.

“Surely this is the most solitary organism in the world,” wrote paleontologist Richard Fortey in his book about the evolution of life.

He was talking about Encephalartos woodii (E. woodii), a plant from South Africa. E. woodii is a member of the cycad family, heavy plants with thick trunks and large stiff leaves that form a majestic crown. These resilient survivors have outlasted dinosaurs and multiple mass extinctions. Once widespread, they are today one of the most threatened species on the planet.

The only known wild E. Woodii was discovered in 1895 by the botanist John Medley Wood while he was on a botanical expedition in the Ngoye Forest in South Africa. He searched the vicinity for others, but none could be found. Over the next couple of decades, botanists removed stems and offshoots and cultivated them in gardens.

Fearing that the final stem would be destroyed, the Forestry Department removed it from the wild in 1916 for safekeeping in a protective enclosure in Pretoria, South Africa, making it extinct in the wild. The plant has since been propagated worldwide. However, the E. woodii faces an existential crisis. All the plants are clones from the Ngoye specimen. They are all males, and without a female, natural reproduction is impossible. E. woodii’s story is one of both survival and solitude.

My team’s research was inspired by the dilemma of the lonely plant and the possibility that a female may still be out there. Our research involves using remote sensing technologies and artificial intelligence to assist in our search for a female in the Ngoye Forest.

The evolutionary journey of cycads

Cycads are the oldest surviving plant groups alive today and are often referred to as “living fossils” or “dinosaur plants” due to their evolutionary history dating back to the Carboniferous period, approximately 300 million years ago. During the Mesozoic era (250-66 million years ago), also known as the Age of Cycads, these plants were ubiquitous, thriving in the warm, humid climates that characterised the period.

Although they resemble ferns or palms, cycads are not related to either. Cycads are gymnosperms, a group that includes conifers and ginkgos. Unlike flowering plants (angiosperms), cycads reproduce using cones. It is impossible to tell male and female apart until they mature and produce their magnificent cones.

Female cones are typically wide and round, and male cones appear elongated and narrower. The male cones produce pollen, which is carried by insects (weevils) to the female cones. This ancient method of reproduction has remained largely unchanged for millions of years.

Despite their longevity, today cycads are ranked as the most endangered living organisms on Earth with the majority of the species considered threatened with extinction. This is because of their slow growth and reproductive cycles, typically taking ten to 20 years to mature, and habitat loss due to deforestation, grazing, and over-collection. Cycads have become symbols of botanical rarity.

Their striking appearance and ancient lineage make them popular in exotic ornamental horticulture and that has led to illegal trade. Rare cycads can command exorbitant prices from $620 (495 pounds) per cm with some specimens selling for millions of pounds each. The poaching of cycads is a threat to their survival.

Among the most valuable species is the E. woodii. It is protected in botanical gardens with security measures such as alarmed cages designed to deter poachers.

AI in the sky

In our search to find a female E.woodii we have used innovative technologies to explore areas of the forest from a vertical vantage point. In 2022 and 2024, our drone surveys covered an area of 195 acres or 148 football fields, creating detailed maps from thousands of photos taken by the drones. It’s still a small portion of the Ngoye Forest, which covers 10,000 acres.

Enlarge / An example of the still images used to train the AI software.

Our AI system enhanced the efficiency and accuracy of these searches. As E. woodii is considered extinct in the wild, synthetic images were used in the AI model’s training to improve its ability, via an image recognition algorithm, to recognise cycads by shape in different ecological contexts.

Plant species globally are disappearing at an alarming rate. Since all existing E. woodii specimens are clones, their potential for genetic diversity in the face of environmental change and disease is limited.

Notable examples include the Great Famine in 1840s Ireland, where the uniformity of cloned potatoes worsened the crisis, and the vulnerability of clonal Cavendish bananas to Panama disease, which threatens their production as it did with the Gros Michel banana in the 1950s.

Finding a female would mean E. woodii is no longer at the brink of extinction and could revive the species. A female would allow for sexual reproduction, bring in genetic diversity, and signify a breakthrough in conservation efforts.

E. woodii is a sobering reminder of the fragility of life on Earth. But our quest to discover a female E. woodii shows there is hope even for the most endangered species if we act fast enough.

Laura Cinti, Research Fellow in bio art & plant behavior, University of Southampton. This article is republished from The Conversation under a Creative Commons license. Read the original article.

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