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Genetics Suggest Our Human Ancestors Very Nearly Went Extinct 900,000 Years Ago

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Thursday, August 31, 2023

A study proposes that the population that gave rise to modern humans may have been reduced to roughly 1,300 reproducing individuals

A study proposes that the population that gave rise to modern humans may have been reduced to roughly 1,300 reproducing individuals

A study proposes that the population that gave rise to modern humans may have been reduced to roughly 1,300 reproducing individuals
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Sea urchin in Sicily at risk of extinction due to popularity as culinary delicacy

Three-year pause in fishing is the only way to prevent disappearance, researchers sayIt is one of Sicily’s most popular dishes: spaghetti ai ricci di mare, or sea urchin spaghetti. Prepared with a simple base of oil and garlic, plates of the stuff are demolished every summer, particularly by the hundreds of thousands of tourists who descend on the island every year.But sea urchins’ status as a culinary delicacy is leading to their gradual disappearance from local waters, and last week researchers said the Sicilian sea urchin, which resides on the sea floor and primarily feeds on algae, could soon become extinct if urgent conservation policies were not implemented. Continue reading...

It is one of Sicily’s most popular dishes: spaghetti ai ricci di mare, or sea urchin spaghetti. Prepared with a simple base of oil and garlic, plates of the stuff are demolished every summer, particularly by the hundreds of thousands of tourists who descend on the island every year.But sea urchins’ status as a culinary delicacy is leading to their gradual disappearance from local waters, and last week researchers said the Sicilian sea urchin, which resides on the sea floor and primarily feeds on algae, could soon become extinct if urgent conservation policies were not implemented.Since that stark warning, a local politician has proposed a three-year ban on all sea urchin fishing in Sicily – but the idea is likely to face stiff opposition from both fishers and restaurateurs.“On the one hand, I understand the need to preserve the sea urchin species,” said Gaetano Serio, a chef at Osteria Lo Bianco in Palermo. “But on the other hand, blocking sea urchin fishing in Sicily for three years would be a tough blow for those of us who work in the restaurant industry. When sea urchin spaghetti is on my menu, we serve up to 40 dishes a day.”The fishing of sea urchins is already restricted in Sicily. According to researchers from the University of Palermo, only 12 fishers hold regular fishing licenses for sea urchins, while hundreds continue to fish them illegally.Their methods are relatively simple, as the urchins can be found at shallow depths. They are also potentially devastating.Presented to the Sicilian government last week, the researchers’ study said a total pause in fishing for at least three years was the only way of staving off extinction.“Unfortunately, the conclusions of this study are disheartening,” said Paola Gianguzza, scientific coordinator of the study. “In the marine-protected areas of Sicily, we have not found any sea urchins nor signs of a healthy population. We would need to halt fishing for at least three years if we wanted to preserve this species.”The stony, purple sea urchins, Paracentrotus lividus, are sensitive to environmental conditions and have also been affected by the climate crisis and pollution, according to the UN’s Food and Agriculture Organisation.But in Sicily it is their status as a delicacy that is driving their decimation. “In Sicily, sea urchins are subject to intense illegal fishing due to their nutritional and economic value,” said Marco Toccaceli from the Council for Agricultural Research and Economics (Crea), a leading Italian research organisation dedicated to the agri-food supply chains. “For this reason, we must intensify enforcement.”Since the publication of the study, Nello Dipasquale, a member of the centre-left Democratic party, has been working on a legislative proposal to ban sea urchin fishing in the island’s waters.“I am, like many others, a lover of sea urchin fishing,” he told the Giornale di Sicilia. “But I believe that we can all give up fishing and enjoying them for three years in order to save a species seriously at risk of extinction. Losing them would be serious damage to the ecosystem. We must intervene as soon as possible.”Angelo Pumilia, chef at the Foresteria Planeta wine resort in Menfi on the south-west coast of Sicily, called for more awareness of the risks of illegal fishing.“It is a serious problem,” he said, claiming that many of his fellow chefs bought urchins from illegal fishers “who sell them at significantly lower prices”.Pumilia, one of Italy’s most celebrated chefs, said: “Just think that 100g of fresh sea urchins from Norway or Japan can cost up to €250 [£217] per gram. A Sicilian illegal fisherman sells them to the restaurant owner for as low as €7 or €10 per 100g. There are channels to legally acquire sea urchins, but they are too expensive for many restaurants.“We, who make quality cuisine and trace every ingredient, buy sea urchins from abroad because here in Sicily, the regulation of this species is too shady and incomplete. There is a need for a general awareness – otherwise we truly risk having to do without one of the main culinary delicacies of our region.”In California, meanwhile, scientists are struggling with the opposite problem: there, the sea urchin population has exploded by 10,000% since 2014 due to the decline in sea otter and starfish populations – two natural predators of sea urchins.Hundreds of millions of purple sea urchins have covered the coast from Baja to Alaska, where they have been devouring the region’s vital kelp forests, causing untold damage to the marine ecosystem. It is estimated that in California, 95% of the kelp forests, which provide shelter and food to a wide range of marine life, have been destroyed and replaced by “urchin barrens” – vast carpets of spiked purple orbs along the ocean floor.

Volcanoes or Asteroid? AI Ends Debate Over Dinosaur Extinction Event

Free-thinking computers reverse-engineered the fossil record to identify the causes of a cataclysm. To address the long-standing debate about whether a massive asteroid impact or...

Dartmouth scientists used an innovative computer model to suggest that volcanic activity, rather than an asteroid impact, was the primary cause of the mass extinction that ended the age of the dinosaurs. This groundbreaking approach opens new avenues for investigating other geological events.Free-thinking computers reverse-engineered the fossil record to identify the causes of a cataclysm.To address the long-standing debate about whether a massive asteroid impact or volcanic activity caused the extinction of dinosaurs and numerous other species 66 million years ago, a team at Dartmouth College took an innovative approach — they removed scientists from the debate and let the computers decide.The researchers report in the journal Science a new modeling method powered by interconnected processors that can work through reams of geological and climate data without human input. They tasked nearly 130 processors with analyzing the fossil record in reverse to pinpoint the events and conditions that led to the Cretaceous–Paleogene (K–Pg) extinction event that cleared the way for the ascendance of mammals, including the primates that would lead to early humans.A New Perspective on Historical Events“Part of our motivation was to evaluate this question without a predetermined hypothesis or bias,” said Alex Cox, first author of the study and a graduate student in Dartmouth’s Department of Earth Sciences. “Most models move in a forward direction. We adapted a carbon-cycle model to run the other way, using the effect to find the cause through statistics, giving it only the bare minimum of prior information as it worked toward a particular outcome.“In the end, it doesn’t matter what we think or what we previously thought — the model shows us how we got to what we see in the geological record,” he said.The model crunched more than 300,000 possible scenarios of carbon dioxide emissions, sulfur dioxide output, and biological productivity in the 1 million years before and after the K–Pg extinction. Through a type of machine learning known as Markov Chain Monte Carlo — which is not unlike how a smartphone predicts what you’ll type next — the processors worked together independently to compare, revise, and recalculate their conclusions until they reached a scenario that matches the outcome preserved in the fossil record.Uncovering the Extinction’s CausesGeochemical and organic remnants in the fossil record capture clearly the catastrophic conditions during the K–Pg extinction, so named for the geological periods on either side of the millennia-long cataclysm. Animals and plants worldwide suffered massive die-offs as food webs collapsed under an unstable atmosphere that — laden with sun-blotting sulfur, airborne minerals, and heat-trapping carbon dioxide — swung wildly from frigid to scorching conditions.While the effect is clear, the cause of the extinction is unresolved. Early theories attributing the event to volcanic eruptions have been eclipsed by the discovery of an impact crater in Mexico known as Chicxulub that was caused by a miles-wide asteroid now thought to be primarily responsible for the extinction event. The theories have begun to converge, however, as fossil evidence suggests a one-two punch unlike anything in Earth’s history: The asteroid may have slammed into a planet already reeling from the massive, extremely violent eruptions of volcanoes in western India’s Deccan Traps.But scientists still do not know — nor agree on — the extent to which each event contributed to the mass extinction. So, Cox and his adviser Brenhin Keller, a Dartmouth assistant professor of earth sciences and study co-author, decided to “see what you would get if you let the code decide.”Modeling Results and Volcanic ImpactTheir model suggested that the outpouring of climate-altering gases from the Deccan Traps alone could have been sufficient to trigger the global extinction. The Traps had been erupting for roughly 300,000 years before the Chicxulub asteroid. During their nearly 1 million years of eruptions, the Deccan Traps are estimated to have pumped up to 10.4 trillion tons of carbon dioxide and 9.3 trillion tons of sulfur into the atmosphere.“We’ve known historically that volcanoes can cause massive extinctions, but this is the first independent estimation of volatile emissions taken from the evidence of their environmental effects,” said Keller, who published a paper last year linking four of Earth’s five mass extinctions to volcanism.“Our model worked through the data independently and without human bias to determine the amount of carbon dioxide and sulfur dioxide required to produce the climate and carbon cycle disruptions we see in the geologic record. These amounts turned out to be consistent with what we expect to see in emissions from the Deccan Traps,” said Keller, who has worked extensively to examine the link between Deccan volcanism and the K–Pg extinction.Asteroid Impact and Modern ContextThe model did reveal a steep drop in the accumulation of organic carbon in the deep ocean around the time of the Chicxulub impact, which likely resulted from the asteroid causing the demise of numerous animal and plant species. The record contains traces of a decrease in temperature around the same time that would have been caused by the large amount of sulfur — a short-term cooling agent — the mammoth meteorite would have ejected into the air when it collided with the sulfur-rich surface on that area of the planet.The asteroid impact also would have likely emitted both carbon and sulfur dioxide. However, the model found that there was no spike in the emissions of either gas at that time, suggesting that the asteroid’s contribution to the extinction did not hinge on gas emissions.Conclusion: Methodological Innovation and Future ApplicationsIn modern context, Cox said, the burning of fossil fuels from 2000 to 2023 has pumped about 16 billion tons of carbon dioxide into the atmosphere per year. This is 100 times greater than the highest annual emission rate scientists project from the Deccan Traps. While alarming on its own, it would still take a few thousand years for current carbon dioxide emissions to match the total amount that spewed forth from the ancient volcanoes, Cox said.“Most heartening is that the results we achieved are broadly physically plausible, which is impressive given that the model could have technically run completely wild without stronger prior constraints,” he said.Interconnecting the processors shortened the time it took the model to analyze such a massive data set from months or years to hours, Cox said. His and Keller’s method can be used to invert other earth systems models — such as those for the climate or carbon cycle — to evaluate geological events for which the outcomes are well known but not the factors that led there. “This type of parallel inversion hasn’t been done in earth sciences models before. Our method can be scaled up to include thousands of processors, which gives us a much broader solution space to explore, and it’s quite resistant to human bias,” Cox said.“So far, people in our field have been more fascinated by the novelty of the method than the conclusion we reached,” he laughed. “Any earth system for which we know the effect but not the cause is ripe for inversion. The better we know the output, the better we’re able to characterize the input that caused it.”Reference: “A Bayesian inversion for emissions and export productivity across the end-Cretaceous boundary” by Alexander A. Cox and C. Brenhin Keller, 28 September 2023, Science.DOI: 10.1126/science.adh3875

Cats have driven many species to extinction. Experts share tactics for reducing feline destruction

Outdoor and feral cats can seriously harm native ecosystems. Here's how to fix it

Cat owners and cat admirers alike tend to be intrigued by their enigmatic companions. When we see an intrepid feline carefully stalking its prey or happily playing with other cats, we ponder the mysteries of its mind and the depths of its soul. What manic misadventures do cats engage in when we're not around? "A free-roaming cat is not filling an ecological niche, or reverting to its ancestral form. It is merely a run-away pet that needs to be brought back inside." Unfortunately, the real world of cats differs significantly from the innocent, whimsical versions depicted in movies like "Cats" and "The Aristocats." In fact, when domesticated cats are allowed to roam freely, they often leave a trail of ecological destruction in their wake. Many species have gone extinct due to domesticated cats being allowed to roam outdoors, and many other animals are suffering immensely because of it. To understand why, it is first important to recognize that domesticated cats can never be "wild," whether they are owned by humans or "feral," meaning a domesticated cat that has no owner. Of course, wild cats exist — not only tigers, but also bobcats and literal wild cats, from which these favored pets evolved. But these cats are native, not invasive and don't spread wherever humans do. By definition, just like cows and chickens, a domesticated cat is biologically incapable of being a natural part of the wilderness. "Just like a stray dog doesn’t become a wolf, a feral cat doesn’t become a wild cat," explained Daniel Joseph Herrera, a PhD student studying urban ecology at the University of Maryland–College Park who has co-authored a 2022 study on domesticated cats being an invasive species. "A free-roaming cat is not filling an ecological niche, or reverting to its ancestral form. It is merely a run-away pet that needs to be brought back inside." "The species most detrimentally impacted by outdoor cats are island species [that] are often naïve to or ill-equipped to handle the enormous threat posed by cats." Herrera said people often confuse the term "feral" with the term "wild" and use this confusion to justify the cat’s continued outdoor life. But it's quite clear that domesticated cats can be dangerous to ecosystems. The question is how dangerous. According to Grant Sizemore, the Director of Invasive Species Programs at the American Bird Conservancy, outdoor cats can negatively impact a wide variety of species from a diverse range of environments around the world, from backyards to oceans. "Those impacts include direct predation, parasite and disease transmission, and indirect effects (e.g., competition)," Sizemore wrote to Salon. "Generally, however, the species most detrimentally impacted by outdoor cats are island species [that] are often naïve to or ill-equipped to handle the enormous threat posed by cats and often have smaller populations than continental wildlife." Sizemore said that this is particularly true of species that are either only as big as cats or slightly smaller, such as the endangered Newell’s Shearwater, "which has nested in burrows in the secluded mountains of Kauaʻi for eons." Outdoor cats are also responsible for the extinction of the Stephen’s Island Wren (or Lyall’s Wren), with Sizemore adding this may be the most famous example of a species now extinct because of cats. "These birds have been ravaged by outdoor cats, even more so than other introduced predators, because cats not only kill the young in the nest but also kill adults, eliminating the chance for that adult bird, which has already survived the trials of youth, to breed again in subsequent years," Sizemore explained. "Sadly, whether on islands or elsewhere, the impacts of cats adds up, and cats have now contributed to the extinction of at least 63 species of birds, mammals and reptiles worldwide." Outdoor cats have a particularly devastating impact on birds, ranking as "the top source of direct, human-caused bird mortality in the United States, killing an estimated 2.4 billion birds every year." Want more health and science stories in your inbox? Subscribe to Salon's weekly newsletter Lab Notes. "In Australia, feral cats were most likely the principal cause of extinction of the pig-footed bandicoot, central hare-wallaby, desert bandicoot, lesser bilby and long-tailed hopping-mouse, amongst others." As Herrera pointed out, bird species are hardly alone in being targeted by outdoor cats. "Free-roaming cats are known for their predation on bird populations, but research has found that cats actually prey on small mammals more than they do birds," Herrera explained. This can include chipmunks, moles, voles, mice and squirrels, which are easier to catch than birds since they cannot fly away. "Additionally, these species may prove a more reliable source of prey since they do not migrate annually like many species of bird do." Although cats are traditionally known for preying on non-native rodents like brown rats, Herrera said "they prefer smaller and easier-to-handle prey such as native small mammals and birds. Previous research has found that cats do not reduce the number of rats in an area, and my own research has found cats and rats to live in relative harmony where people leave cat food outside." Even when cats are not destroying native species through hunting, they can do so through by spreading infections. "In those parts of the world without a long evolutionary history of cats, cats also spread some cat-dependent diseases (such as toxoplasmosis) to many native birds and mammals," explained John C.Z. Woinarski, a professor at the NESP Threatened Species Recovery Hub at Charles Darwin University, in an email to Salon. He added that "in Australia, there would be no toxo were it not for cats" and that "Australia's fauna has been particularly affected by cats, with cats implicated in the extinction of many native mammal species, and the ongoing decline of many threatened birds and mammals." If there is any good news here, it is that humans can solve the problem they helped create. According to Arie Trouwborst, a professor of nature conservation law at Tilburg University, "the only effective way to protect vulnerable wildlife from cats is for people to keep their cats indoors or otherwise within their control — just as we expect pet owners to do with any other animal." He cited the Australian city of Canberra as an example of a government that has done this effectively. "A sympathetic way to work towards a landscape without free-roaming cats, already employed by the Australian authorities in Canberra, is to gradually phase them out," Trouwborst wrote to Salon. "Whereas current outdoor cats may keep roaming the rest of their lives, each newly acquired cat must from now on be kept indoors from the start." He added, "Feral cats are a different category. As cats are one of the world's worst invasive alien species, biodiversity conservation laws and policies require efforts to remove them from the landscape." Woinarski offered suggestions for cat owners who want to protect the environment including de-sexing, registration and preventing cats from roaming, strategies which can be strengthened by government regulation. While the problem of dealing with feral cats is more complicated, he suggested actions like banning the importation of domesticated cats to islands that do not already have them, eradicating cats from the islands that do have them, regulating other threats to species susceptible to cat predation, creating predator-proof enclosures for species particularly threatened by cat predation (which is being heavily done in Australia) and "intensive baiting and other cat control programs at sites of conservation significance." While these measures may seem extreme, Woinarski pointed out that "in Australia, feral cats were most likely the principal cause of extinction of the pig-footed bandicoot, central hare-wallaby, desert bandicoot, lesser bilby and long-tailed hopping-mouse, amongst others." Dr. Sarah Crowley, a senior lecturer at the University of Exeter's Centre for Geography and Environmental Science, argued that there are "several techniques that could help people reduce the amount of wildlife killed by owned domestic cats. The most successful were feeding a meat-rich, complete diet and playing with cats in a way that simulates hunting behaviors (e.g. with a feather wand) for 5-10 minutes a day." It is not merely the wildlife that suffers when outdoor cats are given free rein to roam. As Sizemore observed, "cats are the top source of rabies among domestic animals in the United States and disproportionately expose more people to this disease than wildlife." The animals which roam outdoors "are also about three times more likely to be infected with parasites, which can then be spread to people. Furthermore, cats are a definitive host for the parasite Toxoplasma gondii that causes toxoplasmosis. The parasite can only complete its life cycle in a cat’s digestive tract and is then excreted via feces into the environment, where it can subsequently infect any bird or mammal." These parasites "can cause miscarriages, fetal deformities, blindness, organ failure and death and has been associated with neurodegenerative diseases (e.g., schizophrenia)," Sizemore said. "The risk of toxoplasmosis by cats is an often overlooked but potentially serious consequence of cats roaming the landscape." Read more about invasive species

US Wildlife Agency Explores Cryogenics as a Hedge Against Extinction

This story was originally published by Inside Climate News and is reproduced here as part of the Climate Desk collaboration. The world’s wildlife are facing a barrage of threats caused by climate change, from the loss of suitable habitat to dwindling food supplies. As a result, endangered species across the US are edging closer to extinction at alarming rates—and if they disappear, critical […]

This story was originally published by Inside Climate News and is reproduced here as part of the Climate Desk collaboration. The world’s wildlife are facing a barrage of threats caused by climate change, from the loss of suitable habitat to dwindling food supplies. As a result, endangered species across the US are edging closer to extinction at alarming rates—and if they disappear, critical genetic information could vanish with them.  In a new initiative announced on October 3, the US Fish & Wildlife Service is working with the nonprofit Revive & Restore and other partners to create a “genetic library” of the country’s endangered species—before it’s too late.  “You can have cells that have been in the freezer for decades, and use those to produce animals.” Through a process called biobanking, FWS field staff are gathering biological samples such as blood, tissues and reproductive cells from animals to be cryogenically preserved at extremely low temperatures (at least -256 degrees Fahrenheit) and stored at a USDA facility in Colorado. The samples will also be genetically sequenced and this information will be uploaded to a publicly available database called GenBank, where researchers can study them and compare their genomes to other members of their species. This frozen library of living cells could be crucial for current and future conservation efforts, particularly for helping introduce genetic diversity into captive breeding programs working to rebuild species populations or even for cloning, experts say.  Twenty-first century “conservation challenges require 21st century conservation tools,” Seth Willey, deputy assistant regional director of ecological services for the FWS’s Southwest region, told Inside Climate News in an email. “Biobanking is one such tool that allows us to preserve some of the biodiversity that exists today and ensure it isn’t lost forever.”  Since the project launched in January, partners have already collected and cryopreserved samples from five endangered species, including the Mexican wolf, Florida bonneted bat and Sonoran pronghorn. Though the pilot phase of the program includes just 24 US endangered mammals, the end goal is much more ambitious: to biobank every endangered mammal in the country, creating “a repository for our American legacy” of biodiversity, according to Ryan Phelan, the executive director of Revive & Restore.  Once common across the vast prairies of the Great Plains, the black-footed ferret is now one of the most endangered species in North America, with just around 300 individuals found in the wild. To help rebuild its population, the FWS launched a captive breeding program in 1992, which has introduced thousands of captive-bred black-footed ferrets into the wild since its creation.  However, a ticking time bomb lurks within this species’ genome. Nearly every black-footed ferret is descended from just seven individuals, making their gene pool strikingly similar and leaving entire populations vulnerable to environmental stressors such as disease.  “Cryogenically preserved cell culture samples are an insurance policy against future losses of biodiversity in the wild.” At least, that was the case up until 2020, when history was made at a small conservation center in Fort Collins, Colorado: Scientists successfully cloned a black-footed ferret, nicknamed Elizabeth Ann, using tissue from a living sample frozen in the mid-1980s. This sample was from a black-footed ferret that had no surviving offspring, meaning that many of her genes are genetically diverse from those in the rest of the species. The project was led by many of the same partners in the new biobanking pipeline, including the FWS, Revive & Restore and the San Diego Zoo Alliance.  “This is an extraordinary thing when you can have cells that have been in the freezer for decades, and use those to produce animals that can interbreed with the population and restore the resilience that has been lost because of genetic erosion,” said Oliver Ryder, the director of conservation genetics at the San Diego Zoo Wildlife Alliance. Before being used to clone Elizabeth Ann, the sample was stored at the San Diego Zoo’s Frozen Zoo, one of the world’s largest biobanking facilities, which stores more than 10,000 living cell cultures and reproductive cells from nearly 1,000 taxa. Now, with this new project, the biobanking approach has reached a national level. The federal government “has a responsibility to coordinate actions on behalf of citizens and the loss of biodiversity is a crisis of our time,” Ryder said. “A lot of endangered species are critically small, and they could end up in the same situation as the black-footed ferrets. So why not anticipate, [and] why not use this as a tool in recovery?” Elizabeth Ann the ferret has not yet been introduced to the wild or bred with other populations of black-footed ferrets because scientists are still assessing the potential risks of introducing her genome into the existing gene pool. However, her existence shows how important it is to proactively biobank samples from endangered species, according to Phelan.  “This could not have happened unless some individuals were so prescient 40 years ago to actually bank those living tissues,” she said. “They were biobanking not really knowing even how science would change.”  With this in mind, Phelan and the team at Revive & Restore submitted a proposal to the FWS to create the pilot for the biobanking pipeline program to ensure that future generations have access to these types of living materials. The project relies on a contingent of FWS field biologists—who are often already gathering biological samples from endangered species in the wild—to obtain small tissue biopsies from living animals to be frozen. “Though there are no plans for near term use, cryogenically preserved cell culture samples are an insurance policy against future losses of biodiversity in the wild,” said Willey.  Currently, the biobanking project is just about collecting and storing the living tissues, and cataloging their genomes rather than actively pursuing strategies such as cloning. Yet these species’ genomes could start helping researchers assess genetic diversity and identify at-risk populations in the wild right away. And the frozen samples they store may someday be used to help support conservation technology that doesn’t even exist yet.  

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