Fossils of Webb’s short-tailed mouse (Leggadina webbi) were found at Mount Etna near Rockhampton, while Irvin’s short-tailed mouse (Leggadina irvini), was discovered near Chillagoe at the base of Cape York Peninsula.

Dr Jonathan Cramb from UQ’s School of Earth and Environmental Sciences said the finds show that analysing fossils found in caves could help determine how the local environment had changed over time.

“Caves are great places for the preservation of fossils, partially because they’re natural traps that animals fall into, but also because they’re roosting sites for owls and other flying predators,” he said.

“Owls are exceptionally good at catching small mammals in particular, so the cave floor beneath their roosts is littered with the bones of rodents and small marsupials.

“The accumulation of bones build up over time, providing us with a record of what species were living in the local area, which can stretch back hundreds of thousands of years.

“Many species are only found in certain habitats — for example, hopping mice (Notomys spp.) generally live in deserts, while tree mice (Pogonomys spp.) only live in rainforests — so changes in the fauna tell us about changes in the environment.”

Dr Cramb said the team, including UQ’s Dr Gilbert Price and alumnus Scott Hocknull from the Queensland Museum, was able to confirm a number of environmental changes thanks to the fossils.

“Our findings show that the caves around Mount Etna had gone through a period of local extinction of rainforests, which were replaced by dry to arid habitats less than 280,000 years ago,” Dr Cramb said.

“My colleagues and I wondered if the same environmental change happened elsewhere in Queensland, which is why we were searching the caves near Chillagoe.

“Our analysis of fossils from the caves in north-east Queensland has shown that rainforest extinction was widespread.

“This research shows that, at least in these instances, rainforest extinction is correlated with a sudden shift in climate — a warning that rainforests are particularly vulnerable to climate change.”

The new species of mice were named after UQ palaeontologist Professor Gregory Webb and citizen scientist and caving guide Douglas Irvin.

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“Birds have a unique organ in their airway to produce sounds — it’s like a flute,” says Chad Eliason, a postdoctoral researcher at Chicago’s Field Museum and co-first author of the study. “We don’t know where that organ came from, how and why it evolved. But in this study, when we zoomed out and looked at the windpipes of other animals, we found deep similarities that we didn’t expect.”

Mammals, birds, and reptiles all have a trachea — a tube connecting the nose and mouth to the lungs. And we all have a larynx — a hollow, muscular organ at the top of that tube that helps air pass through to the lungs and keeps food from falling into the airway. In mammals and reptiles, the larynx has little folds of tissue that vibrate when air passes over them, producing sound. In birds, the larynx can’t produce sound — it’s only there for breathing and eating. Instead, birds’ sounds are produced at the bottom of the trachea, just above where the trachea branches into the lungs. This juncture, made of cartilage, is the syrinx.

“The syrinx is a tiny box of cartilage — in a sparrow, it’s about 8 millimeters in diameter, about four times the thickness of a strand of spaghetti,” says Eliason. “It reinforces the airway, and when air passes over the folds in it, it produces a sound: birdsong.”

Since birds have both a syrinx and a larynx, it’s unclear exactly when the syrinx took over sound production duty for the larynx. “Birds’ closest living relatives, crocodiles, produce sound in their throats with a larynx. So how did ancestors of birds transition from making sounds with their larynx to making sounds with their syrinx?” asks Eliason. “If we found fossil evidence of a syrinx in dinosaurs, that would be a smoking gun, but we haven’t yet. In the meantime, we have to look at other animals for clues.”

Eliason and his fellow scientists, including co-first author Evan Kingsley of Harvard Medical School, examined the tracheas of a suite of animals. Cats, mice, and crocs all have a set of fused cartilage rings at the base of the trachea, called the carina, that provides structural support where the trachea branches to the lungs — just like a syrinx does. “Perhaps the syrinx is just a byproduct of reinforcing the airway, like a carina does in other animals,” says Eliason.

The existence of structures like the syrinx and the carina aren’t new to science — people have known about them for decades. But this study provides a new way of looking at them. “We’re deepening our understanding of how these structures are related to each other, and that could help us understand how the syrinx evolved in the first place,” says Julia Clarke, professor at University of Texas at Austin and a leading author of the study.

The study also sheds light on birds’ ability to produce sounds throughout their evolutionary history. According to Eliason and colleagues, there are two ways it could have gone down. In Scenario A, extinct ancestors of birds made sounds with their larynxes, then lost the ability to make sounds with their larynxes and had a period where they couldn’t sing, and then they regained the ability to make sounds with the origin of a syrinx. In Scenario B, bird ancestors made sounds with a larynx, then they developed a syrinx possibly for structural support of the airway, the syrinx became able to produce sound, and after a while, birds only produced sound with their syrinxes and lost the ability to make sounds with their larynxes. This study suggests that Scenario B is more likely. “It seems more intuitive to me that birds’ development of the syrinx would have been step-wise, that they’d have maintained their ability to make sounds with both the larynx and the syrinx, and then gradually lost the ability to make sound with the larynx,” says Eliason. “The other option would have birds and their dinosaur ancestors experiencing a sort of quiet zone when they couldn’t make any sounds. From looking at dinosaurs’ skulls, we know they could hear, and it wouldn’t make sense for them to be able to hear but not be able to make sounds to communicate.” The researchers also note that the presence of a perfectly functional larynx in the closest relatives of birds make Scenario B less likely than the first scenario.

Kingsley says he hopes this study will be useful for all scientists studying how new features evolve. “One of the grand challenges in biology is understanding how novel structures arise, why we see weird traits in some organisms,” he says. “This study gives us an idea of how one of those novel structures, the syrinx, might have come about.” Eliason also notes that the evolution of the syrinx is inextricably linked to the evolution of birdsong, and thus, of birds themselves. “Birdsong is what they use to communicate, to find mates and warn each other of predators. It’s because of the syrinx that birds can produce all these different sounds. There are over ten thousand species of birds, each with a different call — their ability to produce all these sounds could have played a role in generating the bird diversity that we see today.”

The research was funded by the Gordon and Betty Moore Foundation (Grant 4498).

Scientists believe this is evidence that glyphosate might be contributing to the decline of honey bees and native bees around the world.

“We need better guidelines for glyphosate use, especially regarding bee exposure, because right now the guidelines assume bees are not harmed by the herbicide,” said Erick Motta, the graduate student who led the research, along with professor Nancy Moran. “Our study shows that’s not true.”

The findings are published this week in the journal Proceedings of the National Academy of Sciences.

Because glyphosate interferes with an important enzyme found in plants and microorganisms, but not in animals, it has long been assumed to be nontoxic to animals, including humans and bees. But this latest study shows that by altering a bee’s gut microbiome — the ecosystem of bacteria living in the bee’s digestive tract, including those that protect it from harmful bacteria — glyphosate compromises its ability to fight infection.

The researchers exposed honey bees to glyphosate at levels known to occur in crop fields, yards and roadsides. The researchers painted the bees’ backs with colored dots so they could be tracked and later recaptured. Three days later, they observed that the herbicide significantly reduced healthy gut microbiota. Of eight dominant species of healthy bacteria in the exposed bees, four were found to be less abundant. The hardest hit bacterial species, Snodgrassella alvi, is a critical microbe that helps bees process food and defend against pathogens.

The bees with impaired gut microbiomes also were far more likely to die when later exposed to an opportunistic pathogen, Serratia marcescens, compared with bees with healthy guts. Serratia is a widespread opportunistic pathogen that infects bees around the world. About half of bees with a healthy microbiome were still alive eight days after exposure to the pathogen, while only about a tenth of bees whose microbiomes had been altered by exposure to the herbicide were still alive.

“Studies in humans, bees and other animals have shown that the gut microbiome is a stable community that resists infection by opportunistic invaders,” Moran said. “So if you disrupt the normal, stable community, you are more susceptible to this invasion of pathogens.”

Based on their results, Motta and Moran recommend that farmers, landscapers and homeowners avoid spraying glyphosate-based herbicides on flowering plants that bees are likely to visit.

More than a decade ago, U.S. beekeepers began finding their hives decimated by what became known as colony collapse disorder. Millions of bees mysteriously disappeared, leaving farms with fewer pollinators for crops. Explanations for the phenomenon have included exposure to pesticides or antibiotics, habitat loss and bacterial infections. This latest study adds herbicides as a possible contributing factor.

“It’s not the only thing causing all these bee deaths, but it is definitely something people should worry about because glyphosate is used everywhere,” said Motta.

Native bumble bees have microbiomes similar to honey bees, so Moran said it’s likely that they would be affected by glyphosate in a similar way.

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