DAILY DOSE: Chinese study of withheld Covid-19 data raises more questions than it answers.

The Chinese study using the controversial data from early in the pandemic that was only recently made public has been published in Nature. As expected, the study indicates that Wuhan wet market likely acted as ground zero for the outbreak. According to an article in Nature about the study,

Researchers from the Chinese Center for Disease Control and Prevention (China CDC) have published an eagerly awaited analysis1 of swabs collected at a wet market in Wuhan, China, in the early weeks of the COVID-19 pandemic — as well as the underlying data, which the international research community has been calling for since the beginning of the outbreak.

The analysis, published in Nature on 5 April, confirms that swabs from the Huanan Seafood Wholesale Market — which has long been linked to the start of the pandemic — contained genetic material from wild animals and tested positive for SARS-CoV-2. This suggests that it’s possible an animal could have been an intermediate host of a virus that spilled over to infect humans. But researchers say the latest findings still fall short of providing definitive proof that SARS-CoV-2 originated from an animal-to-human spillover event. (The study authors, led by former China CDC director George Gao, did not respond to requests for comment from Nature’s news team, which is editorially independent of Nature’s journal team.)

Still, researchers say that the publication of the genomic data, which have been deposited on open repositories, is crucial — because it will allow further analyses that could offer clues about the pandemic’s origin. “It’s one of the most important data sets we’ve had since the emergence of the pandemic,” says Florence Débarre, an evolutionary biologist at the French National Centre for Scientific Research in Paris, who was part of a team that caused controversy by publishing its own analysis of the China CDC data last month. “They exist because at the time the right things were done.”

Not everyone accepts the findings at face value. One researcher noted that the paper reports the presence of panda DNA among the samples. Killing a panda in China is a crime punishable by death. The presence of panda DNA is more indicative of contamination than dead pandas. That reality makes the samples in question far from ideal. https://bit.ly/418aqR0

A special report by the Associated Press brings to light the degree of destruction overfishing has wrought on the waters surrounding the Bahamas. According to the article,

Scientists, international conservationists and government officials have sounded the alarm that the conch population is fading due to overfishing, and a food central to Bahamians’ diet and identity could cease to be commercially viable in as little as six years…

Conch’s potential demise reflects the threat overfishing poses around the world to traditional foods. Such losses are among the starkest examples of how overfishing has changed people’s lives - how they work, what they eat, how they define themselves.

The overfishing challenges faced by Bahamians are mirrored in places as disparate as Senegal, where overfishing has taken away white grouper, long the basis for the national dish of thieboudienne, and the Philippines, where it has depleted small fish such as sardines that are used in kinilaw, a raw dish similar to ceviche.

Experts predict that if something is not done soon, many species of fish used as food will be extinct. http://bit.ly/3KhTII5

Knowing the tempo of inherited mutations is critical to understanding how species evolve. Yet until recently, the wildly divergent rates at which life can mutate were known for only a handful of species. A recent study published in Nature offers new, more refined insights into the rate of mutations.

Now, a massive analysis of 68 diverse vertebrate species, from lizards and penguins to humans and whales, has made the first large-scale comparison of the rates at which species mutate — a first step toward understanding how quickly they can evolve. The findings, published in the journal Nature, unearthed surprising insights into how the tempo for mutations can change and what sets that pace.

The paper roughly “doubles the amount of mutation-rate estimates we have,” said Michael Lynch, an evolutionary biologist at Arizona State University who was not involved in the study. Now we have a “better idea of the amount of variation within vertebrates.”

With this extensive data, biologists can begin to answer questions about which traits most influence mutation rates and the pace of evolution. “There are things that affect the rate of evolution, [but] we don’t know all of them,” said Patricia Foster, a professor emerita of biology at Indiana University who was not involved in the study. “This is the start.”

The measurements of mutation rates could be critically useful in calibrating the gene-based molecular clocks that biologists use to determine when species diverged, and they offer useful tests of several theories about how evolution works. They also confirm that factors that help set the speed of evolution are themselves subject to evolution. “Germline mutation, like any other trait, is under natural selection,” said Lucie Bergeron, the lead author of the new study.

The most surprising finding that emerged from the data was the wide range of germline mutation rates. When the researchers measured how often the mutations occurred per generation, the species varied by only about fortyfold, which Bergeron said seemed quite small compared to the differences in body size, longevity and other traits. But when they looked at the mutation rates per year rather than per generation, the range increased to about 120-fold, which was larger than previous studies had suggested. https://bit.ly/3ZMnJWn

Thanks for reading. Let’s be careful out there.

IMAGE CREDIT: Xiao Xiao, Chris Newman, Christina D. Buesching, David W. Macdonald & Zhao-Min Zhou.

ON SALE! Charles Darwin Signature T-shirt – “I think.” Two words that changed science and the world, scribbled tantalizingly in Darwin’s Transmutation Notebooks.

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