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The sequenced genomes of the greater mouse-eared bat (Myotis myotis) and five distant cousins are revealing the secrets of bat evolution.

Olivier Farcy

How bats have outsmarted viruses—including coronaviruses—for 65 million years

Although the SARS-CoV-2 virus has sickened more than 14 million people, bats contract similar viruses all the time without experiencing any known symptoms. Now, the newly sequenced genomes of six species spanning the bat family tree reveal how they’ve been outsmarting viruses for 65 million years.

The findings are an “excellent starting point for understanding the superstar immune systems of bats,” says Laurel Yohe, a postdoc at Yale University who studies bat evolution and was not involved with the work.

With more than 1400 species, bats are the second most diverse group of mammals on Earth. They live on every continent except Antarctica, and range in size from two to more than 1000 grams. They fly, they echolocate, and some live up to 41 years—a long time for animals of their size. They are also known to carry many different kinds of viruses, including coronaviruses, with no ill effects.

To discover their secrets, an international consortium launched the Bat1k project, which stands for bat 1000, in 2017 to sequence the genomes of all bat species. Six of those genomes are now complete, the consortium reports today in Nature.

The genomes are more thorough and more accurate than previously sequenced bat genomes, says Jon Epstein, a disease ecologist at EcoHealth Alliance who was not involved with the work. “That allows [researchers] to make some strong comparisons with other animals, including humans.”

The researchers in the consortium did just that, comparing the newly sequenced genomes with those of 42 other mammals, from manatees to people. They found that the bats’ closest relatives aren’t tree shrews, flying lemurs, or even mice (as has been proposed); instead, they formed their own group early on that may share a common ancestor with the mammals that eventually evolved into horses, pangolins, whales, and dogs.

Further analysis revealed bats have disabled at least 10 genes that other mammals use to mount inflammatory responses against infection. But they also have extra copies and modifications of antiviral genes that may explain their high tolerance for disease. Finally, their genome is littered with DNA pieces derived from past viral infections that got incorporated when the viral genomes were replicated.

“These nonbat genes leave a kind of medical record … a diary of previous infections,” Yohe says. That diary reveals that bats have probably had more viral infections than all other mammals over time and have even been infected by viruses thought only to attack birds, the team reports. “The findings highlight bats’ ability to tolerate and survive viral infections more efficiently than other mammals,” says Sharlene Santana, an evolutionary biologist at the University of Washington, Seattle.

The analysis may also resolve the evolutionary origins of bat echolocation, a hunting technique in which bats emit sounds that help them locate insect prey. Some researchers have argued that echolocation evolved later in bat evolutionary history and may even have evolved twice. But the five echolocating bats sequenced have the same versions of several genes involved in hearing, suggesting those versions likely evolved in the ancestor of bats, the team reports.

In the next year, Bat1K researchers plan to sequence 27 more genomes—one bat from each family. They are now seeking funding to do the rest, says Emma Teeling, the project’s co-founder and a zoologist at University College Dublin. Yet these first six genomes will continue to have an impact, says Amy Russell, an evolutionary biologist at Grand Valley State University. “I think this paper will be extremely influential for years to come.”