tetrapods

The fish with the genome 30 times larger than ours gets sequenced

Image of the front half of a fish, with a brown and cream pattern and long fins. — Enlarge / The African Lungfish, showing it’s thin, wispy fins.

When it was first discovered, the coelacanth caused a lot of excitement. It was a living example of a group of fish that was thought to only exist as fossils. And not just any group of fish. With their long, stalk-like fins, coelacanths and their kin are thought to include the ancestors of all vertebrates that aren’t fish—the tetrapods, or vertebrates with four limbs. Meaning, among a lot of other things, us.

Since then, however, evidence has piled up that we’re more closely related to lungfish, which live in freshwater and are found in Africa, Australia, and South America. But lungfish are a bit weird. The African and South American species have seen the limb-like fins of their ancestors reduced to thin, floppy strands. And getting some perspective on their evolutionary history has proven difficult because they have the largest genomes known in animals, with the South American lungfish genome containing over 90 billion base pairs. That’s 30 times the amount of DNA we have.

But new sequencing technology has made tackling that sort of challenge manageable, and an international collaboration has now completed the largest genome ever, one where all but one chromosome carry more DNA than is found in the human genome. The work points to a history where the South American lungfish has been adding 3 billion extra bases of DNA every 10 million years for the last 200 million years, all without adding a significant number of new genes. Instead, it seems to have lost the ability to keep junk DNA in check.

Going long

The work was enabled by a technology generically termed “long-read sequencing.” Most of the genomes that were completed were done using short reads, typically in the area of 100–200 base pairs long. The secret was to do enough sequencing that, on average, every base in the genome should be sequenced multiple times. Given that, a cleverly designed computer program could figure out where two bits of sequence overlapped and register that as a single, longer piece of sequence, repeating the process until the computer spit out long strings of contiguous bases.

The problem is that most non-microbial species have stretches of repeated sequence (think hundreds of copies of the bases G and A in a row) that were longer than a few hundred bases long—and nearly identical sequences that show up in multiple locations of the genome. These would be impossible to match to a unique location, and so the output of the genome assembly software would have lots of gaps of unknown length and sequence.

This creates extreme difficulty for genomes like that of the lungfish, which is filled with non-functional “junk” DNA, all of which is typically repetitive. The software tends to produce a genome that’s more gap than sequence.

Long-read technology gets around that by doing exactly what its name implies. Rather than being able to sequence fragments of 200 bases or so, it can generate sequences that are thousands of base pairs long, easily covering the entire repeat that would have otherwise created a gap. One early version of long-read technology involved stuffing long DNA molecules through pores and watching for different voltage changes across the pore as different bases passed through it. Another had a DNA copying enzyme make a duplicate of a long strand and watch for fluorescence changes as different bases were added. These early versions tended to be a bit error-prone but have since been improved, and several newer competing technologies are now on the market.

Back in 2021, researchers used this technology to complete the genome of the Australian lungfish—the one that maintains the limb-like fins of the ancestors that gave rise to tetrapods. Now they’re back with the genomes from African and South American species. These species seem to have gone their separate ways during the breakup of the supercontinent Gondwana, a process that started nearly 200 million years ago. And having the genomes of all three should give us some perspective on the features that are common to all lungfish species, and thus are more likely to have been shared with the distant ancestors that gave rise to tetrapods.

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

Biology, Ecology, evolution, extinction, paleontology, salamander, Science, tetrapods / Kris Guyer / 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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