Jellyfish study shows scientists that evolution may be 'much more predictable than we expected'

A new study reveals unrelated jellyfish evolved identical genetic mutations, but surprisingly, these matching DNA changes did not result in matching physical traits.

Biologists have always assumed that it is incredibly rare for two different species to independently develop the exact same genetic changes after being separated for millions of years.

However, a new study looking at the DNA of ancient jellyfish shows that evolution repeats itself much more than scientists ever realized.

Across 86 species, lineages that split more than 600 million years ago have repeatedly swapped in the same building block at the same spot in the same protein. It happened far more often than pure chance would allow.

The twist is what those shared changes are not. They mostly have nothing to do with the traits the animals visibly share, such as eyes.

Cory Berger, a postdoctoral researcher in Todd Oakley's lab at UC Santa Barbara, led the work. Colleagues at the University of Kansas, Texas A&M University and the University of Nebraska took part.

Everything here comes from comparing gene sequences across species; no trait was tested in a lab.

"We're studying molecular evolution here - to what extent similar genetic changes occur in different organisms," Berger said. "And that in particular is something we don't know much about."

Rebuilding a very old family tree

The group the team chose, called Medusozoa, takes in the true jellyfish, box jellyfish and the hydroids, which are small branching animals related to them. The team's dating, anchored by 17 fossils, puts the origin of the group at about 685 million years ago.

Before anyone could compare genes, the team had to know who was related to whom and when they split.

They built a tree of 621 species, anchored by the full gene sets of 98 of them, 22 sequenced for this study, and then traced three traits across it.

The results show how often evolution repeats at the level of the body, a pattern biologists call convergent evolution. Eyes, for example, arose at least nine separate times.

The free-swimming medusa stage, the bell-shaped adult most people picture, was lost 41 times. Colonies switched from crusts to upright branching forms 32 times.

"Maybe it's just the case that organisms that have phenotypic convergence who look similar to one another have convergent molecular changes," Berger said, describing the idea the team set out to test.

Genetic change matches kept turning up

The team compared the protein-coding genes of the 86 species, two at a time. This meant 3,570 pairs were compared, across 9,194 gene families.

For each pair, it looked for spots where both lineages had independently changed the same amino acid, one of the building blocks of a protein, to the same new one.

"And then we looked at the patterns of change across those genes. If the same specific change has happened in distantly related species, then we're calling that convergence," said Oakley, the senior author.

The team found 426,322 such matches, under a tenth of a percent of all the branch pairs it tested, and they appeared in 8,991 of the 9,194 gene families.

At those spots, the new amino acid also tended to differ more in its chemistry from the old one than at other changed spots in the same proteins. The team reads that pattern as natural selection rather than accident.

Matches did get rarer as the time since two species split grew longer. But the decline was gentle, and even pairs separated by more than 600 million years shared more changes than a model of pure chance predicted.

Shared genetic changes did not explain it

If evolution reuses genes to build the same trait, species that both evolved eyes, or both lost the medusa stage, should share more genetic changes than other pairs. They didn't. Pairs with a shared trait were statistically indistinguishable from pairs without one.

Genes known to help build eyes did show up a little more often among eye-bearing pairs. But the same genes had also been under the same kind of selection in species with no eyes at all.

What did set the convergent genes apart was their job.

Genes that deal with the outside world, including energy metabolism, immune defense and breaking down foreign chemicals, carried the most repeated changes. Genes that run the cell's internal housekeeping, such as cell division, carried the fewest.

"The amount of genetic similarity indicates that at the genetic level, evolution may be more repeatable and maybe therefore more predictable than we expected," Oakley said.

"But it also means that we still have a huge amount to learn about how the genes function, how that plays out on the whole-organism scale."

Many more questions remain

The team counted only one kind of genetic change, a swap of one amino acid for another. Changes in the DNA that switches genes on and off, which may matter more for body shape, were not part of the analysis.

Also, genes facing the environment may simply evolve faster, which would give them more chances to match.

The bigger gap is the cause. For most shared genetic changes, the pressure that drove them in both lineages is unknown.

The team's own example of a solved case is a pump found in cell membranes. It evolved separately in amphibians, reptiles, mammals and insects to resist the same heart toxins, made by toads and by plants. There, the shared diet explains the shared gene.

The jellyfish data suggest many cases like that are waiting, each with its own explanation. Finding them means measuring the pressures these animals face in the sea as carefully as the team has now measured their genes.

That, the authors wrote, is the next job.

The full study was published in the journal Proceedings of the National Academy of Sciences.

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