Clément Gilbert, an evolutionary genomicist at Paris-Saclay University, thinks the aquatic bias in introners is an echo of what his group found in horizontal gene transfer events. In 2020, their work uncovered nearly 1,000 distinct horizontal transfers involving transposons that had occurred in over 300 vertebrate genomes. The vast majority of these transfers happened in teleost fish, Gilbert said.

If introners find their way into hosts primarily through horizontal gene transfers in aquatic environments, that could explain the irregular patterns of big intron gains in eukaryotes. Terrestrial organisms aren’t likely to have the same bursts of introns, Corbett-Detig said, since horizontal transfer occurs far less often among them. The transferred introns could persist in genomes for many millions of years as permanent souvenirs from an ancestral life in the sea and a fateful brush with a deft genomic parasite.

Introners acting as foreign, invasive elements in genomes could also be the explanation for why they would insert introns so suddenly and explosively. Defense mechanisms that a genome might use to suppress its inherited burden of transposons might not work on an unfamiliar genetic element arriving by horizontal transfer.

“Now that element can go crazy all over the genome,” Gozashti said. Even if the introners are initially harmful, the researchers hypothesize that selective pressures could soon tame them by cutting them out of RNA.

Although horizontal gene transfer and introners share a connection to the aquatic environment, the findings don’t yet show definitively that this is where introners come from. But the discovery of introners’ widespread influence does challenge some theories about how genomes — particularly eukaryotic genomes — have evolved.

Reverberations in the Host

The pervasiveness of recent intron gain may act as a counterweight to some ideas about the evolution of genomic complexity. One example involves a theory of intron evolution developed by Michael Lynch of Arizona State University in 2002. Models suggest that in species with small breeding populations, natural selection can be less efficient at removing unhelpful genes. Lynch proposed that those species will therefore tend to build up heaps of nonfunctional genetic junk in their genomes. In contrast, species with very large breeding populations should not be gaining many introns at all.

But Gozashti, Corbett-Detig and their coauthors found the opposite. Some marine protists with gargantuan breeding populations had hundreds or thousands of introners. In contrast, introners were rare in animals and absent in land plants — both groups with much smaller breeding populations.

The evolutionary arms race between invading genetic elements and the host may have a hand in generating a more complicated genome. The parasitic elements are in “constant conflict” with genetic elements that belong to the host, Gozashti explained, because they compete for genomic space. “All these moving pieces are constantly driving each other to evolve,” he said.

That raises the question of what the intron gains meant for the functional biology of the organisms in which they occurred.

Cedric Feschotte, a molecular biologist at Cornell University, suspects it would be interesting to compare two closely related species, only one of which has experienced an intron swarm in recent evolutionary history. The comparison might help to reveal how influxes of introns could promote the appearance of new genes. “Because we know that bringing in introns can also facilitate the capture of additional exons — so completely new stuff,” he said.

Similarly, Feschotte thinks that profusions of introns might help drive the evolution of families of genes that can change rapidly. Stuffed with new introns, those genes could co-opt the new variability enabled by alternative splicing.

Such rapidly evolving genes are widespread in nature. Venomous species, for instance, often need to remix the complex cocktails of peptides in their venoms at the genetic level to adapt to different prey or predators. The ability of the immune system to generate endlessly diverse molecular receptors also depends on genes that can rearrange and recombine quickly.

Peona warns, however, that although introners could provide benefits to an organism, they might also be totally neutral. They should be considered “innocent until proven guilty of function or anything else.”

“One of the things that’s next is looking at metagenomic data to try to find a case that really is a clear horizontal transfer with the exact same introners in two different species,” Corbett-Detig said. Finding this piece of the puzzle would help flesh out the full story of where most of eukaryotes’ introns have come from.

Irina Arkhipova, a molecular evolutionary geneticist at the University of Chicago Marine Biological Laboratory, is interested in knowing more about how introners are spreading through the genome at such large scales. “It just leaves no trace of the enzyme that was responsible for this massive burst of mobility — that’s a mystery,” she said. “You basically have to catch it in the act while it’s still moving.”

For Gozashti, the discovery of introners in such a wide range of eukaryotes holds a lesson about how to approach fundamental questions about the nature of eukaryotic life: Think broadly. Studies often focus on the sliver of biodiversity represented by animals and land plants. But to understand the important patterns of genomic information underlying all life, “we need to sequence more eukaryotic diversity, more of these protist lineages where we don’t know anything about how they evolve,” he said. “Had we just studied land plants and animals, we never would have found introners.”

Editor’s note: Gozashti is a graduate student in the laboratory of Hopi Hoekstra, who serves on the advisory board for Quanta.