To survive in the frigid ocean waters around the Arctic and Antarctica, marine life evolved many defenses against the lethal cold. One common adaptation is the ability to make antifreezing proteins (AFPs) that prevent ice crystals from growing in blood, tissues, and cells. It’s a solution that has evolved repeatedly and independently, not just in fish but in plants, fungi, and bacteria.
It isn’t surprising, then, that herrings and smelts, two groups of fish that commonly roam the northernmost reaches of the Atlantic and Pacific Oceans, both make AFPs. But it is very surprising, even weird, that both fish do so with the same AFP gene—particularly because their ancestors diverged more than 250 million years ago and the gene is absent from all the other fish species related to them.
A March 2021 paper in Trends in Genetics holds the unorthodox explanation: The gene became part of the smelt genome through a direct horizontal transfer from a herring. It wasn’t through hybridization, because herring and smelt can’t crossbreed, as many failed attempts have shown. The herring gene made its way into the smelt genome outside the normal sexual channels.
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Finally, in 2019, a full sequence for the herring genome was published. It let the team better examine the sequences surrounding the AFP gene, some of which appeared to be “transposable elements” (TEs, or transposons), mobile chunks of DNA that can copy and paste themselves in a genome. The herring genome holds many copies of these TEs, but they are absent from other fish—with one telling exception. Three of them flank the rainbow smelt’s AFP gene, in the same order seen around the herring AFP gene.
Graham thinks that these sequences are “definitive proof” that a small chunk of a herring chromosome made its way into a smelt’s. “If anybody wants to dispute this,” she says, “you know, I don’t see how they possibly could.”
Cédric Feschotte, a genome biologist at Cornell University who was not involved in the study, agrees. “It seems unmistakable when you look at the data,” he says. What really intrigues him, though, is how well this finding lines up with work that he and others are doing on TEs and the rise of new genes.
For instance, in a 2008 study published in the Proceedings of the National Academy of Sciences, he and his colleagues identified a new kind of TE found in a disparate group of vertebrates, including a few species of mammals, a reptile, and an amphibian. These TEs were more than 96 percent identical in these species but were strangely absent from other examined genomes. Because the elements seemed to have appeared suddenly, Feschotte and his colleagues dubbed them “Space Invader elements” (“SPIN elements” for short) and concluded that they must have recently moved horizontally between the sundry lineages. These TEs weren’t merely genetic noise in their new hosts, either: Mice, for example, had obtained a whole new functional gene by co-opting a SPIN-element enzyme.
Since the 2008 SPIN paper, thousands of other horizontal TE transfers between animals have been reported. While these putative horizontal transfers were initially met with surprise, much as Graham’s AFP gene was, the evidence is now undeniable.
For context, it’s worth noting that horizontal transfers can be hard to detect: Over time, ever more mutations accumulate in both the original and the recipient lineages, obscuring similarities in a shared gene. Proving that a gene has been horizontally transferred also depends on demonstrating that it wasn’t once present in other related species and then lost through evolution, which can be difficult when some of those species are extinct.
“The rate of actual horizontal transfer is probably much, much higher than we realize,” Schaack says.
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