DNA usually likes to follow rules. Strands of DNA are copied somewhat faithfully, and the copies are passed from parents to offspring, thus driving evolution as we know it. But, according to new estimates, fifty percent your genome is also composed of renegade DNA that likes to jump from species to species. This rogue DNA, researchers write in a Genome Biology article published Monday, has randomly inserted itself into almost every genome on this planet throughout the evolution of life. They are all that remain of a series of mysterious events from millions of years ago.
Atma Ivancevic, Ph.D., a post-doctoral neurogenetics and bioinformatics researcher and lead author of the paper, began his study by seeking to explain why the same rogue DNA can be found in animals as vastly different as sea urchins and humans. It’s established that most species on earth share a large amount of genetic material — you’ve probably heard the that humans share roughly 99 percent of our DNA with chimps — but these genes are different, says Ivancevic.
“‘Jumping genes’ aren’t actually genes; they are non-coding pieces of ‘junk DNA’,” she tells Inverse in an email. “Think of them like genetic parasites, jumping around the genome to selfishly replicate themselves, and sometimes jumping between species.”
In the past few years, we’ve started to understand the function of these rogue bits of DNA, but we still don’t exactly know what they do. This is the mystery behind jumping genes: They’re breadcrumbs of a DNA trail, scattered throughout the tree of life. Now, thanks to this paper, we might finally find out how they made such a mess.
Ivancevic’s research found that there are two sequences of jumping junk DNA that can be traced across a vast range of species, called BovB and L1. Researchers call these patterns transposable elements (TEs) because they “copy and paste” themselves randomly throughout the genes of animals from sea urchins, to cows, to humans. This strange process, in which a TE invades another species’ genetic material, is called horizontal transfer.
Our standard understanding of reproduction is described by vertical transfer, the assumption that most genetic material is usually passed down from parent to child.
When you draw a family tree, you typically draw children beneath their parents, and in a sense, genes tend to fall along generations in that manner. But some TEs move horizontally across the tree of life, “jumping” from one organism’s DNA to another through a messenger called a “vector.” Scientists don’t fully understand how the process works between species, but they have a hunch about what the vectors might be.
Some organisms, like bacteria, are really good at horizontal transfer of genes and often do so naturally, without a vector. Animals can’t do that, but they can be infected by bacteria, which can then act as vectors. The paper suggests a few likely candidates for this messenger role, including bed bugs, ticks, and locusts, and it also nominates some potential aquatic vector-creatures, like oysters and sea-worms. It’s these vectors that likely moved the two bits of junk DNA sequences, BovB and L1, across species.
What’s really interesting is what happens once the DNA gets there. After a transfer event happens, Ivancevic and her team show, the DNA can replicate rapidly. For instance, BovB is believed to have first arisen in snakes and then “jumped” to cows via horizontal transfer events millions of years ago, where it replicated multiple times. Think of it as doing a standard copy-and-paste, only you hit control-V over and over again.
“To me, the most surprising thing was not the transfer, but the effects to the host genome after transfer,” Ivancevic says. “Now BovB occupies about 25% of the cow genome sequence. That’s a huge change!”
Looking for Big Jumps
To see how far into the tree of life these sequences infiltrated, Ivancevic’s team investigated the genomes of 759 species. They found the BovB sequence in animals as distantly related as snakes, cows, sea urchins, bats and horses (although bats and horses had low numbers of complete BovB sequences). The L1 sequence seemed to be even more prevalent. While 79 species had BovB sequences, 559 species had L1 sequences. Historically, L1 was believed to be only transferred vertically, so finding the L1 sequence in these disparate species was a breakthrough.
BovB has always intrigued researchers because it makes “big jumps” between distantly related species, providing evidence that some kind of horizontal transfer event took place. But previous analysis only turned up a few instances in which L1 sequences made these big jumps, which led researchers to conclude that L1 was probably only passed down vertically.
By casting a wider net, Ivancevic’s team showed that there’s been more genomic jumping around than we once thought. “The use of animals, plants AND fungi, really helped to screen as many genomes as possible with current data. There aren’t many studies which look for cross-Kingdom transfer on a large scale,” she says.
The finding that L1s are present in 559 species was compelling evidence that L1s had made these big jumps. The team points to six previously undiscovered L1 “jumps” in marine species millions of years ago as the possible springboard for this junk gene to enter the DNA of species in completely separate kingdoms.
They write that one of these horizontal events could have popped the L1 sequence into an ancient ancestor of “therian” mammals – animals that don’t lay eggs —between 160 and 191 million years ago. From there, the sequence could have been passed down vertically to all the descendants of those ancient animals, including, perhaps, humans. While L1 is mostly fragmented and inactive in humans, it still composes 17 percent of our genome.
Findings like these illustrate how even the tiniest forces can reshape evolution. Perhaps, millions of years ago, one of our most distant ancestors got into an altercation with a sea-dwelling bloodsucking pest — maybe it was a sea worm — and somehow received an injection of random DNA. Now, millions of years later, those changes persist within us, and we’re still figuring out what roles they play.
“It shows how much random DNA exchanges can shape our evolution,” Ivancevic says.