54 THE SCIENTIST | the-scientist.com
© ISTOCK.COM, INDIANOCEANIMAGERYexpression-altering insertions influence the flies’ stress responses,
and likely behavior and development as well, she notes.^6 Lab stud-
ies suggest that mobile elements account for half or more of all
phenotype-altering mutations in the flies. And in wild popula-
tions, TIPs are common and some are associated with environ-
mental variables such as temperature and rainfall—exactly what
you’d expect if they’re driving adaptation.^7Another line of evidence for this idea is the fact that many TEs
are activated by stress, perhaps serving as a Hail Mary pass for
adaptive mutations. Mirouze points to a 2019 study in yeast as
an example: when yeast cells were subjected to a novel stressor,
the cellular mechanisms that silence transposon activity became
less active and TEs began to move, generating genetic varia-
tion that accelerated the evolution of resistance to the stressor.^8THE CURIOUS CASE OF SEA SNAKES
When University of Adelaide computational biologist David Adelson
and his colleagues set out to annotate the TEs in the genome of the
olive sea snake (Aipysurus laevis), they had no idea how strange the
animals’ transposons would turn out to be. In addition to finding TEs
known from other reptiles, the team discovered seven novel subfami-
lies of transposable elements, many of which appeared to have been
horizontally transferred from unrelated sea creatures (Genome Biol Evol,
12:2370–83, 2020). Intrigued, they investigated the TEs in another
group of marine serpent called sea kraits (Laticauda spp.) and again
found a previously unknown kind of transposon, this time apparently
from sea urchins (Biol Lett, 17: 20210342, 2021).
What was especially intriguing about that TE, which the team dubbed
Harbinger-Snek, is that it underwent massive expansion in the kraits. Now,
some 30 million years after it jumped into the animals—perhaps ferried by
a parasite or virus—Harbinger-Snek elements account for up to 12 percent
of the krait genetic code. And the thousands of copies peppered throughout the genome have landed in some intriguing locations, including potential
regulatory regions and introns, which, although noncoding, can influence how the cell’s machinery behaves when transcribing a gene. “There’s enor-
mous potential for these things to have affected gene expression,” Adelson says, and therefore, to have altered the animals’ physiology or behavior.
A small number of the insertions even appeared to overlap directly with coding regions in proposed genes, providing a more direct path to
functional change. While Adelson cautions that the annotations aren’t robust—one cannot say for sure, yet, that every section currently marked as
a coding region actually is one—it’s certainly possible that at least some of the transposon insertions altered proteins.
Further research suggests that these species weren’t unique. In a preprint posted by Adelson’s team last summer, the researchers claim
that all sea-dwelling snakes have transposons obtained from other marine organisms (bioRxiv, doi:10.1101/2021.06.22.449521, 2021). In
fact, the genomes of all of the Australian snakes Adelson and his collaborators examined had such marine TEs, though the ones in terres-
trial species appeared to be much more degraded, suggesting they were a lot older than the ones only seen in the aquatic snakes.
Adelson says these TEs may help tell the evolutionary story of the sea snakes. Researchers have long thought that Australia’s snake biodiversity
stemmed from a small number of terrestrial snakes that rafted their way to the continent. But the presence of ancient marine TEs suggests the colo-
nizing ancestors were at least semi-aquatic—they were spending enough time in the water to pick up aquatic species’ transposons. After the snakes
moved onto the Australian mainland, they appear to have acquired a transposon from a lizard. Millions of years later, the fully marine sea snakes and
the semi-aquatic sea kraits returned to the water, each gathering new marine TEs in the process.
The data are very preliminary, with population-level studies needed to determine whether TE insertions were advantageous, Adelson says.
But he hypothesizes that, given transposons’ habit of rapidly and dramatically altering the genome, the TEs in Australian snakes could have
directly aided the animals’ evolutionary journey—to the sea in the first place, then from the sea to the land, and especially back to the sea
again. Every time a new transposon entered the genome, he says, it may have provided a burst of genetic diversity, including potentially adap-
tive changes. And if TE insertions that initially aided aquatic living were neutral once the animals slid back onto land, they could have stuck
around for millions of years of terrestrial life, essentially preadapting the snakes to return to the water.
“Perhaps because they had retained some of those amphibious adaptations... [they] could make the transition back to aquatic,” he
muses. “And that’s interesting, because it means that if we’re going to start looking for adaptations in a very recent timeframe for these events,
maybe there are some, but maybe we should be looking at the older ones.”