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Rachel E. Gross/Medill

Nickel, the Shedd Aquarium’s sole giant green sea turtle, flaps toward food. The green sea turtle is one of three turtle species whose recently sequenced genomes support a  genetic link to birds and crocodiles.


Extraordinary origins, unlikely superpowers: the turtle genome unveiled

by Rachel E. Gross
May 13, 2013


Embryos

Illustrations courtesy Naoki Irie. Click on images to enlarge.

 

hourglass

Both the green sea turtle (above) and soft-shell turtle (below) undergo an hourglass model of development, in which they converge into a shared stage with other vertebrates before diversifying.

Nickel the giant green sea turtle glides along the water’s edge, snapping at lettuce.

With her massive bulk (181 pounds of flesh and shell) and lopsided grace (a run-in with a motorboat left her imperfectly buoyant), she just about steals the show from the eels and rays who share her tank at the Shedd Aquarium. But Nickel shies from fame. When feeding time is up, she’ll wedge herself into a corner, away from the eyes of hopeful oglers.

Evolutionarily speaking, Nickel has been eluding scientists for a century. Ancient, toothless and sandwiched in armor, she and her fellow turtles pose a reptilian riddle for biologists.

“How can you have something like a turtle, that looks so different from everything else?” asks Olivier Rieppel, a paleontologist at the Field Museum who still considers turtles an evolutionary mystery even after three decades of studying them.

It’s easy to forget that turtles are wonderfully weird; they’re like a song you’ve played and replayed into familiarity. But a few traits make them truly peculiar. Foremost is that shell, the result of embryonic ribs and vertebrae fused together and grown bony. Creating it seems to have required turtles to develop shoulder blades inside their ribcage. “They’re the only tetrapods that have ever done that in the history of life on earth,” says Brad Shaffer, an evolutionary and conservation biologist at the University of California, Los Angeles. That evolutionary “decision” is what gives turtles their curious scuttle.

Understanding how the shell came about could help us understand more than turtles. It could clue us in to how evolution produces novelties—some say monstrosities—that seem to defy explanation. We’re getting close: in March, the turtle became the second reptile to have its genome sequenced, after Shaffer’s team drafted a blueprint of the western painted turtle, published in Genome Biology. The genomes of two other species—the Chinese soft-shell turtle and the green sea turtle—were announced in Nature Genetics in April as part of a collaboration with the Genome 10K Project, an international effort to create a digital zoo of life’s diversity.

STRANGE LIKE US

Reading those genomes has revealed a host of reptilian superpowers. In the soft-shell turtle, Japanese researchers found genes pointing to an acute sense of smell. More astonishing, Shaffer’s team looked at genes that allow the painted turtle to endure such tortures as extended airlessness and being frozen solid. The neatest part? Those same genes can be found inside you and me. “They’re using the same machinery as we are,” Shaffer says. “They’re just changing the dosages and amounts.”

Same notes, different arrangements—it’s a concept that has emerged as a fundamental theme in genetics. And it’s evident in the first days of a turtle’s life. It means that, while all organisms use many of the same genes, they can achieve vastly different results through how, when, and in which molecular environment they are expressed.

Given their weirdness, you might not expect a turtle to ever resemble a human. But in fact, there is a window of time in which a turtle embryo looks like a chicken or a person: a fleshy, pulsing comma. In each case, the organism first lays down a basic body blueprint—four limbs, one head—before establishing its unique identity. In turtles, that window just happens earlier than most—about seven days in, according to developmental biologist Naoki Irie, who led research on soft-shell turtles embryos at the RIKEN Center for Developmental Biology in Japan.

What does that mean? “Even turtles … could perhaps be bound by a very ancestral body plan they once established at around the dawn of vertebrates,” says Irie.

A TURTLE’S PLACE

The new genomes also help answer a seemingly basic question: how do we classify turtles? The answer isn’t as obvious as you would think. “Up until very recently, we haven’t known who turtles are related to,” Shaffer says.

Once, turtles were considered “living fossils,” relatives of an ancient branch of primitive reptiles, says Rieppel of the Field Museum. In 1994, Rieppel gave them a promotion. He set them in a clade alongside lizards and snakes, by studying fossils and comparing their anatomy. “They flipped from the base to the crown of the reptile tree,” he says now. “This was hugely controversial.” Soon after, molecular studies began flowing in. The verdict: actually, turtles appeared to be more related to crocodiles and birds. 

The new genome research confirms this, marking the strongest support yet. But while molecular evidence is weightier than anatomical similarities (which can be deceiving) Rieppel says it’s not necessarily the last word. The problem is that combining anatomical data with the molecular would be near-impossible—the anatomical signal would be drowned out by the vast size of the genome. “The question is, how do we deal with that conflict?” says Rieppel. “And I don’t know how.”

Irie says the stream of molecular evidence speaks for itself. “I am quite sure of the phylogeny,” he said in an e-mail. Shaffer is more conservative. “I’m feeling better about it,” he says.

UNDER SIEGE

There is a darker reason for having the turtle genome on file. With all their fiber and durability, turtles grow ever rarer. Many fall victim to human appetites (soft-shell turtles are a delicacy in Japan) and carelessness (in addition to the boat-made gash down her shell, Nickel got her name because she was found 10 years ago off Florida’s Gulf Coast with a 1975 coin lodged in her throat).

Of the 331 species that survive, more than half are considered threatened according to the International Union for Conservation of Nature. That makes turtles the most endangered group of vertebrates. Besides a tool to study evolution and development, a genomic library could preserve some of that diversity—even when the animal itself is gone.

Of course, that’s cold comfort for those who cherish turtles as beloved pets, aquatic marvels and icons for conservation. Why do we seem to have such a soft spot for the hard-shelled creatures? Shaffer has an explanation. “Even if you confront one in the wild, rather than it running away or baring its fangs, what do they do?” he says. “They just pull in their shell and sit there. It makes them kind of safe and vulnerable. There’s nothing threatening about a turtle.”