The First Species to Have Every Individual’s Genome Sequenced

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It’s an endearing, giant, flightless, New Zealand parrot, and it’s a poster child for the quantified-self movement.

When humans first settled in New Zealand in the 13th century, they found a wonderland of strange creatures—including a green, bumbling parrot with the face of an owl and the mien of an old gentleman. That was the kakapo—the world’s largest parrot, and its only flightless one. It had a set of endearing traits—a disc of whisker-like facial feathers, a ponderous slow-motion gait, and a habit of awkwardly climbing trees with its beak and large wings—that made it easy to love. It also had a set of unfortunate traits—an inability to fly, a naïveté toward danger, a distinctive earthy smell, and a habit of freezing when threatened—that make it easy to kill.

And so the Māori killed them, to make meals and cloaks. The dogs and rats that accompanied the Māori to New Zealand contributed to the slaughter. And in the 19th century, European settlers and their coterie of stoats, weasels, cats, and dogs dealt the coup de grace. The kakapo vanished. The island’s fjords, which once resounded with the booming calls of amorous males, fell silent. Through the 1950s and 1960s, intensive search parties turned up few traces of kakapo, and the few individuals that were found soon died. It looked as if the kakapo was an ex-parrot, literally pining for the fjords.

But that’s no longer the case. In 1977, scientists discovered a hidden population on southerly Stewart Island—including the all-important females that were missing elsewhere. Twelve years later, New Zealand’s Department of Conservation launched a Kakapo Recovery program and relocated the surviving birds to predator-free sanctuaries.

Almost three decades later, the kakapo—once thought extinct—is one of the most thoroughly studied animals on the planet. Every single one of the last 153 kakapos on the planet is known to researchers. Every one carries a radio transmitter, so scientists know its position, as well as its movements and sex life.

And soon, a team led by Andrew Digby from the Department of Conservation and Bruce Robertson from the University of Otago will sequence the genomes of all of these birds. By the end of this year, the kakapo will become the first species on Earth for which we have a complete genetic record. Forget hipsters and Silicon Valley entrepreneurs: The exemplar of the quantified-self movement is a green, bumbling, oblivion-defying parrot.

The first kakapo to have its DNA fully decoded was a female called Jane. The decoders—Jason Howard and Erich Jarvis from Duke University—were working on a broader effort to sequence the DNA of all 10,000 bird species. They chose the kakapo as one of their focal species at the encouragement of Howard’s daughter, who had become enchanted with the parrot after reading a children’s book about it.

When Digby heard that that one kakapo had been sequenced, he thought: Why not all of them? “We only need to do 124 more and then we’ve got the entire species,” he says. (At the time of the study, there were only 125.) It would be like having the entire library for the animal, rather than a single book.

“Kakapo breeding season prepared me very well for motherhood and the other way round, too.”

DNA will only tell you so much about an animal, but it becomes especially powerful when combined with all the other kakapo data around. For example, their entire genealogy is known because their sex lives are automatically detected and recorded.

When these birds mate, their transmitters detect a distinctive movement—a small, hour-long jiggle. (You can see a dramatic reconstruction in the video below, as Sirocco the kakapo tries to mate with the head of zoologist Mark Carwardine—a literal headfuck that turned him into an instant celebrity.) If a male’s transmitter detects that signature jiggle, it pings all the other transmitters nearby. If one of those belongs to a female, and is also recording a jiggle, it probably means that the two owners are mating.

The islands where the parrots live are studded with data loggers, which suck up the information from any passing kakapo and transmit it to the recovery team. “Every morning, we have a record of all the matings the day before,” says Digby. “These birds don’t have much privacy unfortunately.”

Kakapos breed infrequently. So when there’s a big breeding season, as happens every few years, the recovery team springs into action. “It’s round-the-clock, continual shift work,” says Diedre Vercoe, who manages Kakapo Recovery's dozen or so permanent staff and its hundreds of volunteers. The team catches the males and collects samples of their sperm. If a female hasn’t mated, or has mated with a dud male who’s known to have poor quality sperm, the team artificially inseminates her with sperm from a stud.

When a female eventually lays eggs, the team sneaks into her nest while she’s out foraging, and checks on the health of the eggs. They’ll move eggs between nests to make sure that females aren’t overburdened. When the eggs hatch, a team member sleeps in a nearby tent and weighs the chicks every night. Often, the fruit that these parrots depend on hasn’t ripened yet, and the chicks show signs of malnutrition. In that event, the team pulls them in and rears them by hand, keeping them in the company of other kakapo chicks to ensure that they don’t imprint on humans.

The whole intense, round-the-clock process takes several months. “I liken it to the early months of having a child,” Vercoe says. “Kakapo breeding season prepared me very well for motherhood and the other way round, too.”

the-first-species-to-have-every-individuals-genome-sequenced photo 1A pair of kakapo chicks. (Andrew Digby / New Zealand Department of Conservation)

This is what it takes to save a species. When Digby first talked about sequencing every kakapo, there were 125 of them remaining. Last year, after an intense breeding season, 29 more joined their ranks—an increase of almost a quarter. “We’ve more than tripled the population since the program officially began in 1990, and we have a young and growing population,” says Vercoe. “We’re on the right path.”

These efforts have been a boon for Digby’s sequencing ambitions. Every year, the team catches each bird to check their health and change their transmitters—so collecting blood samples was easy. And the bird’s popularity allowed the team to quickly crowdsource the money they needed—roughly 110,000 U.S. dollars. So far, 81 genomes have been sequenced, and the team recently acquired the money for the 72 other living birds, and 28 individuals who recently died. Digby, with help from Jarvis and Howard, hopes to finish everything by the end of the year.

“We could track the family tree of all individuals of the species from here onward.”

Erich Jarvis thinks that those genomes have interesting evolutionary stories to tell. Along with two other New Zealand parrots, the kea and kaka, the kakapo belongs to the oldest living lineage of parrots. As such, they could provide clues about how some members of the group evolved their intelligence and their aptitude for vocal learning.

Digby also hopes that the 181 genomes will reveal new ways of protecting the growing but still precarious population. For example, kakapo are notoriously infertile. Just half of their eggs hatch (compared to 80 to 90 percent for most birds), and just a third of their chicks eventually fledge. “We suspect their infertility is genetic but we don’t know for sure,” says Digby. “We can look at the genome of every individual and match that against its breeding history—for females, how many eggs they lay, and for males, their sperm quality.”

The birds also suffer from a disease called cloacitis, which Digby calls “crusty bum.” It’s treatable, but no one knows what causes it, or even if it’s an infection. In some individuals, it goes away; in others, it persists and recurs. Digby wants to know if some kakapo are genetically susceptible to the condition.

He also thinks that the genomes could help him and other conservationists to pair the kakapo most efficiently, to maximize the genetic diversity of the species. For example, early studies showed that a male named Gulliver has versions of immune genes that are completely missing in all other kakapo—even his siblings. “Now, he’s a little more important,” says Digby. “We can’t give all of them the same level of attention, so Gulliver gets a little extra. If we’re trying artificial insemination, we’ll try with his sperm a little harder than his brothers.” The full genomes of every kakapo will probably reveal similar differences.

“If we could get the species to survive and repopulate, we could track the family tree of all individuals of the species from here onward,” says Jarvis. “It would be unprecedented.” And if the recovery efforts fail, and the kakapo does become extinct, having the genomes of all remaining individuals would be useful if future scientists attempt to resurrect the species, as many are trying to do for mammoths and passenger pigeons.

Critically, the kakapo project—both the recovery effort and the specific sequencing project—are led by New Zealanders, and done in consultation with Māori. Peter Dearden, a biochemist from the University of Otago, has lamented the fact that the first kiwi genome was sequenced by a German group that included no New Zealanders at all. “It is a sort of colonialism,” he wrote. “It is not necessary, nor appropriate, for these to be scientifically investigated overseas with no links to their place of origin.”

Digby sympathizes. “I’ve worked really hard to make sure that we do as much of this work in New Zealand as possible,” he says. “It’s especially important to maintain the link between genomics and conservation, and you need some contact with the host country to make sure that’s implemented. People can study the genome, and get citations for their papers, but what does that mean for the species?”

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Article The First Species to Have Every Individual’s Genome Sequenced compiled by www.theatlantic.com