Unveiling the genome of the ancient dingo — whose DNA is in every dog in the world

Credit: Karen Black
Credit: Karen Black
“Maybe a dingo ate your baby!” suggested Elaine Benis (Julia Louis Dreyfus) in an episode of Seinfeld in season 3, bumped from season 2 because Larry David thought it not very good. But the phrase stuck.

Elaine’s literary quote harkens back to a 1998 Meryl Streep film, A Cry in the Dark. Streep played Lindy Chamberlain-Creighton, who utters some version of “the dingo’s got my baby!” after her nine-week-old daughter Azaria was taken from the tent that she and her then-husband Michael Chamberlain were sharing while camping in the Northern Territory, Australia.

The film was based on a true story, a tragedy that happened on August 17, 1980. Lindy was convicted of murder and given life in prison while Michael was considered an accessory after the fact and given an 18-month suspended sentence. But legal challenges eventually exonerated both parents. A coroner eventually attributed the baby’s disappearance to “the result of being attacked and taken by a dingo.” So, it happens.

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Dog diversity

Domesticated dogs come in more varieties than do cats. The Cat Fanciers’ Association recognizes 42 breeds, whereas the American Kennel Club claims 190 dog breeds and the World Canine Organization, 340.

Dog breeds make little genetic sense, as if people have been selecting traits that please us – bulging eyeballs, flat faces, drooping bellies – with little regard for the health and fitness of the animals. And now we have all those doodle combinations, not to mention the companies that test canine DNA to reconstruct matings.

Many studies, on tens of thousands of dogs, have identified the ills that plague the high-priced purebred canines. They include dermatitis, early-onset cataracts, blocked aorta, digestive conditions, weird elbows, underactive thyroid, heart and liver disease, and mushy vertebral disks. The basset hound is prone to degenerated joints, twisted stomach, glaucoma, malformed elbows and hips, poor clotting, infections of the loooong ears, and flipped up eyelids.

What would happen if dogs weren’t subjected to selective breeding, what Darwin called artificial selection to refer to his prized pigeons? First you’d get a mutt, which may be one of those banned terms we can’t use anymore. Over millennia, as silly humans restricted gene pools to fashion chihuahuas and St. Bernards and everything in between, the result of leaving the canine genome alone would have been – a dingo.

And that’s why I was excited to learn that a multinational team led by Matt Field from James Cook University in Cairns, Australia, has sequenced a high-quality (few gaps) genome sequence from a 3-year-old named Sandy. She was found as a 4-week-old puppy in a remote region of South Australia in 2014, and genetic testing showed that she was pure dingo – a rarity.

Sandy the dingo.

The researchers compared Sandy’s genome to those of five purebreds (boxer, German shepherd, basenji, Great Dane, and Labrador retriever) and the Greenland wolf, chosen because it hasn’t interbred much with dogs and coyotes.

Their report, “The Australian dingo is an early offshoot of modern breed dogs,” appears in Science. One impetus for the study, the researchers write, was to counter politicians’ questioning the value of conservation efforts of dingoes. Knowing genome sequences could more precisely define the animals and their roles in ecosystems. The Australian Dingo Foundation, near Melbourne, is a dingo preserve that is conserving the gene pool of the original animal.

Preserving wild dogs

Dingoes are modern-day wild dogs. They’re everywhere in Australia, except Tasmania.

Because dingoes interbreed so readily with anything dog-like, it isn’t known whether truly purebred animals exist anymore. In addition to mating with familiar breeds, it’s thought that a dingo crossed to a merle dog from England led to the Australian cattle dog, and that the New Guinea singing dog is a sister subspecies to the dingo. Indeed, I found it odd to see dingoes lumbering around an enclosure in the Melbourne Zoo, as if they were exotic specimens when they look like German shepherds.

A dingo, technically called Canis familiaris dingo, comes in three hues: white, black, and tan. But any mix results in the characteristic sandy ginger color.

Sandy as a puppy.

They were introduced to Australia 5000 to 8500 years ago, possibly even from older domesticated dogs. The first familiar domestic dog breeds were brought to Australia in 1788.

In Australia dingoes have diversified in response to long times spent isolated in specific habitats. Rare mountain dwellers have light coats, whereas their cousins in the desert are redder, and smaller. Whatever their color, dingoes are enemies to farmers, who erect fences and mobilize donkeys to keep the wild canines from eating livestock.

A dingo’s bark comes in short, sharp sounds. Unlike modern dogs that will yap at anything and at anytime, a dingo is more reticent to vocalize, which may have led to the widespread idea that they can’t bark. They can.

I’m not a big fan of dingoes.

Two years ago, a new family moved to a house with a yard that abuts mine. I’d walked on the trail between our properties often, for many years. But one day, two crazed canines, beige with odd faded spots, came tearing across the grass at me, jumping and hollering and baring their teeth. I was petrified. When their owner came out, I flashed back to the Melbourne Zoo and yelled “dingoes!”

My neighboring confirmed that the beasts are half dingo, half Australian shepherd, hence the faded spots. I found a new walking route as they continue to terrorize any human who passes.

What we know about dingo genes

Past studies compared dingo genes to the boxer “reference” genome – which left a lot out because an older genome, the dingo’s, would be more diverse. Comparing short stretches of DNA from a dingo, a golden jackal, three gray wolves, a basenji, and the boxer placed the dingo closest to the domestic dog breeds. Yet another study surveyed SNPs – single sites in the genome that vary among individuals – and found the dingo closest to the Greenland sled dog and the Chinese chow chow.

Another investigation considered molecules in blood plasma as markers of aggression. This study placed dingoes between captive wolves and basenji dogs.

Not surprisingly, the new genome sequencing revealed that the dingo diverged from purebred dog lineages thousands of years ago, and substantially. The genome most closely echoes that of a German shepherd, not a boxer, which it turns out is the farthest-related modern dog with a sequenced genome. And dingoes are closer to wolves than to dogs, which I can attest is true from my neighbors.

One factor that separates the dogs from the dingoes is the wilder animals diet of marsupials and reptiles, in contrast to cereal-based commercial dog chow and table scraps. The differing diets explain why dingoes have only one copy of the salivary amylase gene, which encodes the enzyme that digests starch, but domesticated dog breeds have several copies.

Because of the dietary differences, over time, the microbiomes of domesticated dogs and dingoes  diverged greatly. Comparison of scat samples from German shepherds and dingoes supports this idea. The microbiomes of domestic dogs have greater representation of a trio of bacterial families that break down starchy foods than do residents of the dingo gut.

The researchers expected the dingo genome sequence to confirm what’s already known, and it did:

Our inclusive study reinforces the view that the dingo genome is structurally and evolutionarily distinct from domestic breed dogs, which may translate into functional differences in the ecosystem.

Dingoes eat whatever is walking around, giving them a high-protein, low-fat and low-carb diet. Modern dogs, the newcomers, ate the fat-and-carb-packed diets of the Neolithic period as agriculture bloomed, and continue to do so. And we can thank, or blame, artificial selection for the quirks and oddities of modern dog breeds that we deem attractive and petworthy.

Ricki Lewis, PH.D is a writer for PLOS and author of the book “The Forever Fix: Gene Therapy and the Boy Who Saved It.” Check out Ricki’s website and follow Ricki on Twitter @rickilewis

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