Zoonomia: A genome project cracks mysteries of evolution — and Balto the superdog

Now, nearly a century later, Balto's genetic blueprint is entering the annals of science, thanks to a massive new project that seeks to rewrite our understanding of mammalian evolution, unlocking knowledge that may help treat human disease and stave off species extinction.

The research, published Thursday in 11 papers in the journal Science, also yields valuable insight into the profound question of what makes us unique among species.

This is really an unprecedented view of the evolutionary history of mammalian genomes. We now know which parts of the genome are important in building a mammal.

- Maria Chikina, an assistant professor at the University of Pittsburgh School of Medicine

The work is the result of an international collaboration of more than 100 scientists called the Zoonomia Project that has been building and analyzing a veritable Noah's ark of genomes - 240 mammals in all.

Scouring the genetic blueprints of so many mammals, "we can better understand human genetics," said Carolyn M. Hutter, a division director at the National Human Genome Research Institute. "What does our DNA tell us? How does our DNA function? Where are we similar, and what are the things that make us different?"

By pinpointing parts of the mammalian genome - sometimes just single letters of DNA - that have remained the same through tens of millions of years of evolution, scientists may be able to identify the most crucial parts of our shared genetic makeup, those where change can spell disaster.

"This is really an unprecedented view of the evolutionary history of mammalian genomes," said Maria Chikina, an assistant professor of computational and systems biology at the University of Pittsburgh School of Medicine who was not involved in the research. "We now know which parts of the genome are important in building a mammal."

Earlier scientific studies

Scientists first sequenced the human genome two decades ago in one of this century's biggest scientific breakthroughs. Yet they remain stumped about what much of that DNA does in our bodies. Some parts of the genome randomly mutate across generations with no discernible effect. Other regions stay the same, probably because they encode for a vital protein or something else necessary for life.

To better understand ourselves, geneticists have looked to other mammals. In 2011, the Broad Institute of MIT and Harvard unraveled 29 mammal genomes to help find the most crucial parts of our shared DNA.

"We can actually pinpoint exactly which positions have a function and which don't," said Kerstin Lindblad-Toh, a scientific director at the Broad Institute and one of the Zoonomia consortium's leads.

But Lindblad-Toh and others soon realised they didn't have enough mammals to do a thorough analysis. That's when they began collecting genomes from species ranging from the mighty gray whale to the minuscule bumblebee bat.

Out of all the mammals on their roster, the screaming hairy armadillo has the largest genome, with 5.3 billion chemical base pairs making up its genetic blueprint. The smallest belongs to the common bent-wing bat, at just under 2 billion base pairs. Humans, for comparison, have just over 3 billion base pairs.

With the genomes gathered, the Zoonomia scientists began probing some of biology's toughest questions.

For instance, paleontologists and molecular biologists "used to fight like hell" over when the age of mammals started, said Nicole Foley, a scientist at Texas A&M and lead author of one of the Zoonomia papers. For a while, fossil collections seemed to suggest mammals split into different species after an asteroid wiped out most dinosaurs 66 million years ago. But measuring how different DNA samples of living mammals are from one another can tell geneticists how long ago populations split apart, with earlier work showing the group began to diversify well before that cosmic collision.

Now, a comprehensive analysis using Zoonomia data shows two events - the breakup of the continents more than 100 million years ago and the dinosaur-killing asteroid afterward - each sparked a round of mammal diversification.

"One of the things that's always bugged me as someone that works on mammals is that you can walk up to anybody on the street and you can ask them what happened to the dinosaurs," said Foley, who led a mammal evolution paper. "They know exactly when the dinosaurs went extinct."

"For the longest time," she said, "we haven't known this basic stuff about mammals."

The vast trove of DNA data may also predict extinctions to come, helping policymakers decide where to dedicate limited conservation money.

Even a single organism's genome contains traces of its species' past population size. That information can be used to assess which animals are at risk today, said San Diego Zoo Wildlife Alliance researcher Aryn Wilder. In one paper, her team trained computer programs on three mammalian genomes, and the results show orcas are more worthy of further study to assess threats to them than the Upper Galilee Mountains blind mole-rat or the Java mouse-deer.

The tool does not negate the need for on-the-ground animal surveys, Wilder said. But field work can be costly, and "genomic information can give us an initial assessment of which ones should be prioritized for those really in-depth assessments."

What makes humans distinct from other species

Zoonomia researchers also discovered that sometimes what's left out of the genome turns out to be just as revealing as what's in it.

One research team studied more than 10,000 short sections of genetic code that are found in all other mammals but not in humans a step toward understanding what makes us distinct from other species.

"Many of the [key] differences are in genes that we know are important in building brains," said Steven Reilly, one of the authors of the study and an assistant professor of genetics at Yale University. Many of these small changes help separate the human brain from that of our closest genetic match, the chimpanzee.

"It's little tinkering with these same underlying building blocks" that makes the difference, Reilly said. "I think that's very cool, but a little bit humbling. You'd think we would have a bunch of shiny new parts."

Some key deletions take place near genes that have been linked to distinctly human diseases, such as schizophrenia and bipolar disorder, Reilly said.

The team's work paves the way for scientists to better understand the impact of deletions by reproducing them in the brains of mice, or in artificial human or chimpanzee brains called organoids.

Massive as the Zoonomia project was, mapping the genomes of 240 species only scratches the surface of the mammalian tree. The one elephant, 43 primates, 53 rodents and more than 100 other creatures sampled represent less than 1 per cent of all living mammals.

"There's one species we're missing in there that will annoy me to no end, which is just the raccoon. For some reason, we couldn't get a raccoon DNA sample," said Elinor Karlsson, a director at the Broad Institute who also co-led the Zoonomia group. "How is that the one we're missing?"

Balto's genetic blueprint

While most of the individuals in the Zoonomia studies are anonymous, Balto was chosen in part because of his fame and the fact that his genetic blueprint could be compared with his taxidermied remains, which have been kept for 90 years at the Cleveland Museum of Natural History.

"People already know him, and we're able now to connect him to his genome," said Katherine L. Moon, one of the authors of the Balto paper and a postdoctoral researcher at the University of California at Santa Cruz.

Balto's genetic blueprint is especially interesting because he lived before widespread, human-imposed breeding practices that have set strict physical standards for canines on the show circuit.

Sled dogs were bred not to achieve a specific appearance but to be fast and strong. Scientists discovered that Balto was genetically diverse, with few traces of the kind of inbreeding found in today's pedigreed dogs. Inbreeding can allow rare mutations, including some that cause health problems, to take root in specific breeds.

Balto's DNA reflected his status as an intermediate canine, neither fully domesticated like today's pets, nor wild like coyotes and wolves. Domesticated dogs are genetically suited to digest the starch found in many commercial pet foods. Wild dogs are meat eaters with far less ability to digest starch. Balto's starch-digesting ability fell in between the two groups.

The new paper helps separate sled dog myth from reality.

Born in Nome in 1919, Balto was considered by his owner, Leonhard Seppala, to be a second-string sled dog. Rather than using him for breeding, Seppala had Balto neutered.

However, history records that it was Balto who led the sled on the day it arrived in Nome. More than 150 dogs had helped make the journey from Nenana, but after musher Gunnar Kaasen delivered the diphtheria medicine, he is said to have hugged Balto and declared, "Damn fine dog."

Balto and some of his teammates toured the United States for two years, only to end up on display in a dime museum in Los Angeles. A businessman from Cleveland saw the dogs and agreed to buy them, provided that he could raise the $1,500 purchase price (equivalent to roughly $30,000 today). Factory workers, schoolchildren and others helped raise the money to bring the dogs to Cleveland.

Now, decades later, the sequencing of Balto's genome has laid to rest an old rumor that he was actually a wolf.

"He was not a wolf," Moon said. "He was just a good boy."