In expansive new research out this week, scientists around the world have started to unravel the genetic secrets behind one of nature’s greatest success stories: mammals. They’ve catalogued and compared the genomes of more than 200 mammal species, including elephants, bats, and humans. Among other things, their findings should help us understand the origins of certain mammalian traits, as well as which species are most at risk of extinction in the future.
Mammals aren’t the longest-lasting group of animals on Earth (that honour might belong to sea sponges), nor are we the most plentiful (by combined biomass alone, insects reign supreme there). But we might be one of the pluckiest.
The first mammal-like animals are thought to have emerged 200 million or so years ago, right as dinosaurs and their relatives became the world’s dominant land-dwelling vertebrates. Contrary to popular belief, early mammals did seem to thrive and diversify during this era. But it was the K–Pg extinction event 66 million years ago — likely the result of a giant asteroid impact — that really skyrocketed mammals to the top. Our surviving ancestors took advantage of the power vacuum left behind and gave rise to a wide variety of creatures that have occupied and often conquered just about every niche across the globe. Of course, humans are one of these many species, but we’re actually pretty late to the party, with the first human-like primates only thought to have arrived a few million years ago.
There’s still so much that we don’t understand about the journey that mammals took to get where we are today. That’s why scientists and research organisations decided to embark on a massive collaborative effort, known as the Zoonomia project. The name is a reference to the term coined by Erasmus Darwin, an 18th century English physician, philosopher, and grandfather to Charles Darwin, who set the foundation for the study of evolution. The project is being led by researchers from the Broad Institute at MIT and Harvard, but it has involved the help of more than 150 people.
“Humans are very good at studying humans. And we know an awful lot about humans,” said Elinor Karlsson, one of the project’s leaders and director of the Vertebrate Genomics Group at Broad, in a press conference about the findings. “But when you get out into a lot of other species, we just know surprisingly little about them and what they can do.”
Zoonomia is being billed as the largest resource of mammalian genomes of its kind in the world, with 240 non-human ones collected overall. Some of these were sourced from existing data, but the researchers newly sequenced the genomes of around 130 species and upgraded the genomic data available for a few others. Included in this list are animals like the African savanna elephant, the ghost-faced bat, the jaguar, the Brazilian guinea pig, the Yangtze River dolphin, and the domestic dog. These animals only cover around 4% of all mammalian species, but they should represent about 80% of mammal families in general; they also include over 50 endangered species.
The Zoonomia team didn’t just collect these genomes but also compared them to one another, in hopes of finding important similarities and differences scattered throughout the mammal tree of life. This week, the group has released the initial wave of papers based on these comparisons — 11 in total, all published in the journal Science.
The studies cover lots of ground. One paper appears to show that roughly 10% of the human genome is highly conserved across many other mammal species, meaning that these regions have barely changed over time. These genes, which seem to mostly affect embryonic development and how RNA is expressed, are likely very key to mammals as a whole. The same team also found genes that appear to partly influence traits commonly found in mammals, such as larger brains and a great sense of smell, as well as traits found in only some mammals, like hibernation.
One study might help researchers pinpoint genetic mutations that could raise people’s risk of diseases like cancer. Another provides more support that mammals were diversifying even before the dinosaurs became extinct. Another looked at the genetics of Balto — the famous sled dog who helped save an Alaskan town from a diptheria outbreak in the 1920s — to find clues on how dogs of his time were able to survive their harsh environment.
One paper in particular suggests that we can use these genomes to predict which mammals are most likely to die out, based on factors like their expected population size thousands of years ago. These genomic assessments should be relatively cheap to conduct and could then help inform conservation efforts.
“Tens of thousands of species are at risk of extinction. Identifying those in most urgent need of conservation is often a long and costly process, and delays can further erode the prospects for survival of species on the brink of extinction,” co-lead author Aryn Wilder, a conservation geneticist at the San Diego Zoo Wildlife Alliance, told Gizmodo in an email. “Our work suggests that a genome sequence, even if from only one individual, can provide information to gauge extinction risk, which is especially useful for the >20,000 species considered to be ‘Data Deficient’ by the International Union for Conservation of Nature (IUCN).”
The initial lessons learned from the Zoonomia project will pay off in many different ways, the researchers say, for both humans and other mammals. And the sheer amount of data collected by the team will undoubtedly be used by scientists for years to come. It’s also likely that others will create similar genome projects that cover other broad groups of animals, aided by newer technologies that can provide more precise genetic data.
There is one major area of disappointment for the team, though.
“There’s one species we’re missing in there that will annoy me to no end, which is just the raccoon,” Karlsson said. “Like for some reason, we couldn’t get a raccoon DNA sample. And it was just like, how was that the one we’re missing?”