Oldest DNA Sequenced Yet Comes From Million-Year-Old Mammoths

Genetic material from three ancient molars reveals secrets of about how the Ice Age elephants evolved

Steppe Mammoths
Steppe mammoths evolved shaggy coats over a million years ago, a trait inherited by woolly mammoths. Beth Zaiken / Centre for Palaeogenetics

Woolly mammoths were icons of the Ice Age. Starting 700,000 years ago to just 4,000 years ago, they trundled across the chilly steppe of Eurasia and North America. As ancient glaciers expanded across the Northern Hemisphere, these beasts survived the rapidly cooling temperatures with cold-resistant traits, a characteristic they came by not through evolution, as earlier thought. Woolly mammoths, a new Nature study finds, inherited the traits that made them so successful from a mammoth species closer to a million years old.

The clues come from some incredibly old DNA extracted from a trio of molars uncovered in northeastern Siberia. The oldest is nicknamed the Krestovka mammoth, dated to about 1.2 million years ago. The other two molars are nicknamed the Adycha and Chukochya mammoths, dated to 1 million and 500,000 to 800,000 years old, respectively. The fact that the researchers were able to extract and analyze the DNA from these fossils at all is a landmark. Up until now, the oldest look at ancient genes came from an Ice Age horse that lived over 560,000 years ago. The new mammoth samples double that, taking the title for the oldest DNA yet recovered from fossil remains. “We had to deal with DNA that was significantly more degraded compared to the horse,” says Swedish Museum of Natural History paleogeneticist Love Dalén, an author of the new study.

Understanding such ancient genetic material is a challenge because DNA begins to decay at death. Ancient DNA samples can sometimes become contaminated by modern sources. While preserved snippets of the ancient horse’s DNA were about 78 base pairs long, the fragments of mammoth DNA were about 42-49 base pairs long. Dalén says it can be sometimes difficult to tell which short snippets are from the mammoth and which should be disregarded as modern contamination from bacteria or people. The researchers compared the DNA results of the three teeth to elephants and humans, and discarded any data that seemed like it could have come from humans.

The emerging picture painted by the ancient DNA is different from what researchers expected. “It is indeed a fascinating paper,” says American Museum of Natural History paleontologist Ross MacPhee, who was not involved with the new study, both for setting a new landmark for ancient DNA but also for finding evidence that at least one mammoth species originated as a hybrid.

The story began over a million years ago in Eurasia, when a large species that preceded the woolly mammoth, called the steppe mammoth, Mammuthus trogontherii, lived. These mammoths aren’t as well-known as the woolies and most of what’s been uncovered about them comes from bones alone rather than carcasses with tatters of soft tissue. No one knew whether these beasts were adapted to the cold or not, with the supposition being that the steppe mammoths thrived during warmer interglacial periods and woolly mammoths evolved from the steppe mammoths when the ice expanded its hold on the planet.

Yet the researchers found that the older, million-year-old mammoths had genes for shaggy coats and some other physiological adaptations for life in cold habitats, meaning that the woolies inherited many of their characteristic features. The molar referred to as the Adycha mammoth, at about a million years old and resembling that of a steppe mammoth, contains the genetic markers for these traits even though the mammoth lived hundreds of thousands of years before woolies. What this finding hints, Dalén says, is that many of the critical traits that allowed mammoths to populate cold regions happened much earlier–perhaps during the evolution of the steppe mammoth from its hypothesized ancestor around 1.7 million years ago.

In their genetic analysis, Dalén and colleagues also examined how the three ancient mammoths related to other known specimens and species. The Krestovka mammoth, at about 1.2 million years old, came out as a unique lineage of mammoth that didn’t fit into any previously known species. And this newly discovered mammoth lineage had an important role to play. The researchers hypothesize that Mammuthus columbi–a huge species the roamed North America from 10,500 to 1.5 million years ago–originated as a hybrid between the ancestors of the woolly mammoth and the genetic lineage of the Krestovka mammoth. “That certainly came as a complete surprise to us,” Dalén says.

Oldest DNA Sequenced Yet Comes From Million-Year-Old Mammoths
The molar of the Chukochya mammoth was dated to over 500,000 years old, one of the three samples used in the new study. Love Dalén

That Mammuthus columbi originated as a new species, born of a hybridization event, “has major implications for our understanding of the population structure of Pleistocene megabeasts,” MacPhee says. The ancestors of the woolly mammoth and the Krestova mammoth had diverged from each other for about a million years before a population produced a hybrid that was different from both, giving rise to Mammuthus columbi. More than that, MacPhee notes, “it suggests that mammoths in the Old and New Worlds acted as a hugely distributed metapopulation,” with populations able to interbreed with each other despite looking different from each other.

The study is hardly the final word on the mammoth family tree, of course. Paleogeneticists and paleontologists are just beginning to understand how all these mammoths are related. In North America, for example, some fossils were labeled by 20th century paleontologist Henry Fairfield Osborn as Jefferson’s mammoth and sometimes these fossils are categorized as a unique species. The suspicion among experts is that these mammoths are hybrids between woolly mammoths and Mammuthus columbi, an idea that can be tested against the genetic evidence. North American mammoths dated to about 126,000 to 770,000 years ago, Dalén says, might hold additional genetic clues about how mammoth species hybridized with each other to give rise to new forms of mammoth through time.

Ancient genes are revealing that the Ice Age world was very different from our own. Megafauna thrived through the world’s continents, and those animals may have had genetic connections to each other that extinction has obscured. “We don’t think of megabeast species being able to maintain multicontinental ranges these days, but that must at least be partly due to the fact that humans have disrupted their ranges, population structure and mating opportunities for millennia,” MacPhee says.