The million-year-old genome is here. Mammoth teeth preserved in eastern Siberian permafrost have produced the oldest ancient DNA on record, pushing the technology close to – but perhaps not past – its limits. Genomic DNA extracted from a trio of tooth specimens excavated in the 1970s has identified a new kind of mammoth that gave rise to a later North American species.
Researchers had suspected that ancient DNA could survive beyond one million years, if the right sample could be found. Once an organism dies, its chromosomes shatter into pieces that get shorter over time. Eventually, the DNA strands become so small that — even if they can be extracted — they lose their information content.
Two of the three mammoth molars from Sher’s excavations, retrieved from sediments more than than one million years old, contained so little DNA that Dalén says he would have discarded them had they been younger.
But thanks to advances in sequencing technology and bioinformatics, his team managed to obtain 49 million base pairs of nuclear DNA from the oldest sample, found near a village called Krestovka, and 884 million base pairs from another tooth, called Adycha. Analysis of the DNA suggested that the Krestovka sample was 1.65 million years old, and the Adycha sample around 1.3 million (see ‘Ancient genomes’). The third sample, a 600,000-year-old woolly mammoth tooth dubbed Chukochya, produced nearly 3.7 billion base pairs of DNA, more than the length of its 3.1-billion-base-pair genome.
From their shape, the two oldest teeth looked like they belonged to steppe mammoths, a European species that researchers think pre-dated woolly mammoths and Columbian mammoths (Mammuthus columbi), a North American species. But their genomes painted a more complicated picture. The Adycha specimen was part of the lineage that gave rise to woolly mammoths, but the Krestovka specimen clearly was not.
Dalén’s team found that it belonged to an entirely new lineage. “We can’t say it’s a different species, but it sure looks like it,” he says. Although the Krestovka sample is from Russia, he suspects the lineage became isolated from other steppe mammoths in North America. The team found that Columbian mammoths trace half their ancestry to the Krestovka mammoth lineage, and the other half to woolly mammoths. Dalén estimates that the two lineages mixed more than 420,000 years ago.