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Million-Year-Old Mammoths Sequenced, Giving Insight into Evolution

NEW YORK – Researchers have sequenced three ancient mammoths, including two samples more than 1 million years old, to gain insight into their evolution. According to the researchers, these are the oldest DNA samples to date to be sequenced.

Mammoths arose in Africa about 5 million years ago and colonized much of the Northern Hemisphere. During the Pleistocene, they gave rise to southern mammoths and steppe mammoths as well as, later, to Columbian mammoths and woolly mammoths. By examining genomic data from three mammoth molars from the Early and Middle Pleistocene uncovered in Siberia, an international team of researchers led by Stockholm University's Love Dalén aimed to examine the origins of the Columbian and woolly mammoths. 

As they reported in Nature on Wednesday, they sequenced and pieced together reads from the samples to find that one, dubbed Krestovka based on where the sample was found, belonged to a previously unknown mammoth lineage. This previously unknown lineage further hybridized with the woolly mammoth line to give rise to the Columbian mammoths that lived in North America during the last Ice Age.

"Our expectation was that the two oldest specimens would be from the steppe mammoths, a species that was the direct ancestor of the woolly mammoth," Dalén said during a press briefing. "This ancestral relationship is indeed what we found for one of the million-year-old specimens. However, to our surprise, we found that the other specimen … belonged to a previously unknown genetic lineage of mammoth."

Dalén and his colleagues extracted DNA from three mammoth molars for sequencing. The ancient DNA samples, they noted, were fragmented with high levels of cytosine deamination. They mapped the reads against the African savannah elephant genome and the Asian elephant mitochondrial genome. After applying conservative filters, they had more than 37x coverage of the mitochondrial genomes of all three mammoths and 49 million base pairs of nuclear genomic data from the Krestovka sample as well as 884 million base pairs and 3,671 million base pairs from the other two samples, called Adycha and Chukochya, respectively.

Both geological and molecular data supported the samples' ancient age, with the genetic analysis suggesting the Krestovka samples could be up to 1.6 million years old. The Adycha and Chukochya samples, meanwhile, were estimated to be 1.3 million and 870,000 years old, respectively, by molecular clock analysis.

A phylogenetic analysis placed these three new mammoth samples away from the Late Pleistocene mammoth samples, and highlighted a deep split between the Krestovka mammoth and all other mammoths. The Krestovka mammoth, they found, diverged from other Siberian mammoths about 2 million years ago. This indicated to the researchers that two mammoth lineages lived in Siberia in the later part of the Early Pleistocene, one represented by the Krestovka sample and the other by the Adycha sample and all woolly mammoths.

The mammoth lineage represented by Krestovka is also ancestral to the Columbian mammoth, which lived in North America during the last Ice Age. Through an admixture analysis, the researchers found that the Columbian mammoth is nearly a half-and-half mix of the Krestovka mammoth lineage and the woolly mammoth lineage.

The researchers noted that the Adycha sample appears to belong to a lineage that is ancestral to all woolly mammoths and could give them a glimpse into when woolly mammoths evolved molecular adaptations to the cold, such as changes to thermal regulation and circadian rhythm.

By comparing the Adycha genome to those of woolly mammoths that lived about 700,000 years ago, the researchers found that the gene variants among the woolly mammoths linked to Arctic life were already present in the mammoth lineage 1 million years ago. 

"We don't think there was one very short, rapid burst of adaptations that then led to the evolution of the woolly mammoth," first author Tom van der Valk said during the briefing. "We rather think that this has been more of a gradual process. So over time, the steppe mammoth accumulated adaptations to a colder Arctic environment, and those adaptations have gradually increased up to up late Pleistocene mammoths."

Van der Valk added that 1 million years ago was a time of climatic change and the emergence of new species on Earth, and that while these mammoths are the oldest samples so far to undergo DNA sequencing, their findings suggest that the limit of scientists' ability to sequence ancient DNA has yet to be reached. Other samples from about that age or even slightly older could also be analyzed — particularly if found in permafrost — and provide further insight into the evolution of numerous species, Dalén noted.