The most widely held theory about what happened then is that climate change led to the expansion of grasslands in Africa, which fragmented habitats and spurred many species to evolve.
The new study lends further credibility to the notion that climate change can lead to evolutionary change.
"Ours is one more piece of evidence that definitely supports the idea that climate change is a key event in speciation," lead study author Hofreiter said.
The new research marks a significant departure from previous studies.
Until now, scientists had reconstructed the history of the elephant family primarily using fossil evidence.
Mitochondrial DNA, which is passed on only from mother to child, provides an easy way to trace lineages and is a more accurate source of information. But its use has always been limited, because DNA in ancient fossils begins to breaks down.
Hofreiter and his colleagues, however, developed a way to piece together the genome from small samples of fragmented DNA.
They applied the technique to a mastodon tooth collected in 1999 from Alaska's Ikpikpuk River.
Radiocarbon dating of the collagen in the tooth places its age at at least 50,000 years. But researchers have concluded, based on the dating of other material from the area, that the fossil may be as old as 130,000 years old.
Never before have researchers successfully sequenced a genome from such an ancient piece of bone. Previously, Hofreiter said, the oldest fossil from which scientists were able to extract a complete genome was about 30,000 years old.
In this case, the team cut about 7 ounces (200 grams) from the root of the molar of a mastodon and extracted small fragments of the DNA from bone. By piecing together the overlapping fragments, the team was able to sequence the entire genome.
"It is amazing they were able to extract a complete genome from a bone that old," noted Anna-Sapfo Malaspinas, a researcher at the University of California, Berkeley and one of the authors who helped to analyze the sequencing after the genome was extracted.
Because the animal was encased in permafrost before being exposed to river erosion, the DNA in the mastodon was fairly well preserved, researchers say.
"It is hard, using fossils to come up with accurate dates," Roca, the geneticist, said. "But using DNA makes it easier."
Elephant in the Room
This new research may also put to rest a heated debate about the history of elephants.
"There has been controversy over whether woolly mammoths are more closely related to Asian or African elephants," said Stephen O'Brien, lab chief at the Laboratory of Genomic Diversity.
Both fossil evidence and incomplete mitochondrial genomes had previously indicated that woolly mammoths' closest relatives were African elephants.
Two years ago, however, Hofreiter was also the first to sequence a complete mitochondrial genome from a woolly mammoth. His research contradicted earlier studies because it indicated a tighter kinship to the Asian elephant.
The information extracted from the mastodon, a close relative to both mammoths and elephants, supports Hofreiter's earlier work.
According to O'Brien, studies using incomplete genome sequences from woolly mammoths are likely not as reliable.
"This is the most robust data we have seen to date."
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