Sequencing the nuclear genome of extinct species has always been a challenge for scientists, and so far, only short sequences have been obtained due to the fact that ancient DNA is usually very fragmented and damaged. But in the most recent study of the kind, scientists presented data on several mammoth specimens, however focusing on one in particular, the woolly mammoth, from which they obtained a sequence 100 more extensive than any other previous dataset.

The study, published in the journal Nature this week, is authored by Stephan C. Schuster, professor of biochemistry and molecular biology at Penn. State University, and Webb Miller, from Penn. State University’s Center for Comparative Genomics and Bioinformatics, who lead a team made up of 21 researchers.

“Previous studies on extinct organisms have generated only small amounts of data,” Schuster explained, pointing out that this unprecedented achievement demonstrates that ancient DNA studies can be brought up to the same level as modern genome projects.

The woolly mammoth at the center of this study originated from Africa millions of years ago, but came to populate much of Eurasia and North America until approximately 10,000 years ago. The ice age periods that characterized the northern hemisphere hundreds of thousands of years ago triggered specific changes in these mammoths, such as the shape and size of their bodies, the thick coat, the enormous tusks or the 2-inch layer of insulating fat tissue.

With the help of next-generation DNA-sequencing instruments and a novel approach that reads ancient DNA very efficiently, the Penn. State University scientists assembled data from hair shafts collected from permafrost remains, which according to them, permitted a highly efficient decontamination protocol, leaving the keratin-encased endogenous DNA unharmed.

In this research, the nuclear genome was extracted from hair samples belonging to a mammoth mummy which had been buried in the Siberian permafrost for 20,000 years, and the hair samples of a second mammoth, believed to be at least 60,000 years old. The scientists explained that the hair shaft protects the remnant DNA from degradation and exposure to elements, increasing the chances to extract unharmed DNA.

Out of the 4 billion DNA bases scientists suspect comprise the full woolly mammoth genome, only 3.3 billion DNA bases have been assigned to the mammoth genome, scientists explained. The rest of them could also belong to the mammoth, but the chances are that they belong to other organisms, such as bacteria and fungi, that have contaminated the samples.

The team of researchers used the draft of an African elephant’s genome, which is one of the mammoth’s living relatives, to make a distinction between the sequences that belong to the mammoth and those that belong to other organisms. “Only after the genome of the African elephant has been completed will we be able to make a final assessment about how much of the woolly mammoth’s genome we have sequenced,” Miller explained.

By combining the new-yielded data on the mammoth’s nuclear genome, which comprises the genetic factors responsible for the appearance of an organism, with previously obtained mitochondrial genome, which codes for only 13 of the 20,000 genes of the mammoth, the scientists concluded that the woolly mammoth separated into two groups 2 million years ago, groups that eventually turned into sub-populations. One of these populations became extinct 45,000 years ago, but the other one lived until after the last ice age, 10,000 years ago.

The analysis also revealed stronger connections between modern-day elephants and woolly mammoths than previously believed. As Miller explained, mammoths and modern-day elephants separated 6 million years ago, around the same time humans and chimpanzees separated, but their subsequent evolution occurred at a slower pace.

The next phase of the woolly mammoth project is to try to establish the causes of its extinction. So far, scientists have excluded the human presence as a possible cause, since there were no humans living in Siberia 45,000 years ago. The fact that woolly mammoths were so genetically similar to each other suggests they were susceptible to being wiped by a disease or a change in climate.

While trying to figure out how woolly mammoths went extinct, scientists also explained that deciphering the genome could create the premises to one day bring extinct species back to life.

In this respect, earlier this month, a team of Japanese scientists reported a major breakthrough in cloning, which suggested resurrecting extinct species is not exactly impossible. According to their report, they’ve managed to successfully grow healthy clones from mice frozen 16 years ago in -20C conditions. The experts explained that by using brain nuclei as donors, scientists could one day resurrect animals that have been frozen for long periods of time without cryopreservation.