Debi Poinar, McMaster University
	Paleontologists Alexei Tikhonov, Hendrik N. Poinar, Ross D.E. MacPhee and Clair Flemming in a Siberian ice cave. Dr. Poinar obtained a sample of woolly mammoth DNA from among hundreds of specimens stored there and collaborated with Penn State scientists to partially decode the creature's genome.
	Penn State University
	An analysis of mitochondrial DNA shows that the extinct woolly mammoth is much closer genetically to modern Asian elephants than it is to African elephants.

In Michael Crichton's 1991 novel "Jurassic Park," DNA extracted from ancient blood-sucking insects preserved in amber provided genetic material necessary to recreate Tyrannosaurus rex and its dinosaur buddies.

But in reality, if you're looking for high-quality ancient DNA, nothing beats permafrost, says Stephan C. Schuster, a genomicist at Penn State University.

A week ago, an international team including Dr. Schuster and Penn State colleague Webb Miller, announced they had recovered DNA from a woolly mammoth that had been preserved in the permafrost of northern Siberia for 27,000 years and used a new gene sequencing technology to unravel a portion of its genetic code.

"I'm convinced we'll be able to sequence the entire genome," said Hendrik N. Poinar, a molecular evolutionary geneticist at McMaster University in Hamilton, Canada, and lead author of last week's report in the journal Science.

That will enable researchers to compare and contrast the extinct behemoth's genome, which is almost as large as a human's, with that of the African elephant. And that will allow scientists to get a better idea of what evolutionary changes occurred that caused woolly mammoths and African elephants to diverge 5 million to 6 million years ago, Dr. Poinar said, as well as to better understand why the elephant survived while the mammoth went extinct.

But the study also served as a proof-of-principle exercise to show that a new gene sequencing technology, developed by Carnegie Mellon University graduate Jonathan M. Rothberg of 454 Life Sciences Inc. of Branford, Conn., will make it possible to study all sorts of ancient DNA.

"Any kind of organism that was conserved in frozen ice or permafrost might now be available for genetic analysis," said Dr. Schuster, an associate professor at Penn State's Center for Comparative Genomics and Bioinformatics.

The list includes the woolly rhinoceros, North American lion, extinct species of horses and bison, as well as "a whole slew of smaller animals," Dr. Poinar said. The sequencing of DNA of Neanderthals, a relative of modern humans, might also be possible, though Neanderthal DNA may be less well-preserved, he added.

Dr. Poinar said he knew that new rapid-sequencing technology could make it possible to study the genomes of extinct animals, so he had searched for a well-preserved sample. He found it in a museum in Siberia that stores the remains of about 350 mammoths in a large ice cave, recovering the DNA from the jawbone of a creature recovered from the shore of Lake Taimyr.

At the same time, Penn State had obtained the new 454 sequencer and was looking for a high quality specimen to study. Dr. Poinar said he was acquainted with Dr. Schuster "and it didn't take too long to twist his arm" to reach an agreement to collaborate. The large, international research team also included an authority on woolly mammoths, Ross D.E. MacPhee of the American Museum of Natural History.

Unlike Mr. Crichton's fictional scientists, these researchers have no expectation of actually re-creating the animal, Mammuthus primigenius.

Theoretically, it would be possible to identify all of the differences between the elephant and mammoth genomes and then incorporate those changes in the elephant genome.

"This would require hundreds of thousands of changes," Dr. Schuster said, noting that the technology to accomplish those changes is not available and that the entire enterprise would be extremely expensive. "It would give you an organism that looks like a mammoth," he added, but could only be considered a hybrid, not a true mammoth.

Getting a clean sample
Also last week, researchers in West Germany reported in the journal Nature that they had analyzed mitochondrial DNA from a woolly mammoth and compared it with DNA from African and Asian elephants. They concluded that the mammoth was a much closer relative to the Asian elephant than to the African elephant.

But mitochondrial DNA is much easier to study than DNA from the chromosomes found in a cell's nucleus. A cell contains a thousand more copies of mitochondrial DNA than of the chromosomal DNA, so it's easier to pick out of ancient organisms, Dr. Schuster said.

In fact, one of the major issues involved in analyzing ancient genomes is separating the chromosomal DNA from other contaminants in a sample, such as mitochrondrial DNA and the DNA of bacteria and fungi that would be found in the animal.

Soon after an animal dies, Dr. Schuster explained, the long strands of DNA naturally start breaking apart and, as cell membranes fail, all of these little bits are mixed in with the DNA of other organisms that existed in the animal or later fed off of it.

In Dr. Poinar's study, the researchers found that about half of the DNA they recovered actually came from the mammoth. Many bacterial and other genomes already have been sequenced and, using high-performance computing, the researchers were able to use those genomes to identify bits that didn't belong to the mammoth.

The sequencing is possible because of the technology developed by 454 Life Sciences, Dr. Schuster said. Not only is the machine fast and relatively inexpensive, but the manner in which samples are prepared for analysis is suited for ancient DNA.

Conventional gene sequencing, such as was used by the international Human Genome Project, requires that DNA be divided up and multiplied by inserting the pieces into bacteria. The problem is, Dr. Schuster said, that bacteria only reproduce pieces of DNA that it likes. Some segments of the human genome, for instance, are still unsequenced because bacteria can't reproduce them.

But the 454 sequencing technique dispenses with bacteria. DNA is broken up -- ancient DNA already is highly fragmented -- and each segment is attached to a tiny bead. In a process called emulsion polymerase chain reaction, these beads are isolated from each other and many copies are then made of the attached DNA.

This is important, Dr. Schuster said, because it ensures that all of the DNA gets amplified -- and amplified at the same rate -- making subsequent analysis easier.

The technique was devised in the hope that someday people's genomes could be routinely sequenced to guide medical care. Researchers at Allegheny General Hospital, which also obtained one of the first sequencers, use their device to study various strains of bacteria responsible for ear infections and respiratory disease.

454 Life Sciences, and other groups, have set a goal of sequencing a human genome for $1,000. As early as next year, Dr. Rothberg said, a cost of $100,000 might be possible.

As medical research costs come down, scientists looking at ancient DNA also will benefit, Dr. Schuster said. For now, the researchers are looking for a sponsor to help them complete the sequencing of the woolly mammoth genome, a task that might cost several million dollars.