Saturday, 29 September 2007

DNA Extracted From Woolly Mammoth Hair

Source: Penn State University
Date: September 27, 2007

Science Daily — Stephan C. Schuster and Webb Miller of Penn State, working with Thomas Gilbert from Copenhagen and a large international consortium, discovered that hair shafts provide an ideal source of ancient DNA -- a better source than bones and muscle for studying the genome sequences of extinct animals. Their research achievement, described in a paper to be published in the journal Science on Sept. 28, includes the sequencing of entire mitochondrial genomes from 10 individual woolly mammoths.

Schuster and Miller, working at Penn State's Center for Comparative Genomics and Bioinformatics, and Gilbert, from the Center for Ancient Genetics at the University of Copenhagen, led a team of collaborators that includes a large group of researchers and museum curators from the United States, Russia, Belgium, Denmark, France, Italy, Sweden and the United Kingdom.

The research team obtained hair from 10 woolly mammoths collected from a wide swathe of northern Siberia and with dates of death spanning approximately 38,000 years -- from 50,000 years to 12,000 years ago. Before this study, only seven mitochondrial genomes from extinct animals had been published: four from ancient birds, two from mammoths and one from a mastodon.

"DNA in bones and muscle usually degrades and becomes contaminated with genetic material from other sources such as bacteria, limiting its usefulness in scientific studies," Schuster explained. Because only a tiny proportion of ancient bones and muscle are preserved in such a way that uncontaminated DNA can be recovered, research with such materials has involved laborious efforts, sometimes spanning as long as six years for a single study. In contrast, Miller said, "Once I get the data from the genome sequencer, it takes only five minutes to assemble the entire mitochondrial genome."

The discovery to be published in Science demonstrates that hair clippings can give researchers enormous power and efficiency for divining the genetic makeup of ancient species.

The methods the team members developed for efficiently generating and analyzing large amounts of ancient mitochondrial-genome sequences now position them to generate such data for other extinct species, as well as to sequence the huge nuclear genome of an extinct species. "The data already generated from this study set the stage for the sequencing of a complete mammoth genome," said Schuster.

"We realized that the keratin in hair could protect the DNA it contains from outside influences and hence from the sorts of degradation that affect DNA in other parts of the body, such as bone," Gilbert said. Hair also can more easily be cleaned of environmental contaminants, such as bacteria. The researchers discovered that, even if the hair is washed in a solution that kills and washes off external DNA, the genetic material within the hair is unaffected.

"When people thought of sequencing DNA from hair, the usual assumption was that the material must come from the hair root, which contains recognizable cells, because the hair shaft appears to be dead," Miller explained; "however, we now know that a hair shaft consists essentially of DNA encased in a kind of biological plastic." Protected in this way, the DNA resists damage and readily can be separated from any bacteria that may contaminate the sample. "We discovered, moreover, that the DNA in hair shafts is remarkably enriched for mitochondrial DNA, the special type of DNA frequently used to measure the genetic diversity of a population," Gilbert added.

Several of the hair samples investigated were up to 50,000 years old. One of the samples came from the first specimen ever recorded: the so-called Adams mammoth, found in 1799 and dug out of the permafrost between1804 and 1806 by the botanist Michael Adams and members of the Tungus tribe. This mammoth died around 36,000 years ago. "Hair samples from this find were stored in a Russian museum for 200 years at room temperature, but still allowed for a complete analysis of its mitochondrial genome using only 0.2 grams of hair," Schuster said. As a result, he uses the term "museumomics" for his dream of deriving molecular-genomic-analysis data from the specimens stored in the collections of Charles Darwin, Alexander von Humboldt and Carl von Linne.

The new route to the genetic material of extinct animals also will enable researchers to study the relatedness of individual animals from different populations at a much higher resolution than previously thought possible. "We plan to use hair and other keratin-containing body parts, such as nail and horn, to untangle the secrets of populations that lived long ago, so these populations can send a message from the past about what it might have taken for them to survive," Schuster said. "This discovery is good news for anyone interested in learning more about how species of large mammals can go extinct."

Note: This story has been adapted from a news release issued by Penn State University.
Mammoth hair produces DNA bounty

Last Updated: Friday, 28 September 2007, 03:32 GMT 04:32 UK

A rapid technique for isolating DNA in hair has yielded a mass of new information about woolly mammoths. An international research team says the process should work on other extinct animals, allowing their genetics to be studied in detail for the first time.

The mammoth DNA was taken from the hair shaft which was long thought to be a poor source for the "life molecule".

But the group tells Science magazine that the shaft's keratin material slows degradation and limits contamination.

"The idea has been that all the DNA is in the root and that the shaft is DNA-void, or of much lower quality," explained co-worker Dr Tom Gilbert from the University of Copenhagen, Denmark.

"This is why when we screened a whole load of mammoths, we thought we might be lucky if we took enough hair from one of them. Basically, for every mammoth we tried, it worked. That blew us away," he told the BBC.

Hair and hooves

The traditional route to DNA in ancient samples is through bones and preserved muscle, but any genetic material usually falls apart very soon after death and is prone to contamination from bacteria.

Having a new route to large quantities of well-preserved DNA should be a real boon to scientific research, Gilbert and colleagues say.

The team read the DNA using an established technology known as "sequencing-by-synthesis" - but its application to hair in the context of ancient samples is novel.

"The reason we think hair is so great comes down to the fact that as a structure, hair is made out of this material called keratin," explained Dr Gilbert, who works out of Copenhagen's Center for Ancient Genetics.

"It's a kind of protein that in a very simplistic sense can be viewed as a plastic that the DNA gets embedded in and surrounded by and protected by."

The scientists think the approach will also work for other items built from the durable protein, such as horns, nails, antlers, hooves and even feathers.

They say museum collections must hold countless specimens of recently extinct creatures from which researchers would love to get genetic information but had never bothered because they believed their DNA to be corrupted and beyond analysis.

Ice mummies

Gilbert and colleagues targeted the mammoths' mitochondrial DNA, a special type of DNA frequently used to measure the genetic diversity of populations - how closely different groups of organisms are related to each other.

Where previously only two mitochondrial genomes had been published, the Science paper reports the production of 10 new genomes, including one from the very first mammoth that was studied - the so-called Adams mammoth, which was found in 1799 and has been stored at room temperature for the last 200 years.

"From our experience working with old samples, the colder a sample has been preserved the better the quality of DNA. So, we're looking at permafrost animals -woolly rhino, for example.

"There are also a lot of old bison and horse mummies turning up in the permafrost. It's not just animals, there are humans [too]; there are a lot of mummies around the world with hair, ranging from Egypt, South America to the more cold, better-preserved ones in Greenland."

Asked the classic question about whether it would be possible to clone any extinct creatures back into existence, Dr Gilbert said that even if the full genetic sequence of a mammoth could be retrieved, the technology did not currently exist to turn that biochemical information into a live animal.

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