The poop on DNA (or vice versa)

[Daryl Habel]

All,

Given that there has been some speculation in the past couple of years about the possibility of recovering ancient DNA from MP/UP human coprolites at Gibraltar and the Mount Carmel caves, the following news story seems to indicate the first-ever success has been reported with 8,000 year old remains at Gypsum Cave (Texas).
--------------------------------
The poop on ancient man
 
Fossilized feces are a veritable trove of human DNA and could answer a host of questions about the hunter-gatherer life thousands of years ago. JACOB BERKOWITZ reports

By JACOB BERKOWITZ
Saturday, June 19, 2004 - Page F10

Hendrik Poinar is holding a small plastic vial containing some of the oldest DNA ever extracted from human remains. The snips of genetic material are from a native American who made his home 8,000 years ago in a massive cliff-side rock shelter in southwestern Texas. ...[snip]......"Coprolites are fantastic sources of DNA. It turns out that with bones and poop from the same cave, the poops outdo the bones in terms of DNA yields by up to 10-fold," he says.

Dr. Poinar's molecular coproscopy is doing more than providing an intriguing bottom-up view on the past. He is writing the latest chapter in a surprising Canadian saga that began with a McGill University scientist whose pioneering coprolite work in the 1950s and 60s was initially dismissed.

Now, the power of old poop to tell amazing human stories is being heralded by Dr. Poinar and others in the world's leading scientific journals.

Just six months into Dr. Poinar's current job -- he chose McMaster over offers from Oxford and the University of California at Berkeley -- his four-member research group is meticulously constructing a million-dollar lab. It will soon be among the world's most sophisticated for teasing a string of A, T, C and G base pairs out of coprolites and other sources of ancient DNA, a field known as molecular anthropology.

Dr. Poinar comes naturally to the search for ancient DNA. His father is the "insects-in-amber guy," George Poinar, the Berkeley paleontologist and entomologist whose work is the basis for Michael Crichton's vision of genetically reconstituted dinosaurs, Jurassic Park.

But even with this pedigree, Hendrik Poinar fell into the study of coprolites. Working on his PhD in the mid-1990s at one of the world's leading ancient DNA labs at the University of Munich, he was intrigued by the desiccated doo-doo stored in the basement with the more respectable archeological and paleontological artifacts. The puffball-shaped ice age coprolites were from Gypsum Cave, Nev., just south of Las Vegas.

Other researchers had found it impossible to extract DNA from these or any other coprolites, and written them off as just a lot of old dung....[snip]...

Read the rest of the story at:
CLICK HERE FOR THE URL


Dar

[Jacques Cinq-Mars]

All,

Just an update, from Alan Cooper, on the potential role of the "poo" or "poop" factor in various types of palaeo studies:

Prehistoric poo yields DNA clue

Anna Salleh
ABC Science Online -- Thursday, 31 March 2005

Scientists are about to start searching for piles of ancient dung to find DNA that might help to explain what killed Australia's megafauna.

Professor Alan Cooper of the University of Adelaide says dung in hot, dry environments is one of the best sources of ancient DNA.

"The advantage of dung is that you can get the DNA from the animal that laid the thing, what they ate and the parasites they had," says Cooper.

Cooper is at a palaeontology conference being held at Naracoorte, South Australia this week, where he will announce a new centre for ancient DNA research to study topics including ancient marsupials and hobbit humans.

Cooper says a rich source of ancient DNA has been dung from US caves in Nevada and New Mexico.

"They're absolutely full of ancient dung from giant ground sloths that goes back at least 40,000 years."

He says there is even dung from native Americans dating 10 to 12,000 years.

"There are big piles of it, metres thick. It's so dry it doesn't decompose."

He says he expects to find such rich sources of DNA in Australia given the similarly dry environment.

"[But] I'm a little bit puzzled as to why more of it has not been found in Australia," he says, adding that people may have missed it because it looks like sediment.

The rise and fall of megafauna

Cooper's focus so far been on using ancient DNA to track the extinction of the North America megafauna such as bison, horses, lions and sabre-tooth cats over the past 20 to 30,000 years.

"The question is whether it's human impact or climate change that caused the large mammals to become extinct," he says.

He uses ancient DNA to measure the genetic diversity of particular animals at different points in time and this tells him about population size. The larger the population the more genetic diversity, he says.

He has matched the population changes of North American animals to known records of human presence and climate change and found that climate was the real culprit for their demise.

"You can see exactly what's going on," he says. "The height of the last ice age comes in and it kicks the stuffing out of the population size: it goes into a massive decline."

He says the worst periods for the bison was about 21 to 18,000 years ago, at the height of the last ice age, and again at the end of Pleistocene 10 to 12,000 years ago, when there were a sudden series of climate oscillations.

"Humans may well have done a bit of damage as well but it looks like climate had done the vast majority of it and really put things in dire straits."

Australian work

Now back in Australia after a 10-year post at the University of Oxford, Cooper hopes to examine topics such as coral reef die-offs and the continent's animal extinctions.

He says he hopes to find DNA as old as 30,000 years in Tasmania. The oldest DNA in the world is around 500,000 years old in the permafrost, says Cooper, who says he might find DNA around that age in Antarctic ice cores.

Cooper also hopes to study DNA from the famed hobbit and its habitat in Flores later this year. But he says it will be a challenge to get DNA that goes back 18,000 years from such a hot and humid environment.

"It's a hell of a tall order," he says. "But it's well worth a shot."

Jacques Cinq-Mars