Scientists have unraveled snippets of the genetic code of an extinct bear species, proving a technique that could one day give a glimpse into the behavior of Neanderthals.

left: Skull from the extinct Pleistocene cave bear, Ursus spelaeus. Credit: Joint Genome Institute

Generally speaking, the fossil record is mostly bones and teeth. But bits of DNA - the blueprints of life - sometimes cling to these dry specimens. If the genetic material can be extracted, it can offer a wealth of information about a long-dead creature.

Scientists and science fiction writers have long dreamed of using ancient DNA to resurrect dinosaurs or woolly mammoths. The new study, proving the concept works, also shows it would be very difficult to employ on more ancient creatures.

Edward Rubin of the Department of Energy’s Joint Genome Institute and his colleagues were able to sequence, or decode, a small percentage of the genome from the Pleistocene cave bear, Ursus spelaeus.

"We could have gotten the whole bear genome - we had enough bear DNA," Rubin told LiveScience.

The cave bears (Ursus spelaeus), closely related to modern brown bears, disappeared more than 10,000 years ago. Cave-paintings and fossil evidence suggest that ancient humans had contact with these animals.

Rubin’s team analyzed 40,000-year-old cave bear bones and teeth, collected from two caves in Austria. The relatively cold, dry conditions were optimal for DNA survival.

The scientists identified about 27,000 base pairs in the bear’s DNA code - which, in its entirety, is somewhere around 3 billion base pairs long.

But sequencing the entire code would have been very time-consuming. The scientists consider this bear study merely a proof of principle, as they are more interested in exploring human ancestors.

"The next thing is Neanderthal," Rubin said.

This stocky hominid species is believed to have gone extinct around 29,000 years ago. Having a full or partial Neanderthal genome could tell us things that bones cannot - like what they ate, how their brain was built, or whether they spoke language, Rubin said.

The extraction technique might also be used on the 18,000-year-old remains of the recently discovered Flores Man, nicknamed "the hobbit." However, the diminutive skeletons were found in a tropical environment, which likely accelerated the DNA degradation process.

Besides the fact that DNA falls apart over time, gene sequencing from fossils is hard to do because the DNA that is found is mostly from corpse-eating organisms.

"When we die, we are a nutrient source for microbes and bugs," Rubin said.

To get around this contamination, past studies have focused on DNA from mitochondria. Mitochondria are the energy suppliers in cells, but they also carry their own separate DNA for reproduction. Because there are often thousands of mitochondria in a cell, researchers have had better luck isolating mitochondrial DNA from fossils.

By finding species with similar mitochondrial DNA, biologists have drawn evolutionary family trees. But to learn what an extinct animal looked like or how it behaved, one needs to sequence nuclear, or genomic, DNA, for which there are only two copies per cell.

To go after genomic data, Rubin’s team simply sequenced all the pieces of DNA in a sample - most of which ended up being from microbes - then separated out what DNA belonged to the bear by matching it to the known dog genome.

The full bear genome has not been sequenced, but bears and dogs have similar DNA - having diverged about 50 million years ago. Out of a few million base pairs, the scientists identified less than six percent that was from bear DNA. The results were reported in the June 2 online edition of the journal Science.

"It’s neat work," said Rick Myers from Stanford University, who was not involved in the research. "This is very promising for studying evolutionary relationships in animals that died out not too long ago."

Recently, a separate group of scientists announced an effort to bring back the woolly mammoth from frozen semen. Whether this is possible remains to be seen, since DNA only lasts so long. According to Rubin, 100,000 years is probably the limit.

This would dash any hope of regenerating dinosaurs - a la "Jurassic Park." Even if a small fragment of DNA were to be found in, say, a mosquito trapped in amber, it would be hard to prove that it was 100-million-year-old DNA.

"You always have to worry that it is from a lab worker," Rubin said.

That was one of the reasons the scientists chose to first test their technique with a species not closely related to humans.

"What we found is not from recent contamination, since we have a strict policy: no bears are allowed to work in our lab," Rubin joked.

source; LiveScience

A 50,000-year record of mammals eaten by early humans in southwestern France shows that they basically hunted the same prey. The Neanderthal and Cro-Magnon competed for food.

The paper, published in the online Journal of Archaeological Science, counters the idea proposed by some scientists that Cro-Magnon, who were physically similar to modern man, supplanted Neanderthals because they were more skilled hunters as a result of some evolutionary physical or mental advantage.

"This study suggests Cro-Magnon were not superior in getting food from the landscape," said lead author Donald Grayson, a University of Washington professor of archaeology. "We could detect no difference in diet, the animals they were hunting and the way they were hunting across this period of time, aside from those caused by climate change.

"So the takeover by Cro-Magnon does not seem to be related to hunting capability. There is no significant difference in large mammal use from Neanderthals to Cro-Magnon in this part of the world. The idea that Neanderthals were big, dumb brutes is hard for some people to drop. Cro-Magnon created the first cave art, but late Neanderthals made body ornaments, so the depth of cognitive difference between the two just is not clear."

The study also resurrects a nearly 50-year-old theory first proposed by Finnish paleontologist Björn Kurtén that modern humans played a role in the extinction of giant cave bears in Europe. Cro-Magnon may have been the original "apartment hunters" and displaced the bears by competing with them for the same caves the animals used for winter den sites.

Grayson and his colleague, Francoise Delpech, a French paleontologist at the Institut de Prehistoire et de Geologie du Quanternaire at the University of Bordeaux, examined the fossil record left in Grotte XVI, a cave above the Ceou River, near its confluence with the Dordogne River. The cave has a rich, dated archaeological sequence that extends from about 65,000 to about 12,000 years ago, spanning the time when Neanderthals flourished and died off and when Cro-Magnon moved into the region. Neanderthals disappeared from southwestern France around 35,000 years ago, although they survived longer in southern Spain and central Europe.

The researchers were most interested in the transition from the Middle to Upper Paleolithic, or Middle to Late Stone Age.

Neanderthals occupied Grotte XVI as far back as 65,000 years ago, perhaps longer. Between 40,000 and 35,000 years ago, people began making stone tools in France, including at Grotte XVI, that were more like those later fashioned by Cro-Magnon. However, human remains found with these tools at several sites, were Neanderthal, not Cro-Magnon. Similar tools but no human remains from this time period were found in Grotte XVI and people assumed to be Cro-Magnon did not occupy the cave until about 30,000 years ago.

The researchers examined more than 7,200 bones and teeth from large hoofed mammals that had been recovered from the cave. The animals – ungulates such as reindeer, red deer, roe deer, horses and chamois were the most common prey – were the mainstay of humans in this part of the world, according to Grayson.

He and Delpech found a remarkable dietary similarity over time. Throughout the 50,000-year record, each bone and tooth assemblage, regardless of the time period or the size of the sample involved, contained eight or nine species of ungulates, indicating that Neanderthals and Cro-Magnon both hunted a wide variety of game.

The only difference the researchers found was in the relative abundance of species, particularly reindeer, uncovered at the various levels in Grotte XVI. At the oldest dated level in the cave, reindeer remains accounted for 26 percent of the total. Red deer were the most common prey at this time, accounting for nearly 34 percent of the bones and teeth. However, as summer temperatures began to drop in Southwestern France, the reindeer numbers increased and became the prey of choice. By around 30,000 years ago, when Cro-Magnon moved into the region, reindeer accounted for 52 percent of the bones and teeth. And by around 12,500 years ago, during the last ice age, reindeer remains accounted for 94 percent of bones and teeth found in Grotte XVI.

Grayson and Delpech also looked at the cut marks left on bones to analyze how humans were butchering their food. They found little difference except, surprisingly, at the uppermost level, which corresponds to the last ice age.

"It is possible that because it was so cold, people were hard up for food," Grayson said. "The bones were very heavily butchered, which might be a sign of food stress. However, if this had occurred earlier during Neanderthal times, people would have said this is a sure sign that Neanderthals did not have the fine hand-eye coordination to do fine butchering."

In examining the Grotte XVI record, the researchers also found a sharp drop in the number of cave bears from Neanderthal to Cro-Magnon times.

"Cave bears and humans may have been competing for the same living space and this may have led to their extinction," Grayson said. He added that it is not clear if the decline and eventual extinction of the bears was driven by an increase in the number of humans or increased human residence times in caves, or both.

"If we can understand the extinction of any animal from the past, such as the cave bear, it gives us a piece of evidence showing the importance of habitat to animals. The cave bear is one of the icons of the late Pleistocene Epoch, similar to the saber tooth cats and mammoths in North America. If further study supports Kurtén’s argument, we finally may be in a position to confirm a human role in the extinction of a large Pleistocene mammal on a Northern Hemisphere continent."

source: Science Daily