Showing posts with label dna. Show all posts
Showing posts with label dna. Show all posts

Sunday, February 5, 2012

How Neanderthal Are You? Your DNA Has the Answer

In a survival of the fittest, modern humans bested the Neanderthals, who went extinct about 30,000 years ago. But even to this day, we can find traces of these boorish people in our DNA.
A new labs feature from biotech startup 23andMe shows just how Neanderthal you are, anywhere between 1 and 4 percent. (Full disclosure: While I have no stake in 23andMe, my boyfriend is a software engineer at the Mountain View-based company.)
The results can be surprising. If you looked at my hairy boyfriend, the only person whose DNA profile I have access to, you might assume he’s more of a caveman, but in reality I’ve got 0.2 Neanderthal percentage points on him. At 2.7 percent, my DNA ranks me in the 63rd percentile of the unrefined kind.
What are the implications of this finding? Well, the scientific community is figuring it out. It’s still a mystery why Homo sapiens survived over Homo neanderthalensis. By looking at our DNA, scientists can find the most recent evolutionary changes.

Wednesday, January 25, 2012

Rare Chinese white dolphin gets DNA bank

A Hong Kong conservation group said Saturday it has set up a DNA bank for the rare Chinese white dolphin, also known as the pink dolphin, in a bid to save the mammals facing a sharp population decline.
There are about 2,500 Chinese white dolphins in the Pearl River Delta region, the body of water between Macau and Hong Kong, with the majority of the mammals in Chinese waters and the rest in Hong Kong.
But experts say their number has dropped significantly in the past few years due to overfishing, an increase in maritime traffic, water pollution, habitat loss and coastal development.
In a bid to save the dwindling population, the Ocean Park Conservation Foundation Hong Kong said it had joined hands with a Chinese university to set up a DNA bank, which will also spearhead a genetic research project.
"We hope to offer the scientific community a standardised genetic analysis platform to assess the sustainability of Chinese white dolphin populations," Judy Chen, the foundation chairwoman said in a statement.
"The collected data will provide important reference to governments in the region for developing critical strategies of Chinese white dolphin conservation," she added.
The biological samples of these dolphins will be sent to the DNA bank to investigate the environmental impacts on the mammal, the statement said.
The Chinese white dolphins, a sub-species of the Indo-Pacific humpback dolphins, are unique for their pink skin. They are listed as "near threatened" by the International Union for Conservation of Nature.
The mammal was the official mascot at the handover ceremony when the former British colony returned to Chinese rule in 1997, while dolphin watching is a favourite tourist attraction in Hong Kong.
Its population in Hong Kong has dropped from an estimated 158 in 2003 to only 75 in 2010, according to the Hong Kong Dolphin Conservation Society.

Wednesday, December 28, 2011

Dino-Chicken: Wacky But Serious Science Idea of 2011

Paleontologist Jack Horner has always been a bit of an iconoclast. In the 1970s, Horner, the curator of paleontology at the Museum of the Rockies in Bozeman, Mont., and his friend Bob Makela discovered a Maiasaura nesting site, painting the first picture of dinosaurs as doting moms and dads. He's also been at the forefront of research suggesting that dinosaurs were fast growing and warm-blooded.

But Horner's newest idea takes iconoclasm to a new level. He wants, in short, to hatch a dinosaur.

Or something very much like one, at least. Horner, who served as a technical advisor for the "Jurassic Park" movies, has no illusions that the technique in that movie — extracting dino DNA from mosquitoes in amber — would work. DNA degrades too quickly, for one thing. Dinosaur DNA has proved impossible to extract from actual dinosaur bones, never mind blood-sucking insects.

"If you actually had a piece of amber and it had an insect in it, and you drilled into it, and you got something out of that insect and you cloned it, and you did it over and over and over again, you'd have a room full of mosquitoes," Horner said in a February 2011 TED Talk in Long Beach, Calif. TED, or Technology, Entertainment and Design, is a nonprofit focusing on "ideas worth spreading."

Read more here:
http://www.livescience.com/17642-chickenosaurus-jack-horner-create-dinosaur.html

Monday, November 7, 2011

Study Finds Culprits To Ice Age Mammal Extinctions

A research team involving over 40 academic institutions around the world is trying to tackle the question of what caused extinctions in the Ice Age.

The study found that the extinction of mammals like the woolly rhinoceros and woolly mammoth was not due to humans or climate change.

The team found using ancient megafauna DNA, climate data and the archeological record that humans played no part in the extinction of the wooly rhino or the musk ox in Eurasia.

The researchers believe these two mammals’ demise could be entirely explained by climate change.
However, the experts say that humans could have had part of the responsibility for leading to the extinction of the wild horse and the bison in Siberia.

“Our findings put a final end to the single-cause theories of the Ice Age extinctions, and suggests that care should be taken in making generalizations not just regarding past and present species extinctions but also those of the future,” Professor Eske Willerslev’s Center for GeoGenetics at the Natural History Museum said in a statement. “The impacts of climate change and human encroachment on species extinctions really depends on which species we’re looking at.”

The authors of the study found no clear pattern in their data distinguishing species that went extinct from species that survived.

“The fact that we couldn’t pinpoint what patterns characterize extinct species – despite the large and varying amount of data analyzed – suggests that it will be challenging for experts to predict how existing mammals will respond to future global climate change,” Eline Lorenzen, professor at the University of Copenhagen, said in a press release.

The study was published in the journal Nature.

http://www.redorbit.com/news/science/1112414031/study-finds-culprits-to-ice-age-mammal-extinctions/index.html

Thursday, October 13, 2011

Black Death bug DNA reconstructed

Fragments of 700-year-old DNA from the bug responsible for the Black Death have been pulled from the teeth of four plague victims buried in east London.

Scientists used the degraded strands to reconstruct the entire genetic code of the deadly bacterium - the first time experts have succeeded in drafting the genome of an ancient pathogen, or disease-causing agent.

The researchers found that a specific strain of the plague bug Yersinia pestis caused the pandemic that killed 100 million Europeans - between 30% and 50% of the total population - in just five years between 1347 and 1351.

They also learned that the strain is the "mother" of all modern bubonic plague bacteria.

"Every outbreak across the globe today stems from a descendant of the medieval plague," said lead scientist Dr Hendrik Poinar, from McMaster University in Canada. "With a better understanding of the evolution of this deadly pathogen, we are entering a new era of research into infectious disease."

Although rare, bubonic plague continues to kill some 2,000 people around the world each year.
The scientists, reporting their findings in the journal Nature, analysed the skeletal remains of four individuals exhumed from an East Smithfield "plague pit" sited under what is now the Royal Mint in London.

Tiny scraps of Yersinia pestis DNA were obtained from the victims' dental pulp, and from these fragments, the researchers were able to reconstruct virtually the whole of the bug's genetic code, or genome.

The same techniques could now be used to study the genomes of other ancient pathogens, say experts.
"This will provide us with direct insights into the evolution of human pathogens and historical pandemics," said co-author Dr Johannes Krause, from the University of Tubingen in Germany.

http://www.blogger.com/post-create.g?blogID=4348728589329576621

Monday, September 12, 2011

Aids research creates glowing cats (via Jessica Heard)

Green glowing cats have been created by gene scientists working on the Aids virus.

The spooky-looking moggies had their DNA modified with a gene from a fluorescent jellyfish. Placed under blue light, their fur, claws and whiskers emit an eerie green glow.

The purpose of the study was to show how a natural protein that prevents macaque monkeys developing Aids can do the same in cats.

Scientists in the US used the jellyfish gene to track the gene for the protein. Both were inserted into the DNA of adult tabby cats, which gave birth to luminous kittens.

Cats are susceptible to their own version of the HIV virus that triggers Aids, called FIV (Feline Immunodeficiency Virus).

Normally the immune systems of cats and humans are overwhelmed by the viruses.

But macaque monkeys possess "restriction factor" proteins that can stop the viruses invading immune cells.

When cats were genetically engineered to produce one of these factors, TRIMcyp, FIV replication was reduced.

Two male cats and one female with the genes were born and survived. The male passed the genes down to kittens of his own, which emitted a weaker glow.

Eric Poeschla, from the Mayo Clinic in Rochester, New York state, who led the study, reported in the journal Nature Methods: "One of the best things about this biomedical research is that it is aimed at benefiting both human and feline health. It can help cats as much as people."

http://uk.news.yahoo.com/aids-research-creates-glowing-cats-170133077.html

Friday, August 26, 2011

The downside of sex with Neanderthals (via Rob Chambers)

Some modern humans carry immune genes that originated in Neanderthals and a related species. But these genes may have come at a price
One question seemed to hang in the air more than any other when scientists first turned the powerful techniques of modern genetics on the fragile and damaged remains of ancient humans: did we or didn't we? Have sex with them, that is.

The answer came after years of painstaking work, when material extracted from the leg of a Neanderthal and the fingerbone of a Denisovan, an apparent sister species, yielded readable DNA. It turned out that most of us have some of their genes. The Neanderthals contributed up to 4% of modern Eurasian genomes, while the Denisovans contributed roughly 4-6% of modern Melanesian genomes. That doesn't happen by holding hands.

And so the scene was set. Hundreds of thousands of years ago, early humans in Africa split into several groups, among them Homo sapiens, Neanderthals and their apparent sister species, the Denisovans. The Neanderthals headed for West Asia and Europe, the Denisovans to East Asia. Our ancestors left Africa much later, and arrived in Eurasia where the others had set up home. Cue amorous encounters, and surely a fair amount of less than amorous contact.

But the question of whether our ancestors mated with these other human-like groups was always just the starting point for a line of inquiry. With interbreeding now well-established the intriguing question is, what came of it? How did our ancestors' antics shape the people we are today?

A glimpse of the legacy of those ancient encounters is revealed in a study reported today in the US journal, Science. An international team of scientists, led by Stanford University, scoured the Neanderthal and Denisovan genomes for gene variants that are central to the immune system. These genes belong to a group known as the HLA class I genes, which govern the body's ability to recognise and destroy dangerous pathogens.

By comparing the HLA genes of modern human populations with those from Denisovans and Neanderthals, the scientists identified a handful that could be traced back to ancient sexual encounters between the groups. One variant, known as HLA-B*73, likely arose in modern humans after cross-breeding with Denisovans. The variant is most common in West Asian populations, the region where the mating probably happened.

The Neanderthals contributed a string of HLA gene variants, or alleles, to the modern Eurasian population's gene pool, the study found.

There was good reason for Neanderthal and Denisovan immune system genes to have spread through the populations of modern humans who encountered them. Both Neanderthals and Denisovans had established themselves long before modern humans arrived. Their immune systems had adapted to the threats of the local environment. When those genes crossed into modern humans, they conveyed an advantage. Natural selection took care of the rest.

But the scientists think there was a downside. Inheriting Denisovan or Neanderthal immunity genes will have helped modern humans to fight the diseases of the day, but beyond the age of reproductive maturity they might have a more harmful effect, turning our immune systems on ourselves.

Paul Norman, a co-author on the paper, put it like this: "There's enormous genetic variation in people's immune systems and that can control how different people fight different diseases. This could go some way to explaining why some people are better at fighting some infections than others, but we think it also goes some way to explaining why some people are susceptible to autoimmune diseases."

Autoimmune diseases are conditions that arise when the immune system turns its firepower on the body, usually when it mistakenly identifies the body's tissues as foreign, and so potentially dangerous.

"The vast majority of autoimmune diseases have been shown by genome-wide association studies to be associated with particular HLA alleles and we find a couple of those in Denisovans," Norman added. "So it looks to me like modern humans have acquired these alleles, but we weren't kind of prepared for them, we hadn't grown up with them, and in some circumstances, they can start to attack us as well as the viruses and other pathogens."

The group is now investigating a gene variant called HLA-B51, which came from cross-breeding with Neanderthals and has already been linked to Behcet's disease, a rare and chronic inflammatory condition.

How else might immune genes inherited from Neanderthals and Denisovans affect the health of modern humans? The question is intriguing and will differ from population to population. Here, at least, is a worthy successor to the question of "did we or didn't we?"
http://www.guardian.co.uk/science/blog/2011/aug/25/neanderthal-denisovan-genes-human-immunity>

Friday, August 19, 2011

Dreaded carp: Can they be stopped?

DNA from the invasive silver carp has been found at 22 sites in the St. Croix River, a development that has deepened despair about the imminent arrival of the notorious leaping fish and doubts that state and federal officials can do anything to stop it.

The Minnesota Department of Natural Resources announced Thursday that 22 of 50 water samples taken between St. Croix Falls and Franconia tested positive for silver carp DNA. The samples did not test positive for the other three species of Asian carp that are believed to moving upriver from Illinois, and another 50 samples from the Mississippi River were negative.

The results are not conclusive evidence that the fish are living and breeding in the St. Croix -- none has been found in the river -- or that they are absent from the Mississippi, DNR officials said. The DNA could have come from dead carp, live carp someone dumped in the river or fish pellets used in hatcheries.

Still, it ratchets up the fear considerably, they said.

"This is disappointing news," said DNR Commissioner Tom Landwehr.

The four species of Asian carp have caused enormous ecological damage in the Illinois and Missouri Rivers, where they are well established. The carp eat 40 percent of their body weight every day in plankton and bugs, squeezing out every other creature up the food chain, from sunnies to fish-eating birds.

"They become the most dominant organism in the system," said Byron Karns, a biologist with the National Park Service. "They topple the food chain."

Much national attention has focused on stopping the carp from moving into the Great Lakes through a shipping channel in Chicago, and five states -- Michigan, Minnesota, Ohio, Pennsylvania and Wisconsin -- have filed a federal lawsuit demanding the closure of the shipping channel.

The threat to Minnesota and Wisconsin waters has not attracted similar concern from federal agencies or Congress. That's partly because the Mississippi is a long river running through multiple states, managed by many federal agencies but with no one in charge, said Paul Labovitz, superintendent of the National Park Service's Mississippi National River and Recreation Area.

"It's like the invader of the body snatchers are at the door and we have no generals to fight back," said Mark Peterson, executive director of Audubon Minnesota.

Taken alone, the new DNA results are not likely to change that, officials said.

"We need a fish," Landwehr said Thursday.

So far, no silver carp have been caught in the St. Croix. Two bighead carp -- a cousin of the silver carp -- have been caught in the river, one in 1996 and another on April 18 of this year.

This month the DNR will contract with commercial fishermen to look for the carp up and down the St. Croix. As early as next week, DNR staff will be on the river with nets and boats outfitted with electric shocking capabilities to search for fish.

An Asian Carp Task Force brought together in January by National Park Service officials will also conduct more DNA testing in both rivers.

Meanwhile, the DNR will issue notices to anglers and boaters to keep an eye out for the silver carp, which can be hard to miss. The fish is known for its astonishing ability to leap 10 feet out of the water and even knock people out of their boats.

The far more difficult question is what to do if -- or when -- they find live carp. There is no surefire way to stop the fish.

In the short term, Landwehr said, the state will seek emergency authority to close the lock and dam at the Ford Bridge in Minneapolis.

Long-term, state and federal officials also said they will pursue a tool used elsewhere, an acoustic bubble barrier. The fish don't like the bubbles, and the acoustics can be changed to deter carp but not desirable fish.

But bubblers are not guaranteed to work, either. And just the material to construct one would cost $7 million, officials said. The only likely place on the Mississippi narrow enough for such a barrier would be at mouth of the St. Croix at Prescott, they said.

Another option is reconstruction of the Coon Rapids dam. The Legislature appropriated $16 million to carp-proof it this year. That could preserve the state's $4 billion recreational fishing industry north of the Twin Cities but would mean sacrificing the lower length of the Mississippi, including Lake Pepin, and the Minnesota River to carp invaders. And it could be only temporary. Some who have studied it say it would work for only 10 or 15 years and might not be adequate at times of high water.

The most effective solution is also the most politically difficult -- permanently closing the locks at the Ford Bridge or the St. Anthony Falls in downtown Minneapolis.

But that would require an act of Congress, and by the time that happens it might be too late.
"I don't think we need to wait to find the fish," said Peterson of the Audubon Society. "The fish are going to find us. It's just a matter of time."

Josephine Marcotty
http://www.startribune.com/local/east/127521753.html

Friday, August 12, 2011

Animal's genetic code redesigned (via Dawn Holloway)

Researchers say they have created the first ever animal with artificial information in its genetic code.


The technique, they say, could give biologists "atom-by-atom control" over the molecules in living organisms.

One expert the BBC spoke to agrees, saying the technique would be seized upon by "the entire biology community".

The work by a Cambridge University team, which used nematode worms, appears in the Journal of the American Chemical Society.

The worms - from the species Caenorhabditis elegans - are 1mm long, with just a thousand cells in their transparent bodies.

What makes the newly created animals different is that their genetic code has been extended to create biological molecules not known in the natural world.

Genes are the DNA blueprints that enable living organisms to construct their biological machinery, protein molecules, out of strings of simpler building blocks called amino acids.

Just 20 amino acids are used in natural living organisms, assembled in different combinations to make the tens of thousands of different proteins needed to sustain life.

Expanded palette
But Sebastian Greiss and Jason Chin have re-engineered the nematode worm's gene-reading machinery to include a 21st amino acid, not found in nature.

Dr Chin of the Laboratory of Molecular Biology (where Francis Crick and James Watson first cracked the structure of DNA) describes the technique as "potentially transformational": designer proteins could be created that are entirely under the researchers' control.

The development builds on techniques first developed at the Scripps Research Institute, in La Jolla, US, where Dr Chin worked 10 years ago.

The genetic code comes in four DNA letters, A,C,G and T; the genetic machinery reads it in words three letters long, called codons, which stand for the individual amino acid blocks to be built into a growing protein.

At Scripps, researchers showed in a paper in PNAS how one of those three letter words could be re-assigned, so that cells would read it as an instruction to incorporate an unnatural amino acid, one not normally found in living organisms. But that was in the bacterium E. coli; until now, no one had succeeded in doing the same in a whole animal.

Jonathan Hodgkin, professor of genetics at Oxford University, welcomes the new development, saying it "creates exciting new opportunities for research on C. elegans".

New tricks
Closer to home, Dr Mario de Bono, an expert on C elegans, who is also at the Laboratory of Molecular Biology, predicts "this sort of news travels like wildfire" among research biologists, adding that the method could be applied to a wide range of animals.

So far it is just a proof of principle - the artificial protein that is produced in every cell of the nematode worm's tiny body contains a fluorescent dye that glows cherry red under ultraviolet light. If the genetic trick failed, there would be no glow.

But Dr Chin says any artificial amino acid could be chosen to produce specific new properties. Dr de Bono suggests the approach could now be used to introduce into organisms designer proteins that could be controlled by light.

Indeed, the two are planning to collaborate on a detailed study of neural cells in the nematode brain, aiming to activate or deactivate individual neurons in precise ways with tiny laser flashes.

Dr Chin rather modestly admits he's "incredibly pleased" to have succeeded in a project he had avoided until a year and a half ago, for fear that other well-established competitors would get there quicker.

On the other hand, Dr de Bono compares the invention with the Nobel-prize winning work on green fluorescent protein, which are now part of the standard kit in biology labs across the world.


By Roland Pease

BBC Radio Science
http://www.bbc.co.uk/news/science-environment-14492948

Sunday, July 24, 2011

All Non-Africans Part Neanderthal, Genetics Confirm

If your heritage is non-African, you are part Neanderthal, according to a new study in the July issue of Molecular Biology and Evolution. Discovery News has been reporting on human/Neanderthal interbreeding for some time now, so this latest research confirms earlier findings.

Damian Labuda of the University of Montreal's Department of Pediatrics and the CHU Sainte-Justine Research Center conducted the study with his colleagues. They determined some of the human X chromosome originates from Neanderthals, but only in people of non-African heritage.

"This confirms recent findings suggesting that the two populations interbred," Labuda was quoted as saying in a press release. His team believes most, if not all, of the interbreeding took place in the Middle East, while modern humans were migrating out of Africa and spreading to other regions.

The ancestors of Neanderthals left Africa about 400,000 to 800,000 years ago. They evolved over the millennia mostly in what are now France, Spain, Germany and Russia. They went extinct, or were simply absorbed into the modern human population, about 30,000 years ago.

Neanderthals possessed the gene for language and had sophisticated music, art and tool craftsmanship skills, so they must have not been all that unattractive to modern humans at the time.

"In addition, because our methods were totally independent of Neanderthal material, we can also conclude that previous results were not influenced by contaminating artifacts," Labuda said.
This work goes back to nearly a decade ago, when Labuda and his colleagues identified a piece of DNA, called a haplotype, in the human X chromosome that seemed different. They questioned its origins.

Fast forward to 2010, when the Neanderthal genome was sequenced. The researchers could then compare the haplotype to the Neanderthal genome as well as to the DNA of existing humans. The scientists found that the sequence was present in people across all continents, except for sub-Saharan Africa, and including Australia.

"There is little doubt that this haplotype is present because of mating with our ancestors and Neanderthals," said Nick Patterson of the Broad Institute of MIT and Harvard University. Patterson did not participate in the latest research. He added, "This is a very nice result, and further analysis may help determine more details."

David Reich, a Harvard Medical School geneticist, added, "Dr. Labuda and his colleagues were the first to identify a genetic variation in non-Africans that was likely to have come from an archaic population. This was done entirely without the Neanderthal genome sequence, but in light of the Neanderthal sequence, it is now clear that they were absolutely right!"

The modern human/Neanderthal combo likely benefitted our species, enabling it to survive in harsh, cold regions that Neanderthals previously had adapted to.

"Variability is very important for long-term survival of a species," Labuda concluded. "Every addition to the genome can be enriching."

http://news.discovery.com/human/genetics-neanderthal-110718.html

Monday, July 18, 2011

Male and female giant pandas prefer different habitats

Male and female giant pandas prefer to use different habitats, say scientists.

Female pandas frequent high altitude conifer forests and mixed forests on steeper slopes, whereas males roam more widely, researchers found.

Females prefer these areas as they provide den sites for birthing and dense bamboo cover in which baby pandas can hide.

The discovery could inform strategies for conserving wild pandas and releasing them back into the wild.

Details are published in the Journal of Zoology.

Dunwu Qi and Fuwen Wei of the Institute for Zoology at the Chinese Academy of Sciences in Beijing and colleagues studied the movements of giant pandas within the Liangshan Mountains of south central China.

They conducted transect surveys recording the presence of pandas by sight or by their droppings.

By studying the DNA in fecal samples, the researchers could determine the sex of the pandas encountered.

Giant pandas are solitary animals confined to highly fragmented montane forests in remote China.


Scientists well understand the basic type of habitat pandas need to survive, which tends to be forests above 1500m rich in bamboo, the pandas' main food.

The animals generally avoid higher peaks lacking bamboo and lower areas dominated by people.

But the specific requirements of males and females has been largely ignored until now.

The scientists' study confirmed that both sexes prefer to live in areas at higher altitudes and with high forest cover.

But female pandas are more picky than males.

They tend to limit their movements to within high altitude conifer forests and mixed forests, as well as historically clear-felled forest.

They also prefer habitat that slopes at between 10 and 20 degrees.


Such areas are better for raising young. Female pandas are selective about their den sites and often make dens in stands of large conifer trees more than 200 years old.

That also suggests that den sites may be limited in logged areas.

Males, in contrast, range more widely, covering areas that overlap the ranges of several females.

This segregation of the sexes should be accounted for in conservation and management efforts to safeguard the giant panda, say the researchers.

In particular, it should be recognised that female giant pandas have a narrower habitat preference than males.

That means they are likely to be disproportionately affected by habitat loss and people exploiting the forest.

It should also be taken into account when breeding programmes release giant pandas back into the wild.

Roads don't appear to have as great an impact on the movements of giant pandas as previously thought, say the researchers.

Females are often found near abandoned logging trails, though this could be an artefact of the number of roads of this type that crisscross the region.

Males tend to frequent habitat close to roads used by vehicles, perhaps due to their need to move greater distances to find prospective female mates.

By Matt Walker

Editor, BBC Nature
http://www.bbc.co.uk/nature/14153997

Tuesday, July 5, 2011

Belly button biomes begin to blossom

Peter Aldhous, San Francisco bureau chief

The human navel should be designated as a bacterial nature reserve, it seems. The first round of DNA results from the Belly Button Biodiversity project are in, and the 95 samples that have so far been analysed have turned up a whopping total of more than 1400 bacterial strains. In 662 cases, the microbes could not even be classified to family, "which strongly suggests that they are new to science", says team leader Jiri Hulcr of North Carolina State University in Raleigh.

The project was conceived as a light-hearted exercise in science communication, but is making a serious contribution to the understanding of microbial diversity. Since New Scientist wrote about the initiative in April, samples of bacteria taken when volunteers swabbed their navels with Q-tips have had their "DNA barcodes" read by sequencing the gene for 16S ribosomal RNA, widely used in studies of bacterial evolutionary relationships.

My own sample was among 10 per cent of those in the first round in which reactions to amplify the DNA present failed - so the next installment of the comparison of my belly button biome with that of fellow science writer Carl Zimmer will have to wait for another day. Still, Zimmer has already been having some fun with his results, finding among other things that his belly button hosts Georgenia bacteria, previously found in Asian soils.

Results like this reflect our ignorance of microbial diversity, Hulcr suggests: the inhabitants of our navels seem weird because biologists haven't sampled sufficiently extensively to document the full diversity of microbial life in a variety of habitats. He likens reactions to the first round of belly button results to the astonishment of the first European explorers seeing African big game - which today seem commonplace. "Now you're expecting rhino and elephants," Hulcr says.

Also, identifying bacteria to species is difficult. Noah Fierer's team at the University of Colorado, Boulder, classified them into "operational taxonomic units" having 16S ribosomal RNA gene sequences that differed by 3 per cent or less. Apply this standard to mammals, Hulcr explains, and dogs and cats would be lumped together. It means that a "match" between a belly button strain and a species known from the deep ocean, for instance, may actually represent two microbes separated by several million years of divergent evolution.

Although the total number of strains recorded was large, the results so far indicate that a small group of about 40 species accounts for around 80 per cent of the bacterial populations of our belly buttons. "It is tempting to think of the abundant species as the good, core biome of bacteria and the rare ones as transients, struggling to take hold, sometimes at our expense," says Rob Dunn, author of The Wild Life of Our Bodies, and head of the lab in which Hulcr works.

Confirming that theory will require studies on a new scientific frontier: belly button ecology.

http://www.newscientist.com/blogs/shortsharpscience/2011/06/peter-aldhous-san-francisco-bu.html

Thursday, April 14, 2011

Cornwall falcon DNA database aims to prevent thefts

14 April 2011 Last updated at 11:42

Animal health experts are taking DNA samples from newly-born peregrine falcon chicks in Cornwall to try to catch unscrupulous bird dealers.

The work is being carried out to allow identification if any are found in suspicious circumstances in captivity.

Officials from the government's Animal Health Agency said they obtained the birds' DNA from feathers in nests.

The county has about 50 breeding pairs of falcons on cliffs along the north coast.

Nest patrols

The move is part of work to prevent chicks from being stolen during the current breeding season and being sold on to dealers, particularly dealers abroad.

The head of compliance at the Animal Health and Veterinary Laboratories Agency, Nevin Hunter, said there had been "significant issues" across the UK and falcons had been targeted in particular.

He said: "In one example, a man was arrested at Birmingham Airport last year trying to smuggle 14 eggs taken from fives sites in south Wales.

"We know there is a premium for wild-taken falcons."

Devon and Cornwall was rated as the third worst area in England for the killing of birds of prey, according to the RSPB last September.

Devon and Cornwall Police said the DNA would help trace any birds back to individual nests if they were stolen from Cornwall.

As well as the DNA database, patrols by police and bird lovers are being stepped up to protect the birds in the county during the breeding season.


http://www.bbc.co.uk/news/uk-england-cornwall-13078195

Monday, March 28, 2011

Unknown Animals Nearly Invisible Yet There

Individuals of the bryozoan Alcyonidium diaphanum
stretch out their tentacles to filter food particles
out of the water. (Credit: Judith Fuchs.)
ScienceDaily (Mar. 22, 2011) — Bryozoans (moss animals) are a group of aquatic invertebrates that are found in great variety throughout the world, with well over 100 species in Sweden alone. Yet little is known about them. Researchers at the University of Gothenburg have now studied Swedish bryozoan species using DNA techniques.

"There are currently over 6 000 known species of Bryozoa. Earlier studies were based on visible characteristics of these animals, which is not sufficient to decide how the species are related to each other. To understand the evolution of bryozoans and how they are related to other animals, it is necessary to use molecular data, that's to say DNA," says Judith Fuchs of the Department of Zoology at the University of Gothenburg.

When Bryozoa were discovered in the 16th century, they were regarded as plants. Later on they were found to have a nervous system, muscles and an intestinal system and were classified as animals. On their own, bryozoans are barely visible to the naked eye, but like coral animals all bryozoans build colonies that reach several centimetres in size and some species build colonies of over 30cm.

In her thesis, Fuchs has studied the evolution and relationships of Bryozoa using molecular data (DNA) from more than 30 bryozoan species, most collected in Sweden. The results show that this animal group developed from a common ancestor that probably lived in the sea. Two groups of Bryozoa evolved from this common ancestor: a group that stayed in the marine environment and another that evolved in freshwater. The DNA studies of the larval stage of Bryozoa can also contribute to a better understanding of the evolution of life cycles and larval stages of other multicellular animals.

Together with her supervisor, Matthias Obst, over a period of four years she has also taken part in the marine inventory of the Swedish Species Project along the west coast of Sweden. The collection of all marine bottom-living animals is based on more than 500 samples from 400 locations.

"We found as many as 120 marine bryozoan species in our waters, and many of them had not been previously known in Sweden. We also found a completely new species of Bryozoa. This is a very small bryozoan with characteristic spikes on its surface, which I have described in my thesis."

To date, 45 per cent of the bryozoans collected in the inventory have been determined.

"Sweden has a very rich bryozoan fauna. On your next trip to the beach you might perhaps take a closer look at seaweed or pebbles. If you see a white covering with small holes in it, you have found a bryozoan colony for yourself."

There are currently over 6 000 known species of Bryozoa. Earlier studies were based on visible characteristics of these animals, which is not sufficient to decide how the species are related to each other. To understand the evolution of bryozoans and how they are related to other animals, it is necessary to use molecular data, that's to say DNA," says Judith Fuchs of the Department of Zoology at the University of Gothenburg.

http://www.sciencedaily.com/releases/2011/03/110322105740.htm

Experts DNA test England's adders to help halt decline

28 March 2011

Ecologists are running DNA tests on adders to check their genetic diversity amid fears the UK's only venomous snake is vanishing from the wild.

A recent study found that numbers of the reptile had declined since 2007.

Conservationists believe inbreeding in small, isolated populations could lead to a further decrease in numbers.

Experts from Natural England, the Zoological Society of London and Oxford University are taking swabs from the reptiles at 16 sites across England.

Ecologist Nigel Hand has already carried out health checks and collected DNA samples from five snakes at a Surrey Wildlife Trust site and 27 adders from an area in Norfolk.

Once captured, the reptiles are placed in a plastic tube to measure their length and protect the handler from their bite.

A swab is taken and they are marked before they are released back into the wild.

The DNA is then analysed to see whether larger or smaller populations have different levels of genetic variety.

Jim Foster, of Natural England, said: "With around a third of adder populations now restricted to isolated pockets of habitat, and with only a handful of snakes per sites, they could be especially vulnerable."

It is estimated that there are 1,000 populations of adder in the country with some groups made up of fewer than 10 adults.

Mr Foster said the tests would also help them understand why some adders had been found with abnormalities including malformed scales and missing eyes.

He added: "In the longer term, the last resort option is whether we should move animals between populations, artificially encouraging them to mix."

http://www.bbc.co.uk/news/uk-england-12878563

Monday, March 21, 2011

Craig Venter’s Genetic Typo

David M. Ewalt
Mar. 14 2011 - 12:00 pm

In May 2010, geneticist J. Craig Venter and his team made news by creating the first “synthetic life form,” replacing the genetic code in a bacterium with DNA they’d composed on a computer.

But during a presentation delivered Monday morning at the South By Southwest convention in Austin, Texas, Venter talked about two ways the landmark innovation went wrong.

In order to distinguish their synthetic DNA from that naturally present in the bacterium, Venter’s team coded several famous quotes into their DNA, including one from James Joyce’s A Portrait of the Artist of a Young Man: “To live, to err, to fall, to triumph, to recreate life out of life.”

After announcing their work, Venter explained, his team received a cease and desist letter from Joyce’s estate, saying that he’d used the Irish writer’s work without permission. ”We thought it fell under fair use,” said Venter.

The synthetic DNA also included a quote from physicist Richard Feynman, “What I cannot build, I cannot understand.”

That prompted a note from Caltech, the school where Feyman taught for decades. They sent Venter a photo of the blackboard on which Feynman composed the quote –and it showed that he actually wrote, “What I cannot create, I do not understand.”

“We agreed what was on the Internet was wrong,” said Venter. “So we’re going back to change the genetic code to correct it.”

http://blogs.forbes.com/davidewalt/2011/03/14/craig-venters-genetic-typo/

Monday, February 14, 2011

William S. Burroughs' Preserved Poop Inspires 'Bio-Art' Piece

Feb 11, 2011 – 3:16 PM
David Moye

Controversial 20th-century novelist William S. Burroughs was best known for his novel "Naked Lunch," and now two "bio-artists" are hoping to turn the remains of his last lunches into art.

Adam Zaretsky and Tony Allard are the creators of "Mutate or Die: A W.S. Burroughs Biotechnical Bestiary," an ongoing project that basically turns a piece of Burroughs' poop into a piece of art.

Burroughs died in 1997 at the age of 83 in Lawrence, Kan., and the poop being used belongs to a family friend and is covered in epoxy, presumably until it could be used for a higher purpose such as this.


Artists Adam Zaretsky and Tony Allard are creating an art piece using a piece of poop that was once in the colon of controversial writer William S. Burroughs.
Courtesy Adam Zaretsky
Artists Adam Zaretsky and Tony Allard are creating an art piece using a piece of poop that was once in the colon of controversial writer William S. Burroughs.
Zaretsky, who has a background in biotech, and Allard, a college professor in San Diego, say their plan is to "take a glob" of the preserved poop, isolate the DNA and make lots of copies of it.

After that, they will soak the DNA dust in gold dust and load it into a "gene gun," a modified air pistol used to insert DNA into plants, worms, rats and humans for experiments.

The DNA dust collected from the poop will be loaded into the pistol, which will then be shot into a mix of blood, poop and semen and then, according to the artists, be declared either a "living bio-art," a "new media print," a "living cut-up literary device" or a mutant sculpture.

Allard admits the concept is, for many people, like poop itself: not easy to grasp even if you're fully aware of its purpose.

"The main response we get from people is, 'Are you serious?' " he told AOL News. "But this is not your typical art project. We see this as a paradigm shift from representational art, since, in this case, the art is in the living organism."

The idea for turning Burroughs' poop into art dates back to October 1996, when Allard was living in Kansas City, Mo., and tried to get the author's DNA sequenced at the scanning electron microscope at the University of Missouri at Kansas City.

That didn't happen, but Allard was able to make things happen after he met Zaretsky at a symposium.

"He asked me what I could do with [Burroughs'] s--t," Zaretsky said. "I told him we could isolate and amplify the DNA from the turd and make a bucket of DNA, and I could throw it in his face.

"But, I also mentioned that if we could raise some money for a gene gun, I could shoot the genes into his balls. After some fundraising, I think we have ourselves a potential to go on a gonad bender."

Allard believes this attempt to make what he calls a "transgenic mutation" fits in better with the spirit of Burroughs' work than the original plan. It also has the complete approval of Burroughs' estate.

"One of Burroughs' most famous quotes is 'Mutate or die!' and mutants run through his work," Allard said.

So do bodily fluids. The mixing of Burroughs' poop and DNA with blood and semen belonging to others is meant to be sort of a shout-out to the author's pioneering "cut-up" technique of writing, in which he cut random book pages in half and mismatched them with other pages.
And the fact that the DNA is being shot with a gun is also an allusion to the 1951 incident when Burroughs shot and killed his wife while playing a drunken game of "William Tell."

But Allard says just the fact they are doing this with DNA is what is truly Burroughsian about the project.

"In the scientific community, transgenic mutations are common," he said. "A piece of corn might have the gene of a flounder to keep it drought-resistant. However, there are controls. It's normalized.

Allard says the randomness of this project flushes that notion down the toilet.

"The exact sciences are obsessed with tight controls over random factors," he said. "They don't do things like this just to see what will happen, but this is what we're interested in. Burroughs was opposed to any kind of control system. He believed in diversity through mutation, which is what this is."

Although Allard and Zaretsky have joked that the combination of blood, sperm and poop could somehow create a race of Burroughs-bred turd monsters, Allard is quick to point out that the amount of the writer's DNA in the poop is actually small.

"The amount of DNA in the s--t is fairly minuscule; it's more like the DNA of what was in his gut at the time," he said.

But the reaction to the project has been robust in just the few days since they announced it -- and that reaction is the first part of what they expect to be a two- to three-year project.

"The first part is announcing the project and having the public comment on it, but we probably won't extract the DNA sample until the fall," he said. "We're creating a context for a dialog.

"In most cases, s--t is an ending point. Here, it's a starting point."

http://www.aolnews.com/discuss/2011/02/11/william-s-burroughs-preserved-poop-inspires-bio-art-piece

Tuesday, January 11, 2011

Researchers to drill for ancient DNA in 'hobbit' tooth

Prospects of recovering ancient DNA from boosted by study on teeth.

January 5, 2011

Nature News

By Cheryl Jones


Scientists are planning an attempt to extract DNA from the "hobbit" Homo floresiensis, the 1-meter-tall extinct distant relative of modern humans that was unearthed in Indonesia, following a study that suggests problems in standard sampling methods in ancient-DNA research could have thwarted previous efforts.

This year, geneticists at the Australian Centre for Ancient DNA (ACAD) at the University of Adelaide hope to recover DNA from a roughly 18,000-year-old H. floresiensis tooth, which was excavated in 2009 from the Liang Bua site on the Indonesian island of Flores.

The premolar has been kept cold, and has been handled as little as possible to prevent contamination with modern DNA. But little, if any, of the ancient DNA is likely to have survived the heat and moisture of the tropics, and any that has may be highly fragmented.

Tony Djubiantono, director of the Indonesian National Centre for Archaeology in Jakarta, where the tooth is held, says that developments in DNA extraction techniques could overcome previous sampling problems, and have exciting potential for understanding the evolutionary history of H. floresiensis.

If the DNA can be extracted, comparing its sequence to that of other species could settle disputes over classification. For instance, Peter Brown, a paleoanthropologist at the University of New England in Armidale, Australia, who described and named the species in 2004, is rethinking his initial classification. At first he put the species in the human genus Homo, but he now suspects that the hobbit's ancestors left Africa before Homo evolved so the species could belong to a different or new genus.

Teething troubles

Five years ago, two teams, one from ACAD and one from the Max Planck Institute of Evolutionary Anthropology in Leipzig, Germany, attempted to recover DNA from another H. floresiensis tooth excavated in 2003. Both attempts failed.

Now, a team led by Christina Adler, a geneticist at ACAD, has found that standard sampling procedures could be responsible for the failure to get DNA from the hobbit and some other ancient specimens.

Adler's team--which included some researchers involved in the original H. floresiensis DNA recovery attempt--compared the impacts of various sampling techniques on DNA from the mitochondria of 40 human specimens from around the world, which had been dated up to 7,500 years old. The results have been accepted for publication in the Journal of Archaeological Science.

Most genetics research on ancient teeth has focused on the inner tooth tissue, dentine, but Adler's team found that cementum, the coating of the root, was a richer source of DNA.

Drilling is a technique commonly used to sample teeth and bone, because it minimizes damage to the precious specimen. But Adler's team found that the heat generated at standard drill speeds of more than 1,000 revolutions per minute (RPM) destroys DNA rapidly, causing yields to be up to 30 times lower than for samples pulverized in a mill. Reducing the drill speed to 100 RPM alleviated the problem.

The Max Planck team sampled dentine from the hobbit tooth in its early attempt to recover DNA, but it is unclear what drill speed was used. And although the ACAD scientists used the lower drill speed, they also concentrated on dentine. They will target cementum in their next attempt.

Small chance

Adler says that several ancient specimens that previously failed to yield DNA might now warrant re-sampling. She is surprised that ancient-DNA researchers commonly choose to drill at high speeds for samples, because dentists have long known that this harms their patients' teeth. "This is a case of a lack of communication between two specialist fields that are both working on similar things independently," she says.

Matthew Collins, a specialist in ancient-protein analysis who is based at the University of York, UK, says that Adler's team's results will "help to ensure that we minimize the destruction of molecules during sampling of precious fossils, and potentially enable us to reach even further back in time to recover sequence information."

However, he is pessimistic about the chances of winkling DNA out of H. floresiensis, saying that the molecules are probably too fragmented owing to high temperatures at the excavation site.

But the ACAD scientists think that it is worth making an attempt on their H. floresiensis tooth. They have been encouraged by their successful extraction of DNA from a 6,000-year-old pig tooth from the site in 2007.

http://www.scientificamerican.com/article.cfm?id=researchers-to-drill-for-hobbit

Researchers to drill for ancient DNA in 'hobbit' tooth

Prospects of recovering ancient DNA from boosted by study on teeth.

January 5, 2011

Nature News

By Cheryl Jones


Scientists are planning an attempt to extract DNA from the "hobbit" Homo floresiensis, the 1-meter-tall extinct distant relative of modern humans that was unearthed in Indonesia, following a study that suggests problems in standard sampling methods in ancient-DNA research could have thwarted previous efforts.

This year, geneticists at the Australian Centre for Ancient DNA (ACAD) at the University of Adelaide hope to recover DNA from a roughly 18,000-year-old H. floresiensis tooth, which was excavated in 2009 from the Liang Bua site on the Indonesian island of Flores.

The premolar has been kept cold, and has been handled as little as possible to prevent contamination with modern DNA. But little, if any, of the ancient DNA is likely to have survived the heat and moisture of the tropics, and any that has may be highly fragmented.

Tony Djubiantono, director of the Indonesian National Centre for Archaeology in Jakarta, where the tooth is held, says that developments in DNA extraction techniques could overcome previous sampling problems, and have exciting potential for understanding the evolutionary history of H. floresiensis.

If the DNA can be extracted, comparing its sequence to that of other species could settle disputes over classification. For instance, Peter Brown, a paleoanthropologist at the University of New England in Armidale, Australia, who described and named the species in 2004, is rethinking his initial classification. At first he put the species in the human genus Homo, but he now suspects that the hobbit's ancestors left Africa before Homo evolved so the species could belong to a different or new genus.

Teething troubles

Five years ago, two teams, one from ACAD and one from the Max Planck Institute of Evolutionary Anthropology in Leipzig, Germany, attempted to recover DNA from another H. floresiensis tooth excavated in 2003. Both attempts failed.

Now, a team led by Christina Adler, a geneticist at ACAD, has found that standard sampling procedures could be responsible for the failure to get DNA from the hobbit and some other ancient specimens.

Adler's team--which included some researchers involved in the original H. floresiensis DNA recovery attempt--compared the impacts of various sampling techniques on DNA from the mitochondria of 40 human specimens from around the world, which had been dated up to 7,500 years old. The results have been accepted for publication in the Journal of Archaeological Science.

Most genetics research on ancient teeth has focused on the inner tooth tissue, dentine, but Adler's team found that cementum, the coating of the root, was a richer source of DNA.

Drilling is a technique commonly used to sample teeth and bone, because it minimizes damage to the precious specimen. But Adler's team found that the heat generated at standard drill speeds of more than 1,000 revolutions per minute (RPM) destroys DNA rapidly, causing yields to be up to 30 times lower than for samples pulverized in a mill. Reducing the drill speed to 100 RPM alleviated the problem.

The Max Planck team sampled dentine from the hobbit tooth in its early attempt to recover DNA, but it is unclear what drill speed was used. And although the ACAD scientists used the lower drill speed, they also concentrated on dentine. They will target cementum in their next attempt.

Small chance

Adler says that several ancient specimens that previously failed to yield DNA might now warrant re-sampling. She is surprised that ancient-DNA researchers commonly choose to drill at high speeds for samples, because dentists have long known that this harms their patients' teeth. "This is a case of a lack of communication between two specialist fields that are both working on similar things independently," she says.

Matthew Collins, a specialist in ancient-protein analysis who is based at the University of York, UK, says that Adler's team's results will "help to ensure that we minimize the destruction of molecules during sampling of precious fossils, and potentially enable us to reach even further back in time to recover sequence information."

However, he is pessimistic about the chances of winkling DNA out of H. floresiensis, saying that the molecules are probably too fragmented owing to high temperatures at the excavation site.

But the ACAD scientists think that it is worth making an attempt on their H. floresiensis tooth. They have been encouraged by their successful extraction of DNA from a 6,000-year-old pig tooth from the site in 2007.

http://www.scientificamerican.com/article.cfm?id=researchers-to-drill-for-hobbit

Tuesday, December 7, 2010

Neanderthals: how needles and skins gave us the edge on our kissing cousins

The Neanderthal genome tells us we were very similar: in fact we interbred. But intellect and invention meant that we lived while they perished, says Robin McKie


On the ground floor of the Natural History Museum in London, arrays of Formica-covered cabinets stretch from floor to ceiling and from one end of the great building to the other. Some of nature's finest glories are stored here: pygmy hippo bones from Sicily, mammoth tusks from Siberia and skulls of giant sloths from South America.


Many treasures compete for attention, but there is one sample, kept in a small plywood box, that deserves especial interest: the Swanscombe skull. Found near Gravesend last century, it is made up of three pieces of the brain case of a 400,000-year-old female and is one of only half-a-dozen bits of skeleton that can be traced to men and women who lived in Britain before the end of the last ice age. Human remains do not get more precious than this.

However, the Swanscombe find is important for another, crucial reason: the skull is that of a Neanderthal, that race of shadowy, evolutionary cousins of our own species who made complex stone tools and who once thrived in Europe before being wiped about 35,000 years ago, not long after modern humans had emerged from their African birthplace and had begun to spread across the planet.

"This woman was clearly a member of a very successful tribe of hunter-gatherers to judge from the thousands of stone axes they left behind at Swanscombe," says Professor Chris Stringer, research leader in human origins at the museum.

The reason for the Neanderthals' extinction has been pondered by scientists for 150 years without resolution. These bulky but brainy people have stubbornly refused to give up their secrets. However, a series of remarkable projects has recently shed new light on the Neanderthals and their relationship with modern humans. For the first time, scientists think we may unravel the mystery of their fate. It is a remarkable story that takes us from London to fossil sites across France, Spain, eastern Europe and Africa and – most important of all – to the Max Planck Institute for Evolutionary Anthropology in Leipzig.

The contrast between the institute and the dusty glories of the Natural History Museum could not be greater. The central concourse of this huge glass and concrete building has been fitted with a climbing wall – four storeys high – while a baby grand piano stands, mysteriously, at its foot. "We are encouraged to breakfast, lunch and dine here and to swap ideas," explains geneticist Svante Pääbo. "Hence the piano and climbing wall. We need to take our minds off things occasionally."

Certainly, its researchers deserve relaxation. Set up in 1997 and lavishly funded by the German government as part of its reunification of the country, the institute – in Leipzig, in the former German Democratic Republic – has already pioneered some striking research which culminated this year with completion of the sequencing of a Neanderthal genome.

By any account, this was an extraordinary undertaking. Scientists only succeeded in unravelling the three billion units of DNA that make up the human genome in 2000. Yet within 10 years, Pääbo did the same for a species that had died out more than 30,000 years ago using only bones from Vindija cave in Croatia as his source material. It was simply "fabulous" research, says Ian Tattersall of the American Museum of Natural History.

To create the genome, Pääbo and his team used dentists' drills to extract pill-sized samples of bone cells which were then broken up to reveal the DNA in their nuclei. The risk of researchers contaminating samples with their own DNA required them to wear full-body suits, masks and gloves all the time while air pressure in the laboratory was kept high so no contamination could blow in. And when the team went home, the room was irradiated.

It was a draining, four-year effort. Yet it produced results, with Pääbo outlining the 60% complete Neanderthal genome in May. "Now we can look for areas in the human genome where a change may have swept rapidly through us since we separated from Neanderthals," he said.

However, there was an added sensational aspect to Pääbo's work. He compared his Neanderthal genome with those of five modern humans, from South Africa, western Africa, France, China and New Guinea and found the last three possessed small amounts of Neanderthal DNA. The explanation is intriguing.

At some point during humanity's exodus from Africa, interbreeding between the two species must have taken place, probably when they met 100,000 years ago as Homo sapiens began to move into Neanderthal territory in the Levant. Then, as our species continued to spread round the globe, that Neanderthal DNA was carried with us. Hence it appears in non-Africans but not in Africans. The idea that humans and Neanderthals made love and not war millennia ago generated headlines round the world. "Our work is not about understanding Neanderthals," added Ed Green, one of Pääbo's team. "It's about understanding us."

Certainly, the notion that modern humans and Neanderthals were not just evolutionary cousins but were evolutionary kissing cousins does suggest differences between us may have been relatively slight. We had to be close to interbreed, surely? Thus it was just bad luck that doomed them and not us, a point stressed by Clive Finlayson, of the Gibraltar Museum.

He describes Neanderthals as expert ambush hunters who used thick vegetation to stalk their prey. By contrast, modern humans, who had evolved on the African savannah, were better long-distance runners who could chase their prey over open land. Crucially, as modern humans – or Cro-Magnons, as these early invaders of Europe are also known – entered Europe, climatic change began thinning its dense woodlands and opening up the landscape, giving them a key advantage over Neanderthals. "The roulette wheel of life favoured one and not the other in a particular place and time. A slight change of time, place, climate or fortunes and a Neanderthal might have been writing these lines," Finlayson wrote recently in the Times.

In short, we just got lucky. Apart from some differences in physique and behaviour, we were really very close to one another, it is argued. It sounds plausible. Yet many other scientists dispute this idea and point to a series of recent studies which undermine notions that Neanderthals were the intellectual equals of modern humans. A powerful example is provided by Tom Higham at the Oxford Radiocarbon Accelerator Unit who has used new dating techniques to study artefacts found at Grotte du Renne.

In the 1950s, archaeologists at this key site in central France dug up delicately carved pieces of bone and pierced teeth that had been worn as necklaces. These were attributed – by studying soil layers – to Neanderthal craftsmen and hailed as clear demonstrations of their artistic genius and capacity for symbolic expression. In fact, the artefacts are just about the only evidence so far uncovered which shows Neanderthals had artistic and symbolic talents. Hence the importance of Grotte du Renne.

Higham's work was published in the Proceedings of the US National Academy of Sciences last month and made uncomfortable reading for many researchers. He found that some pieces of Grotte du Renne jewellery that were attributed to Neanderthal "craftsmen" were only 21,000 years old – 10,000 years after the last Neanderthal had died. As timing issues go, this is a tricky one. As Higham says: "This is a site with problems."

In fact, it is now clear that layers of soil must have become mixed up over the millennia and that delicate artwork attributed to Neanderthals was the handiwork of Cro-Magnons. "Thus the single most impressive and widely cited pillar of evidence for the presence of complex symbolic behaviour among the Neanderthal populations in Europe has now effectively collapsed," says Paul Mellars of the University of Cambridge.

In short, the idea that Neanderthals possessed the same capacity for sophisticated expression and thought as modern humans has received a possibly mortal blow, raising serious questions about their intellectual prowess and ability to withstand their rivals, Homo sapiens. This is not to say that Neanderthals were grunting brutes, as was once alleged. They almost certainly possessed considerable skill, some language and a fair measure of compassion to judge from the number of Neanderthals who had clearly been cared for by their tribes after suffering injuries.

Nevertheless, it seems clear that an "intellectual and social gulf" separated them from Homo sapiens, says archaeologist Brian Fagan, in his new book, Cro-Magnon. "What gave our ancestors the edge was their intellectual awareness and imagination, their ability not only to co-operate with others but also to plan ahead and think of their surroundings as a living, vibrant world." We were a class apart, in other words.

But which specific traits gave us such an advantage that we were propelled to global glory at the expense of the Neanderthals? In the suite of behaviours that we evolved in Africa 150,000 years ago, what were the characteristics that really made a difference and can therefore be considered as defining human attributes? There are many candidates – complex language and superior memory, for example. However, among many scientists there appears to be consensus that imagination and opportunism were critical attributes.

This meant, says Fagan, that we learned to use local materials – antler, bone and ivory – in ways Neanderthals simply could not imagine. In one case, this resulted in "one of the most revolutionary inventions in history: the eyed needle, fashioned from a sliver of bone or ivory," he adds. While Neanderthals shivered in rags in winter, humans used vegetable fibres and needles – created by using stone awls – to make close-fitting, layered clothing and parkas: the survival of the snuggest, in short.

A slightly different interpretation is given by Steve Churchill of Duke University, in North Carolina. He believes it was the invention of the first projectile weapons that really did it for Homo sapiens. Bows and arrows as well as spear-throwers – special sticks with hooks – allowed hunters to hurl projectiles with greatly improved accuracy and distance. (An Aborigine still uses a spear-thrower known as a woomera.)

The consequences of these inventions were also profound. It meant Cro-Magnons could kill animals from a considerable – and rather safe – distance of between 20 and 40 metres. Neanderthals continued to fight close up and personal, often to their cost. "Spear-throwers meant you could fire a couple of shots off and not worry about being stamped on or trampled by an angry mammoth," says Churchill.

Evidence for this hypothesis is elusive, though Churchill has found that Cro-Magnon skeletons have signs of strain that suggest they were using such devices. Neanderthals do not.

However, it is unclear whether we used these weapons directly against Neanderthals. Most probably, we just got the best food long before they did. "If you look at other carnivore competitors living in Europe then – cave lions and cave hyenas – these also died out," added Churchill. "We took their food."

Stringer agrees: "If early modern humans had better ways of coping with rapid climate change, such as sewn clothing and more efficient weapons, they would have been more likely to survive. That is not to say modern humans always survived, since populations of both species only existed in their thousands in Europe then. Nevertheless, the effect would have been cumulative. We multiplied and the Neanderthals did not."

Robin McKie

The Observer,