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genetic clues

International experts have identified the creature that gave rise to all the placental mammals – a huge group that includes whales, elephants, dogs, bats and us.

The international effort mapped out thousands of physical traits and genetic clues to trace the lineage.

Their results indicate that all placental mammals arose from a small, furry, insect-eating animal.

A report in Science resolves the debate as to when the creature lived; it came about after the demise of dinosaurs.

That had been a hotly debated question over years of research.

Placental mammals – as opposed to the kind that lay eggs, such as the platypus, or carry young in pouches, such as the kangaroo – are an extraordinarily diverse group of animals with more than 5,000 species today. They include examples that fly, swim and run, and range in weight from a couple of grams to hundreds of tonnes.

A wealth of fossil evidence had pointed to the notion that the group, or clade, grew in an “explosion” of species shortly after the dinosaurs’ end about 65 million years ago.

But a range of genetic studies that look for fairly regular changes in genetic makeup suggested that the group arose as long as 100 million years ago, with mammals such as early rodents sharing the Earth with the dinosaurs.

Deciphering the very distant past on the basis of fossils and animals that are around today is inherently a subjective business.

“Comparative anatomy” – in which, for example, the forelimbs of a number of fossils are compared to establish which are most closely related – was the entire toolbox for the earliest palaeontologists. The era of genetics ushered in a more incisive tool to compare similarities across species.

But the new work tackles the question of placental mammals in unprecedented detail, developing a database of physical and genetic data some 10 times larger than any used previously – and taking a decidedly modern take on it.

“Anatomy and research in palaeontology had a very 19th Century veneer to it – that we would sit in small groups in a lab with a fossil describing it,” said lead author of the study Maureen O’Leary of Stony Brook University in New York, US.

“That is a very effective and important part of what we do, but by trying to bring this into the 21st Century and using new software, we were able to really band together as a group of experts and tackle a much larger problem,” she said.

International experts have identified the creature that gave rise to all the placental mammals

International experts have identified the creature that gave rise to all the placental mammals

To build the database, the team gathered more than 4,500 details of phenotype – diet, lengths of limbs, shapes of teeth, length of fur if any, and so on – from 86 different species that are around today, and from 40 fossils of extinct animals.

To that they added some 12,000 detailed images and genetic information for all of the current species, putting all the data into what Dr. Maureen O’Leary called “a supermatrix – essentially like a spreadsheet, filled with observations and images, to create a really rich description of mammals we’d sampled”.

That, in essence, allows not just one or a few researchers to log details and make comparisons of, for example, fossil or genetic data; it becomes a problem shared – in this case, among 23 co-authors.

“That really wasn’t possible until we developed this software called Morphobank. Our experts in China or Brazil or Canada or the US or just across the hall could all be working in one place at the same time,” Dr. Maureen O’Leary said.

By noting which traits have been preserved down the lineage and how they are expressed, the team was able to feed their phenotypic and genetic data into standard software that makes relationship and age estimates – suggesting the ancestral animal lived just 200,000 years after the extinction event that saw the end of the dinosaurs.

It also yields informed guesses as to the traits of the ancestral animal that gave rise to them all – incorporating those traits into an artist’s conception of what it would have looked like.

The result resolves a long-standing debate, but Dr. Maureen O’Leary said it could also contribute to a new way of tackling such debates.

“I think that it will go a long way toward showing people a way forward for using all the data… both DNA and anatomy. I think that had been an intimidating kind of project because of its scale,” she said.

“Now that we can do that…we are sort of iteratively working and refining the <<Tree of Life>> in that way.”

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A race to unlock genetic clues behind living to 100 is set to begin next year, after a US team announced it will compete for the $10 million Genomics X Prize.

Genetic entrepreneur Dr. Jonathan Rothberg is entering the challenge to identify genes linked to a long, healthy life.

His team – and any other contenders – will be given 30 days to work out the full DNA code of 100 centenarians at a cost of no more than $1,000 per genome.

The race will start in September 2013.

Under the rules of the Archon Genomics X Prize, teams have until next May to register for the competition.

A race to unlock genetic clues behind living to 100 is set to begin next year, after a US team announced it will compete for the $10 million Genomics X Prize

A race to unlock genetic clues behind living to 100 is set to begin next year, after a US team announced it will compete for the $10 million Genomics X Prize

Dr. Jonathan Rothberg’s team from Life Technologies Corporation in California is the first to formally enter the race.

Being able to sequence the full human genome at a cost of $1,000 or less is regarded as a milestone in science.

It is seen as the threshold at which DNA sequencing technology becomes cheap enough to be used widely in medicine, helping in diagnosis and in matching drugs to a patient’s genetic make-up.

One hundred people aged 100 have donated their DNA for the project.

Scientists believe people who reach a very old age may have certain rare changes in their genes which protect against common diseases of later life, such as heart disease and cancer.

If these genes can be identified by analyzing the DNA codes of centenarians, it will help scientists search for new medical treatments and perhaps ways to prolong life.

However, many sample DNA sequences will be needed in order to get the accuracy needed to pinpoint changes on the scale of a few genetic letters among the three billion in the human genome.

Dr Jonathan Rothberg, a geneticist and entrepreneur, said the DNA of 100 centenarians is a good start towards finding “the fountains of youth”.

He said: “One hundred people will give you a hint. One thousand will make you reasonably sure. Ten thousand will let you say, <<Hey, these are the genes involved in cancer or heart disease>>.”

Dr. Craig Venter is the originator of the prize and one of the main players in the race to sequence the first human genome, which was completed in 2003.

He said he could never have imagined that genome sequencing would come this far in so little time.

Dr. Craig Venter: “I can’t emphasize [enough] how impressed I am with the progress of technology and the dropping of the cost.

“If they can do a human genome in two hours with one little machine, it’s just stunning. We have come a long way.”

The X Prize Foundation offers awards for solutions to modern scientific challenges, from space to the human genome.

Any data gleaned from the X Prize will be shared with other scientists in the field, to aid the quest for insights into ageing.