Posts Tagged ‘dna’

Bone Analysis sheds new light on ill-fated arctic expedition

March 27, 2011

English Heritage 18.03.2011 – Original article here

New isotope analysis and forensic facial reconstruction undertaken by a team led by English Heritage has shed new light on the doomed 1845 British voyage of Arctic exploration led by Sir John Franklin, in which all 129 people on board perished.

Analysis of the only surviving complete skeleton has offered new clues as to why the expedition was lost, a mystery that has sparked debate ever since. Some have suggested that scurvy or tuberculosis may have been causes of debilitation and death on the expedition, but no evidence of these diseases was found on the bones, and DNA tests proved negative for tuberculosis. Work is still ongoing on samples from the remains to analyse for lead to see if lead poisoning from the expedition’s canned food or from their water supply was a factor.

The study has also revealed that the identity of the skeleton is unlikely to be Henry LeVesconte, a Lieutenant aboard one of the ships, a conclusion that has been widely accepted since the skeleton was first examined in 1872 by Thomas Henry Huxley, one of the foremost biologists of the age.

Daguerreotype of Goodsir (left, copyright: National Maritime Museum) and the facial reconstruction

The remains thought to be Le Vesconte’s, and those of one other sailor, were the only ones ever to be returned to Britain. The lieutenant’s bones were buried beneath the Franklin Expedition monument at the old Royal Naval College in Greenwich. Renovations in 2009 of the memorial meant that the remains had to be exhumed and temporarily moved. This gave an opportunity for English Heritage to study the remains and to evaluate the twin questions of the identity of this particular skeleton and the reasons for loss of the expedition.

Henry LeVesconte grew up in Devon. However, analysis of stable isotopes from the teeth of the skeleton shows that it is unlikely that this individual grew up there, but more likely that he spent his childhood in NE England or eastern Scotland.

Moreover, 14 of the 24 officers on the expedition had their portraits taken by the newly devised Daguerreotype photographic process prior to embarkation.  A forensic facial reconstruction was undertaken using the skull of the skeleton, and it seemed to match quite closely the appearance of Harry Goodsir, an assistant surgeon and naturalist on the voyage.

Dr Simon Mays, skeletal biologist at English Heritage, said: ‘ The study of human remains and in turn our understanding of the past has benefited immensely from the advance of science and technology. The disappearance of Franklin’s heroic crew became a cause celebre in Victorian England, and the reasons for its loss continue to be debated. Our study offers some important clues to take the debate further.

‘The identity of the skeleton is difficult to ascertain but the new evidence seems to show that it is unlikely to have been Henry LeVesconte. The facial resemblance to Harry Goodsir is striking, and the isotope evidence is consistent with it being him, but the identification is not 100% certain because some officers on the voyage were not photographed.  However, tissue samples from the remains were retained so attempts at a DNA match with a living direct descendant of Goodsir can be made should anyone come forward.’

In May 1845, an expedition of two ships, commanded by Sir John Franklin and sponsored by the Royal Navy, set out from England to try and discover the Northwest Passage trade route to Asia. The expedition’s disappearance caused a sensation in Britain, prompting huge rescue efforts that helped map much of the vast and remote polar archipelago of the Canadian Arctic.

The study was undertaken at the request of the Greenwich Foundation for the Old Royal Naval College and with the consent of a LeVesconte relative at English Heritage’s laboratories in Portsmouth and at the Universities of Bradford and Surrey between 2009 and 2011. The remains have been reburied under the memorial.

Resurrected Mammoth Blood Very Cool

May 5, 2010

Professor Alan Cooper is pictured here with a mammoth bone. (Credit: University of Adelaide)

(University of Adelaide via ScienceDaily, 3 May 2010) — A team of international researchers has brought the primary component of mammoth blood back to life using ancient DNA preserved in bones from Siberian specimens 25,000 to 43,000 years old. Studies of recreated mammoth hemoglobin, published May 3 in Nature Genetics, reveal special evolutionary adaptations that allowed the mammoth to cool its extremities down in harsh Arctic conditions to minimize heat loss. “It has been remarkable to bring a complex protein from an extinct species, such as the mammoth, back to life,” says Professor Alan Cooper, Director of the Australian Centre for Ancient DNA (ACAD) at the University of Adelaide, where the mammoth hemoglobin sequences were determined. This is true paleobiology, as we can study and measure how these animals functioned as if they were alive today.” Professor Cooper is an Australian Research Council Future Fellow and a member of the University’s Environment Institute. “We’ve managed to uncover physiological attributes of an animal that hasn’t existed for thousands of years,” says team leader Professor Kevin Campbell of the University of Manitoba, Canada. “Our approach opens the way to studying the biomolecular and physiological characteristics of extinct species, even for features that leave no trace in the fossil record.” The project began over seven years ago when Professor Campbell contacted Professor Cooper, who was then based at the University of Oxford, to suggest resurrecting mammoth hemoglobin.

Original article here

Neither Neanderthal nor sapiens: new human relative IDed

March 30, 2010
By John Timmer | Last updated 3 days ago

At a press conference yesterday, researchers announced the completely unexpected: a Siberian cave has yielded evidence of an entirely unknown human relative that appears to have shared Asia with both modern humans and Neanderthals less than 50,000 years ago. The find comes courtesy of a single bone from individual’s hand. Lest you think that paleontologists are overinterpreting a tiny fragment, it wasn’t the shape of the bone that indicates the presence of a new species—it was the DNA that it contained.

The paper that describes the finding comes courtesy of the Max Planck Institute’s Svante Pääbo, who has been actively pursuing the sequencing of the Neanderthal genome. It seems likely that this particular bone fragment was targeted due to suspicions that it might also provide an additional Neanderthal sequence. The site, called Denisova, is in the Altai Mountains of southern Siberia, an area that has had hominins present as early as 125,000 years ago. The sample itself came from a layer of material that dates from between 30,000 and 50,000 years ago. Neanderthal DNA was found in a sample from the same time period less than 100km away, while artifacts indicate that modern humans were also present in the region by 40,000 years ago.

So, there was no apparent reason to suspect that the bone would yield anything more than a familiar sequence. And in fact, most of the first half of the paper simply describes the methods used to construct a complete sequence of the mitochondrial DNA, including over 150-fold coverage of the genome, and an alignment program designed to account for the errors typical of ancient DNA sequences. About the only surprise here is that Pääbo’s group has switched from using 454 sequencing machines to those made by Illumina.

Various checks indicate that the sequence the authors obtained contains damage that’s typical of ancient DNA, and that it all comes from a single individual. So far, quite typical.

Things got quite unusual when they attempted to align the sequence to the mitochondrial DNA from the hominin species that were likely to be present at that time and place: human and Neanderthal. Instead of clustering with one or the other, the Denisova mitochondrial genome was a clear outlier, having about 385 differences with the typical human mitochondrial genome. In contrast, Neanderthals only differ from modern humans by an average of 202. The obvious interpretation is that the Denisova lineage split off before modern humans and Neanderthals did. If we accept that Neanderthals are a distinct species of hominin (and we do), then this sample clearly represents yet another one.

Building a tree with the chimpanzee genomes and assuming a divergence time of 6 million years, the data indicates that the Denisova lineage diverged about a million years ago. At that point, Homo Erectus was already a global species, but our human ancestors were still in Africa. That suggests that the Denisova variant probably originated in, or at least near, Africa as well, although there’s no way to tell whether it was a distinct species before it started migrating, or whether it became an isolated population because of a migration.

The paper is in the format of a Nature letter, which allows only a paragraph for discussion. The authors use that space primarily to note that, 40,000 years ago, southern Siberia was a very busy place as far as hominins are concerned, with at least three different species present within a very narrow time frame. If we accept that the Indonesian hobbits are yet another distinct species—and the relevant community seems to be leaning that way—then it appears that there were at least four distinct hominin species cohabiting the globe in the very recent past.

As surprising as that is, it’s only a small fraction of the implications of this work. For starters, there’s the whole idea that we can identify a new species without having any idea what it actually looked like—in fact, without having any idea of whether it would be physically distinct enough from any of the other hominin species around that we’d even have known it were a separate species based on the bones.

The authors also briefly touched on a separate issue: this ability will be unevenly distributed in space and time. DNA simply lasts longer in cool climates, as evidenced by the recent announcement that DNA had been obtained from a polar bear sample that was over 100,000 years old. So, any species that was stuck near the equator—like the hobbits—are unlikely to be in on the DNA revolution. This is especially unfortunate given the fact that, as noted above, a lot of the most interesting action in hominin origins seem to have been taking place in Africa.

Then there’s the whole question of what else we might be missing. Avoiding contamination issues with modern DNA is easiest if the entire excavation is designed around a sterile technique from the start, meaning bones that have been previously excavated aren’t ideal. At the moment, at least, sequencing from a single sample is also pretty labor intensive (this paper had seven authors), meaning we aren’t likely to be able to just start sequencing any bone fragments we stumble across. Figuring out how to prioritize what might be informative will be a real challenge.

If that seems like a lot of questions for a short and fairly technical paper (and it is), it’s a product of the fact that this paper seems truly exceptional. Because of the rich history of most fields of science, there aren’t a whole lot of truly unexpected results, since you typically know that there are people working in a given area. But this finding is truly a stunning one, and really seems to be a complete surprise.

Nature, 2010.

Original article here.

Man’s early ancestors are pictured together for the first time

March 28, 2010

By Daily Mail Reporter
26th March 2010
A mysterious species of ancient human has been discovered in a cave in southern Siberia. Nicknamed X-Woman, scientists say the human lived alongside our ancestors tens of thousands of years ago. The discovery, which could rewrite mankind’s family tree, was made after analysis of DNA from a fossilised finger bone.

human ancestors

Back in the beginning: Living 6.8million years ago this is Sahelanthropus tchadensis. Parts of its jaw bone and teeth were found nine years ago in the Djurab desert, Chad, and from this scientists created this model head

human ancestors

This young woman lived between 100,000 and 90,000 years ago. Her skull and mandible were found in a cave in Israel in 1969 along with the remains of 20 others. The size of their skulls was higher than that of the average person today

Experts believe the finger belonged to a child who died 48,000 to 30,000 years ago.

It was thought only two species of early humans lived at that time – the ancestors of modern man and the Neanderthals, who died out soon afterwards.

But the DNA evidence published in the journal Nature reveals a third species.

The latest study was based on an analysis of ‘mitochondrial’ DNA – a genetic code passed from mothers to children.

Researcher Dr Svante Pääbo said the code was different from that of Neanderthals and modern humans and was ‘a new creature that’s not been on our radar screens so far’.

The scientists are unable to say what X-Woman looked like and are even unsure if the finger belonged to a male of female, but Dr Pääbo said they named her X-Woman ‘because its mitochondrial and we want to take a feminist tack on this’.

The discovery of the ‘X-Woman’ comes as scientists revealed images of what man looked like millions of years ago.

Gathering bone fragments from across the globe, paleoanthropologists used sophisticated research methods to form the 27 model heads, which are on show at the Senckenberg Natural History Museum in Frankfurt, Germany.

The exhibition goes back seven million years to sahelanthropus tchadensis and traces the numerous stages of man culminating with modern-day homo sapiens.

Each of the heads is used to tell its story: where they lived; what they ate; and what killed them.

It shows how researchers today use satellite image analysis and computer tomography.

There is little doubt that Africa is the cradle of humanity and this is where the most ancient of the remains were unearthed. But clues to other pre-human species have been found in the Middle East and Far East.

Only a few thousand fossils of pre-human species have ever been discovered and entire sub-species are sometimes known only from a single jaw or fragmentary skull.

human ancestors

This skull was fashioned from a skull and jaw found in the remains of 17 pre-humans (nine adults, three youths and five children) which were discovered in the Afar Region of Ethiopia in 1975. They are believed to have lived 3.2million years ago

human ancestors

Meet ‘Mrs Ples’ who was unearthed in Sterkfontein, South Africa in 1947. Her whole skull was found and it is believed she lived 2.5million years ago. Sediment traces found on the inside of her skull indicate to scientists that she died by falling into a chalk pit

human ancestors

The skull of this male adult was found on the western shore of Lake Turkana in Kenya in 1985. He is believed to have lived in 2.5million years ago. The shape of the mouth indicates that he had a strong bite and that he could chew sinewy plants

human ancestors

This species of sub-human – Homo rudolfensis – was found in Koobi Fora, Kenya, in 1972. The adult male is believed to have lived about 1.8million years ago. He used stone axes ate meat and plants and lived on the wooded edge of Lake Turkana in Eastern Africa

human ancestors

Researchers shaped this skull on the basis of this discovery of ‘Zinj’ in 1959. The adult male lived 1.8million years ago in the Olduvai Gorge of Tanzania. He would have fed himself on seeds, plants and roots which he dug out with bones

human ancestors

The near-complete skeleton of ‘Turkana Boy’, a male adolescent aged about 13, was found in Nariokotome, Kenya, in 1984. He lived 1.6million years ago. His teeth and skull bear a close resemblance to discoveries in Asia of homo erectus

Experts are often forced to resort to educated guesswork to fill in the gaps in research to come up with images of human ancestors.

Each new discovery means paleoanthropologists have to rethink the origins of man’s ancestors.

The previously held concept of primitive man – characterised by a large brain and the ability to manufacture tools – has had to be changed by researchers.

European natives of primitive man, homo heidelbergensis, are believed to have been able to make perfect javelins from wood 400,000 years ago and are also thought to have had the ability to plan for the future.

Neanderthals are also now thought to have had far more culture and craft skills than earlier research indicated.

human ancestors

Discovered in Java, Indonesea, this skull belonging to ‘Sangiran 17’ is believed to have belonged to an adult male who probably lived around 800,000 years ago. He was found by an Indonesian farmer hacking away in a field. Sangiran is believed to have used fire

human ancestors

The discovery of this adult male in Sima de los Huesos, Spain, in 1993 points to an early stage in the evolution of neanderthal man due to the shape of his face. ‘Miquelon’ was around 1.75m tall and lived about 500,000 to 350,000 years ago. His remains were found with that of 31 others which led researchers to believe this was a burial site

human ancestors

The skull and jaw of this female ‘hobbit’ was found in Liang Bua, Flores, Indonesia, in 2003. She was about 1m tall and lived about 18,000 years ago. The discovery brought into question the belief that Homo sapiens was the only form of mankind for the past 30,000 years. Homo sapiens are the primate species to which modern humans belong

human ancestors

The ‘Old man of La Chapelle’ was recreated from the skull and jaw of a male found near La Chapelle-aux-Saints, in France in 1908. He lived 56,000 years ago. His skeleton indicated he suffered a number of illness including arthritis and had numerous broken bones. This was not noticed when he was first discovered and gave rise to the mistaken belief that neanderthal man was a hunched individual. His relatively old age of between 40 to 50 indicates he was looked after by a clan

Climate change may have shaped polar bear origins

March 7, 2010

Allison Cross, NunatsiaqOnline march 3. 2010
“The polar bear is an evolutionary young species that split off from brown bears”

DNA extracted from a polar bear fossil found in Norway is giving scientists rare insight into the origin of the species, suggesting that polar bears may have evolved from brown bears in response to climate change in the past.

“Our results confirm that the polar bear is an evolutionary young species that split off from brown bears some 150,000 years ago and evolved extremely rapidly,” said researcher Charlotte Lindqvist, from State University of New York at Buffalo.

“Perhaps adapting to the opening of new habits and food sources in response to climate changes,” Lindqvist said.

But the polar bears’ success in weathering temperature fluctuations over the past 150,000 years doesn’t necessarily mean the bears, like those living in Canada’s North, can make it through global warming today, the researchers said.

Lindqvist explores the evolutionary origins of polar bears in a paper she co-authored with researchers from Penn State University and the University of Oslo, and published recently in the journal Proceedings of the National Academy of Sciences.

Polar bear fossils are rare, but in 2004, a geologist from Iceland found a fossil jawbone and canine tooth in the Svalbard archipelago of Norway, north of the mainland.

After the find, Lindqvist drilled into the bone and tooth to extract powder that could be analyzed. Scientists then sequenced the mitochondrial DNA, which tends to reveal the most useful characteristics when examining the evolution of a species.

Knowing the age of polar bears actually helps scientists better determine which major climate events they lived through, Schuster said.

But it would be wrong to assume that because polar bears were resilient in the past, they are just as resilient now, Schuster said.

“You have to be… careful because a polar bear from 50,000 years ago or 100,000 years ago might have been a different animal,” he said. “There is always a constant change.”

Polar bears live their lives on the ice, so when they die, their remains often sink to the bottom of the ocean or are picked apart by scavengers.

There are only two known polar bear fossils in the world, said Stephan Schuster, from Penn State’s Centre for Comparative Genomics and Bioinformatics, and only one contains any DNA.

Many scientists believe that polar bears in Canada, and elsewhere in the world, are threatened by a loss of their sea ice habitat as a result of warming temperatures.

“The polar bear may be more evolutionarily constrained because it is today very specialized,” Lindqvist said. “[It is] physically and behaviourally well-adapted to living on the edge of Arctic ice, subsisting on a few species of seals.”

There is significant concern that polar bears across the world will become “extirpated,” which means to disappear or retreat from a region, although continue to live in other areas.

Andrew Derocher, a polar bear biologist at the University of Alberta in Edmonton, said some estimates peg the polar bear as being much older than 150,000 years.

Some research indicates they have been around 700,000 years, or for even as long as one million years, he said.

“I don’t think the research tells us very much [about the future] of polar bears,” he said. “But it helps to fill in some of the gaps about the past. That’s really where our understanding of the evolution of polar bears is really challenging us.”

Original article here

Nunatsiaq Online seem to be reporting on a story featured in the national broadcasting company of Norway, NRK.
NRK article here (norwegian only)

Ancient Man in Greenland Has Genome Decoded

February 14, 2010

New York Times/NICHOLAS WADE February 10, 2010
The genome of a man who lived on the western coast of Greenland some 4,000 years ago has been decoded, thanks to the surprisingly good preservation of DNA in a swatch of his hair so thick it was originally thought to be from a bear.

An artist’s impression of “Inuk.” Nuka Godfredsen.

This is the first time the whole genome of an ancient human has been analyzed, and it joins the list of just eight whole genomes of living people that have been decoded so far. It also sheds new light on the settlement of North America by showing there was a hitherto unsuspected migration of people across the continent, from Siberia to Greenland, some 5,500 years ago.

The Greenlander belonged to a Paleo-Eskimo culture called the Saqqaq by archaeologists. Using his genome as a basis, a team of researchers from the University of Copenhagen determined that the Saqqaq man’s closest living relatives were the Chukchis, people who live at the easternmost tip of Siberia. His ancestors split apart from Chukchis some 5,500 years ago, according to genetic calculations, implying that the Saqqaq people’s ancestors must have traveled across the northern edges of North America until they reached Greenland.

The team, led by Morten Rasmussen and Eske Willerslev of the University of Copenhagen, decoded the genome from four tufts of hair dug out of the permafrost at Qeqertasussuk, on the west coast of Greenland. The hair was excavated in 1986 and kept in a plastic bag in the National Museum of Denmark. It was found with other waste, and the scientists speculate that it was the result of a haircut.

There it moldered, unfrozen, until discovered by Dr. Willerslev, an expert on ancient DNA. Having spent two months digging for ancient human DNA in Greenland without finding any human remains, he concluded that ancient Greenlanders must have disposed of their dead by laying them on the sea ice. Only on complaining of his bad luck to a friend did he learn that the friend’s father had found the hair sample 20 years earlier.

No traces of the Saqqaq people have been found in North America, said Michael H. Crawford, an expert on circumpolar populations at the University of Kansas and a co-author of the report. Because the land bridge that once connected Siberia and Alaska had long since foundered, the Saqqaq people might have crossed to Alaska on the winter ice or could have used the boats on which they hunted fish and seals. They evidently kept to Arctic latitudes, perhaps because more southerly regions were already occupied by the Inuit, or because they were better adapted to life in the Arctic, Dr. Rasmussen said.

The Saqqaq man’s genome is so complete that the Danish researchers have been able to reconstruct his probable appearance and susceptibility to disease from the genetic information in his genome. They conclude that he would have had brown eyes because of variations, at four positions along his DNA, that are associated with brown eye color in East Asians.

He has the East Asian version of a gene known as EDAR, which endows people with hair that is thicker than that of most Europeans and Africans. Another gene suggests that he would have had dry earwax, as do Asians and Native Americans, not the wet earwax of other ethnic groups.

Perhaps reflecting the so far somewhat limited reach of personal genomics, the researchers note that the ancient Greenlander was at risk for baldness, a surprising assessment given that all that remains of him is his hair. Dr. Rasmussen said he assumed the man died young.

Biologists used to think that DNA would be found only in the cells at the roots of the hair, not in the keratin of which the hair shaft is made. But it now seems that the cells become incorporated into the growing shaft and their DNA is sealed in by the keratin, protecting it from attack by bacteria and fungi.

The Danish researchers, using an advanced DNA sequencing technology developed by Illumina of San Diego, reported that they were able to decode 80 percent of the ancient Greenlander’s genome to a high degree of accuracy. Their findings appear in the journal Nature.

An ever present danger in analyzing ancient human DNA is contamination, particularly from modern human DNA from all the archeologists and curators who have touched the samples. The Danish researchers said they took precautions to exclude this and other contaminants, and they seem to have succeeded.

Original article here