Category Archive 'DNA'
22 Jul 2009
Jonathan Shaw in Harvard Magazine explains that studies of population DNA suggest that an effective policy of sexual apartheid practiced by the newly arrived Anglo-Saxons could have eliminated British male Y chromosomal DNA in as few as five generations. The Spanish conquistadores in Colombia and the Vikings in Scotland and Ireland left similar DNA patterns, in which the male heredity of the modern population is overwhelming traceable to the invaders, but female mitochondrial DNA predominantly descends from the conquered population.
Moral? Successful invaders get the girls. At some level, history amounts to a contest over who gets to reproduce his DNA, and who does not.
There are no signs of a massacre—no mass graves, no piles of bones. Yet more than a million men vanished without a trace. They left no descendants. Historians know that something dramatic happened in England just as the Roman empire was collapsing. When the Anglo-Saxons ﬁrst arrived in that northern outpost in the fourth century a.d.—whether as immigrants or invaders is debated—they encountered an existing Romano-Celtic population estimated at between 2 million and 3.7 million people. Latin and Celtic were the dominant languages. Yet the ensuing cultural transformation was so complete, says Goelet professor of medieval history Michael McCormick, that by the eighth century, English civilization considered itself completely Anglo-Saxon, spoke only Anglo-Saxon, and thought that everyone had “come over on the Mayﬂower, as it were.” This extraordinary change has had ramiﬁcations down to the present, and is why so many people speak English rather than Latin or Celtic today. But how English culture was completely remade, the historical record does not say.
Then, in 2002, scientists found a genetic signature in the DNA of living British men that hinted at an untold story of Anglo-Saxon conquest. The researchers were sampling Y-chromosomes, the sex chromosome passed down only in males, from men living in market towns named in the Domesday Book of 1086. Working along an east-west transect through central England and Wales, the scientists discovered that the mix of Y-chromosomes characteristic of men in the English towns was very different from that of men in the Welsh towns: Wales was the primary Celtic holdout in Western Britannia during the ascendance of the Anglo-Saxons. Using computer analysis, the researchers explored how such a pattern could have arisen and concluded that a massive replacement of the native fourth-century male Britons had taken place. Between 50 percent and 100 percent of indigenous English men today, the researchers estimate, are descended from Anglo-Saxons who arrived on England’s eastern coast 16 centuries ago. So what happened?
21 Jan 2009
Scientific evidence has been found that currently unknown forms of stored data beyond DNA may function in the transmission of inherited traits.
Scientists at the Centre for Addiction and Mental Health (CAMH) have detected evidence that DNA may not be the only carrier of heritable information; a secondary molecular mechanism called epigenetics may also account for some inherited traits and diseases. These findings challenge the fundamental principles of genetics and inheritance, and potentially provide a new insight into the primary causes of human diseases.
12 Jan 2009
Everyone with blue eyes shares a common matrilineal ancestor who lived between 6000 and 10000 years ago.
19 Aug 2008
The New York Times summarizes an article on European Genetics from Current Biology which arrives the conclusion that it could very likely be possible to identify the nationality of Europeans by genetic testing.
Europe has been colonized three times in the distant past, always from the south. Some 45,000 years ago the first modern humans entered Europe from the south. The glaciers returned around 20,000 years ago and the second colonization occurred about 17,000 years ago by people returning from southern refuges. The third invasion was that of farmers bringing the new agricultural technology from the Near East around 10,000 years ago.
The pattern of genetic differences among present day Europeans probably reflects the impact of these three ancient migrations, Dr. Kayser said.
The map also identifies the existence of two genetic barriers within Europe. One is between the Finns (light blue, upper right) and other Europeans. It arose because the Finnish population was at one time very small and then expanded, bearing the atypical genetics of its few founders.
The other is between Italians (yellow, bottom center) and the rest. This may reflect the role of the Alps in impeding free flow of people between Italy and the rest of Europe.
Correlation between Genetic and Geographic Structure in Europe article
08 Aug 2008
Results show modern humans, Neandertals diverged 660,000 years ago
An international consortium of researchers reports in the Aug. 8 Cell that for the first time the complete sequence of mitochondrial DNA from a Neandertal has been deciphered. Comparison of the Neandertal sequence with mitochondrial sequences from modern humans confirms that the two groups belong to different branches of humankind’s family tree, diverging 660,000 years ago.
That date is not statistically different from previous estimates of the split between humans and Neandertals, says Erik Trinkaus, a paleoanthropologist at Washington University in St. Louis. The sequence also doesn’t reveal what happened to drive Neandertals to extinction, but it does clear up some discrepancies in earlier studies. ...
At 16,565 bases long, the new sequence is the largest stretch of Neandertal DNA ever examined. The DNA was isolated from a 38,000-year-old bone found in a cave in Croatia.
“It’s a nice accomplishment and the next important step toward completing the Neandertal genome,” says Stephan Schuster of Pennsylvania State University in University Park. Schuster is part of a group that is sequencing the genomes of the mammoth and other extinct animals, but was not involved in the current study. “It’s a nice landmark on the way to saying what makes modern humans so special.”
In order to know exactly how modern humans and Neandertals differ, scientists will need to examine DNA from the Neandertal’s entire genome. The sequence reported in the new study was generated as part of a project to decode Neandertal DNA, but it contains information only about DNA from mitochondria.
Mitochondria are organelles that generate energy for a cell. Inside each mitochondrion is a circular piece of DNA that contains genes encoding some of the key proteins responsible for power generation. Mitochondria are passed down from mothers to their children. Scientists use variations in mitochondrial DNA as a molecular clock to tell how fast species are evolving.
Scientists have previously examined a short piece of Neandertal mitochondrial DNA known as the hypervariable region, but this new complete sequence helps clear up some ambiguities from studies comparing Neandertals and humans, says John Hawks, a biological anthropologist from the University of Wisconsin–Madison.
Some modern humans have several changes in the hypervariable region that made it seem as if Neandertals are more closely related to modern humans than humans are to each other.
“Comparing the complete mitochondrial DNA genomes of a Neandertal and many recent humans presents a very different picture,” Hawks says. “Humans are all more similar to each other, than any human is to a Neandertal. And in fact the Neandertal sequence is three or more times as different, on average, from us as we are from each other. This change from the earlier picture is a purely statistical one, but it makes a clearer picture.”
Human and Neandertal mitochondrial DNAs differ at 206 positions out of the 16,565 examined, while modern humans differ at only about 100 positions when compared with each other.
17 Jul 2008
British newspapers report that living residents of Nienstedt, a village in the foothills of the Harz Mountains in Lower Saxony, have been found by DNA analysis to be relatives of 3000-year-old Bronze Age inhabitants of the same area interred in the nearby Lichtensteinhöhle cave.
The good news for two villagers in the Söse valley of Germany yesterday was that they have discovered their (127th times)-great grandparents.
The bad news is that their long-lost ancestors may have grilled and eaten other members of their clan.
Every family has its skeletons in the cave, though, so Manfred Hucht-hausen, 58, a teacher, and 48-year-old surveyor Uwe Lange remained in celebratory mood. Thanks to DNA testing of remarkably well-preserved Bronze Age bones, they can claim to have the longest proven family tree in the world. “I can trace my family back by name to 1550,” Mr Lange said. “Now I can go back 120 generations.”
Mr Lange comes from the village of Nienstedt, in Lower Saxony, in the foothills of the Harz mountain range. “We used to play in these caves as kids. If I’d known that there were 3,000-year-old relatives buried there I wouldn’t have set foot in the place.”
The cave, the Lichtensteinhöhle, is made up of five interlocked natural chambers. It stayed hidden from view until 1980 and was not researched properly until 1993. The archaeologist Stefan Flindt found 40 skeletons along with what appeared to be cult objects. ...
Analysis showed that all the bones were from the same family and the scientists speculated that it was a living area and a ceremonial burial place.
About 300 locals agreed to giving saliva swabs. Two of the cave family had a very rare genetic pattern – and a match was found.
The bones of 40 people were shielded from the elements by calcium deposits that formed a protective skin around the skeletons.
All the remains turned out to be from the same family group who had a distinctive – and rare – DNA pattern.
When people in the local area were tested with saliva swabs, two nearby residents turned out to have the same distinctive genetic characteristic.
Manfred Huchthausen, a 58-year-old teacher, and Uwe Lange, a 48-year-old surveyer, now believe they are even more local than either of them thought.
Inma Pazos at iGENEA Forum provides more specific information.
(translated & abridged)
DNA analysis really found that 15 of 22 skeletons were relatives, constituting several generations of a family clan. In 2007, about 300 DNA samples of today’s indigenous population in Osterode-am-Harz were collected and tested for possible affinity. Susann Hummel, a leading anthropologist, has identified eleven living persons as descendants of the cave burials.
Ten lines of mtDNA haplogroup H, four of haplogroup U, two of the haplogroup J and three of the haplogroup T were identified. A further breakdown in the sub-groups succeeded in identifying U5b, T2 and J1b1. In another case, membership in sub-group U2 was considered very likely.
25 Apr 2008
Human beings may have had a brush with extinction 70,000 years ago, an extensive genetic study suggests. The human population at that time was reduced to small isolated groups in Africa, apparently because of drought, according to an analysis released Thursday.
The report notes that a separate study by researchers at Stanford University estimated the number of early humans may have shrunk as low as 2,000 before numbers began to expand again in the early Stone Age.
“This study illustrates the extraordinary power of genetics to reveal insights into some of the key events in our species’ history,” Spencer Wells, National Geographic Society explorer in residence, said in a statement. “Tiny bands of early humans, forced apart by harsh environmental conditions, coming back from the brink to reunite and populate the world. Truly an epic drama, written in our DNA.”
Wells is director of the Genographic Project, launched in 2005 to study anthropology using genetics. The report was published in the American Journal of Human Genetics.
Previous studies using mitochondrial DNA — which is passed down through mothers — have traced modern humans to a single “mitochondrial Eve,” who lived in Africa about 200,000 years ago.
The migrations of humans out of Africa to populate the rest of the world appear to have begun about 60,000 years ago, but little has been known about humans between Eve and that dispersal.
The new study looks at the mitochondrial DNA of the Khoi and San people in South Africa which appear to have diverged from other people between 90,000 and 150,000 years ago.
The BBC reports the study’s conclusion that mankind nearly split into two separate species at the same time.
Ancient humans started down the path of evolving into two separate species before merging back into a single population, a genetic study suggests.
The genetic split in Africa resulted in distinct populations that lived in isolation for as much as 100,000 years, the scientists say.
This could have been caused by arid conditions driving a wedge between humans in eastern and southern Africa.
Behar et al., The Dawn of Human Matrilineal Diversity, The American Journal of Human Genetics (2008), doi:10.1016/j.ajhg.2008.04.002
31 Jan 2008
Genetic studies apparently have found a mutation which took place 6-10,000 years ago and is the cause of the eye color of all blue-eyed humans alive on the planet today.
But aren’t the divergences of the predominant European Ydna and mtDNA haplogroups a good deal older than that?
Hat tip to Karen L. Myers.
03 Dec 2007
The region around Liverpool was once a major Viking settlement, according to a genetic study of men living in the area.
The research tapped into this Viking ancestry by focusing on people whose surnames were recorded in the area before its population underwent a huge expansion during the industrial revolution. Among men with these “original” surnames, 50% have Norse ancestry.
The find backs up historical evidence from place names and archaeological finds of Viking treasure which suggests significant numbers of Norwegian Vikings settled in the north-west in the 10th century. “[The genetics] is very exciting because it ties in with the other evidence from the area,” said Professor Stephen Harding at the University of Nottingham, who carried out the work with a team at the University of Leicester led by Professor Mark Jobling.
They used historical documents, including a tax register from the time of Henry VIII, to identify surnames common in the region. They then recruited 77 male volunteers with “original” surnames, and looked for a genetic signature of Viking ancestry on the Y chromosome. They report in Molecular Biology and Evolution that a Y chromosome type, R1a, common in Norway, is also very common among men with original surnames.
06 Nov 2007
US scientists say an animal found in Texas is not the chupacabra – or goat-sucker – of American myth, but a coyote with a hair loss problem.
DNA tests on the carcass found at a ranch south-east of San Antonio yielded a virtually identical match to coyote DNA, biologist Mike Forstner said.
The coyote was one of three found dead by rancher Phylis Canion this summer.
Central American myth has long spoken of a vampire-like creature that slays livestock by sucking out their blood.
The chupacabra is said to attack its victims at night, leaving a trail of carcasses with their throats torn out.
Mr Forstner said that he himself had assumed the creature brought in for testing at Texas State University was a domestic dog but “the DNA sequence is a virtually identical match to DNA from the coyote”.
Ms Canion and some of her neighbours discovered the 40-pound (18-kg) carcasses of three of the animals over four days in July outside her ranch in Cuero, 90 miles (145km) south-east of San Antonio.
She said she had saved the head of one of them to get it properly tested.
Additional hide samples have been taken to try to determine the cause of the animal’s hair loss, Mr Forstner said.
16 Oct 2007
92-lb. (41.82 kg) animal shot October 1, 2006 in Troy, Vermont
Rutland Herald 10/10:
A 92-pound (41.82 kg) canine shot in Troy last October may be the first confirmed wolf to roam the Green Mountains in more than a century, Vermont officials said Tuesday.
A yearlong investigation into the genetic makeup of the large animal, initially mistaken for a coyote, found “a substantial amount of wolf ancestry,” according to John Austin of the Vermont Fish and Wildlife Department.
“We’re trying to be cautious in how we interpret these results,” Austin said Tuesday. “What the information tells us is that the genetic composition, the size of animal … suggests it’s largely of wolf ancestry.”
The animal, shot by a farmer in a Vermont town along the Canadian border Oct. 1, 2006, could well have been a wolf. But scientists say it likely wasn’t wild. Genetic tests conducted at four laboratories, including the U.S. Fish and Wildlife Service’s forensics laboratory in Ashland, Ore., traced the ancestry of the animal to two separate and geographically distinct populations of wolves. The animal, according to lab conclusions, was almost certainly bred in captivity.
Peggy Struhsacker, a wolf specialist for the Natural Resources Defense Council, examined the animal after it was shot last October and said Tuesday that laboratory testing supported her initial hunches.
“I looked at all the traits and characteristics of it and believed it was possibly a full wolf or a high-percentage animal because it had all physical characteristics,” Struhsacker said. “That being said, it had too many other characteristics that made me feel it wasn’t a wild wolf.”
The animal’s shoddy coat, uniform nail wear and well-fed gut, she said, all indicated the canine was a domestic pet.
The animal’s origins have significant implications for the state. If the animal was indeed a wild wolf migrating from an existing pack in southern Quebec, it would signal the reappearance of an animal extirpated from the state in the 1800s.
“We’re really interested in trying to determine the origin of large canids when they turn up in New England,” said Kim Royar, a wildlife biologist with the Vermont Fish & Wildlife Department. “If it turns out, like the lab suggested, that this animal is of domestic origin, then basically we would assume it had been released into the wild by somebody who had bred it for sale. What we’re interested in is documenting whether there is movement of wolves from wild populations … in eastern Canada down to New England.”
Royar said the state has no evidence that such movement has occurred, though reports of wild wolves in Maine and New Hampshire suggest wolf populations may be crossing into the northeastern United States.
Michael Amaral, endangered species specialist for the U.S. Fish and Wildlife Service, said the discovery should signal a warning to hunters in the state. The wolf is protected by the federal Endangered Species Act and hunters who shoot them, mistakenly or intentionally, he said, face stiff fines.
“Gray wolves, even if they are of captive origin, are a protected species,” Amaral said. “I think the important message for Vermont’s hunters is it’s not beyond the realm of possibility that wolves can get to northern Vermont from existing wolf populations in Canada.”
Charlie Hammond, the man who shot the wolf in Troy, won’t be prosecuted, according to Amaral.
“Because it appears that this animal was of domestic origin … and other circumstances, we are not prosecuting in this case,” Amaral said.
Steve Mcleod is executive director of the Vermont Traditions Coalition, an organization that lobbies on behalf of hunters, farmers and other groups opposed to the reintroduction of the gray wolf to Vermont. He said a resurgence of the animal in the state would signal the decline of deer populations.
“There would be a deer slaughter that would result,” Mcleod said. “The white tail deer is the signature species of Vermont and it would really drastically change the balance of deer in the state over time.”
Austin said the department will have to pinpoint the origin and genetic makeup of the animal before it can fully understand the implications the discovery has for Vermont.
“What we haven’t done is ask an objective wildlife genetics expert … to help us understand what all this information now means to us,” Austin said. “What are the implications of that to wildlife conservation in Vermont? We’re going to work hard to get those answers.”
Vermont Fish & Wildlife Report
A 72 lb. (32.66 kg.) canine was shot in Glover, Vermont in 1997. DNA testing found it was of Gray wolf (Canis lupus) mixed with possibly coyote and domestic dog.
Reports of sightings of unfamiliar canines in Androscoggin County, Maine go back to 1991, and just over a year ago a canine thought to fit the descriptions found in previous accounts killed by an automobile on Route 4 in that county was photographed.
29 Jun 2007
New York Times:
Some 10,000 years ago, somewhere in the Near East, an audacious wildcat crept into one of the crude villages of early human settlers, the first to domesticate wheat and barley. There she felt safe from her many predators in the region, such as hyenas and larger cats.
The rodents that infested the settlers’ homes and granaries were sufficient prey. Seeing that she was earning her keep, the settlers tolerated her, and their children greeted her kittens with delight.
At least five females of the wildcat subspecies known as Felis silvestris lybica accomplished this delicate transition from forest to village. And from these five matriarchs all the world’s 600 million house cats are descended.
A scientific basis for this scenario has been established by Carlos A. Driscoll of the National Cancer Institute and his colleagues. He spent more than six years collecting species of wildcat in places as far apart as Scotland, Israel, Namibia and Mongolia. He then analyzed the DNA of the wildcats and of many house cats and fancy cats.
Five subspecies of wildcat are distributed across the Old World. They are known as the European wildcat, the Near Eastern wildcat, the Southern African wildcat, the Central Asian wildcat and the Chinese desert cat. Their patterns of DNA fall into five clusters. The DNA of all house cats and fancy cats falls within the Near Eastern wildcat cluster, making clear that this subspecies is their ancestor, Dr. Driscoll and his colleagues said in a report published Thursday on the Web site of the journal Science.
The wildcat DNA closest to that of house cats came from 15 individuals collected in the deserts of Israel, the United Arab Emirates, Bahrain and Saudi Arabia, the researchers say. The house cats in the study fell into five lineages, based on analysis of their mitochondrial DNA, a type that is passed down through the female line. Since the oldest archaeological site with a cat burial is about 9,500 years old, the geneticists suggest that the founders of the five lineages lived around this time and were the first cats to be domesticated.
Wheat, rye and barley had been domesticated in the Near East by 10,000 years ago, so it seems likely that the granaries of early Neolithic villages harbored mice and rats, and that the settlers welcomed the cats’ help in controlling them.
Unlike other domestic animals, which were tamed by people, cats probably domesticated themselves, which could account for the haughty independence of their descendants. “The cats were adapting themselves to a new environment, so the push for domestication came from the cat side, not the human side,” Dr. Driscoll said.
Cats are “indicators of human cultural adolescence,” he remarked, since they entered human experience as people were making the difficult transition from hunting and gathering, their way of life for millions of years, to settled communities.
Until recently the cat was commonly believed to have been domesticated in ancient Egypt, where it was a cult animal. But three years ago a group of French archaeologists led by Jean-Denis Vigne discovered the remains of an 8-month-old cat buried with its human owner at a Neolithic site in Cyprus. The Mediterranean island was settled by farmers from Turkey who brought their domesticated animals with them, presumably including cats, because there is no evidence of native wildcats in Cyprus.
The date of the burial far precedes Egyptian civilization. Together with the new genetic evidence, it places the domestication of the cat in a different context, the beginnings of agriculture in the Near East, and probably in the villages of the Fertile Crescent, the belt of land that stretches up through the countries of the eastern Mediterranean and down through what is now Iraq.
09 Dec 2006
Scientific fact threatening primitive superstition poses a hazard to remote indigenous tribes, proclaims this Sunday’s Times, in this weekly front-page sob story.
At issue is whether scientists who need DNA from aboriginal populations to fashion a window on the past are underselling the risks to present-day donors. Geographic origin stories told by DNA can clash with long-held beliefs, threatening a world view some indigenous leaders see as vital to preserving their culture.
They argue that genetic ancestry information could also jeopardize land rights and other benefits that are based on the notion that their people have lived in a place since the beginning of time.
Liberal egalitarianism rates not only naked savagery as equal to modern civilization, it also considers primitive cultures’ self-deluding myths as privileged from the challenge of fact.
23 Nov 2006
Scientists have discovered a dramatic variation in the genetic make-up of humans that could lead to a fundamental reappraisal of what causes incurable diseases and could provide a greater understanding of mankind.
The discovery has astonished scientists studying the human genome – the genetic recipe of man. Until now it was believed the variation between people was due largely to differences in the sequences of the individual ” letters” of the genome.
It now appears much of the variation is explained instead by people having multiple copies of some key genes that make up the human genome.
Until now it was assumed that the human genome, or “book of life”, is largely the same for everyone, save for a few spelling differences in some of the words. Instead, the findings suggest that the book contains entire sentences, paragraphs or even whole pages that are repeated any number of times.
The findings mean that instead of humanity being 99.9 per cent identical, as previously believed, we are at least 10 times more different between one another than once thought – which could explain why some people are prone to serious diseases.
The studies published today have found that instead of having just two copies of each gene – one from each parent – people can carry many copies, but just how many can vary between one person and the next.
The studies suggest variations in the number of copies of genes is normal and healthy. But the scientists also believe many diseases may be triggered by an abnormal loss or gain in the copies of some key genes.
Another implication of the finding is that we are more different to our closest living relative, the chimpanzee, than previously assumed from earlier studies. Instead of being 99 per cent similar, we are more likely to be about 96 per cent similar.
09 Oct 2006
Alfred Tennyson opined that simple faith (was more) than Norman blood, and Tennyson may well be right.
Stephen Oppenheimer, one of the most prominent British autorities on DNA research, is contending that there simply isn’t all that much Norman blood around in Britain anyway, nor Celtic, nor Roman, nor Anglo-Saxon.
According to Oppenheimer,
Everything you know about British and Irish ancestry is wrong. Our ancestors were Basques, not Celts. The Celts were not wiped out by the Anglo-Saxons, in fact neither had much impact on the genetic stock of these islands…
The genetic evidence shows that three quarters of our ancestors came to this corner of Europe as hunter-gatherers, between 15,000 and 7,500 years ago, after the melting of the ice caps but before the land broke away from the mainland and divided into islands. Our subsequent separation from Europe has preserved a genetic time capsule of southwestern Europe during the ice age, which we share most closely with the former ice-age refuge in the Basque country. The first settlers were unlikely to have spoken a Celtic language but possibly a tongue related to the unique Basque language.
Another wave of immigration arrived during the Neolithic period, when farming developed about 6,500 years ago. But the English still derive most of their current gene pool from the same early Basque source as the Irish, Welsh and Scots. These figures are at odds with the modern perceptions of Celtic and Anglo-Saxon ethnicity based on more recent invasions. There were many later invasions, as well as less violent immigrations, and each left a genetic signal, but no individual event contributed much more than 5 per cent to our modern genetic mix…
based on the overall genetic perspective of the British, it seems that Celts, Belgians, Angles, Jutes, Saxons, Vikings and Normans were all immigrant minorities compared with the Basque pioneers, who first ventured into the empty, chilly lands so recently vacated by the great ice sheets.
By “Basque pioneers,” Oppenheimer is referring to female-line mitochondrial DNA haplogroup H1.
mtDNA Haplogroups in general.
Oppenheimer has a new book on all of this, titled The Origins of the British: A Genetic Detective Story.