Strands of 1,000-year-old DNA from 10 Viking skeletons have been retrieved, a team of scientists claims.

Of particular interest to us, is this paragraph from the research article:

Among present day Scandinavians Hg I constitutes <2%, however, we have previously observed a markedly higher frequency (10–20%) of Hg I in Danish Iron Age and Viking Age population samples. With the observation of Hg I for subject G6 this trend is also seen for the Viking population sample from Galgedil. Interestingly, Hg I shows a low frequency (1 out of 114 subjects) among other ancient populations in Italy, Spain, Great Britain, and early central European farmers.

If true, the achievement would be notable, since many researchers say it is impossible to recover authentic DNA from ancient humans.

Jorgen Dissing of the University of Copenhagen and colleagues say they retrieved the genetic material from the freshly sampled teeth of skeletons dating back to around A.D. 1000 and found at a non-Christian burial site called Galgedil on the Danish island of Funen.

Wearing protective suits, the researchers removed the teeth from the jaw at the moment the skeletons were unearthed, where they had lain untouched for 1,000 years. Subsequent laboratory procedures were carefully controlled to avoid contamination with modern human DNA.

In the past few years, several studies have shown that it is possible to recover authentic ancient human DNA if strict measures are taken to avoid contamination.

“The present work provides further evidence that retrieval of authentic DNA from ancient humans is indeed a possible undertaking provided adequate precautions are observed,” the authors wrote in this week’s issue of the journal PLoS ONE.

Although “Viking” often refers to pirates and robbers at sea, recent research has indicated that the Vikings were also traders to the fishmongers of Europe. Dissing and his colleagues are interested in family relationships among populations of Vikings and genetic variation among them. The team has also obtained DNA sequence results on other ancient humans — from an early Christian cemetery dating from A.D. 1000 to A.D 1250, two Roman Iron Age settlements from A.D. 0 to A.D. 400 and Greenland Inuit from about A.D. 1450.

Severe problems connected with the retrieval and analysis of DNA from ancient organisms (such as the scarcity of intact molecules) are further aggravated in the case of ancient humans. This is because of the great risk of contamination with abundant DNA from modern humans.

Humans are involved in the analysis every step of the way, from excavation to laboratory analyses. This means that many previous results have subsequently been disputed as attributed to the presence of contaminant DNA from modern humans in the lab and the field.

However, analysis of the Viking DNA showed no evidence of contamination with extraneous DNA, Dissing said, and typing of the DNA gave reproducible results and showed that these individuals were just as diverse as contemporary humans.

Analysis of DNA from the remains of ancient humans provides valuable insights into such questions as the origin of genetic diseases, migration patterns of our forefathers and tribal and family patterns.

“A reliable retrieval of authentic DNA opens the way for a valuable use of prehistoric human remains to elucidate the genetic history of past and extant populations,” the authors wrote.
from LiveScience

Full Article

The human race was divided into two separate groups within Africa for as much as half of its existence, says a Tel Aviv University mathematician. Climate change, reduction in populations and harsh conditions may have caused and maintained the separation.

Dr. Saharon Rosset, from the School of Mathematical Sciences at Tel Aviv University, worked with team leader Doron Behar from the Rambam Medical Center to analyze African DNA. Their goal was to study obscure population patterns from hundreds of thousands of years ago.

Rosset, who crunched numbers and did the essential statistical analysis for the National Geographic Society’s Genographic Project, said the team was trying to understand the timing and dynamics of the split into at least two separate groups.

“We wanted to look into the ancient history of our species. How did we live throughout most of our existence as a species? Did we live as one — or were we fractured into small groups? Until now, it wasn’t really clear,” says Rosset.

A Picture of the Ancient Past

Researchers believe that about 60,000 years ago, modern humans started their epic journeys to populate the world. This time period has been the primary focus of anthropological genetic research. However, relatively little is known about the demographic history of our species over the previous 140,000 years in Africa.

Read the rest of this entry »

Dorothy Rosenberg’s sister called her recently to give her some news about a long-lost relative - a really, really long-ago-lost relative.

Rosenberg, 80, who belongs to the Alaskan Tlingit tribe, learned through DNA testing that an iceman who died 200 to 300 years ago in the wilds of British Columbia is one of her ancestors.

The iceman could be a legendary Arctic trader celebrated in tribal lore. But even if he’s not, the twenty-something man - found draped in squirrel pelts and wearing a hat made of roots - is being welcomed as kin by his California cousins.

“We are also Jewish,” said Aaron Rosenberg, Dorothy Rosenberg’s youngest son who lives in Hollywood. “We are the best of both tribes.”

Three sheep hunters found the human remains in a melting glacier in 1999 on land in British Columbia, part of the traditional territory of the Champagne and Aishihik First Nations. The tribe named him Kw day D n Ts’inchi, meaning “Long Ago Person Found” in the Southern Tutchone language.

DNA testing recently traced the remains to 17 people in Alaska and Canada, including Dorothy Rosenberg’s sister, Harryet Rappier, who lives in Juneau, Alaska. She called recently to deliver the news.

“She said her DNA matched the man in the ice,” said Dorothy Rosenberg of Canyon Country. “That goes for me.”

Her family - including sons Mark and Ben who live with their mother - expect to find more family members through the DNA results.

“It could be just the beginning of our family tree,” said Ben Rosenberg, 49.

The man - believed to have died in his early 20s - was wearing a spruce-root hat and a robe made of Arctic ground-squirrel pelts. It’s thought that he died between 1670 and 1850, said Lawrence Joe, director of the tribe’s Heritage Land and Resources department.

Some southeast Alaskans believe Long Ago Person Found is Kaakaldeini, who was immortalized in song and stories, said Kathy Dye, spokeswoman for Sealaska Heritage Institute.

According to oral tradition, Kaakaldeini was hurt while on a trade trip to Canada. When a storm rolled in, he told his companions to leave him, fearing that if they carried him, they would go too slowly and all die in the storm. His companions piled blankets on him, left and he was never seen again.

Extensive travel between Canada and Alaska is documented in tribal oral traditions, Dye said.

After the discovery, the tribe - along with government groups - convened a discovery committee and led the culture, artifact and DNA studies. The Royal BC Museum and the government’s BC Archaeology Branch oversaw preservation and research of the remains, which were cremated in 2001.

In 2000, a DNA study was launched to determine whether Long Ago Person Found had any living descendants in Canada and Alaska. The Sealaska Heritage Institute, a nonprofit that represents the Tlingit, Haida and Tsimshian people of southeast Alaska, worked with the Champagne and Aishihik First Nations on the Alaskan participants.

The DNA results were released last month at a symposium about the discovery in Victoria, British Columbia. Of the nearly 250 people tested, 17 in Alaska and Canada were found to be related to the man.

“The DNA results are not a surprise to native people here but it’s good to see science validating oral histories,” Dye said. “It proves the truth of oral histories to the general public.”

For the Rosenbergs, the excitement continues. Phone calls to the Canyon Country home start with a news flash about their famous relative.

Although Dorothy Rosenberg has lived in Southern California longer than in Alaska, she kept those strong ties to her roots.

The family would travel to Alaska every couple of years, meandering through villages. Her mother gave her sons their tribal names.

Aaron Rosenberg uses his, Eech ya, or face of the coral reef, as part of his e-mail address. He also speaks the Tlingit language and can sing a love song and the tribe’s national anthem.

“We were the first Americans,” the 42-year-old said. “We are the true Americans.”
from Daily News

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.

It would be the longest period for which modern human populations have been isolated from one another. But other scientists said it was still too early to reconstruct a meaningful picture of humankind’s early history in Africa. They argue that other scenarios could also account for the data.

At the time of the split - some 150,000 years ago - our species, Homo sapiens, was still confined to the African continent.

The latest conclusions are based on analysis of mitochondrial DNA in present-day African populations. This type of DNA is the genetic material stored in mitochondria - the “powerhouses” of cells. It is passed down from a mother to her offspring, providing a unique record of maternal inheritance.

“We don’t know how long it takes for hominids to fission off into separate species, but clearly they were separated for a very long time,” said Dr Spencer Wells, director of the Genographic Project.
“They came back together again during the Late Stone Age - driven by population expansion.”

Although present-day people carry a signature of the ancient split in their DNA, today’s Africans are part of a single population. The researchers compiled a “family tree” of different mitochondrial DNA groupings found in Africa and found that a major split occurred near the root of the tree as early as 150,000 years ago.

On one side of this divide are the mitochondrial lineages now found predominantly in East and West Africa, and all maternal lineages found outside Africa. On the other side of the divide are lineages predominantly found in the Khoi and San (Khoisan) hunter-gatherer people of southern Africa. Many African populations today harbor a mixture of both.

Scientists think the most likely scenario is that two populations went their separate ways early in our evolutionary history which then gave rise to separate human communities localized to eastern and southern Africa that evolved in isolation for between 50,000 and 100,000 years. This divergence could have been related to climate change: recent studies of ancient climate data suggest that eastern Africa went through a series of massive droughts between 135,000-90,000 years ago.

Lead author Doron Behar, from the Rambam Medical Center in Israel commented: “It is possible the harsh environment and changing climate made populations migrate to other places in order to have a better chance of survival.

“Some of them found places where they could and - perhaps - some didn’t. More than that we cannot say.”

Dr Wells told BBC News: “Once this population reached southern Africa, it was cut off from the eastern African population by these drought events which were on the route between them.”

Modern humans are often presumed to have originated in East Africa and then spread out to populate other areas. But the data could equally support an origin in southern Africa followed by a migration to East and West Africa.

The genetic data show that populations came back together as a single, pan-African population about 40,000 years ago. This renewed contact appears to coincide with the development of more advanced stone tool technology and may have been helped by more favorable environmental conditions.

“[The mixing] was two-way to a certain extent, but the majority of mitochondrial lineages seem to have come from north-eastern Africa down to the south,” said Spencer Wells.

But other scientists said different scenarios could explain the data. Like Dr Sarah Tishkoff, an expert on African population genetics from the University of Pennsylvania, said the Khoisan might once have carried many more of the presumed “East African” lineages but that these could have been lost over time.

“Although there is very deep divergence in the mitochondrial lineages, that can be different from inferring when the populations diverged from one another and there can be many demographic scenarios to account for it,” she told BBC News.

She added: “As a general rule of thumb, when mitochondrial genetic lineages split, it will usually precede the population split. It can often be difficult to infer from one to the other.”

The University of Pennsylvania researcher stressed it was not possible to pinpoint where in Africa the populations had once lived - complicating the process of reconstructing scenarios from genetic data.

The Genographic Project’s findings are also consistent with the idea - held for some years now - that modern humans had a close brush with extinction in the evolutionary past.

The number of early humans may have shrunk as low as 2,000 before numbers began to expand again in the Late Stone Age.

from BBC News

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.”

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, who appear to have diverged from other people between 90,000 and 150,000 years ago.

The researchers led by Doron Behar of Rambam Medical Center in Haifa, Israel, and Saharon Rosset of IBM T.J. Watson Research Center in Yorktown Heights, New York, and Tel Aviv University concluded that humans separated into small populations before the Stone Age, when they came back together and began to increase in numbers and spread to other areas.

Eastern Africa experienced a series of severe droughts between 135,000 and 90,000 years ago, and researchers said this climatological shift may have contributed to the population changes, dividing into small, isolated groups that developed independently.

Paleontologist Meave Leakey, a Genographic adviser, said: “Who would have thought that as recently as 70,000 years ago, extremes of climate had reduced our population to such small numbers that we were on the very edge of extinction?”

Today, more than 6.6 billion people inhabit the globe, according to the U.S. Census Bureau.

The research was funded by the National Geographic Society, IBM, the Waitt Family Foundation, the Seaver Family Foundation, Family Tree DNA and Arizona Research Labs

source: CNN Technology

Russia’s Czar Nicholas II, seated second from left, Czarina Alexandra, center rear, and their family are shown in this undated file photo. Bottom row left to right, Princess Olga, Czar Nicholas II, Princess Anastasia, Prince Alexei and Princess Tatiana. Top row left to right, Princess Maria and Princess Alexandra.

DNA test results to be announced within months on bone fragments found in Russia last year could prove that none of Czar Nicholas II’s family escaped execution in the Bolshevik Revolution — not even Anastasia, the teenage princess whose identity various women have claimed over the decades.

Evgeny Rogaev, who heads a genetic research team working in Moscow and at the University of Massachusetts Medical School in Worcester, is not immune to the effect his work could have on how his fellow Russian citizens view that turbulent chapter in their history.

He keeps pictures of the royal family carefully tucked inside a folder near charts of DNA sequences, but does not display them. Likewise, he shields any sight of the remains from everyone except the other researchers, out of respect for whomever the remains represent.

“Murders occurred. Children were murdered,” he said this week, choosing his words carefully. “I will not make a show of it. That is my ethics.”

For Rogaev, a professor at UMass and Moscow State University, ensuring the accuracy of the DNA tests is paramount.

“In an expert work, it cannot be about emotions. It must be about collection of scientific evidences, and that is why this DNA is so powerful to study,” he said.

Rogaev is reviewing the genetic material at the request of the Russian Federation Prosecutor’s Office as part of its reopened investigation of the deaths of the royal family.

Nicholas II, Empress Alexandra, 13-year-old Crown Prince Alexei, the prince’s four older sisters and their four attendants were taken prisoner in 1917. Even though the czar already had abdicated his throne, their captors fatally shot all the prisoners on July 17, 1918, in a basement room of a house in the city of Yekaterinburg.

DNA testing determined skeletal remains unearthed from shallow graves in a nearby mining pit in 1991 were most likely those of the couple and three of their four daughters.

The daughters were believed to be 22-year-old Olga, 21-year-old Tatiana and 17-year-old Anastasia, although some people speculate the last set of remains belonged to the similarly sized 19-year-old Maria.

Researchers suspect the bone shards discovered last summer, burned and doused with acid, are those of Alexei and Maria. They were found in the area where one of the professed killers said their bodies had been destroyed.

The remains found in 1991 were reburied with honors in 1998 in the imperial-era capital of St. Petersburg. It was shadowed by doubts at the time, including from the Russian Orthodox Church and some Romanov relatives, over the authenticity of the genetic results.

Nevertheless, the church canonized the royal family in 2000.

Rogaev, who was called to help verify the remains’ authenticity in 1997 and 1998, said he knows many people with opinions on both sides. He compares it to the emotions that Americans have about their legendary public figures and families, such as the Kennedys, and says the DNA tests are the best way to be certain about the Romanovs’ fate.

“In science, what you conclude to be true comes from the results you find. When I see the results, I accept the results as the fact,” he said.

No clear explanation exists about why the suspected remains of the prince and one of his sisters were destroyed with more violence than those of the czar, empress and three of their daughters.

Some researchers think that after shooting the family, the killers tried to destroy as much of their remains as possible, but ran out of time after starting to destroy two of the smallest bodies with fire and sulfuric acid. Some have said the killers thought monarchists might try to memorialize the burial place as a shrine if the bodies’ locations were known.

The bone fragments were so badly damaged that Rogaev and other researchers first had to determine whether enough uncontaminated genetic material still existed for testing.

The delicate work proved that, indeed, useful DNA could be extracted from a very small amount of the material — a critical fact, since they wanted to preserve as much of the bone fragments as possible out of respect for the victims.

The researchers are comparing DNA from the recently discovered remains with those of Empress Alexandra, who was a granddaughter of Britain’s Queen Victoria and a distant relative of Prince Philip, the husband of Queen Elizabeth II. The prince, whose DNA might offer important points of reference for comparison, has not provided DNA so far, but researchers are reviewing published information related to the family, Evgeny said.

Renowned forensic scientist Henry Lee endorsed Rogaev’s approach and called the case a prime example of science settling questions about the past.

“It’s an interesting project, and DNA is opening up a lot of new frontiers in solving crime and answering questions of history,” said Lee, a former Connecticut public safety commissioner and founder of the forensic science program at the University of New Haven.

A representative of the Romanovs urged caution after the remains were found last summer. They have tried without success for years to persuade Russian authorities to declare Nicholas and his family victims of political repression.

“I will be deeply happy if the remains of (Alexei) and Maria have really been found,” Nikolai Romanov, identified by Channel One as the head of the family, told the station by telephone from Switzerland. “But it is always necessary to treat such epochal events with caution.”
from Yahoo News

A 30-year-old systems administrator from a small village close to Madurai in Tamil Nadu has been identified as one of the direct descendants of the first ever settlers in India, who had migrated from the African coast some 70,000 years ago.

The DNA of Virumandi Andithevar, one of the circa 700 inhabitants of Jothimanickam village, matched the white chromosome marker scientifically labeled “M130″, which is a gene found only among the descendants of the African migrants who had spread across the world tens of thousands of years ago. “This young man and 13 members of his nine-generation clan carried the same marker in their genes. It means that his ancestors in all probability settled in this village several generations ago,” said Prof. Rm Pitchappan, who led a team of scientists tracking the “M130″ DNA.

“M130 is actually present sporadically among the population along the Western Ghats and around Madurai,” said Dr Pitchappan, who heads the School of Biological Sciences at Madurai Kamaraj University. His research was part of the “Genographic Project”, a global initiative launched by National Geographic and a team of reputed scientists for unraveling the mystery of human migration. “The genetic studies carried out using M130 told us about the first human migration to India. We identified the marker of the first coastal migration in our Madurai samples. The search took us to Virumandi, who belongs to the Piramalai Kallar community, whose DNA matched M130, establishing him as one of the direct descendants of the first migrant from the African coast, who must have come here some 70,000 years ago,” Dr Pitchappan said.

Virumandi is elated with the news. “This is God’s gift to me, to be told that my roots go back to 70,000 years. They used to say that our village of 700 people had spawned from just three ancestors and I had often wondered from where and when they came. Now I have the answer — they came 70,000 years ago from Africa,” Virumandi said.

It took five years to establish the DNA link between Virumandi and the first migrants to the subcontinent. The studies also proved that though the migration to India took place some 70,000 years ago, the first settlement in the South happened about 10,000 years later.

“More than half of the Australian aborigines carry this M130 gene. The marker is also present among some people in Philippines and the tribals of Malaysia,” said Dr Pitchappan.

The Genographic Project will gather all data in collaboration with indigenous and traditional people around the world. The public is invited to join the project by purchasing a Genographic Project public participation kit. The proceeds from the sales go to further field research and the Genographic Legacy Fund, which in turn supports indigenous conservation and revitalization projects.

from The Asian Age

Poop shows humans lived in North America more than 14,000 years ago

Discovered in a cave in Oregon, fossil feces yielded DNA indicating these early residents were related to people living in Siberia and East Asia, according to a report in Thursday’s online edition of the journal Science.

“This is the first time we have been able to get dates that are undeniably human, and they are 1,000 years before Clovis,” said Dennis L. Jenkins, a University of Oregon archaeologist, referring to the Clovis culture, well known for its unique spear-points that have been studied previously.

Humans are widely believed to have arrived in North America from Asia over a land-bridge between Alaska and Siberia during a warmer period. A variety of dates has been proposed and some are in dispute.

Few artifacts were found in the cave, leading Jenkins to speculate that these people stayed there only a few days at a time before moving on, perhaps following game animals or looking for other food.

The petrified poop — coprolites to scientists — is yielding a look at the diet of these ancient Americans, Jenkins said. While the analysis is not yet complete, he said there are bones of squirrels, bison hair, fish scales, protein from birds and dogs and the remains of plants such as grass and sunflowers. The oldest of several coprolites studied is 14,340 calendar years old, said co-author Eske Willerslev, director of the Centre for Ancient Genetics at Denmark’s University of Copenhagen.

“The Paisley Cave material represents, to the best of my knowledge, the oldest human DNA obtained from the Americas,” he said. “Other pre-Clovis sites have been claimed, but no human DNA has been obtained.”

The date for the new coprolites is similar to that of Monte Verde in southern Chile, where human artifacts have been discovered, added Willerslev. Jenkins said it isn’t clear exactly who these people living in the Oregon caves were, since there were few artifacts found. He said there was one stone tool, a hand tool used perhaps to polish or grind or mash bones or fat.

“We are not saying that these people were of a particular ethnic group. At this point, we know they most likely came from Siberia or Eastern Asia, and we know something about what they were eating, which is something we can learn from coprolites. We’re talking about human signature,” he said.

“If you are looking for the first people in North America, you are going to have to step back more than 1,000 years beyond Clovis to find them,” Jenkins said.

The Clovis culture has been dated to between 13,200 and 12,900 calendar years ago and is best known by the tools left behind.

Michael Waters, director of the Center for the Study of the First Americans at Texas A&M University, said the find, along with indications of human presence at other locations, adds to the evidence for a pre-Clovis human presence in North America.

“The genetic evidence from the coprolites from Paisley Caves is also consistent with the current genetic data for the peopling of the Americas — that the earliest inhabitants of the Americas came from Northeast Asia,” added Waters, who was not part of the research team.

Jenkins said that discoveries like those in the Oregon caves “help us to reconstruct the American past.”

“Our heritage is really important and it is important to the majority of the American public. If you don’t know where you come from, it’s hard to have a feeling of community, of participation.”

To make sure the Oregon cave material hadn’t been contaminated with modern DNA, the researchers tested more than 50 people who worked at the site. The DNA testing indicated that the feces belonged to Native Americans in two groups that can be traced to Siberia and East Asia.

In their paper the researchers dated the coprolites at 12,300 “carbon years” before the present. Prior to 3,000 years ago, carbon years differed from calendar years, resulting in the date of approximately 14,300 calendar years for the coprolites.

The research was funded by the Museum of Natural and Cultural History, University of Oregon; Association of Oregon Archaeologists and the Marie Curie Actions program.
from Yahoo News article

Scientists reshape Y chromosome haplogroup tree gaining new insights into humanancestry

Wednesday, April 2, 2008 –The Y chromosome retains a remarkable record of human ancestry,since it is passed directly from father to son. In an article published online today in GenomeResearch (www.genome.org), scientists have utilized recently described genetic variations on thepart of the Y chromosome that does not undergo recombination to significantly update and refinethe Y chromosome haplogroup tree. The print version of this work will appear in the May issue ofGenome Research, accompanied by a special poster of the new tree.

Human cells contain 23 pairs of chromosomes: 22 pairs of autosomes, and one pair of sexchromosomes. Females carry a pair of X chromosomes that can swap, or recombine, similarregions of DNA during meiosis. However, males harbor one X chromosome and one Ychromosome, and significant recombination between these dissimilar sex chromosomes does not occur. Therefore, the non-recombining region of the Y chromosome (NRY) remains largelyunchanged over many generations, directly passed from father to son, son to grandson, and so on, along with genetic variations in the NRY that may be present. Scientists can use geneticvariations, such as single nucleotide polymorphisms (SNPs), on the Y chromosome as markers of human ancestry and migration.

In 2002, the Y Chromosome Consortium (YCC) constructed a tree of 153 haplogroups based upon 243 unique genetic markers. In this report, researchers led by Dr. Michael Hammer of the University of Arizona recognized the need to revisit the Y chromosome haplogroup tree and incorporate the latest data. “The YCC effort in 2002 was a landmark in mapping the then known 300 or so Y-linked SNPs on a single tree, and getting the community to use the same nomenclature system,” explains Hammer. “The rate of SNP discovery has continued to increase
over the last several years, as are publications on Y chromosome origins and affinities. While this new information is useful, ironically it also brings with it the danger of introducing more chaos into the field.”

Hammer’s group integrated more than 300 new markers into the tree, which allowed the resolution of many features that were not yet discernable, as well as the revision of previous arrangements. “The major lineages within the most common African haplogroup, E, are now all sorted out, with the topology providing new interpretations on the geographical origin of ancient sub-clades,” describes Hammer. “When one polymorphism formerly described as unique, but recently shown to have reversed was replaced by recently reported markers, a sub-haplogroup of haplogroup O, the most common in China, was considerably rearranged,” explains Fernando
Mendez, a co-author of the study.

In addition to improving the resolution of branches, the latest reconstruction of the tree allows estimates of time to the most recent common ancestor of several haplogroups. “The age of [haplogroup] DE is about 65,000 years, just a bit younger than the other major lineage to leave Africa, which is assumed to be about 70,000 years old,” says Hammer, describing an example of the fine resolution of age that is now possible. “Haplogroup E is older than previously estimated, originating approximately 50,000 years ago.”

Furthermore, Hammer explains that this work has resulted in the addition of two new major haplogroups, S and T, with novel insights into the ancestry of both. “Haplogroup T, the clade that Thomas Jefferson’s Y chromosome belongs to, has a Middle Eastern affinity, while haplogroup S is found in Indonesia and Oceania.”

“More SNPs are being discovered, and we anticipate the rate to increase with the 1000 Genomes Project,” says Hammer, referring to the wealth of human genetic variation data that will soon be available. While this report represents a significant advance in mapping ancestry by Y chromosome polymorphisms, it is certain that future discoveries will necessitate continual revisions to the Y chromosome haplogroup tree, helping to further elucidate the mystery of ourorigins.

FTDNA Press Release

Good idea?

After two decades, Sean Reid of Surrey, British Columbia, discovered that he had a son. Fred Turley of Des Plaines, Ill., learned he didn’t have a daughter. And Wendy Lieb of Lewis Center, Ohio, made certain that her son was not the claimed father of a girlfriend’s baby.

All three situations were determined by a $29.99 kit on a drugstore shelf named Identigene by Sorenson Genomics of Salt Lake City.
Sales in three western states — Washington, Oregon and California — were so brisk last fall that Rite Aid Corp. expanded the product this week to some 4,300 stores in 30 states across the country.

“Everyone is purchasing the tests because they’re curious,” said Fogg, who expects to sell at least 52,000 tests this year. “They’re looking to establish questions about their own child or their own paternity.”

But for genetics experts, drugstore marketing of DNA testing raises questions of accuracy and ethics.

“From our perspective, direct-to-consumer genetic tests raise all the same issues for lax government oversight, potentially misleading or false advertising and the potential for making profound medical decisions on the basis of poorly interpreted or understood results,” said Rick Borchelt, a spokesman for the Genetics and Public Policy Center at Johns Hopkins University.

Reliability

The paternity kits have taken their place on store shelves next to other diagnostic tests that don’t rely on DNA, including those for pregnancy, HIV and blood sugar, said Michael S. Watson, executive director of the American College of Medical Genetics.

Unlike genetic tests for health conditions, tests that use DNA to determine paternity are fairly simple to provide and fairly easy to interpret, said Watson. They’re subject to limited oversight, however, with no review required by the Food and Drug Administration and no certification required under the federal Clinical Laboratory Improvement Amendments, or CLIA.

The Identigene kit includes swabs for collecting cell samples from the inside of the cheeks of the child and the alleged father. Collection of the mother’s cells is optional, but strongly recommended to strengthen the results. The swabs are packaged and mailed to the Sorenson laboratory in Salt Lake City where they’re analyzed.

The Sorenson lab is accredited by the AABB, the agency formerly known as the American Association of Blood Banks.

Results are reported online, by phone or by mail in three to five business days. They come back as a probability figure that verifies paternity with 98 percent to 99 percent accuracy, Watson said.

Total cost is about $150, including the price of the kit and a $119 laboratory processing fee. For another $200, users can purchase validated tests that meet legal requirements for determining paternity, Fogg said.

Legal Concerns

But Susan Crockin, a lawyer who specializes in reproductive technology, said consumers shouldn’t count on the tests standing up in court.

“The jury’s still very much out on these tests in terms of reliability and establishing a chain of custody,” said Crockin, a consultant for the Johns Hopkins public policy center.

Most of the users who have been buying the kits — which have gone on sale for as low as $17.99 — don’t plan to use the results to resolve legal issues, Fogg acknowledged. Instead, most are looking to answer social questions. And that’s where the complexity comes in.

Because the cell samples are taken in private, there’s the potential for fraud and deception, noted Charo, the ethics expert.

“I can imagine rather peculiar circumstances in which somebody has a swab taken without their knowledge,” she said. “It raises questions about informed consent.”

Even when people do consent, the results can be unsettling. Watson estimates that between 5 percent and 10 percent of genetic tests he’s conducted show a child is not related to the presumed father.

“It could break up families,” Watson said. “Some will be broken because that was the goal. Others will be broken up and that wasn’t the goal.”

But people who’ve used the at-home tests swear by the ease, the accuracy — and the results.

A Smithsonian Team Gives Unearthed Body a Name

William T. White, 14 years of age, from Accomack County on Virginia’s Eastern Shore, died in 1852 of pneumonia. All dressed up in a white burial suit and put into an iron coffin, he was left behind when the cemetery where he was buried in Northwest Washington moved a decade after his death. And there he stayed, forgotten, while the city continued to grow above him - and 155 years passed by.

He was accidentally unearthed by a construction crew in 2005 and researchers at the Smithsonian Institution vowed to find out who he was. But this historical drama / detective story took a couple of wrong turns in the process.

Smithsonian anthropologist Douglas W. Owsley stated the boy had been about five feet tall and probably sickly because of a hole between two chambers in his heart. He had been buried in a cemetery that probably belonged to Columbian College, the precursor to George Washington University, in what is now Columbia Heights, and had been a student at the college preparatory school when he died Jan. 24, 1852.

It’s All In The Case

Back to the beginning though - the research began with the coffin; the Fisk and Raymond “metallic burial case” was a big clue. Such airtight coffins were expensive, most affordable by the rich and were popular between 1850 and 1860. It was opened in August 2005 to be examined by a team of pathologists.

The body was extremely well preserved and the fashion of pleated shirt and vest with cloth-covered buttons, flared trousers, darned socks and ankle-length underdrawers seemed to indicate the 1850s. An autopsy concluded that the boy probably died of lobar pneumonia.

The grave was found in the now-residential neighborhood of Columbia Heights. Columbian College had once been there, and a page from a 1970 history of George Washington University stated that the old college had a cemetery. Further research showed that the original cemetery was moved in 1866 from the periphery of the college grounds to the main campus. And it was during this move that the iron coffin was probably left behind. This might have been because the tombstone was absent or had been misplaced during the Civil War, when the college was the site of two sprawling military hospitals, the researchers said.

Dead Ends

The team began reading lists of obituaries from the 1850s compiled from local newspapers and jumped too quickly at an item in the May 27, 1852 edition of Washington’s Daily National Intelligencer that had an obituary for Lemuel P. Bacon, 12, the son of Columbian’s president, Joel Bacon. It seemed perfect - “seemed.”

With samples of the dead boy’s mitochondrial DNA ( which can be traced and matched via female descendants over many generations), Hull-Walski and Scott developed a Bacon family tree and located a descendant in Texas. But that descendant’s DNA did not match. Dead End Number One. It is never that easy, as we genealogical researchers know!

Continuing with the obits, the Jan. 28, 1852 edition of the Intelligencer carried a brief obituary for a William Taylor White, of Accomack, who had died “at college hill” four days earlier. In a digest of old wills for Accomack County, they found one in which a guardian had left White money for his education. This time, Scott said, “we really felt like we had the right person.”

However, the course of genealogy never runs smooth - when the researchers saw that the same digest contained the will of a Levin White, who had a son named William T., they “assumed” he must have been the boy’s late father. But when a descendant of Levin White was located in Baltimore and her DNA did not match. Dead End Number Two.

The team had also found an obituary for a William Henry White, who had died Sept. 29, 1852, at the age of 14. There was no connection to the college, but the boy’s father, Mathias, had been a Pennsylvania Avenue undertaker who used Fisk and Raymond coffins. Again a descendant was traced, this time to suburban Maryland - but again the DNA did not match. Dead End Number Three.

The Tide Turns

It was now summer 2006, and the team had been working on the case for a year. The boy’s body was being preserved at the museum, encased in a white body bag inside a metal cooler, but no closer to knowing who he was.

That Spring, a clue came by accident. Searching through a computer database of the Washington Intelligencer, Hull-Walski stumbled on another notice of the death of William T. White. Not an obituary, but a heartfelt “resolution” drawn up by his college friends, expressing their anguish at the loss of one who “was bound to us by the tenderest ties of friendship.” Somehow it had not turned up in prior research, but it reinforced to Hull-Walski that, despite the DNA, William T. White had to be the coffin boy. She showed the notice to Scott. “It’s him,” she told her colleague. But where had they gone wrong?

“So we started again,” Hull-Walski said. She appealed to colleagues on the Eastern Shore, where White was born, explaining the problem and asking for help and a local genealogist called her with the news that the Levin White she thought was William’s father, and whose family tree she had traced, was from a different White clan.

Later, two acquaintances visiting an Accomack records office found an 1850 court document that referred to White’s status as an orphan — and listed the name of his deceased father, William A. White. There was the research mistake, Hull-Walski realized, and that’s why the DNA didn’t match. “It was a relief,” she said.

The Tie That Binds

The identification was made after museum researchers, led by Deborah Hull-Walski and Randal Scott, figured out that the youth might be White, constructed a 788-person family tree — a diagram that stretched the length of a wall — and tracked down a descendant in Lancaster, Pa.

Linda Dwyer, 64, a night clerk in a convenience store, matched to a sample of DNA taken from the boy’s left shinbone. “I think it’s awesome,” Dwyer said, adding that she believes she is White’s great-great-great-grandniece. “The whole technology of finding me and putting it all together. . . . It’s so cool.”

Yes it is Linda, yes it is.

source: Wash Post Article

MADRID, Spain - A small piece of jawbone found in a cave in Spain is the oldest known fossil of a human ancestor in Europe. This also shows that people lived on the continent much earlier than previously believed.

This fossil was found last year at Atapuerca in northern Spain, along with stone tools and animal bones, and is up to 1.3 million years old. That would be 500,000 years older than remains from a 1997 find that prompted the naming of a new species: Homo antecessor, or Pioneer Man, possibly a common ancestor to Neanderthals and modern humans — and this find seems to be from the same species, researchers said.

The timing of the earliest occupation of Europe by humans that emerged from Africa has been controversial for many years. Some archeologists believe the process was a stop-and-go one in which species of hominins — a group that includes the extinct relatives of modern humans — emerged and died out quickly only to be replaced by others, making for a very slow spread across the continent, Carbonell said in an interview.

Until now the oldest hominin fossils found in Europe were the Homo antecessor ones, also found at Atapuerca, but at a separate digging site, and a skull from Ceprano in Italy.

Carbonell’s team has tentatively classified the new fossil as representing an earlier example of Homo antecessor. And, critically, the team says the new one also bears similarities to much-older fossils dug up since 1983 in the Caucasus at a place called Dmanisi, in the former Soviet republic of Georgia. These were dated as being up to 1.8 million years old.

“This leads us to a very important, very interesting conclusion,” Carbonell said. It is this: that hominins which emerged from Africa and settled in the Caucasus eventually evolved into Homo antecessor, and that the latter populated Europe not 800,000 years ago, but at least 1.3 million years ago.

“This discovery of a 1.3 million-year-old fossil shows the process was accelerated and continuous; that the occupation of Europe happened very early and much faster than we had thought,” Carbonell said.

Chris Stringer, a leading researcher in human origins at the Natural History Museum in London and not involved in the project, said Carbonell’s team had done solid dating work to estimate the antiquity of the new Atapuerca fossil by employing three separate techniques — some researchers only use one or two — including a relatively new one that measures radioactive decay of sediments.

“This is a well-dated site, as much as any site that age can be,” Stringer said.

But he also expressed some caution about Carbonell’s conclusions.

First of all, the newly found jawbone fragment, which measures about two inches long and has teeth attached to it, preserves a section not seen in the equivalent pieces found at Atapuerca in 1997. So assigning both to the same species must be provisional, Stringer said.

And on the broader issue of tracing the new fossil back to the species unearthed at Dmanisi — Carbonell’s big leap arguing continuity — Stringer said this too must be tentative because it is based on just a piece of a front of a jawbone and the time lapse is half a million years.

“That is a long period of time to talk about continuity,” Stringer said.

Still, there are similarities between the two and this along with other archaeological evidence, suggests southern Europe did in fact begin to be colonized from western Asia not long after humans emerged from Africa — “something which many of us would have doubted even five years ago,” Stringer said.

Carbonell says that with the finding of human fossils 1.3 million years old in Europe, researchers can now expect to find older ones, even up to 1.8 million years old, in other parts of the continent.

“This has to be the next discovery,” he said. “This is the scientific hypothesis.”

from This Article

Two brothers slain by Native Americans — and a niece who was kidnapped and made an American Indian bride.

If Obama’s great-great-great-great-great-great-grandfather Christian Gutknecht had an adventurous life, it’s lost to history. But the fate of his brothers and their families could fill a TV mini-series.

Christian and his brothers, Hans Michael and George, all emigrated to the New World from Germany on separate ships in the mid-1700s. All three went by Goodnight once they arrived.

Both Hans — also known as John Michael, or just Michael — and George were slaughtered by American Indians in separate late-18th century attacks in frontier Kentucky.

“They pioneered into the Kentucky wilderness among the earliest of those who went there; the blood of both brothers, spilled in Indian warfare, helped make it ‘the dark and bloody ground,’ ” wrote descendant S.H. Goodnight in The Good(k)night Family (Gutknecht) Family in America (1936).

George was killed in 1780 in a British-led raid by 500 Canadians and Native Americans on Ruddell’s Station in frontier Kentucky. Five of his children were captured by American Indians.

His daughter Elizabeth had two sons by a Native American before she returned to her family.

“George was massacreed in the most barbrous manner while his children were scattered among the Indians,” according to a family letter written in 1883 letter. “My father was taken to Detroit and sold to the French and taken to Canada. Elizabeth never got to her people until she was twenty two years old.”

Accounts vary on exactly how Hans Michael met his fate.

One version has him being killed by Indians while his family was part of wagon train of pioneers heading from North Carolina toward what is now Mercer Co., Ky., in 1781.

His son was wounded, and his pregnant wife escaped into the woods, where a search party found her days later “lying prostrate upon the ground in a semi-conscious state, her face covered with a blanket,” according to the unattributed family account published in a newspaper in 1973.

But a version passed down in old family letters has Indians attacking Hans Michael and his son while the two were apparently travelling alone. According to this version, they were returning to their Kentucky settlement after a trip to North Carolina to retrieve some of their possessions. Native Americans killed — and scalped — Hans Michael and wounded his son, who was able to escape.

“The Indians came upon them at their camp fire, killed the father,” a descendant wrote in 1883. “They shot the son, the arrow entered one side and came out at the other, and the surprising part is in that condition he made his way to the horses, stopped the bell, concealed himself and the next day went to the white settlements.”

******

“Great grandfather was killed by the Indians and John was shot but got away in Ky. and one of my grand aunts was stolen by the Indians and had two sons by the Indians before she got back to her folks.”

Source: Family letter written by John S. Goodnight in 1884 and reprinted in The Good(k)night Family (Gutknecht) Family in America by S.H. Goodnight (1936).

******

“The family version of the removal to Kentucky and the killing of Michael Goodnight by Indians is told in this manner:

“‘After locating and building a cabin at Harlan’s Station in what later became Mercer County, [Hans] Michael Goodnight returned to North Carolina and then set out again to Kentucky in July 1781, with his family and household effects. They were a party of a caravan composed of other pioneer families, who were guarded by thirty armed men.

“‘No serious mishap befell the emigrant train until it arrived within half a day’s journey of Harlan’s Station, where a camp was pitched for the night. All was secure but at midnight, the fearful cry of the savage was heard, followed by gun shots, screams and confusion.

“‘Michael Goodnight was killed in the first onslaught and his son, John, was severly wounded, but he succeded in making his escape. Mrs. Goodnight was expecting another child at the time; she fled into the dark forest.

“‘Many of the immigrants were massacred, but a few escaped to the station where the alarm was given. A party was made up to search for Mrs. Goodnight and she was found two days later in woods lying prostrate upon the ground in a semi-conscious state, her face covered with a blanket.

“‘She was taken to Harlan’s Station, where four months later, January 1, 1782 a son, Isaac Goodnight, was born. A curious circumstance, preserved in the family traditions, is that from his birth until the day of his death Isaac could never go to sleep without covering his face.’”

Source: Unattributed historical family account printed in the Harrodsburg Herald, Harrodsburg, Ky., on Jan. 18, 1973.

******

Excerpt from 1883 family letter:

“The two brothers, John (Michael) and George, in the days of General Logan and Boon emegrated to the state of Kentucky and met sad misfortune. George and his entire family except two sons who were in the service were captured I think at Kentons [Ruddell's] station.

“George was massacreed in the most barbrous manner while his children were scattered among the Indians. My father was taken to Detroit and sold to the French and taken to Canada. Elizabeth never got to her people until she was twenty two years old.

“John (Michael) and his son John went back after some of their goods which they had to pack on horses for want of roads, the Indians came upon them at their camp fire, killed the father. They shot the son, the arrow entered one side and came out at the other and the surprising part is in that condition he made his way to the horses, stopped the bell, concealed himself and the next day went to the white settlements.

“I have given the outlines of our people in America. . . . . .

Respectfully, Farewell,

S. W. Goodnight.
article link

The Village of Eyam

It’s hard to prove the causative agent was a virus because of course in those days there were no blood tests for viruses. And today it’s impossible to extract viral DNA from 700 year-old skeletal remains. But in the last few years some evidence has emerged that seems to support the viral theory.

There may not have been blood tests, but in England at least there were parish records from about 1540. They give a detailed picture of what happened to the inhabitants of even the smallest village - births, deaths, marriages, and baptisms. One such village was Eyam, a lead-mining village in the county of Derbyshire in an area known as the Peak District, in central England.

The Black Death suddenly struck this tiny village in September 1665. The town’s rector persuaded the villagers to quarantine themselves to prevent the disease from spreading through the region. During the period of isolation, food was left for the villagers at a well on the parish boundary high up on the hill above the village, and paid for by coins which were dipped in vinegar to disinfect them. It seemed to work, because none of the surrounding areas were affected by the plague. A year later, the first outsiders ventured into Eyam. About half the town had survived.

Genetic View

In 1996, researchers from the National Institutes of Health in Washington D.C. led by Dr Stephen J O’Brien, tracked down the modern day descendants of Eyam from parish records and tested their DNA. They were curious to know whether the survivors shared any genetic similarity that had helped their ancestors resist the plague. They found high levels of a gene mutation called CCR5-delta 32 amongst the descendants. CCR5 is a gene that codes for a protein on the surface of white blood cells which acts as a receptor for other molecules involved in inflammation

These researchers knew about this protein from previous research on HIV which showed that HIV can slip past the protein, using it as a gateway to get inside and kill white cells. But people who have the mutated form of the gene - CCR5-delta 32 - don’t have this protein and their white cells won’t allow HIV in. So people with the mutation are resistant to HIV infection - they either don’t get HIV at all or are much slower to get it than people who have the normal gene.

Here was the mutation showing up again in the population of Eyam. And not just Eyam. Areas of Europe that had been affected by the plague (including America, which was mostly settled by European plague survivors and their descendants) also had unusually high levels of CCR5-delta 32 - about fourteen per cent of the population compared to two percent in areas that never experienced the Black Death - such as Asia and Africa.

The big jump in the percentage of the population with the mutation has been calculated to have occurred around 700 years ago - around the time of the first major plague epidemic, say Duncan and Scott.

It appears that, beginning 700 years ago, the Black Death increased the genetic frequency of CCR5-delta 32 mutation in the Caucasian gene pool. This protected these populations from later epidemics of both the Black Death and also HIV. The populations of Asia, and Africa had no such protection - and this also explains why HIV/AIDS has spread more quickly there. It also appears that, like HIV, the Black Death was caused by a virus, say Duncan and Scott.

They say that during the period of the Great Pestilence there were probably two separate plagues - a viral hemorrhagic fever in Europe, the Black Death; and a bubonic plague in Asia and parts of the Mediterranean coast caused by Yersinia.

The Black Death

Both epidemics are examples of an evolutionary struggle that has gone on for millions of years between disease causing micro-organisms and hosts. If a micro-organism mutates into a form that makes transmission easier - to a new host for example - then it has the advantage. If the host in turn develops a mutation that protects it from the micro-organism, or develops immunity to it, then it has an advantage over that micro-organism.

The Black Death, dying out in the 17th century, lost the fight. The last great epidemic was in 1670 - after that smallpox took over as the number one infectious disease killer. The Black Death was a victim of its own success. It killed so many of the population so quickly that those left either had genetic resistance or immunity. It had nowhere to go. Bubonic plague was more successful from an evolutionary point of view. It was (and is) deadly too, but it caused sporadic outbreaks in isolated areas, leaving the rest of the population disease free possibly to be infected in future. So bubonic plague survives.

But both epidemics were only possible because of the increased movement of people from place to place. In the Middle Ages, disease could only spread as fast as a person could walk or a ship could sail. In the twenty first century, a new disease could cross the globe by air in twenty-four hours, say Duncan and Scott. Will there another epidemic? Undoubtedly. Will it be as deadly as the Black Death? It’s possible. If it happens in the twentieth first century it will travel much faster than two miles a day.
from ABC net AU

DNA Proves Immunity to Bubonic Plague and HIV

People with a genetic mutation that makes them more resistant to the AIDS virus probably have smallpox to thank, according to two population geneticists at the University of California, Berkeley.

About 10 percent of Europeans have a mutation that disables a protein the Human Immunodeficiency Virus (HIV-1) uses to slip into immune system cells. HIV-1 has a harder time infecting people who have a mutation in one of the two genes that code for this receptor protein, and if these people become infected, their disease progresses more slowly. Those with mutations in both copies of the gene are almost completely resistant to the virus.

This genetic mutation arose as recently as 700 years ago, and some researchers have suggested that the bubonic plague that devastated Europe periodically over the past 1,000 years may have selected for the mutation by sparing those who lacked one or both copies of the gene.

In a paper appearing this week in the online Early Edition of The Proceedings of the National Academy of Sciences, the two UC Berkeley researchers argue that smallpox, not bubonic plague, is the most likely cause of the spread of this mutation throughout the European population in such a short time. That is, the same genetic mutation that confers resistance to HIV-1 protects against death from smallpox.

“Our population genetic model finds that genetic selection from plague wouldn’t have been sufficient to drive the frequency of this genetic mutation to its current level,” said Alison P. Galvani, a Miller Postdoctoral Fellow at UC Berkeley. “It was sufficient for smallpox.”

Bubonic plague hasn’t been a major source of death in Europe or elsewhere for the last 250 years, while smallpox was only eradicated in 1978, at the same time AIDS appeared. The survival advantage this genetic mutation provided against smallpox has thus been transferred to AIDS, the authors noted.

Following a 1998 paper that linked the gene deletion with bubonic plague, “bubonic plague had been cited as a classical example of a historical selection pressure acting on a clinically important locus,” she said. That classic example now changes, with smallpox replacing the plague.

The gene produces a receptor, called CCR5, that is the main entry port for HIV-1 into T cells and macrophages. While most people around the world have two CCR5 genes or alleles, about 10 percent of Europeans, on average, lack one of the alleles. They thus produce fewer CCR5 receptors, which hinders initial infection by HIV-1 and slows spread within the body once an immune cell has been infected. Those lacking both alleles produce no CCR5 receptor.

Based on a population genetics model, Galvani and Montgomery Slatkin, a UC Berkeley professor of integrative biology, argue that bubonic plague could not have caused such a rapid spread of this genetic mutation throughout Europe. Even though the Black Death pandemic killed off 25-40 percent of all Europeans during its run through the continent between 1346 and 1352, bubonic plague was historically a sporadic disease with an average annual death rate of only a few percent during the 400-year period it afflicted Europe. Transmitted by fleas infesting rats, it killed people of all ages.

Smallpox, on the other hand, was a continuous presence in Europe for 2,000 years, and almost everyone was exposed by direct person-to-person contact. Most people were infected before the age of 10, with the disease’s 30 percent mortality rate killing off a large part of the population before reproductive age.

“When you remove children from a population, you remove more of the reproductive potential for the species, compared to losing older people, who are not reproducing,” Galvani said.

Other diseases common at the time, including measles, polio, whooping cough, rubella, scarlet fever, chicken pox and influenza, also targeted children, but fatalities were typically only a few percent and could not have exerted strong influence on the frequency of this genetic mutation.

The smallpox virus also has more biological similarities to HIV-1 than does bubonic plague, the authors point out. Plague is a bacterial disease, and there is no evidence that the bacterium, Yersinia pestis, uses the CCR5 receptor in infection. The bacteria actually reproduce outside immune cells.

Smallpox, on the other hand, is a virus based on RNA, just like HIV, she said. And there is some evidence that smallpox, Variola major, uses chemokine receptors like CCR5 to enter cells.

The researchers said the geographic distribution of smallpox also correlates better with the frequencies of the CCR5 deletion in Europe.

“The Scandinavian countries in particular have very high frequencies of this deletion allele - 14 to 16 percent - which some people have taken to mean that Vikings dispersed the deletion,” Galvani said. “But it could also be due to smallpox hitting Scandinavian countries harder. There were certainly some big smallpox epidemics in Scandinavia, whereas plague affected the continent more, in particular Italy and France.”

Polymorphisms, the technical term for small differences in peoples’ genomes, are probably often the result of disease, Galvani said. Sometimes they even lead to other diseases, such as the documented case of sickle cell anemia resulting from selection for resistance to malaria.

“There are probably other alleles that have been selected by disease, but we just haven’t found them,” she said. “Diseases have the potential to exert strong selection. There is an arms race between the host to resist and clear infection and the pathogen to evade the resistance. That leads hosts to develop polymorphisms, and then the pathogen to respond by evolving its own polymorphisms, and so on - there is a constant battle.”

from Science Daily

Nearly all of today’s Native Americans in North, Central and South America can trace part of their ancestry to six women whose descendants immigrated around 20,000 years ago, a DNA study suggests. Furthermore, they passed their mtDNA to about 95 percent of Native Americans, researchers said.

The women lived between 18,000 and 21,000 years ago, though not necessarily at exactly the same time, he said. The work was published this week by the journal PLoS One. Perego is from the Sorenson Molecular Genealogy Foundation in Salt Lake City and the University of Pavia in Italy.

The researchers created a “family tree” that traces the different mitochondrial DNA lineages found in today’s Native Americans. By noting mutations in each branch and applying a formula for how often such mutations arise, they calculated how old each branch was. That indicated when each branch arose in a single woman.

The six “founding mothers” apparently did not live in Asia because the DNA signatures they left behind aren’t found there, Perego said. They probably lived in Beringia, the now-submerged land bridge that stetched to North America, he said. Connie Mulligan of the University of Florida, an anthropolgist who studies the colonization of the Americas but didn’t participate in the new work, said it’s not surprising to trace the mitochondrial DNA to six women. “It’s an OK number to start with right now,” but further work may change it slightly, she said. That finding doesn’t answer the bigger questions of where those women lived, or of how many people left Beringia to colonize the Americas, she said Thursday.

The estimate for when the women lived is open to question because it’s not clear whether the researchers properly accounted for differing mutation rates in mitochondrial DNA, she said. Further work could change the estimate, “possibly dramatically,” she said.
from Daily Times

European colonization (or conquering) of South America resulted in a dramatic shift from a native American population to a largely mixed one, a genetic study has shown. It is not surprising that the study suggests male European settlers mated with native and African women, and slaughtered the men - though areas like Mexico City “still preserve the genetic heritage” because these areas had a high number of natives at the time of colonization. All according to the journal Public Library of Science Genetics.

The international team of researchers wrote:

“The history of Latin America has entailed a complex process of population mixture between natives and recent immigrants across a vast geographic region.

“Few details are known about this process or about how it shaped the genetic make-up of Latin American populations.”

Clear signature

The study examined 249 unrelated individuals from 13 Mestizo populations (people from a mixed European/native American origin) in seven countries, ranging from Chile in the south to Mexico in the north.

Not only did the European settlers take away land and property, they also took away the women

“There is a clear genetic signature,” explained lead author Andres Luiz-Linares from University College London.

“The initial mixing occurred predominately between immigrant and European men and native and African women.”

Furthermore, the study showed that it was a pattern that was uniform across Latin America, but within the genetic landscape of Latin America, there were variations.

“We see it in all the populations we examined, so it is clearly a historical fact that the ancestors of these populations can be traced to matings between immigrant men and native and African women.”

“The Mestizo with the highest native ancestry are in areas which historically have had relatively large native populations,” they reported.

This included Andean regions and cities such as Mexico City, where major civilizations were already established by the time Europeans reached the continent in the late 15th Century.

“By contrast, the Mestizo with the highest European ancestry are from areas with relatively low pre-Columbian native population density and where the current native population is sparse,” they added.

Bloody Past

Explaining the fate of native males when the Europeans arrived, Professor Luiz-Linares said: “It is a very sad and terrible historical fact, they were basically annihilated.

“Not only did the European settlers take away land and property, they also took away the women and, as much as possible, they exterminated the men.”

As well as providing an insight into the past, the team hopes that the findings will also help shape studies aimed at identifying and analyzing diseases.
from BBC News

MITOMAP, the human mitochondrial genome database, has recently published a paper in Nucleic Acids Research announcing the completion of a full human mtDNA phylogenetic tree. [read full article]

This tree, available here (in pdf) was constructed from 2959 mtDNA coding region sequences. I find it hard to deal with because of the wide format. It lists mutations and the study that identified each particular sequence, the tree labels each mutation as a substitution mutation, a silent mutation, a tRNA or rRNA mutation, a mutation in the noncoding region, or a pathological mutation. MitoMap also provides another valuable tool, tables of mtDNA polymorphisms with source information.

The tree will potentially be very useful to both researchers and genetic genealogists by providing a quick and easy way to characterize new sequences. Anyone interested in learning more about their haplogroup or how their haplogroup fits into the human mtDNA tree will find the new mtDNA phylogenetic tree extremely informative.

Note: there is another tree view that I prefer located HERE

JOHN TOPP | March 13th, 2008 at 7:21 am

I am a South African of European descent belonging to the I MtDNA haplogroup. My MtDNA readings are as follows:
MtDNA HVRI variation: 16129g-A; 16223C-T; 16391G-A
MtDNA HVRII variation: 73A-G; 146T-C; 150C-T; 152T-C; 199T-C; 207G-A; 250T-C; 263A-G

KC | February 23rd, 2008 at 1:22 am

This is amazing! Finally, a site for our tiny little group. I’m KC, from California. I did the Nat. Geog. Genographic project so I don’t have as many numbers as you, but here they are:
16129A, 16189C, 16223T, 16391A, 16519C