Newsletter #9
Asian Haplogroups N & O Spread After Native Americans Left Asia About 12,000 Years Ago
European Journal of Human Genetics (2007) 15, 204�211.
A counter-clockwise northern route of the Y-chromosome haplogroup N from Southeast Asia towards Europe
S. Rootsi et al.
A large part of Y chromosome lineages in East European and East Asian human populations belong to haplogroup (hg) NO, which is composed of two sister clades N-M231 and O-M175. The O-clade is relatively old (around 30 thousand years (ky)) and encompasses the vast majority of east and Southeast Asian male lineages, as well as significant proportion of those in Oceanian males. On the other hand, our detailed analysis of hg N suggests that its high frequency in east Europe is due to its more recent expansion westward on a counter-clock northern route from inner Asia/southern Siberia, approximately 12�14 ky ago. The widespread presence of hg N in Siberia, together with its absence in Native Americans, implies its spread happened after the founder event for the Americas. The most frequent subclade N3, arose probably in the region of present day China, and subsequently experienced serial bottlenecks in Siberia and secondary expansions in eastern Europe. Another branch, N2, forms two distinctive subclusters of STR haplotypes, Asian (N2-A) and European (N2-E), the latter now mostly distributed in Finno-Ugric and related populations. These phylogeographic patterns provide evidence consistent with male-mediated counter-clockwise late Pleistocene�Holocene migratory trajectories toward Northwestern Europe from an ancestral East Asian source of Paleolithic heritage.
Healthcare Providers Challenged to Educate Themselves on Genetics
Nature Reviews Genetics 8, 151-157 (February 2007)
Alan E. Guttmacher et al.
To biomedical researchers, this is the 'genome era'. Advances in genetics and genomics such as the sequence of the human genome, the human haplotype map, open access databases, cheaper genotyping and chemical genomics have already transformed basic and translational biomedical research. However, for most clinicians, the genome era has not yet arrived. For genomics to have an effect on clinical practice that is comparable to its impact on research will require advances in the genomic literacy of health-care providers. Here we describe the knowledge, skills and attitudes that genomic medicine will require, and approaches to integrate them into the health-care community.
Ethnic Groups Proved to Have Varying Responses to Complex Diseases
Nature Reviews Genetics 8, 91 (February 2007) |
Common genetic variants account for differences in gene expression among ethnic groups
Spielman, R. S. et al.
Polymorphic genetic variants contribute to differences between individuals on the cellular level in producing proteins involved in disease. These authors analyzed 4,000 genes from several ethnic groups. Around 1,000 of these genes showed differences between populations. This finding provides an important step on the way to understanding the genetics of susceptibility to complex diseases.
Y-chromosomal Evidence for a Limited Greek Contribution to the Pathan Population of Pakistan
E3b Lineages are Key
European Journal of Human Genetics (2007) 15, 121�126; published online 18 October 2006
By Firasat, S. et al.
Three Pakistani populations residing in northern Pakistan, the Burusho, Kalash and Pathan claim descent from Greek soldiers associated with Alexander's invasion of southwest Asia. Earlier studies have excluded a substantial Greek genetic input into these populations, but left open the question of a smaller contribution. We have now typed 90 binary polymorphisms and 16 multiallelic, short-tandem-repeat (STR) loci mapping to the male-specific portion of the human Y chromosome in 952 males, including 77 Greeks in order to re-investigate this question. In pairwise comparisons between the Greeks and the three Pakistani populations using genetic distance measures sensitive to recent events, the lowest distances were observed between the Greeks and the Pathans. Clade E3b1 lineages, which were frequent in the Greeks but not in Pakistan, were nevertheless observed in two Pathan individuals, one of whom shared a 16 Y-STR haplotype with the Greeks. The worldwide distribution of a shortened (9 Y-STR) version of this haplotype, determined from database information, was concentrated in Macedonia and Greece, suggesting an origin there. Although based on only a few unrelated descendants, this provides strong evidence for a European origin for a small proportion of the Pathan Y chromosomes.
Sami Came from Volga-Ural Region of Russia
European Journal of Human Genetics (2007) 15, 115�120.
A recent genetic link between Sami and the Volga-Ural region of Russia
By Max Ingman and Ulf Gyllensten1
The genetic origin of the Sami is enigmatic and contributions from Continental Europe, Eastern Europe and Asia have been proposed. While the majority of mtDNA diversity in the northern Swedish, Norwegian and Finnish Sami is accounted for by haplogroups V and U5b1b1, the southern Swedish Sami have other haplogroups and a frequency distribution similar to that of the Continental European population. Stratification of the southern Sami on the basis of occupation indicates that this is the result of recent admixture with the Swedish population. The divergence time for the Sami haplogroup V sequences is 7600 YBP (years before present), and for U5b1b1, 5500 YBP amongst Sami and 6600 YBP amongst Sami and Finns. This suggests an arrival in the region soon after the retreat of the glacial ice, either by way of Continental Europe and/or the Volga-Ural region. Haplogroup Z is found at low frequency in the Sami and Northern Asian populations but is virtually absent in Europe. Sami Z lineages may be grouped with those from Finland and the Volga-Ural region of Russia. This suggests that some Sami lineages shared a common ancestor with lineages from the Volga-Ural region as recently as 2700 years ago, indicative of a more recent contribution of people from the Volga-Ural region to the Sami population.
DNA Study Concludes Shawnee war chief Blue Jacket was a Native American, not legendary Dutch Caucasian
Research Revises Popular Legend
Advance for release
Friday, December 1, 2006
Columbus (December 1, 2006) . . . The great Shawnee war chief Blue Jacket, who played a pivotal role in the early history of southwestern Ohio, was not the legendary Dutch Caucasian named Marmaduke Van Swearingen, according to research published today in The Ohio Journal of Science.
Barring any questions of the paternity of the Chief's single son who lived to produce male heirs, the �Blue Jacket-with-Caucasian-roots" legend is not based on reality,� said Carolyn D. Rowland, an analyst at Forensic Bioinformatics, Inc. in Fairborn, Ohio, and lead author of the report.
Using the tools of modern molecular biology and genetics Rowland and her colleagues tested the issue of paternity by analyzing cheek tissue samples collected from six direct male line descendants of George I Blue Jacket, son of Chief Blue Jacket and his wife Metis� Baby. Similarly, researchers collected samples from the Swearingen male line from two direct male descendants also six generations removed from Charles Swearingen; and one each from direct descendants of Marmaduke Swearingen's paternal great-uncles, Samuel Swearingen and John Swearingen.
According to the article, if it is accepted that George I was Chief Blue Jacket's son, it can be reasonably concluded that the famous Shawnee war chief was in fact a Native American and that the popular story surrounding his relatedness to Dutch settlers is without merit.
Written and oral accounts have claimed that the young Marmaduke Van Swearingen was captured by the Shawnee while he was wearing a blue linsey blouse or hunting shirt. That article of clothing is then said to have given rise to his Indian name when he became enamored with and dedicated to the way of the Shawnee and, ultimately, became Chief of the Shawnee by the age of twenty-five.
The paternally inherited Y chromosome, the focus of this research, has become a particularly important tool for such genealogical reconstructions as well as other purposes including forensics, molecular archaeology, nonhuman primate genetics and human evolutionary studies. The Thomas Jefferson/Sally Hemings affair and the identification of the remains of Christopher Columbus are among the more prominent oral traditions that have been directly tested by such DNA comparisons.
The lead author of the report, Ms. Carolyn Rowland, is currently an analyst at Forensic Bioinformatics, Inc. in where she reviews case files including GenophilerTM output, laboratory notes and serological results associated with forensic DNA testing. She has reviewed and consulted with the lead attorneys of more than 400 cases over the past four years.
Other authors included R. V. Van Trees, Major, USAF (Ret.), historian, genealogist and author; Marc S. Taylor, technical advisor to the Quincy TV series and lead scientist at Technical Associates in Ventura, CA; Dr. Michael Raymer, Associate Professor in the Department of Computer Science and Engineering at Wright State University; and Dr. Dan Krane, Associate Professor of Biological Sciences at Wright State University.
Vikings Left Little Genetic Trace in Ireland
European Journal of Human Genetics (2006) 14, 1288�1294. doi:10.1038/sj.ejhg.5201709; published online 6 September 2006
"The scale and nature of Viking settlement in Ireland from Y-chromosome admixture analysis"
By Brian McEvoy, Claire Brady, Laoise T Moore and Daniel G Bradley
Smurfit Institute of Genetics, Trinity College, Dublin, Ireland
You may want to consider returning your "Viking Certificate." According to a new study of Y chromosome lineages among Irish males with surnames seeming to indicate Norse ancestry, the Vikings did not leave as much of an imprint on the Irish population as many people would like to think. After all, they only stayed for a couple of centuries in most cases before going back to Norway. That's not much time to leave a sizable genetic legacy, even if you are a Viking.
ABSTRACT
The Vikings (or Norse) played a prominent role in Irish history but, despite this, their genetic legacy in Ireland, which may provide insights into the nature and scale of their immigration, is largely unexplored. Irish surnames, some of which are thought to have Norse roots, are paternally inherited in a similar manner to Y-chromosomes. The correspondence of Scandinavian patrilineal ancestry in a cohort of Irish men bearing surnames of putative Norse origin was examined using both slow mutating unique event polymorphisms and relatively rapidly changing short tandem repeat Y-chromosome markers. Irish and Scandinavian admixture proportions were explored for both systems using six different admixture estimators, allowing a parallel investigation of the impact of method and marker type in Y-chromosome admixture analysis. Admixture proportion estimates in the putative Norse surname group were highly consistent and detected little trace of Scandinavian ancestry. In addition, there is scant evidence of Scandinavian Y-chromosome introgression in a general Irish population sample. Although conclusions are largely dependent on the accurate identification of Norse surnames, the findings are consistent with a relatively small number of Norse settlers (and descendents) migrating to Ireland during the Viking period (ca. AD 800�1200) suggesting that Norse colonial settlements might have been largely composed of indigenous Irish. This observation adds to previous genetic studies that point to a flexible Viking settlement approach across North Atlantic Europe.
Genetic breakthrough reveals
differences between humans
Scientists hail genetic discovery that will change human understanding
By Steve Connor, Science Editor, The Independent
Published: 23 November 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.
HapMap Takes Leap Forward
Nature Genetics - 38, 1251 - 1260 (2006)
A worldwide survey of haplotype variation and linkage disequilibrium in the human genome
By Conrad D. F. et al.
Recent genomic surveys have produced a high level of information, and the HapMap project has raised high hopes for mapping genetic determinants of complex human disease, but only in a small number of human populations. Haplotype structure is reported here in 927 individuals representing 52 populations, a significant increase. The geographic distribution of haplotypes reflects human history. The emerging HapMap will be helpful for the design of genome-wide association mapping studies in nearly all human populations.
Neanderthal Genetic Secrets About to Be Unraveled
Nature, 16 November 2006
Neanderthal Genomics
Editor's Summary
Neanderthal traits appear in the human fossil record of Europe and western Asia about 400,000 years ago and vanish about 30,000 years ago. The Neanderthals are our closest extinct relatives, so as DNA technology advances the tantalizing prospect of identifying genetic changes characteristic of fully modern humans comes closer. A 38,000-year-old Neanderthal bone of sufficiently high quality to allow the extraction of more than a million base pairs has now been identified: it was originally found Vindija cave in Croatia (pictured on the cover) in 1980. Comparison of its DNA with the chimp and human genomes reveals that Neanderthal and human ancestors � like humans but unlike apes � had a small effective population size. The technology used in this work offers the prospect of a draft Neanderthal genome within two years.
Home Ancestry Test Uses
Same DNA Evidence as TV Shows
SANTA FE, N.M. -- (September 19, 2006) -- DNA Consulting has introduced a home DNA test that can unravel one's ancestry based on the same genetic markers used by detectives on TV shows. The company's DNA Fingerprint Test determines 16 genetic markers that make each of us unique and compares them to a database that can explain an individual's particular ethnic mix, or genetic signature. No two people have the same signature, composed of an equal number of genes inherited from mother and father, and from their parents, on and on back in time.
The new addition to genetic genealogy allows people to see their Top Ten closest matches in 180 populations. Previous products were limited to revealing the direct male or direct female lineage, based respectively on Y chromosome markers we receive from our father or on mitochondrial DNA passed to us by our mother. DNA Fingerprint Test looks at all our inheritance. It is as simple as collecting cheek cells at home with a cotton swab and mailing the sample back to the lab. It can be ordered online at www.dnaconsultants.com.
While other tests concentrated on populations in the past and human migration patterns, DNA Fingerprint's matches are to living persons. According to principal investigator Donald N. Yates, it is the first test to address such questions as, "Why do I have the physical appearance that I have?" and, "Do I have any Scandinavian, Chinese or English in my total genetic makeup?"
"The ancestry results are current, practical and very accurate," said Yates, "The accompanying report is valid for other family members and makes an unusual high-tech present for birthdays, marriages and anniversaries."
The 16 markers analyzed by the test include the so-called CODIS markers that are standard in the forensic profession. Individual test scores are input into a public database called OmniPop. Unlike criminal cases, however, all matches are anonymous. All results are confidential.
DNA Fingerprint sells for $250.00 and is an exclusive new product offering of DNA Consulting.
Myths of British History
Prospect, October 2006
Everything you know about British and Irish ancestry is wrong, according to geneticist Stephen Oppenheimer. Our English 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. And a form of English, not Celtic, was spoken in most places before the Roman invasion. Phylogenetic studies have overturned many of the commonly held beliefs about British history. Read article.
I'm Irish and German . . . Think Again
New DNA Fingerprint Test Uncovers
Deep Ancestry That May Contain Surprises
Houston Chronicle, September 30, 2006
Carolina Miranda thought she was purely Hispanic. But when she took the new DNA Fingerprint test for ancestry she learned she had matches with Poland and Mozambique.
Her experience inspired a young journalism student sure that she was Irish and Polish and German to go on the same journey into the past. "I was shocked to see that my strongest genetic roots were in Spain, followed closely by the Himalayan region of India," said Asheley Herzog. "Other top matches included Turkey, Norway, Romania and Saudi Arabia -- places I'd never dreamed of identifying with. And I apparently should not waste time searching for long-lost relatives at Oktoberfest parties this year: Germany graced the bottom of the list, barely beating Northern Italy as a contributor to my genetic profile."
Read article.
Human Lymphocyte Antigens
Studied for Disease Association
By P.I.W. de Bakker et al.
Nature Genetics 38:1166 - 1172
Published online: 24 September 2006
For the first time, scientists have created a high-resolution haplotype map for disease association studies in humans.
The proteins encoded by Human Lymphocyte Antigen (HLA) genes are highly diverse, yet their variation is a crucial determinant for a large number of infectious and autoimmune diseases. Identification of causes for disease is difficult because linkage disequilibrium extends across multiple genes. The international team of scientists therefore set out to characterize the classical HLA genes and more than 7,500 common SNPs across four population samples. The analysis provides a sweeping new basis for the study of disease associations.
New Research Overturns
Single Origin of Man
Nature Reviews Genetics 7, 669-680 (September 2006)
"Reconstructing human origins in the genomic era"
By Daniel Garrigan and Michael F. Hammer
Analyses of recently acquired genomic sequence data are leading to important insights into the early evolution of anatomically modern humans, as well as into the more recent demographic processes that accompanied the global radiation of Homo sapiens. Some of the new results contradict early, but still influential, conclusions that were based on analyses of gene trees from mitochondrial DNA and Y-chromosome sequences. In this review, we discuss the different genetic and statistical methods that are available for studying human population history, and identify the most plausible models of human evolution that can accommodate the contrasting patterns observed at different loci throughout the genome.
Database of Mission Indians
Now Online for Researchers
August 8, 2006
Reclaiming a neglected part of California's past, historians Monday unveiled an immense data bank that for the first time chronicles the lives and deaths of more than 100,000 Indians in the Spanish missions of the 18th and 19th centuries.
In an eight-year effort, researchers at the Huntington Library in San Marino used handwritten records of baptisms, marriages and deaths at 21 Catholic missions and two other sites from between 1769 and 1850 and created a cross-referenced computerized repository that is now open to public access.
The database should be a big boon to families researching their Southwest Indian ancestor who was adopted.
Role of Natural Selection in Evolution Proved on Genetic Level
From the article "A Map of Recent Positive Selection in the Human Genome," by Benjamin F. Voight et al., PloS Biology 4/3: March 2006
A team of evolutionary biologists have created the first comprehensive map of genes involved in natural selection, using newly available, dense, single nucleotide polymorphism (SNP) data from the International HapMap Project. "Signals of natural selection are incredibly widespread across the human genome," one of the researchers was quoted as saying in the New York Times (July 24, 2006).
"Everywhere we look, there appears to be very widespread signals of natural selection in many genes and many processes."
Examples of recent selection were demonstrated by high resolution study of the human genome in populations all over the world, but this factor in evolution was strongest in the Yoruba of sub-Saharan Africa.
Different genetic signals responsible for different physical attributes such as skin color and fitness were "clocked" for the first time.
Read more.
Scientists Plan to Rebuild Neanderthal Genome
By NICHOLAS WADE
The New York Times, July 20, 2006
Researchers at the Max Planck Institute for Evolutionary Biology in Leipzig, Germany, plan to reconstruct the genome of Neanderthals, the archaic human species that occupied Europe from 300,000 years ago until 30,000 years ago until being displaced by modern humans.
The genome will initially be reconstructed using DNA extracted from Neanderthal bones that are 45,000 years old, which were found in Croatia, though bones from other sites may be analyzed later.
The project is a collaboration between Dr. Svante Paabo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, and 454 Life Sciences, a Connecticut company that has developed a new method of sequencing, or decoding, DNA.
The sequencing of Neanderthal DNA, long a forlorn hope, suddenly seems possible more
Roots of Human Family Tree Shallower Than Previously Believed
Santa Fe New Mexican/Associated Press
July 1, 2006
By Matt Crenson
Humphrey Bogart
Brooke Shields is probably a descendant of Lucrezia Borgia. Humphrey Bogart is probably a descendant of the prophet Muhammad. And so it goes. Geneticists used to believe that "everybody on earth descends from somebody who was around as recently as the reign of Tutankhamen," according to an article titled "Brotherhood of Man." But revised thinking on their part puts the most remote common ancestor(MRCA)in a much more modern timeframe, so that nearly everyone alive can claim Charlemagne and Ghengis Khan as an ancestor, if statistics and random mating hold true.
The reason is that many, many lines die out. Those that survive have huge numbers of descendants within a few generations, and all of us have huge numbers of ancestors going back to a small genetic pool about a thousand years ago. So a 13-marker Y-STR match such as those reported in Male DNA Ancestry products from DNA Consulting relates to a relatively recent timeframe, unlike previous theories that a match went back many thousands of years to a common male ancestor.