Newsletter #6
NEWSWEEK COVER STORY: DNA Testing
It is connecting lost cousins and giving families surprising glimpses into their pasts. Now scientists are using it to answer the oldest question of all: where did we come from?
We Are Family: Father Bill Sanchez (back row, right) learned that his genes share characteristics of an ancient Jewish line. Some of his relatives closely match the signature, too.
By CLAUDIA KALB
Newsweek
Feb. 6, 2006 issue - Brian Hamman had always wondered: what was up with his great-grandfather Lester? Hamman, an avid genealogist, could trace his patrilineal line back to 19th-century rural Indiana, but there was a glitch in the family records. Great-Grandpa Lester, the documents showed, was born before his parents were married. So was Lester really a Hamman? Was Brian? Three years ago DNA tests confirmed the lineage and a simple family mystery was solved: Lester's parents had hooked up before they walked down the aisle on July 25, 1898. Lester was indeed a Hamman, and so is Brian. "I'm delighted," he says....
Genetic Link to Parkinson's Discovered in Ashkenazic and Sephardic Jews, Arabs, North Africans
By Rick Weiss
From the Washington Post, January 26, 2006
Researchers said yesterday that they have identified a single genetic mutation that accounts for more than 20 percent of all cases of Parkinson's disease in Arabs, North Africans and Jews, a big surprise for a major disease in which genetics was thought to play a relatively minor role.
The discovery raises the delicate question of whether some people should be offered tests to see if they harbor the predisposing glitch -- a tough call, as there is no known way to prevent the disease.
Parkinson's affects at least 500,000 Americans and has no cure, though drugs can slow its progression.
To view the entire article, go here,.
Human Genome Reveals More Individual Variation Than Thought
From Nature Reviews Genetics 7, 85-97 (February 2006)
By Lars Feuk, Andrew R. Carson and Stephen W. Scherer
The first wave of information from the analysis of the human genome revealed SNPs to be the main source of genetic and phenotypic human variation. However, scientists have now uncovered an unexpectedly large extent of 'structural variation' in the human genome. Structural variants can comprise millions of nucleotides within every genome, spelling big news for understanding human diversity and disease susceptibility.
Celtic DNA Has Origins on the Atlantic Facade of Europe, not in Central Europe
By Brian McEvoy et al.
Am. J. Hum. Genet. 75 (2004) 693-702
Celtic languages are now spoken only on the Atlantic facade of Europe, mainly in Britain and Ireland, but were spoken more widely in western and central Europe until the collapse of the Roman Empire in the first millennium A.D. It has been common to posit a central European "homeland" for the Celtic peoples. New mtDNA data, however, display patterns significantly similar to Y-chromosome and indicate a shared ancestry throughout the Atlantic zone, from northern Iberia to western Scandinavia, that dates back to the end of the last Ice Age.
Read full article
Linkage Disequilibrium Lower in African Americans?
From Genes and Immunity (2005) 6, 723�727. July 28, 2005
Linkage disequilibrium across the human genome is generally lower in West Africans and African Americans than Europeans. However, in one region of the DNA rich in immune genes, scientitists have found significantly more examples of apparent positive selection in West African and African American populations.
Scientists in Nature Magazine
Challenge Out of Africa Thesis
An Asian perspective on early human dispersal from Africa
BY ROBIN DENNELLI and WIL ROEBROEKS
Dec. 22, 2005
Nature vol. 438, pp. 1099-1104
The past decade has seen the Pliocene and Pleistocene fossil hominin record enriched by the addition of at least ten new taxa, including the Early Pleistocene, small-brained hominins from Dmanisi, Georgia, and the diminutive Late Pleistocene Homo floresiensis from Flores, Indonesia. At the same time, Asia's earliest hominin presence has been extended up to 1.8 Myr ago, hundreds of thousands of years earlier than previously envisaged. Nevertheless, the preferred explanation for the first appearance of hominins outside Africa has remained virtually unchanged. We show here that it is time to develop alternatives to one of palaeoanthropology's most basic paradigms: 'Out of Africa 1'.
Written in stone
From the Editor of Nature Magazine
Dec. 15, 2005
A collection of stone tools from East Anglia has been dated at around 700,000 years old, making them the the earliest signs of human activity in northern Europe by about 200,000 years. Humans were present in sunnier southern Europe before 750,000 years ago, but until now there were no traces of human activity north of the Alps before half a million years ago. The flint artefacts found at Pakefield, near Lowestoft, extend human activity in Britain and the entire northern European landmass back to an antiquity we're more used to from southern Europe. The tools are from the well known Cromer Forest-bed Formation, which has yielded Ice Age fossils for over a century. But this find was notable as the 32 worked flints, including the scraper shown on the cover, were in a clearly datable stratigraphic context. Go to tinyurl.com/d2zko for video clips of the press conference announcing this discovery.
Associated Article: Archaeology: Life on the Costa del Cromer
By WIL ROAEBROEKS
Flint fragments from eastern England constitute the earliest known evidence of human occupation of Britain. The climate was balmy, and the environment was home to a wide range of animals and plants.
Associated Letter: The earliest record of human activity in northern Europe
Simon A. Parfitt, Ren� W. Barendregt, Marzia Breda, Ian Candy, Matthew J. Collins, G. Russell Coope, Paul Durbidge, Mike H. Field, Jonathan R. Lee, Adrian M. Lister, Robert Mutch, Kirsty E. H. Penkman, Richard C. Preece, James Rose, Christopher B. Stringer, Robert Symmons, John E. Whittaker, John J. Wymer and Anthony J. Stuart
The colonization of Eurasia by early humans is a key event after their spread out of Africa, but the nature, timing and ecological context of the earliest human occupation of northwest Europe is uncertain and has been the subject of intense debate. The southern Caucasus was occupied about 1.8 million years (Myr) ago, whereas human remains from Atapuerca-TD6, Spain (more than 780 kyr ago) and Ceprano, Italy (about 800 kyr ago) show that early Homo had dispersed to the Mediterranean hinterland before the Brunhes�Matuyama magnetic polarity reversal (780 kyr ago). Until now, the earliest uncontested artefacts from northern Europe were much younger, suggesting that humans were unable to colonize northern latitudes until about 500 kyr ago. Here we report flint artefacts from the Cromer Forest-bed Formation at Pakefield (52� N), Suffolk, UK, from an interglacial sequence yielding a diverse range of plant and animal fossils. Event and lithostratigraphy, palaeomagnetism, amino acid geochronology and biostratigraphy indicate that the artefacts date to the early part of the Brunhes Chron (about 700 kyr ago) and thus represent the earliest unequivocal evidence for human presence north of the Alps.
Gene Piracy of Third World People Criticized
A review of international and UK-based ethical guidelines for researchers conducting nontherapeutic genetic studies in developing countries
By SHORMILA ROY CHOUDHURY and LESLIE A. KNAPP
European Journal of Human Genetics (2006) 14, 9�16.
21 September 2005
Initiation and implementation of nontherapeutic genetic research projects, sponsored by developed countries and conducted in developing countries, requires careful consideration and awareness of procedures that ensure ethical research. This article reviews, and discusses controversies surrounding, the ethical principles established internationally and recommended by institutions in the UK for designing and implementing nontherapeutic genetic research studies. Before project commencement, the researcher should submit proposals to appropriate ethics committees and, wherever possible, seek guidance from experienced researchers. The researcher must also be aware of his/her responsibilities when conducting research with human participants. Responsibilities include respecting autonomy, privacy and confidentiality of participants, respecting social and cultural differences, providing appropriate information to participants, obtaining informed consent and offering appropriate compensation for participation. Finally, researchers involved in human genetics studies must also consider specific issues and public concerns when collecting biological samples. This includes using anonymised samples, considering future use of samples and ensuring confidentiality of results.
Get into Your Pet's Genealogy
After the cloning of the first dog and assembling of the complete dog gene along with haplotypes for different breeds, can DNA testing for pedigree dogs be far behind? We suggest www.familydogdna.com. . . .
Summary by the EDITOR of Nature
Dec. 8, 2005
The genome of the domestic dog is arguably the most interesting of the 5,500 species of mammals on Earth, genetically speaking. The remarkable diversity between breeds, created by a brief period of intensive human-driven selection for behavioural and physical traits, means that its sequence contains critical clues to understanding genome evolution and organization, and predisposition to disease. In this issue, Lindblad-Toh et al. publish the high-quality draft sequence of the dog genome � that of female boxer Tasha � and outline some of the genetic differences between breeds. Comparative analysis with humans and rodents provides a general perspective on gene and genome evolution. And see Books and Arts for a review of the book of the genome.
News and Views: Genomics: The dog has its day
By HANS ELLEGREN
Domestication and selective breeding have transformed wolves into the diversity of dogs we see today. The sequence of the genome of one breed adds to our understanding of mammalian biology and genome evolution.
Study Suggests 'Y' the Male Chromosome Will Endure
By DAVID BROWN
The Washington Post
September 5, 2005
To paraphrase Mark Twain, reports of the impending death of the human Y chromosome have been greatly exaggerated.
Research published last week revealed that the chromosome of maleness -- which under the microscope looks as worn down and misshapen as a stubbed-out cheroot -- is actually healthy and holding up fine against the ravages of evolutionary time.
It turns out the human Y has barely changed in the last 6 million years. All its important parts still work. Predictions that it will cease to exist in another 10 million years -- and with it, men as we know them -- may be wrong.
In Chimpanzee DNA, Signs of Y Chromosome's Evolution
By NICHOLAS WADE, The New York Times
Published: September 1, 2005
Scientists have decoded the chimp genome and compared it with that of humans, a major step toward defining what makes people human and developing a deep insight into the evolution of human sexual behavior.
The comparison pinpoints the genetic differences that have arisen in the two species since they split from a common ancestor some six million years ago.
Chimpanzees and people possess almost identical sets of genes, so the genes that have changed down the human lineage should hold the key to what makes people human.
Biologists suspect that only a handful of genes are responsible for the major changes that reshaped the apelike ancestor of both species into a human and that these genes should be identifiable by having evolved at a particularly rapid rate.
Dental DNA reveals our ancient roots
By Leigh Fenly
UNION-TRIBUNE STAFF WRITER
August 24, 2005
ASHLAND, Ore. -- Paleontologist Timothy Heaton was used to finding 35,000-year-old remains of brown bear, black bear, hoary marmot and antelope in On Your Knees Cave, a tight opening tucked in the dense hemlocks of Alaska's vast Tongass National Forest. But on the last day of excavation in 1996, as Heaton was filling a final bag of sediment, he came upon something quite different.
A lower jaw. A pelvic bone. Obsidian worked into a spear point.
Unmistakable evidence of an ancient human.
Since, the effort to tease clues from the 10,300-year-old remains, �the oldest ever found in Alaska or Canada,� has involved myriad research laboratories, most recently the Molecular Anthropology Lab at UC Davis.
A tooth from On Your Knees Cave Man � wrapped in cotton and shipped via Federal Express � arrived there in 2003. Brian Kemp, a Ph.D. candidate, removed the tooth's crown and hammered out a quarter-gram portion of root. He subjected it to bleach, a decalcifying chemical and a protein-devouring enzyme. With a silica extraction, he got the tooth's DNA to jump out of the solution.
With the same process forensic scientists use to link DNA to criminals, Kemp tricked the purified DNA into copying itself millions of times. The resulting sequences, �the oldest DNA ever extracted from human remains in the Americas,� revealed some of the old man's secrets.
Kemp's analysis, which he will submit to Nature, confirmed the Ice Age remains as male and established his maternal ancestry as Asian.
From differences in the genetic sequences, Kemp is now able to argue that the cave man's DNA represents a new ancient lineage in North America. Comparing that DNA to modern-day sequences, he also is suggesting changes to some scientists' estimates of the time of the first migrations to the New World.
In the months to come, the results will likely be strenuously argued. Less debatable is the fact that Kemp's work gets us closer to understanding who first peopled North America and offers a glimpse at the tantalizing future of genetic anthropology.
The human genome stores vast amounts of information on the movements, relationships and adaptations of past populations. In the last decade, after some embarrassing missteps and exaggerated claims, DNA technology has begun to reveal some of that dormant information.
The promise is huge, says Nina Jablonski, an anthropologist at the California Academy of Sciences. "As the early problems get solved, we're going to have the framework to learn about relationships among ancient people. DNA is going to answer all our questions about who is related to whom."
To follow this conversation for long you need a vocabulary word: mitochondrial DNA.
Most people are familiar with nuclear DNA – our genes that come to us courtesy of our mother and father, when the sperm fertilizes the egg and both sets of genes mix.
As a tool for genetic anthropologists, nuclear DNA is troublesome because all that reshuffling of genes makes it tough to trace a direct genetic line from individual to individual.
But the mitochondria, the cell's energy-producing bodies, also have tiny genomes, and these are inherited only from our mothers. Because there is no mixing with male genes, Smith explains, mitochondrial DNA stays the same from generation to generation, except when random mutations occur.
And mitochondrial DNA is abundant in cells compared to nuclear DNA and therefore more likely to be extracted. It will never be enough to clone an early cave man, but for Kemp, Smith and other genetic anthropologists, mitochondrial DNA is the mother lode.
"This is what's allowing us to construct a history where there is no written record," Smith says.
The reason they can do this is because the rate of mutation in mitochondrial DNA remains constant over time – in each individual, from prehistory to modern-day, changes occur at the same rate. That rate of change is used as a measuring stick for time known as the molecular clock.
To make sense of all the mutations, scientists group individuals with similar sets of mutations into families known as haplogroups. Haplogroups are further divided into smaller groups called haplotypes. OYKCM belongs to haplotype D, one of five founding lineages that appear in North America. But his haplotype is rare.
"When I first saw it, I wasn't sure what I was looking at," Kemp says. "He was D-something else."
The D-something-else genetic sequence is like a fingerprint of inherited mutations. Kemp wanted to find out if anyone living today had anything similar. From a genetic database of 3,500 Native Americans, he found 47 individuals living in North and South America who belong to the same haplotype. These are the cave man's relatives, inheritors of his same fingerprint of mutations.
The 47 are widely spread, from California to Tierra del Fuego. Some belong to California's Chumash tribe, Ecuador's Cayapa tribe and the Tarahumara in Mexico. This wide dispersal is an important clue to the geographic reach of the cave man's family and the migratory routes they might have taken.
Mitochondria can be inherited from both parents
* 17:01 23 August 2002
* NewScientist.com news service
* BY DANNY PENMAN
Mitochondria may not be inherited solely through the maternal line, according to new research that promises to overturn accepted biological wisdom.
If confirmed by other researchers, the findings could have huge implications for evolutionary biology and biochemistry.
Robert Sanders Williams, from Duke University Medical Center in North Carolina, says the findings are "remarkable and unanticipated. This is more than a mere curiosity. It asserts the principle that it can occur in humans. It could have significant implications for the study of human evolution and the migrations of populations," he says.
DNA Machine May Advance Genetic Sequencing for Patients
By NICHOLAS WADE
Published: August 1, 2005
A new kind of machine for decoding DNA may help bring costs so low that it would be feasible to decode an individual's DNA for medical reasons. The machine, developed by 454 Life Sciences of Branford, Conn., was used to resequence the genome of a small bacterium in four hours, its scientists report in an article published online today by the journal Nature. Read the article in The New York Times.
Vive la difference!
By Charles Lee
Until very recently, it was widely touted that the complete DNA sequences of any two human beings were 99.9% identical. A new study refutes this notion through a comprehensive comparison of two individual genomes which detects hundreds of new structural genomic variants. The article appears in Nature Genetics 37, 660 - 661 (2005).
Heart Drug for Blacks Endorsed
Racial Tailoring Would Be a First; Idea Stirs Debate
By Rob Stein
Washington Post Staff Writer
Friday, June 17, 2005; Page A01
Federal health advisers yesterday endorsed the approval of a drug to treat heart failure in African Americans, which would make the controversial pill the first medicine targeted at a specific racial group. Read article.