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  • DNA links 10,000-year-old man to tribal descendants

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    DNA links 10,000-year-old man to tribal descendants
    Wednesday, August 24, 2005

    DNA tests on a 10,300-year-old man discovered in Alaska links him to 47
    tribal descendants in North and South America, The San Diego Union-Tribune
    Paleontologist Timothy Heaton extracted DNA from "On Your Knees Cave Man"
    and compared it to a database of Native people. He found 47 descendants
    belonging to tribes as diverse as the Chumash in California, the Zapotec in Mexico
    and the Quechua of Peru.
    The connection was uncovered by examining the haplotype, or DNA mutation, of
    the ancestor and his descendants. According to researchers, there are five
    different haplotypes found among all Native Americans.
    On Your Knees Cave Man was found in the Tongass National Forest in Alaska in
    1996. The U.S. Forest Service worked with the Klawock Tribe and the Craig
    Tribe on the excavation. Tribal members participated and observed the dig. The
    tribes agreed to the DNA test, which was restricted to two teeth.
    Get the Story:
    _Long in the tooth _
    ( (The San Diego
    Union-Tribune 8/24)
    _Politics plagued bones of Kennewick Man _
    (The San Diego Union-Tribune 8/24)

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    Dental DNA reveals our ancient roots
    By Leigh Fenly
    August 24, 2005

    / University of Colorado, Boulder
    A cast of the human jaw found in On Your Knees Cave on Prince of Wales
    Island in southeastern Alaska. UC Davis researchers have sequenced DNA from two
    of the teeth - - the oldest ever extracted from ancient American remains
    * _Politics plagued bones of Kennewick Man_
    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.
    _Graphic: Kinship with On Your Knees Cave Man_
    ( 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."
    DNA's promise
    At the moment, Kemp is relating to a cup of coffee. He's joined by his
    peers: his adviser, David Glenn Smith, the respected director of Davis' Molecular
    Anthropology lab; Ripan Malhi and Jason Eshleman, former students of Smith's
    and partners in science and business; and John McDonough, Smith's jovial lab
    They are earnest, confident, energized. Smith alone – who brought them all
    here, literally and figuratively – has a quiet air.
    Earlier this morning, each had muscled through PowerPoint presentations
    describing their work at an American Association for the Advancement of Science
    seminar at Southern Oregon University in Ashland. Now, in the sleek new, brick
    library on campus, they are warming to shop talk. Teeth, for instance, and
    Don't worry that it's not good enough for anyone else to hear... just sing, sing a song.sigpic

  • #2
    / University of Colorado, Boulder
    The entrance to On Your Knees Cave in southeastern Alaska. A lower jaw, some
    pelvic bones, ribs and backbones of a 10,300-year-old skeleton were
    excavated from the cave in 1996.
    The field is so new, it's only now becoming clear that teeth are more likely
    than bone to give up their DNA. The difficulties recovering any DNA from
    ancient material are vast, since DNA begins to degrade immediately after death,
    as water, oxygen and microbes attack it. But teeth, encased in enamel and
    partly protected by the jaw bone, are turning out to be better harborers of
    DNA. They have become the prizes in the DNA lab.
    "In my 200 samples, I didn't have a single tooth," laments Eshleman, drawing
    a face.
    Malhi ribs him. "Oh, it's OK, Jason."
    Eshleman's DNA studies – using bones – are helping make sense of
    California's huge number of Native American languages. He's also found new evidence of
    a very early coastal migration down the West Coast.
    Similarly, Malhi is using DNA data to measure the impact of European contact
    on the genetic diversity of Native Americans who populated the Columbia
    The two have also founded Trace Genetics Inc., in Richmond, a private
    company that has helped 1,000 people determine their Native American ancestry. For
    one woman, adopted as a child, this was the first time she'd known for sure:
    She is Native American, descended from Na-Dene speaking tribes.
    In all such work, the single biggest hurdle is defeating contamination. The
    PCR process, used to create millions of copies of DNA, has been compared to
    a Xerox machine, although Malhi prefers to call it a "contamination factory."
    "Lots of times I've done a sampling and gotten my own DNA sequence," he says
    That's because DNA is lying about everywhere. "What is it – we each shed
    millions of skin cells every day?" wonders McDonough. Each DNA-rich cell – lying
    on a lab bench, tucked into a glove – is waiting to hook onto an ancient,
    degraded sample.
    In the 1990s, it was contaminated samples that led to false claims for DNA
    sequences of dinosaurs and million-year-old plants and insects. Smith's lab at
    Davis, one of the largest in the country, is a model for containment and
    sterilization processes. Access to the lab is strictly limited. Equipment is
    bleached and decontaminated on a regular basis. On file are the DNA records of
    every employee, past and present, to compare to new results.
    Whenever possible, Smith recommends duplicating the work. Kemp sequenced a
    second tooth from On Your Knees Cave Man (OYKCM) in the lab of Malhi and
    Eshleman. "When it came up the same," he says, "I knew the results were true."
    Mother lode
    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.
    Beyond migration questions, haplogroup studies can indicate conquest,
    assimilation and language development – filling in a broad canvas with small
    strokes. "It's easy to get seduced by the big questions," says Smith, "but what
    we're interested in are the smaller questions of what happened after the
    peopling of the New World. We're interested in the intricacies."
    One example is Eshleman's studies showing haplotype A occurring primarily in
    British Columbia and the Channel Islands – suggesting an early southerly
    migration along the West Coast.
    Mitochondrial DNA creates a partial record, to be sure, because it only
    traces female populations. (The male trademark Y chromosome is notoriously
    difficult to sequence in ancient samples, although Kemp was lucky to identify it in
    Even so, DNA data may clarify the contentious debate surrounding the timing
    of the first migrations to the New World.
    Parallel dates
    Here Kemp has tread, too.
    In the late 1990s, scientists used DNA studies to propose that people first
    advanced upon the continent from Asia as much as 40,000 years ago. But data
    from numerous archaeological sites across the Americas have placed the
    migration at closer to 10,000 to 12,000 years ago.
    Kemp has used OYKCM as a measuring stick to come up with dates much closer
    to the archaeological record. "Because we know that this guy represents the
    oldest known example of this lineage, that places a minimum date on the
    emergence of the lineage," he explains.
    In other words, OYKCM represents one end of the measuring stick. At the
    other end are the 47 people who belong to his haplotype. According to the rules
    of the molecular clock, this makes it possible to measure the genetic changes
    between OYKCM and the modern samples and calculate the time it would have
    required for those changes to occur.
    "My calibration shows that the changes were occurring two to four times
    faster than previously thought," Kemp says. "It means some people have
    overestimated the time. It wasn't so long ago."
    That makes some of his colleagues wrong – and previous DNA data flawed –
    but Kemp is satisfied. "I hope the impact of my paper will be to bring the
    molecular timing more in line with the archaeological record," he says. "This is
    what you want your work to do."
    Don't worry that it's not good enough for anyone else to hear... just sing, sing a song.sigpic


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