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

**Blackbear** · 08-27-2005, 06:51 PM

JAMES DIXON
/ 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
Plateau.
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
wryly.
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
OYKCM.)
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."

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

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

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