Oldest New World human DNA.

[Jacques Cinq-Mars]

All,

Here is an interesting short Nature “news” that speaks of the extraction and analysis of DNA from a tooth belonging to 10,300 year old human fossil uncovered in a cave called “On Your Knees”, located on Prince of Wales Island, off the southeastern Alaskan mainland.

Dalton, Rex, 2005. Caveman DNA hints at map of migration. Nature 436: 162.

The oldest sample of human DNA ever isolated in the Americas is providing a glimpse of how people spread across the land masses. The DNA was extracted from teeth, more than 10,000 years old, found in a cave on the northern tip of Prince of Wales Island, off southern Alaska. Researchers compared the pattern of mutations in the DNA against those in thousands of samples. They found matches with 47 Native Americans from tribes living in areas ranging from North America to Tierra del Fuego, showing how the caveman’s descendants must have spread.

“I could hardly believe what I found,” says molecular anthropologist Brian Kemp from the University of California, Davis, who reported the results last month at a regional meeting of the American Association for the Advancement of Science in Ashland, Oregon.

The work, which has yet to undergo peer review, indicates how genetic techniques are giving researchers a new window on genetic migration, says Kemp. Cooperation between scientists and Native American tribes on the project is cited as an example of how science and traditional cultures can coexist — in stark contrast to the case of Kennewick man, bitterly disputed for nine years before studies finally began last month (see Nature 436, 10; 2005).

The DNA was extracted from teeth on a mandible found in 1996 in On Your Knees Cave, named by the explorer who first crawled inside in 1993. Carbon dating in 1997 showed the remains to be from someone living 10,300 years ago. Attempts to extract DNA from the bone failed, so Kemp spent two years probing the teeth. Working in high-containment facilities to prevent contamination, he and his colleagues finally managed to isolate fragments of mitochondrial DNA, which is passed down the maternal line, and Y chromosome DNA, which is passed from father to son.

The researchers compared the mitochondrial DNA with nearly 3,500 Native American sequences available in public databases. They found 47 matches, mostly from modern individuals but some from samples up to 1,500 years old. More than half of the matches were with members of the the Cayapa coastal tribe in Ecuador. Others were with members of the Chumash tribe of California, the Klunk Mound people in Illinois, the Tarahumara of Chihuahua in Mexico and the Mapuche and Yaghan tribes of Chile.

The caveman belonged to ‘lineage D’, one of the five founding lineages believed to have settled in the Americas more than 10,000 years ago. Lineage D is thought to have originated in Asia, and researchers also found a close match with a member of the Han ethnic group from Qingdao in eastern China.

“This is an exciting frontier,” says co-author James Dixon, an archaeologist at the University of Colorado, Boulder, who first dated the remains. But he adds that it will be important to repeat the work with other samples.

The local Tlingit and Haida tribes welcomed the project, which supports their concept of ‘haa shagoon’, learning from their ancestors. “We went right to the tribes within 24 hours of finding the bones, asking them to be a partner,” says Terence Fifield, the US Forest Service archaeologist for the region.

“We viewed the remains as offering us knowledge,” says Rosita Worl, a Tlingit tribal member who is a Harvard-trained cultural anthropologist. “We wanted the knowledge for current and future generations.”

For the original article -- that includes a nifty little map, click HERE.

Jacques Cinq-Mars

[Daryl Habel]

The 1-page article in Nature is not very informative.  Here is more information, the abstract for the original presentation made to the American Association for the Advancement of Science meeting last month (mentioned in the Nature article), forwarded here here with permission of one of the co-authors, Jason Eshleman.

Analysis of Ancient DNA from an Individual from Prince of Wales Island:
Implications for the Peopling of the New World, BRIAN M. KEMP, DAVID
GLENN SMITH, JASON ESHLEMAN, RIPAN S. MALHI, JOHN MCDONOUGH, E. DEBORAH
BOLNICK, JAMES DIXON, TIMOTHY H. HEATON, TERENCE FIFIELD, and ROSITA
WORL


Ancient mitochondrial and Y-chromosome DNA were successfully extracted
from the teeth of an individual dated to 9,880 ± 50 (CAMS- 32038) and
9,730 ± 60 (CAMS-29873) excavated from On Your Knees Cave (site
49-PET-408) on Prince of Wales Island in Southeast Alaska.  d13C
values of 12.1 and 12.5% suggest a diet of marine foods, so the date
should be adjusted to c. 9,200 14C ybp.  The mitochondrial DNA (mtDNA)
of this individual belongs to haplogroup D and the Y-chromosome to
haplogroup Q-M3*, which also confirms that the sex of the individual
was male.  This individual's mitochondrial haplotype (based on his
hypervariable region I+II sequences) does not represent the basal
haplogroup D lineage, demonstrating that multiple founder lineages of
this haplogroup reached the New World.   This haplotype matches or
closely matches published sequences of Native American mtDNA found in
populations of both North and South America, being found in
approximately 1% of living Native Americans.  The known date associated
with this sample allows for the calibration of the molecular clock and
can be used to assess the accuracy of earlier estimates of the timing
of the peopling of the New World based on molecular diversity.  This
sample also establishes a minimum date for the emergence of the M3
Y-chromosome mutation, which is believed to have occurred early during
the settlement of the New World.

Thanks, Jason.

Dar

[Doug]

Since Q3 is rekoned to be about 10,000 years old, it is a major discovery to find it in a 10,000 year old tooth. Now we have to believe that either Q3 is significantly older than 10,000 years or that they had an amazing stroke of good fortune and found the remains of the only Q3 bearer on Earth 10,000 years ago.

Doug

The 1-page article in Nature is not very informative.  Here is more information, the abstract for the original presentation made to the American Association for the Advancement of Science meeting last month (mentioned in the Nature article), forwarded here here with permission of one of the co-authors, Jason Eshleman.

Analysis of Ancient DNA from an Individual from Prince of Wales Island:
Implications for the Peopling of the New World, BRIAN M. KEMP, DAVID
GLENN SMITH, JASON ESHLEMAN, RIPAN S. MALHI, JOHN MCDONOUGH, E. DEBORAH
BOLNICK, JAMES DIXON, TIMOTHY H. HEATON, TERENCE FIFIELD, and ROSITA
WORL


Ancient mitochondrial and Y-chromosome DNA were successfully extracted
from the teeth of an individual dated to 9,880 ± 50 (CAMS- 32038) and
9,730 ± 60 (CAMS-29873) excavated from On Your Knees Cave (site
49-PET-408) on Prince of Wales Island in Southeast Alaska.  d13C
values of 12.1 and 12.5% suggest a diet of marine foods, so the date
should be adjusted to c. 9,200 14C ybp.  The mitochondrial DNA (mtDNA)
of this individual belongs to haplogroup D and the Y-chromosome to
haplogroup Q-M3*, which also confirms that the sex of the individual
was male.  This individual's mitochondrial haplotype (based on his
hypervariable region I+II sequences) does not represent the basal
haplogroup D lineage, demonstrating that multiple founder lineages of
this haplogroup reached the New World.   This haplotype matches or
closely matches published sequences of Native American mtDNA found in
populations of both North and South America, being found in
approximately 1% of living Native Americans.  The known date associated
with this sample allows for the calibration of the molecular clock and
can be used to assess the accuracy of earlier estimates of the timing
of the peopling of the New World based on molecular diversity.  This
sample also establishes a minimum date for the emergence of the M3
Y-chromosome mutation, which is believed to have occurred early during
the settlement of the New World.

Thanks, Jason.

Dar

[Daryl Habel]

From National Geographic News, comes a story dated Feb 2, 2007.

First Americans Arrived Recently, Settled Pacific Coast, DNA Study
Says

Stefan Lovgren
for National Geographic News
February 2, 2007

"A study of the oldest known sample of human DNA in the Americas
suggests that humans arrived in the New World relatively recently,
around 15,000 years ago.
The DNA was extracted from a 10,300-year-old tooth found in a cave on
Prince of Wales Island off southern Alaska in 1996.
The sample represents a previously unknown lineage for the people who
first arrived in the Americas.
The findings, published last week in the American Journal of Physical
Anthropology, shed light on how the descendants of the Alaskan
caveman might have spread.
Comparing the DNA found in the tooth with that sampled from 3,500
Native Americans, researchers discovered that only one percent of
modern tribal members have genetic patterns that matched the
prehistoric sample.
Those who did lived primarily on the Pacific coast of North and South
America, from California to Tierra del Fuego at the southernmost tip
of South America (see map).
This suggests that the first Americans may have spread through the
New World along a coastal route...."

There's more. The full story at:
http://tinyurl.com/284jhu

The story is based on an "Early View" research article published this
week in the American Journal of Phhysical Anthropology:

Kemp, B.M., Malhi, R.S., McDonough, J., Bolnick, D.A., Eshleman,
J.A., Rickards, O., Martinez-Labarga, C., Johnson, J.R., Lorenz,
J.G., Dixon, E.J., Fifield, T.E., Heaton, T.H., Worl, R., and Smith,
D.G. (2007).

ABSTRACT. Mitochondrial and Y-chromosome DNA were analyzed from
10,300-year-old human remains excavated from On Your Knees Cave on
Prince of Wales Island, Alaska (Site 49-PET-408). This individual's
mitochondrial DNA (mtDNA) represents the founder haplotype of an
additional subhaplogroup of haplogroup D that was brought to the
Americas, demonstrating that widely held assumptions about the
genetic composition of the earliest Americans are incorrect. The
amount of diversity that has accumulated in the subhaplogroup over
the past 10,300 years suggests that previous calibrations of the
mtDNA clock may have underestimated the rate of molecular evolution.
If substantiated, the dates of events based on these previous
estimates are too old, which may explain the discordance between
inferences based on genetic and archaeological evidence regarding the
timing of the settlement of the Americas. In addition, this
individual's Y-chromosome belongs to haplogroup Q-M3*, placing a
minimum date of 10,300 years ago for the emergence of this
haplogroup. Am J Phys Anthropol, 2007. © 2007 Wiley-Liss, Inc.

Abstract available at:
http://www3.interscience.wiley.com/cgi-bin/abstract/114082833/ABSTRACT
or:
http://tinyurl.com/3asg2l

For those reading from 'recent posts', this is a continuation of an earlier thread which begins HERE.

Dar