DNA Sheds Light on North American Migration

Dental DNA reveals our ancient roots
By Leigh Fenly
UNION-TRIBUNE STAFF WRITER
August 24, 2005

JAMES DIXON
/ 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 [Photo]

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 manager.

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 contamination.

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. [Photo]

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

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."
{The orginal article has a great map showing probably migration patterns based on DNA matches]