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Stanford Report, November 8, 2000

Why study the Y: Chromosome reveals path of ancestral humans


About 89,000 years ago the grandfather of all modern men was born in Africa. His sons and extended family lived close to home for many years, but then a handful of adventurous young men traveled far afield, and their descendents set foot in Europe, Asia and Australia. Many years after their departure, a second group of male wanderers -- and perhaps even a third -- set out to make their way in the world. The descendents of these other wanderers followed the steps of their distant relatives into new continental pockets and raised families of their own. So reads their genetic story, say Stanford researchers, as written in the DNA that comprises the Y chromosomes of their modern-day descendants.

Deciphering this chapter in the story of the Y chromosome has been the avid pursuit of Stanford researchers Peter Underhill, PhD, senior research scientist in the Department of Genetics, and Peter Oefner, PhD, senior research scientist in the Department of Biochemistry and associate director of the Stanford Genome Technology Center. They are using the small DNA differences between different men's Y chromosomes to figure out how populations from around the world are related, and where and when these populations evolved.

"Each gene has its own molecular ancestor," said Underhill. "The idea all along, through this molecular anthropology approach that [emeritus professor of genetics] Luca Cavalli-Sforza pioneered, is to look at the genetic history of genes and see if we can infer or deduce something about human history and human populations."

Only men carry a Y chromosome. Females have two X chromosomes, whereas males have one X and one Y. And, unlike the 22 pairs of non-sex chromosomes each human has, there is almost no opportunity for the Y chromosome to swap or share its DNA with another chromosome. So all the information in a man's Y chromosome is passed to his son -- and every man's Y chromosome carries a virtual pedigree of his male family history.

"The Y is somewhat unique," said Underhill "It has this unique storytelling component to it. That's why the Y chromosome was very revealing about the history of Thomas Jefferson and his descendants. What we've done, instead of looking at one family of 8 generations, is to look back over three or four thousand generations at the history of our species."

By analyzing the Y chromosomes of men from different populations, Oefner, Underhill and their colleagues estimate that the African grandfather -- the most recent common ancestor to all living men -- lived sometime between 40,000 and 140,000 years ago, most probably about 89,000 years ago. Twenty-three thousand years later, the first of these modern humans migrated out of Africa.

Although the Y chromosome is passed intact from father to son, once in a while an alteration will occur in the chromosome's DNA. A single DNA letter will incorrectly replace another, causing a permanent change in the chromosome's genetic sequence. Such a change is the start of a new Y lineage because the change will be inherited by all future male descendants. It is these lineages that Oefner and Underhill use to track the movements of ancestral men and the populations they founded.

"Differences are very rare [on the Y chromosome] -- approximately one in every 5,000 to 50,000 base pairs. But in genetics it's the differences that really tell the story," said Oefner.

The two scientists have now found 160 DNA substitutions on the Y chromosome. They have catalogued these changes in 1062 men from 21 populations and have concluded that a small group of East Africans (Sudanese and Ethiopians) and Khoisan, from Southern Africa, are the closest present-day relatives of the original ancestral male lineage.

The genetic data also revealed that there were at least two migrations of modern humans into the Americas. People in the first migration traveled to the Americas from Africa via East Asia. The second wave of immigrants traveled from Africa through Central Asia into North America. According to the researchers, the predominant Y chromosomes in Native American populations today are most closely related to individuals in Central Asia.

To confirm their theories and help pinpoint the timing of population movements across the continents, the researchers are also studying DNA that is passed only from mothers to daughters.

Comparing data collected from the two genetic systems, the researchers find consistency in the estimates of the timing of the various migratory events out of Africa.

The two scientists are continuing to analyze DNA from more people in addition to studying DNA markers on other chromosomes to sharpen their genetic picture of our earliest human ancestors. "There is not one genetic system to explain the entire history of the human genome," said Underhill. "Different genes have different histories. But when several genes are telling the same story, you're more confident that you've got the history right."

Oefner and Underhill and an international team of collaborators published their latest results in the November issue of Nature Genetics and the November 10 issue of Science. Stanford co-authors of the papers include Ronald Davis, PhD, professor of biochemistry and genetics, and director of the Stanford Genome Technology Center; Peidong Shen, research associate at the center; Cavalli-Sforza; Alice Lin and Giuseppe Passarino, PhD, research assistant and visiting researcher respectively in the department of genetics; and Marcus Feldman, PhD, professor of biological sciences.

Ornella Samino, PhD, contributed to the project as a visiting researcher in Cavalli-Sforza's lab. Wei Yang and Erin Kauffman, previously research assistants at the Stanford Genome Technology Center, also contributed.