University of Arizona

A photomicrograph shows an X chromosome at left, alongside a shrunken Y chromosome. The Y chromosome is passed down exclusively from father to son and can serve as an indicator of male-line human diversity.

Scientists say an African-American male's odd genetic signature suggests that the human Y chromosome's lineage goes back further in time than they thought — perhaps due to interbreeding with other populations such as Neanderthals.

"This really upsets a lot of ideas, but at the same time, it's understandable if we accept that human populations were structured in the past so that there were little pockets of diversity," said Michael Hammer, an evolutionary biologist at the University of Arizona who is one of the authors of a study published in the American Journal of Human Genetics.

The study focuses on the analysis of a DNA sample that was obtained from an African-American living in South Carolina and submitted to the Genographic Project, a National Geographic effort aimed at mapping human origins and migration. The funny thing about this sample is that it didn't match up with any of the previously known genetic signatures for the Y chromosome, which is passed down from father to son.

"Nobody expected to find anything like this," Hammer said in a news release.

A team led by Fernando Mendez, a researcher in Hammer's lab, analyzed more than 240,000 DNA base pairs on the African-American's Y chromosome. A comparison of the differences between the mystery genetic signature and previously known signatures led the team to conclude that the most recent common ancestor for the entire group lived about 338,000 years ago.

That goes further back than the fossil record goes for anatomically modern humans, Hammer said. "The fossil record speaks to 195,000 years or 200,000 years," he said. It also goes further back than the previous date for the most recent common ancestor based on Y-chromosome analysis, which is in the range of 142,000 years.

The researchers followed up on their discovery by searching through a genetic database for African populations, and turned up 11 men from western Cameroon who had virtually the same genetic signature.

Hammer said there could be two explanations for the previously unidentified Y-chromosome type: Either the genetic heritage of anatomically correct humans really does go back much further than what's reflected in the fossil record — or other populations, such as Neanderthals or the more recently identified Denisovans, interbred with modern humans. Anthropologists refer to that pattern of divergence followed by renewed interbreeding as introgression.

The results are "more consistent with introgression of an odd lineage," Hammer told NBC News. Over the past few years, scientists have been coming around to the view that such interbreeding did take place early in the history of our species. Recent analysis of Neanderthal and Denisovan DNA has indicated that a part of their genetic heritage survives in modern-day humans.

Melissa Wilson Sayres, a geneticist at the University of California at Berkeley who played no role in Hammer's study, said the new findings were "exciting" because they pointed to a Y-chromosome lineage more ancient than any others. "They just happened to come across this one Y chromosome that was hidden for so long, and it's very likely that there are more hidden Y chromosomes around the world," she told NBC News.

She said one of the biggest debates in the study of human genetics has to do with how to match mutation rates with time scales — and she expects this latest study to add to the debate. For example, some might continue to argue that the most recent common ancestor lived more recently than 338,000 years ago. "It will still be the oldest Y-chromosome heritage that we have, but I can foresee that some people might disagree with that specific age," she said.

More about our genetic origins:

• Y chromosome is an evolutionary marvel
• Humans had sex with now-extinct relatives
• So who didn't have sex with Neanderthals?

In addition to Hammer and Mendez, the authors of "An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree" include Thomas Krahn, Bonnie Schrack, Astrid-Maria Krahn, Krishna R. Veeramah, August E. Woerner, Forka Leypey Mathew Fomine, Neil Bradman, Mark G. Thomas and Tatiana M. Karafet. The authors acknowledged Jacqueline Johnson and her male cousins, the descendants of Albert Perry (South Carolina) and participating Family Tree DNA customers.

Alan Boyle is NBCNews.com's science editor. Connect with the Cosmic Log community by "liking" the log's Facebook page, following @b0yle on Twitter and adding the Cosmic Log page to your Google+ presence. To keep up with Cosmic Log as well as NBCNews.com's other stories about science and space, sign up for the Tech & Science newsletter, delivered to your email in-box every weekday. You can also check out "The Case for Pluto," my book about the controversial dwarf planet and the search for new worlds.

Christine Cox / NBC News file

Researchers say genetic genealogy databases can be leveraged to unlock more sensitive genetic information.

Researchers have shown that it's possible to link your identity to supposedly secret genetic information about your predisposition to diseases, merely by analyzing family-tree databases and other publicly available information.

"It was quite surprising," said Yaniv Erlich, a genetic researcher at the Whitehead Institute for Biomedical Research. "When we got the first family, I was surprised. ... It's as if you opened a box that for a long time was locked."

Erlich led the research team whose work is being published in this week's issue of the journal Science. The team's study already has led to a tightening of security measures for federally sponsored genetic databases.

The security-cracking trick relies on the availability of genetic information linked to surnames in a variety of public family-tree databases. DNA samples from males can be tested to look at dozens of genetic markers on the Y-chromosome that change only rarely from generation to generation. If the markers from two individuals with the same surname are a close match, that's a tip-off that the two are closely related, even if they don't know each other.

Tens of thousands of people (including yours truly) make that information public in hopes that someone else will match up with their results. The genealogical markers aren't linked to disease or other specific traits. But under the right circumstances, they could provide an opening for links with other, more sensitive genetic information.

How the secrets were revealed
Erlich and his colleagues conducted a three-step process to see how easy it'd be to use that opening. First, they analyzed anonymous Y-chromosome data from a public database for the 1000 Genomes Project, to come up with the DNA coding for markers that are used for genealogical purposes. Then they compared those markers against entries in the two largest family-tree databases, Ysearch and the Sorenson Molecular Genealogy Foundation.

The researchers said their analysis projected a success rate of 12 percent for recovering the surnames of U.S. Caucasian males. Another 5 percent would theoretically be linked up with the wrong surnames. They said upper- to middle-class Caucasian males were easier to identify, presumably because they're more likely to participate in the family-tree databases.

Once the surnames were identified, the third step was to look at other publicly available sources to go from the surname to a specific individual: Some genetic databases, for example, include information about the age and the state of residence of an anonymous participant, and even the number of children and their birth order. Those clues were added to information gleaned from other sources, ranging from public-record search engines to obituaries.

The researchers linked five specific individuals in three separate families with supposedly anonymous genetic records. The process took three to seven hours for each family pedigree, the scientists said. Then they traced those three family-tree pedigrees to find other connections between relatives and sensitive genetic data. "In total, surname inference breached the privacy of nearly 50 individuals from these three pedigrees," the researchers wrote.

"We show that if, for example, your Uncle Dave submitted his DNA to a genetic genealogy database, you could be identified," Melissa Gymrek, a member of the Erlich Lab and the Science paper's principal author, explained in a news release. "In fact, even your fourth cousin Patrick, whom you've never met, could identify you if his DNA is in the database, as long as he's paternally related to you."

What is to be done with data?
Erlich and his colleagues made a point not to reveal the identities of those individuals, and said they were not advocating a clampdown on the availability of genetic information.

"Quite the opposite," Erlich said. "We found the gene for two devastating pediatric disorders by analyzing the data in public databases. Using these databases, we gave hope to these families and to other parents. We don't want to take away these databases. ... What we really want to do here is to have this really mature conversation about privacy — to tell people we cannot completely protect the privacy, but also to tell them about the benefits."

For years, experts have worried that sensitive genetic data could be used to discriminate against patients, potential employees or would-be insurance customers. Such discrimination is illegal when it comes to employment or health insurance, but the law doesn't cover life insurance, disability insurance or long-term care insurance. Theoretically, an insurer could search through genetic records and turn you down because you have a genetic predisposition to, say, Alzheimer's disease. 

In a Science policy paper, representatives of the National Human Genome Research Institute and the National Institute of General Medical Sciences at the National Institutes of Health said it was time to "re-examine how to balance the protection of research participants ... with the societal benefits likely to be gained through the enhanced research that broad data sharing facilitates."

They said NIH "acted swiftly to mitigate future risks" by working with the NIGMS' genetic repository to shift the data about the age of study participants out of public view and into a controlled-access area of the database.

"That reduces the risk," Erlich said. "It creates another fence."

And what about the genealogical genetic data? Max Blankfeld, vice president for operations and marketing at Family Tree DNA, said his company has been dealing with privacy issues for more than a decade — and doesn't expect the latest research to lead to policy changes. Family Tree DNA has been running the Ysearch database as a free public resource for a decade, but does not force any of its more than 400,000 participants to use it.

"People voluntarily post their information in that database, and therefore it has nothing really to do with the vast majority of the people who take the test and choose to have it protected by Family Tree DNA," Blankfeld said. "This data, we don't share with anyone."

More about genetic ancestry:

• DNA takes on a family's mysteries
• Update on Irish roots: The wearin' o' the genes
• Gene-tracing project gets an upgrade

In addition to Erlich and Gymrek, the authors of "Identifying Personal Genomes by Surname Inference" include Amy McGuire, David Golan and Eran Halperin. The work was supported by the National Defense Science and Engineering Graduate Fellowship, the Edmond J. Safra Center for Bioinformatics at Tel Aviv University, and a gift from James and Cathleen Stone.

The authors of the Science policy paper, "The Complexities of Genomic Identifiability," include Laura Rodriguez, Lisa Brooks and Erick Green of NHGRI and Judith Greenberg of NIGMS.

Alan Boyle is NBCNews.com's science editor, and also the administrator of the Boyle Surname Project at Family Tree DNA.

Connect with the Cosmic Log community by "liking" the log's Facebook page, following @b0yle on Twitter and adding the Cosmic Log page to your Google+ presence. To keep up with Cosmic Log as well as NBCNews.com's other stories about science and space, sign up for the Tech & Science newsletter, delivered to your email in-box every weekday. You can also check out "The Case for Pluto," my book about the controversial dwarf planet and the search for new worlds.