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.

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Neanderthals like the one depicted in this museum reconstruction died out tens of thousands of years ago, but geneticist George Church says it may be possible to bring their DNA back into the gene pool.

Pioneering Harvard geneticist George Church suggests that the day is coming when we'll want to reverse-engineer the Neanderthal genome and pass the now-extinct creatures' advantages to our own progeny. All that's needed would be an "extremely adventurous female human" to serve as a surrogate mother.

During an interview with the German magazine Der Spiegel, Church was asked whether a Neanderthal baby would be born in his lifetime. "That depends on a hell of a lot of things," the 58-year-old replied, "but I think so."

Is he serious?

Well, Church is serious about the promise of synthetic biology, which involves tinkering with the chemical components of DNA to add artificial twists to the code of life. Microbes could be tweaked to produce better biofuels or harness solar power. White blood cells could be rejiggered to fight cancer or other diseases, using a tamed form of the HIV virus. And extinct species could be brought back to life through a combination of cloning and genetic engineering.

The species-resurrection scenario would involve inserting the reconstructed nuclear genetic material from the extinct creature into the living egg of a closely related present-day species, sparking the cell into dividing, and then implanting the resulting embryo into the womb of a female from the present-day species. It's been discussed in the context of using elephants to bring back mammoths, or chicken hens to bring back dinosaurs. 

Technically speaking, the progeny wouldn't be a mammoth or a dinosaur, but rather an elephant or chicken exhibiting the genetic traits of their long-departed relatives. A similar technique could be applied using Neanderthal DNA: Chunks of reconstructed genetic code could be used to reprogram human cells and produce increasingly Neanderthal-like stem cells.

"If we do that often enough, then we would generate a stem cell line that would get closer and closer to the corresponding sequence of the Neanderthal," Church told Der Spiegel. "We developed the semi-automated procedure required to do that in my lab. Finally, we assemble all the chunks in a human stem cell, which would enable you to finally create a Neanderthal clone."

In the current political, ethical and technological climate, there's no way this scenario could come to pass. Researchers are closing in on a high-quality Neanderthal genome, but they're not quite there yet. The Russian and Korean scientists behind the mammoth-cloning project say they're years away from doing their experiment. And the idea of getting humans involved in cloning experiments is still the stuff of science fiction.

However, Church's point is that the Neanderthal genetic code may be so valuable that the hurdles will be worth overcoming.

"Neanderthals might think differently than we do," he told Der Spiegel. "We know that they had a larger cranial size. They could even be more intelligent than us. When the time comes to deal with an epidemic or getting off the planet or whatever, it's conceivable that their way of thinking could be beneficial."

Theoretically, it might be possible to create a whole population of neo-Neanderthals and see how they differ from the usual breed of Homo sapiens, Church said.

"Curiosity may be part of it, but it's not the most important driving force," Church said. "The main goal is to increase diversity. The one thing that is bad for society is low diversity. This is true for culture or evolution, for species and also for whole societies. If you become a monoculture, you are at great risk of perishing. Therefore the re-creation of Neanderthals would be mainly a question of societal risk avoidance."

Does the idea of Neanderthal surrogate motherhood sound sensible when he puts it that way? Or does it still sound like a science-fiction nightmare? Feel free to weigh in with your comments below.

More about the DNA frontier:

• How sex with Neanderthals made us stronger
• Neanderthal DNA lives on in some of us
• How synthetic biology will change us

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.

M. Hofreiter / K. Fiusterweier

Researchers say some Neanderthals may have had pale skin and red hair similar to that of some modern humans. Explaining the genetic similarities, however, can lead to a tangled tale.

One of the most titillating tales in the study of human origins — focusing on whether Neanderthals interbred with modern humans — has just gotten more tangled.

Over the past couple of years, studies of Neanderthal DNA samples painstakingly extracted from ancient bones have suggested that contemporary non-Africans can trace up to 4 percent of their genetic code to our long-extinct Neanderthal cousins. The genomes of modern-day Africans, in contrast, have virtually nothing in common with the Neanderthals. Researchers assumed that the genetic contribution for the non-Africans was passed down through cross-species sex during the time that Neanderthals and Homo sapiens lived in close proximity in Europe, tens of thousands of years ago.

However, there's another possibility: Maybe that common genetic code was passed down from the common ancestor of Homo sapiens and Homo neanderthalensis, hundreds of thousands of years ago in Africa. Today, researchers at the University of Cambridge reported in the Proceedings of the National Academy of Sciences that such a scenario provides a better fit for the genetic data. They say there's no need to assume that anatomically modern humans did the Neanderthal nasty, a process known more scientifically as hybridization. 

"Our work shows clearly that the patterns currently seen in the Neanderthal genome are not exceptional, and are in line with our expectations of what we would see without hybridization," the lead researcher, Andrea Manica, said in a Cambridge news release. "So, if any hybridization happened — it's difficult to conclusively prove it never happened — then it would have been minimal and much less than what people are claiming now."

Modeling population dynamics
Manica and his colleagues set up a computer model for the last half-million years of population dynamics, with the assumption that there were two migrations from Africa. The first migration led to the settlement of Europe by the ancestors of the Neanderthals, hundreds of thousands of years ago. Then, around 300,000 to 350,000 years ago, the route from north Africa to Europe was cut off somehow. The European and north African populations showed gradual genetic divergence, but still retained a bit of common heritage from their mutual ancestors.

When the second migration from Africa took place, around 60,000 to 70,000 years ago, the north Africans who dispersed to Europe and Asia would carry that extra bit of genetic similarity with them. But the Africans who lived farther south and stayed behind on the continent wouldn't have as much genetic kinship with the Europeans.

The researchers found that their model did a fine job of accounting for the existing data without Neanderthal sex.

So what do the researchers behind the earlier DNA studies say? That's where it gets really interesting: One study, published online in April in Molecular Biology and Evolution, contends that ancient population dynamics alone can't account for the genetic patterns seen in the DNA from Neanderthals and modern humans. Another study, posted on the arXiv preprint server and due for publication in PLOS Genetics, takes a closer look at a genetic pattern known as linkage disequilibrium — and concludes that modern humans and Neanderthals interbred somewhere between 37,000 and 86,000 years ago. Nature's Ewen Callaway delves into the details surrounding those claims and counterclaims.

Either-or proposition?
So, to recap: Some scientists say the population dynamics that were in effect hundreds of thousands of years ago can explain genetic similarities between populations, even if those populations never interbred. Others say the evidence is getting stronger that modern humans and Neanderthals really did mate when they met up in Europe, tens of thousands of years ago.

University of Washington geneticist Joshua Akey says both sides just might be right.

"To me, I don't think it's a case of either-or," he told me. "I think that both things can be going on."

Akey and other researchers recently published a study in the journal Cell suggesting that a mysterious "Neanderthal sibling species" made a genetic contribution to the DNA of modern-day Africans. He said that interpreting whether genetic similarities come from a common ancestor (a process known as archaic population structure) or from more recent cross-species sex (a process that Akey calls introgression) is a tricky but essential task for those who study human origins.

"Ultimately, it's important that we come to a consensus as to one process or the other, but I find them both to be interesting interpretations," Akey said. "Introgression is a sexier mechanism, but even if it turns out to be a case of archaic population structure, that still tells us something about our past that we didn't know before."

So did modern humans do it with Neanderthals or not? And to what extent? Today, maybe it's a tangled tale, but that won't necessarily be the case forever. Akey said he was optimistic that researchers will be able to "tease apart" the different influences from the two processes within the next year or so.

Update for 2:10 a.m. ET Aug. 14: In a follow-up email, Akey clarified his view on the "did they do it" question, leaning toward the affirmative:

"Although I do think that both ancestral population structure and introgression are not mutually exclusive events, the recent papers from David Reich and Monty Slatkin show pretty compelling evidence that introgression of Neanderthal lineages into anatomically modern humans occurred. Thus, the real debate moving forward will be about the relative contributions of these two processes."

More about ancient hominid sex:

• Neanderthal-human sex rarely produced kids
• Ancestors had sex with mysterious human cousins
• How sex with Neanderthals made us stronger

Cambridge's Anders Eriksson is Manica's co-author on the paper published by the Proceedings of the National Academy of Sciences, titled "Effect of Ancient Population Structure on the Degree of Polymorphism Shared Between Modern Human Populations and Ancient Hominins."

Authors of the study in Molecular Biology and Evolution are Melinda Yang, Anna-Sapfo Malaspinas, Eric Durand and Montgomery Slatkin.

Authors of the preprint destined for PLOS Genetics are Sriram Sankararaman, Nick Patterson, Heng Li, Svante Pääbo and David Reich.

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 dwarf planet and the search for new worlds.