A recent study has found that the common ancestor of all Y-chromosomes lived approximately 338,000 years ago, vastly surpassing previous estimates (100–140,000 years). Unlike most genetic studies, this one did not begin in a university — though it soon landed in the laboratory of Michael Hammer at the University of Arizona. Instead, it started with the customers of Family Tree DNA. Among all the samples the company tested and classified, one stood out.
Submitted by the relatives of Albert Perry, an African-American from South Carolina, this Y-chromosome was like none seen before. After careful study, the new variant, now called the A00 haplotype, turned out to be different from the ancestor of all previously known human Y chromosomes at 59 positions in about 240,000 genetic letters of sequence. Knowing that the rate of mutation of Y-chromosomes today is one per two billion letters per year, researchers could deduce when A00 branched from the rest of us. Analysis of over 5600 samples from Africa found this chromosome in just 11 people (0.2%), who made up 6.3% of the people of Mbo ancestry from Cameroon who were tested.
The identification of a rare, ancient Y chromosome doesn't change very much. The handful of mutations identified are very unlikely to have any actual effect, because the Y chromosome carries only a handful of genes, most narrowly tailored for the purpose of being male, among vast tracts of "junk DNA." Nor should we be surprised to find a rare genetic variant in Africa, a treasury of human genetic diversity. The known pattern of early human migrations as anatomically modern humans arose about 200,000 years ago and this does not challenge spread throughout Africa and to the rest of the world.
The "Y-chromosomal Adam" (though he really should be called "Noah" according to the Genesis metaphor) is defined merely as the man who by chance had two sons who both still have living descendants. In theory, this man could have lived long after, and in this case long before, the evolution of the human race, as we know it. Species evolve gradually, generally as large populations, so they inherit much of the diversity of their ancestors.
There is also a "mitochondrial Eve," from whom sequences passed through only a female lineage from a last common ancestor 200,000 years ago. Now that Adam is more than 50% older than Eve, there could be some mild embarrassment for those who argued that factors such as polygyny accounted for the former discrepancy of a younger Adam. Even so, evidence of a higher female migration rate is not based solely on the last common ancestor, so we shouldn't forget that a much older "Eve" might merely be waiting for someone to type the right sample.
The question that A00 really raises is how and where it managed to "hide out" in the human population for so long. Ordinarily, a process called "genetic drift" slowly removes unusual variants from the gene pool by random chance. A mathematical formula worked out by pioneers of population genetics during the World War I, long before DNA was discovered, predicts the time to gene extinction under certain ideal conditions. What determines it is the population size and the population structure. Finding this A00 gives a strong hint that early populations may have had much more "structure" than imagined—in other words, that isolated groups held on in different areas or ecological niches, preserving their individual genetic oddities by having relatively little to do with one another.
This is a complicated issue, difficult to analyze completely even in model modern studies where people track things like the genetics of weevils among the islands of the Galapagos, where the history and migration patterns are known. The authors didn't try to say whether the isolated population holding onto this Y chromosomal variant was anatomically modern humans or something else. But they could not resist pointing out that the Mbo live less than 500 miles away from Iwo Eleru, a site where humans buried their dead 13,000 years ago, whose features appeared to be intermediate between those of modern-day humans and those of Neanderthals or Homo erectus.
Comparison of the A00 haplotype specimens from Albert Perry and the Mbo suggests that the common ancestor of all known A00s was about 17,000 years ago. It is possible that this particular Y chromosome was imported from some other human subspecies, which has since been assimilated or gone extinct.
If so, this would not be the first time such "introgression" (hybridization) has been proposed. Eurasians are thought to have somewhere between 1–4% DNA from the Neanderthals, while Melanesians may have up to 6% DNA from another group called Denisovans. No contribution is known — yet — from some other species or varieties of humans living at that time, such as Homo rhodesiensis, Homo floresiensis, and a presently unnamed but apparently new group unearthed from the Red Deer and Longlin caves of China. By all appearances, modern humans were a wave that swept aside an untold number of rivals; yet with rare and subtle clues like this we are reminded that perhaps some trace of their heritage remains among us.