An extremely rare African American Y chromosome found in an individual who submitted his DNA to a company specializing in DNA analysis to trace family roots pushes back the time of the most recent common ancestor for the Y chromosome lineage tree to 338,000 years ago.

The Y chromosome is one of the two sex-determining chromosomes in humans. It is found only in males – the normal male has one X and one Y chromosome. Unlike the other human chromosomes, the majority of the Y chromosome does not exchange genetic material with other chromosomes, which makes it simpler to trace ancestral relationships among contemporary lineages. If two Y chromosomes carry the same mutation, it is because they share a common paternal ancestor at some point in the past. The more mutations that differ between two Y chromosomes the farther back in time the common ancestor lived.

A new study, published online in the American Journal of Human Genetics, suggests that the newly discovered lineage branched from the Y chromosome tree before the first appearance of anatomically modern humans in the fossil record.

“Our analysis indicates this lineage diverged from previously known Y chromosomes about 300,000 ago, a time when anatomically modern humans had not yet evolved,” said senior study author Prof Michael Hammer of the University of Arizona. “This pushes back the time the last common Y chromosome ancestor lived by almost 70 percent.”

“The most striking feature of this research is that a consumer genetic testing company identified a lineage that didn’t fit anywhere on the existing Y chromosome tree, even though the tree had been constructed based on perhaps a half-million individuals or more. Nobody expected to find anything like this.”

About 300,000 years ago falls around the time the Neanderthals are believed to have split from the ancestral human lineage. It was not until more than 100,000 years later that anatomically modern humans appear in the fossil record. They differ from the more archaic forms by a more lightly built skeleton, a smaller face tucked under a high forehead, the absence of a cranial ridge and smaller chins.

Prof Hammer said that the newly discovered Y chromosome variation is extremely rare. Through large database searches, his team eventually was able to find a similar chromosome in the Mbo, a population living in a tiny area of western Cameroon in sub-Saharan Africa.

“This was surprising because previously the most diverged branches of the Y chromosome were found in traditional hunter-gatherer populations such as Pygmies and the click-speaking KhoeSan, who are considered to be the most diverged human populations living today.”

“Instead, the sample matched the Y chromosome DNA of 11 men, who all came from a very small region of western Cameroon,” Prof Hammer said. “And the sequences of those individuals are variable, so it’s not like they all descended from the same grandfather.”

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Bibliographic information: Fernando L. Mendez et al. An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree. The American Journal of Human Genetics, 28 February 2013; doi: 10.1016/j.ajhg.2013.02.002