Human Y chromosome much older than previously thought

Mar 04, 2013 by Daniel Stolte
Human sex-determining chromosomes: X chromosome (left) and the much smaller Y chromosome.

(Phys.org) —University of Arizona geneticists have discovered the oldest known genetic branch of the human Y chromosome – the hereditary factor determining male sex.

The new divergent lineage, which was found in an individual who submitted his DNA to Family Tree DNA, a company specializing in to trace family roots, branched from the tree before the first appearance of anatomically in the fossil record.

The results are published in the .

"Our analysis indicates this lineage diverged from previously known Y about 300,000 ago, a time when anatomically modern humans had not yet evolved," said Michael Hammer, an associate professor in the University of Arizona's department of ecology and and a research scientist at the UA's Arizona Research Labs. "This pushes back the time the last common Y chromosome ancestor lived by almost 70 percent."

Unlike the other , 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 lived.

Originally, a DNA sample obtained from an African American living in South Carolina was submitted to the National Geographic Genographic Project. When none of the used to assign lineages to known Y chromosome groupings were found, the DNA sample was sent to Family Tree DNA for sequencing. Fernando Mendez, a in Hammer's lab, led the effort to analyze the DNA sequence, which included more than 240,000 of the Y chromosome.

Hammer said "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. 

Hammer said 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," Hammer said. "And the sequences of those individuals are variable, so it's not like they all descended from the same grandfather."

Hammer cautions against popular concepts of "mitochondrial Eve" or "Y chromosome Adam" that suggest all of humankind descended from exactly one pair of humans that lived at a certain point in human evolution.

"There has been too much emphasis on this in the past," he said. "It is a misconception that the genealogy of a single genetic region reflects population divergence. Instead, our results suggest that there are pockets of genetically isolated communities that together preserve a great deal of human diversity."

Still, Hammer said, "It is likely that other divergent lineages will be found, whether in Africa or among African-Americans in the U.S. and that some of these may further increase the age of the Y chromosome tree."

He added: "There has been a lot of hype with people trying to trace their Y chromosome to different tribes, but this individual from South Carolina can say he did it."

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More information: www.cell.com/AJHG/abstract/S0002-9297(13)00073-6

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Lurker2358
1.4 / 5 (11) Mar 04, 2013
A half million individuals is only one twentieth of one percent of living humans. This is not nearly enough to be seriously called a profile of the modern human genome. You would need at least a 50% plus one majority, and you still won't get all the odds and ends.

Then there's the fact you have next to nothing for your fossil/ archaeologic human genome. What? Some absurdly small number like 2 or 3 useful samples in the time frame you're making a comparison?
verkle
1.2 / 5 (9) Mar 04, 2013
Hammer cautions against popular concepts of "mitochondrial Eve" or "Y chromosome Adam" that suggest all of humankind descended from exactly one pair of humans that lived at a certain point in human evolution.


I don't understand why he makes this caution. It doesn't make sense.

dschlink
3 / 5 (4) Mar 04, 2013
Unfortunately, christians, that are not young-earth christians, use the idea of one pair as proof of the creation of the race by god.
C_elegans
4.8 / 5 (6) Mar 04, 2013
This is remarkable because it implies that the Mbo have been more or less genetically isolated for hundreds of thousands of years.
SoylentGrin
4.8 / 5 (6) Mar 04, 2013
I don't understand why he makes this caution.

Because popular concepts aren't accurate. Every sexually reproducing species has a "mitochondrial Eve". It's a position (that can change) that represents an individual that current populations have in common. It doesn't mean one individual gave rise to the current population.
"Mitochondrial Eve" had ancestors and contempories as well. She wasn't a lone individual who gave birth to everyone. Popular concepts don't take the more accurate, complex picture into account; they're too simplistic.
Lurker2358
1.6 / 5 (7) Mar 04, 2013
Unfortunately, christians, that are not young-earth christians, use the idea of one pair as proof of the creation of the race by god.


You wouldn't necessarily find the Biblical Eve (and certainly not Adam,) through DNA analysis anyway, regardless of whether or not time spans are literal, which they aren't.

The Bible claims humans have inter-bred with other intelligent species (some sub-group of what are called "angels") on at least one occasion, and possibly two or more occasions, producing various classes of what were called "Nephilim" (mostly giants but also other forms). It is therefore conceivable that ancient humanoid fossils are not necessarily "pure blood" humans, nor necessarily "purely terrestrial" in origin.

If there is any truth to these claims, which actually appear in several different middle-eastern traditions, then the DNA profile of ancient humans and so-called common ancestors is muddied, because some will lack a common male ancestor before these events.
Narcotect
5 / 5 (5) Mar 04, 2013
WHY are there still religious nutters- that's the real genetic mystery
Bartolo
not rated yet Mar 06, 2013
Why does this have to be an early branch-off and not a later one? If it were an older one it would have had much more chance to spread through other geographical areas in Africa. Genetic mutations can happen at any time and according to my logic the more isolated (if that's even true it's really that isolated) this mutation is the more likely it is to be recent.

Could someone explain to me why this should be an early branch and couldn't be a later one?