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Y Chromosome Studies Suggest Modern Men Share Nearly 200,000-year-old Ancestor

NEW YORK (GenomeWeb News) – A pair of studies appearing online today in Science refute the notion that the common male ancestor of modern humans is significantly younger than his female counterpart.

For the first of the two studies, Stanford University's Carlos Bustamante and colleagues from the US and France did genome sequencing on 69 men from nine human populations in an effort to retrace the time to men's most recent common ancestor — nicknamed the Y chromosomal "Adam."

Results of their analysis suggest the shared male ancestor lived some 120,000 to 156,000 years ago. That's tens of thousand of years earlier than some past estimates, and around the same age mitochondrial "Eve." The shared common ancestor of modern human women was around some 99,000 to 148,000 years ago, based on patterns in the maternally inherited mitochondrial DNA assessed in the same study.

"Our findings suggest that, contrary to previous claims, male lineages did not coalesce significantly more recently than female lineages," Bustamante and his co-authors wrote.

Past estimates suggested that the Y chromosome coalescent time may have been as recent as 50,000 years ago, they noted, which is far more recent than the timeframes that have been proposed for modern humans' most recent common mitochondrial ancestor.

The team suspected that the discrepancy might be related to a dearth of extensive Y chromosome sequence data from across human populations.

To address that possibility, the researchers sequenced the Y chromosomes of 69 men from populations around the world, including representatives from Namibia's San population, members of the Mbuti Pygmy population in the Democratic Republic of Congo, Baka Pygmies and Nzebi individuals from Gabon, and Mozabite Berbers from Algeria.

Samples from outside of Africa came from individuals in Cambodia, Pakistan's Pashtun population, the Yakut population in Siberia, and Mexico's Mayan population.

After tossing out sequences from centromeres, constitutive heterochromatin, and the like, the team mapped nearly 23 million bases of each individual's Y chromosome to the existing reference sequence.

From there, the group narrowed in further, focusing on roughly 10 million bases of what was thought to be the most reliable Y chromosome data.

Within those sequences, researchers tracked down 11,640 SNPs. Together with well-established demographic events, the variants made it possible to estimate the Y chromosome's yearly substitution rate and, from there, determine the phylogenetic relationships between the populations tested, as well as the time to the most recent shared Y chromosome ancestor.

"Essentially, we've constructed a family tree for the Y chromosome," first author David Poznik, a graduate student in Bustamante's Stanford lab, said in a statement. "Prior to high-throughput sequencing, the tree was based on just a few hundred variants."

"We now have a more complete structure, including meaningful branch lengths, which are proxies for the periods of time between specific branching events," he added.

By working backwards in the Y chromosome tree, for instance, the researchers estimated that modern humans share a Y chromosome ancestor going back 120,000 to 156,000 years.

To see how that jibed with the time to the most recent common ancestor for the maternally inherited mitochondrial DNA, they did a similar mitochondrial sequence analysis using data for the 69 men and for two-dozen women sampled from seven populations. From that data, they landed on an estimated age of 99,000 to 148,000 years for modern humans' shared female ancestor.

The results indicate that the predecessors of existing Y chromosome and mitochondrial DNA lineages likely lived at roughly the same time. What's less clear, though, is why each of those lineages persisted, was passed along, and diversified to generate the Y chromosome and mitochondrial groups present in modern humans today.

"Some lineages die out, some are successful," Poznik said. "But it's also possible that there may be elements of human demographic history that predispose these lineages to coalesce at certain times."

For another Science study, an independent team from Italy, the US, and Spain explored Y chromosome coalescent times using low-coverage genome sequence data for more than 1,200 men from the Italian island of Sardinia.

Within around 9 million bases of sequenced representing male-specific Y chromosome regions, authors of that study tracked down almost 12,000 SNPs that they used in a phylogenetic analysis of European Y chromosome haplogroups.

To more fully refine relationships in the tree, the researchers folded in existing European sequence data, including sequences for Ötzi the Iceman, as well as newly generated sequences for individuals from northern Italy, Tuscany, Corsica, and Spain's Basque region.

Again, the Y chromosome data proved useful for exploring relationships between populations — particularly population histories within Sardinia itself. Using mutation rates gleaned from the Y chromosome phylogeny, meanwhile, the team came up with its own Y chromosome coalescent of between 180,000 and 200,000 years.