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Y Chromosome Tree Reshaped

NEW YORK (GenomeWeb News) – A group of scientists today unveiled a newly revised version of the Y chromosome haplogroup tree including information from hundreds of previously unincorporated genetic markers. 
The researchers, based at the University of Arizona and Stanford University, have reworked the Y chromosome haplogroup tree for the first time in five years or so, incorporating nearly 600 additional genetic markers to create more than 300 reorganized haplogroups in 20 clades. Their paper, which appeared online today in the journal Genome Research, describes these re-arrangements and their implications for future work assessing Y chromosome polymorphisms.
The Y chromosome is the sex chromosome that’s passed from fathers to sons. Because it contains regions that don’t change much over long periods of time, the Y chromosome is useful for determining human history and lineage. Genetic variation on the Y chromosome has been analyzed to inform studies on everything from genealogy and evolutionary biology to forensics and medical genetics.
The first Y chromosome phylogeny tree was created in 2002. That tree, called the Y Chromosome Consortium tree, contained 153 haplogroups based on 243 genetic markers. A modified version of the tree was published the following year. But it hasn’t been updated since.
In the intervening years, more and more Y chromosome polymorphisms have been identified during SNP studies, re-sequencing projects, and other research. Consequently, researchers’ understanding of the relationships between different Y chromosome haplogroups has changed.
“The rate of SNP discovery has continued to increase over the last several years, as are publications on Y chromosome origins and affinities,” senior author Michael Hammer, an evolutionary biologist at the University of Arizona, said in a statement. “While this new information is useful, ironically it also brings with it the danger of introducing more chaos in the field.”
This work is intended to make sense of that chaos. Hammer and his colleagues added 586 new mutations and 13 recurrent mutations that broadened and rearranged the tree. The result: 311 distinct haplogroups organized into 20 major clades designated clade A to clade T. This adjustment involved merging some clades and splitting others. 
“As we show, many of the newly discovered polymorphisms require topological changes to the tree, as well as new nomenclature to define the lineages,” the authors wrote.
The new tree also provides new estimates about when various clades shared a common ancestor, indicating that some groups are older or younger than previously believed. In contrast to prior estimates, which were largely based on microsatellite variation, the new estimates rely on SNP data applied without assumptions about population history or demographics.
Even so, the authors noted, there are still known mutations that need to be incorporated into the new tree. And much more data will be generated in the future as the cost of sequencing and SNP typing decreases.
Finally, the researchers called for increased access to cell lines with known Y chromosome polymorphisms to augment future Y chromosome research.
“The Y chromosome research community would also benefit from a set of publicly accessible cell line DNAs that could be used as positive controls for all the known markers,” they wrote. “[W]e suggest that typing of the current markers on the widely available CEPH-HGDP panel would be a highly desirable goal for a future study.”

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