New Y-chromosome haplogroup tree

UPDATE (Apr 2):

The report is now online. Unfortunately, the supplementary information is not yet online.

UPDATE 2:

I think that the Genographic Project has a lot of rewriting to do in their Atlas of the Human Journey given the proposed dates for the major haplogroups. For example, the oft-repeated claim that R1b has something to do with the Cro-Magnons is no longer tenable.

UPDATE 3:

The supplementary material can be found here (pdf).

Genome Research DOI: 10.1101/gr.7172008

New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree

Tatiana M. Karafet et al.

Markers on the non-recombining portion of the human Y chromosome continue to have applications in many fields including evolutionary biology, forensics, medical genetics, and genealogical reconstruction. In 2002, the Y Chromosome Consortium published a single parsimony tree showing the relationships among 153 haplogroups based on 243 binary markers and devised a standardized nomenclature system to name lineages nested within this tree. Here we present an extensively revised Y chromosome tree containing 311 distinct haplogroups, including two new major haplogroups (S and T), and incorporating approximately 600 binary markers. We describe major changes in the topology of the parsimony tree and provide names for new and rearranged lineages within the tree following the rules presented by the Y Chromosome Consortium in 2002. Several changes in the tree topology have important implications for studies of human ancestry. We also present demography-independent age estimates for 11 of the major clades in the new Y chromosome tree.

Link

A new Y-chromosome haplogroup tree will be published in Genome Research. Here is the public release:

The Y chromosome retains a remarkable record of human ancestry, since it is passed directly from father to son. In an article published online today in Genome Research (www.genome.org), scientists have utilized recently described genetic variations on the part of the Y chromosome that does not undergo recombination to significantly update and refine the Y chromosome haplogroup tree. The print version of this work will appear in the May issue of Genome Research, accompanied by a special poster of the new tree.

...

Hammer’s group integrated more than 300 new markers into the tree, which allowed the resolution of many features that were not yet discernable, as well as the revision of previous arrangements. “The major lineages within the most common African haplogroup, E, are now all sorted out, with the topology providing new interpretations on the geographical origin of ancient sub-clades,” describes Hammer. “When one polymorphism formerly described as unique, but recently shown to have reversed was replaced by recently reported markers, a sub-haplogroup of haplogroup O, the most common in China, was considerably rearranged,” explains Fernando Mendez, a co-author of the study.

In addition to improving the resolution of branches, the latest reconstruction of the tree allows estimates of time to the most recent common ancestor of several haplogroups. “The age of [haplogroup] DE is about 65,000 years, just a bit younger than the other major lineage to leave Africa, which is assumed to be about 70,000 years old,” says Hammer, describing an example of the fine resolution of age that is now possible. “Haplogroup E is older than previously estimated, originating approximately 50,000 years ago.”

Furthermore, Hammer explains that this work has resulted in the addition of two new major haplogroups, S and T, with novel insights into the ancestry of both. “Haplogroup T, the clade that Thomas Jefferson’s Y chromosome belongs to, has a Middle Eastern affinity, while haplogroup S is found in Indonesia and Oceania.”