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

¹ ARL Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA; ² Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; ³ Department of Genetics, Stanford University, Stanford, California 94305, USA; ⁴ Department of Anthropology, University of Arizona, Tucson, Arizona 85721, USA

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.

E-mail mfh{at}u.arizona.edu; fax (520) 626-8050.

[Supplemental material is available online at www.genome.org.]

Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.7172008.

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