Scientists reshape Y chromosome haplogroup tree gaining new insights into human ancestry

Wednesday, April 2, 2008 –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.

Human cells contain 23 pairs of chromosomes: 22 pairs of autosomes, and one pair of sex chromosomes. Females carry a pair of X chromosomes that can swap, or recombine, similar regions of DNA during meiosis. However, males harbor one X chromosome and one Y chromosome, and significant recombination between these dissimilar sex chromosomes does not occur. Therefore, the non-recombining region of the Y chromosome (NRY) remains largely unchanged over many generations, directly passed from father to son, son to grandson, and so on, along with genetic variations in the NRY that may be present. Scientists can use genetic variations, such as single nucleotide polymorphisms (SNPs), on the Y chromosome as markers of human ancestry and migration.

In 2002, the Y Chromosome Consortium (YCC) constructed a tree of 153 haplogroups based upon 243 unique genetic markers. In this report, researchers led by Dr. Michael Hammer of the University of Arizona recognized the need to revisit the Y chromosome haplogroup tree and incorporate the latest data. “The YCC effort in 2002 was a landmark in mapping the then known 300 or so Y-linked SNPs on a single tree, and getting the community to use the same nomenclature system,” explains Hammer. “The rate of SNP discovery has continued to increase over the last several years, as are publications on Y chromosome origins and affinities. While this new information is useful, ironically it also brings with it the danger of introducing more chaos into the field.”

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.