A Nomenclature System for the Tree of Human Y-Chromosomal Binary Haplogroups

Subjects and Methods

YCC Cell Lines

The Y Chromosome Consortium (YCC) is a collaborative group involved in an effort to detect and study genetic variation on the human NRY. The YCC was initiated in 1991 by Michael Hammer and Nathan Ellis with the following goals: (1) to establish a repository of lymphoblastoid cell lines (YCC cell line repository) derived from a sample of males representing worldwide populations, (2) to provide DNA isolated from these cell lines to investigators searching for polymorphisms on the NRY, and (3) to establish a common database containing the results of typing DNAs from the Repository cell lines at as many Y-specific polymorphic sites as possible (YCC Newsletter: http://ycc.biosci.arizona.edu/newsletters/YCC_Newsletter_1.pdf). Lymphoblastoid cell lines were established at the New York Blood Center from blood donated by volunteers who gave informed consent. Additional cell lines were donated by Luca Cavalli-Sforza, Trefor Jenkins, Judy Kidd, and Ken Kidd; or were purchased from the Coriell Institute. See Table 1 for a list of the YCC cell lines, as well as associated geographic, ethnic, and linguistic information.

Other DNA Samples

In constructing the tree, a great deal of phylogenetic information was retained from previous studies. When markers from different laboratories mapped on the same branch of the tree, an attempt was made to determine the order of mutational events. Towards this end, a variety of samples was provided by each of the participating laboratories, all of which were obtained with informed consent. These samples represented known haplogroups that were not present in the YCC cell line DNAs and thus served to map many additional markers on the haplogroup tree.

Genotyping SNPs and Indels

The protocols for genotyping many of the 237 polymorphic sites analyzed have been published (see Underhill et al. 2000, 2001; Hammer et al. 2001, and references therein); some of these assays were converted from conventional RFLPs and DNA sequence data (e.g., Jobling 1994; Hammer et al. 1997; Pandya et al. 1998; Bergen et al. 1999; Shinka et al. 1999; Bao et al. 2000). The remainder will be published in future manuscripts. Recurrent mutations, observed at SRY10831, 12f2, MSY2, M116, M64, M108, P37, and P41 are counted as distinct polymorphisms. A table listing all published markers included in this survey and primer information is available as supplementary data on the Genome Research web site.

Terminology

The terms 'haplogroup' and 'haplotype' have various, overlapping definitions in the literature. Here, we use the terminology of de Knijff (2000) in which 'haplogroup' refers to NRY lineages defined by binary polymorphisms. The term 'haplotype' is reserved for all sublineages of haplogroups that are defined by variation at STRs on the NRY (Y-STRs). Mutations labeled with the prefix "M" (standing for "mutation") were published by Underhill et al. (2000; 2001). Many of the mutations with the prefix "P" (standing for "polymorphism") were described by Hammer et al. (1998, 2001). The eight recurrent mutational events are indicated by their mutation name followed by a or b.

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