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

Introduction

Recent years have witnessed an explosion in data from the non-recombining portion of the Y chromosome (NRY) in human populations. This explosion has been driven, in part, by the many recently discovered polymorphisms on the NRY. There has been a keen interest in using polymorphisms on the NRY to examine questions about paternal genetic relationships among human populations since the mid-1980s (Casanova et al. 1985). In more recent years these polymorphisms have found use in DNA forensics (Jobling et al. 1997), genealogical reconstruction (Jobling, 2001), medical genetics (Jobling and Tyler-Smith 2000) and human evolutionary studies (Hammer and Zegura 1996). The low level of polymorphism on the NRY hindered research for many years. By the end of 1996 there were fewer than 60 known polymorphisms on the NRY. Most of these (~80%) were long-range polymorphisms (detectable by pulsed-field electrophoresis), conventional restriction fragment length polymorphisms (RFLPs), or short tandem repeats (STRs). Until 1997, there were only 11 known binary polymorphisms that could be genotyped by PCR-based methods (Hammer 1994; Seielstad et al. 1994; Hammer and Horai 1995; Whitfield et al. 1995; Santos et al. 1995; Jobling et al. 1996; Underhill et al. 1996). These included single nucleotide polymorphisms (SNPs), an Alu insertion polymorphism, and a deletion. Then, in 1997 Underhill et al. (1997) published 19 new PCR-based binary polymorphisms that were discovered by a novel and efficient mutation detection method known as denaturing high performance liquid chromatography (DHPLC). This method has since been used to discover more than 200 SNPs and small insertions/deletions (indels) on the NRY (Shen et al. 2000, Underhill et al. 2000; Hammer et al. 2001). These polymorphisms are particularly useful because of their low rate of parallel and back mutation, which makes them suitable for identifying stable paternal lineages that can be traced back in time over thousands of years. As the number of known binary polymorphisms increased, so did the number of publications and the number of different systems used to name these binary haplogroups. Currently, there are at least seven different nomenclature systems in use, making it very difficult to compare results from one publication to the next. Our purpose here is twofold: (1) to construct a highly resolved tree of NRY binary haplogroups by genotyping most published PCR-based markers on a common set of samples, and (2) to describe a new nomenclature system that is flexible enough to allow the inevitable changes that will result from the discovery of new mutations and NRY lineages. We hope that the nomenclature presented here will be adopted by the community at large and will improve communication in this highly interdisciplinary field.

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