The Y Chromosome Consortium Unified Tree For Y Haplogroups

The Rosenta Stone for interpreting the plethora of Y chromosome haplogroups listed in the literature was published by the Y Chromosome Consortium (YCC) in the February 2002 issue of Genome Research (YCC 2002). The YCC is an international group of scientists lead by Michael Hammer from the University of Arizona, Peter Underhill from Stanford University, Mark Jobling from Leicester University, and Chris Tyler-Smith who at that time was at Oxford University. Their paper entitled 'A nomenclature system for the tree of human Y chromosomal binary haplogroups' opened the way for an easier understanding of seven previously published methods for describing information from the same SNP markers. The 'YCC tree' as it is commonly called describes the position of almost 250 bi-allelic markers in differentiating 153 different haplogroups (YCC 2002).









C D E E3a F* G H I J J2 K* L M N O P* Q R R1 R1b R1b3


A slightly modified and updated YCC tree was published in August 2003 (Jobling and Tyler-Smith 2003).

Figure 9.9 highlights the major branches of the YCC tree along with some of the Y-SNP markers that help define the various branches. For example, observation of the derived allele for M2 in a sample classifies it into the E3a haplogroup. Y chromosome haplogroup designation and characterization has greatly benefited from the YCC tree.

Before 2002, if a 'G' (derived state) was observed in a sample when typing the M2 (sY81 or DYS271) marker, then the sample could be reported as belonging to Haplogroup (Hg) 8 by Jobling's nomenclature (Jobling and Tyler-Smith 2000), Hg III by Underhill's naming procedure (Underhill et al. 2000), or Hg 5 by Hammer's description (Hammer et al. 2001). On the YCC tree, M2 derived alleles define the Hg E3a. Needless to say, the unified and universal nomenclature is much easier to understand and permits comparisons of results across laboratories.

A number of the SNP typing technologies reviewed in Table 8.2 have also been used for Y-SNP typing (Butler 2003). Two of the more popular SNP typing methodologies have been allele-specific primer extension (ASPE) and allele-specific hybridization (ASH). Vallone and Butler (2004) observed complete concordance comparing ASPE and ASH in almost 4000 Y-SNP allele calls.

Figure 9.9 Y Chromosome Consortium tree with 18 major haplogroups (A-R). Representative Y-SNP markers that define each haplogroup are listed next to the branch point. The most common African-American haplogroup is E3a. The most common Caucasian (European) haplogroup is R1b/R1b3.



Y chromosome testing is beginning to play a role in addressing some interesting historical questions (see D.N.A. Box 9.1) as well as aiding efforts in genealogical family history research (see D.N.A. Box 9.2). The use of Y chromosome

Genetic legacy of Genghis Khan

In a study of more than 2100 males from Central Asia, a team of scientists lead by Chris Tyler-Smith from the University of Oxford found that approximately 8% of those studied had a unique Y chromosome lineage. These samples formed a central star-cluster that possessed the following Y-STR profile (repeat numbers in parentheses after each marker): DYS389I (10), DYS389II (26), DYS390 (25), DYS391 (10), DYS392 (11), DYS393 (13), DYS388 (14), DYS425 (12), DYS426 (11), DYS434 (11), DYS435 (11), DYS436 (12), DYS437 (8), DYS438 (10), and DYS439 (10). An analysis of at least 16 additional markers in the form of Y-SNPs placed all of these samples in haplogroup C*(xC3c), which is common in Asia (see Jobling and Tyler-Smith 2003). By making some assumptions regarding mutation rates and a generational time of 30 years, these researchers were able to calculate a time to the most recent common ancestor for these particular Y-lineages of ~1000 years ago. The highest frequency was in Mongolia leading to the assumption that it was the source of these particular male lineages, but it was spread throughout 16 different populations in Asia. Interestingly the geographical distribution of these populations closely matches the area of Genghis Khan's former Mongol Empire. The evidence that this Y-lineage was from Genghis Khan (circa 1162-1227) and his close male-line relatives was strengthened by a match to a group in Pakistan who by oral tradition consider themselves direct male-line descendants of Genghis Khan. Thus DNA testing can reveal some interesting historical clues into our past as a human race.


Zerjal, T., et al. (2003) The genetic legacy of the Mongols. American Journal of

Human Genetics, 72, 717-721. Jobling, M.A. and Tyler-Smith, C. (2003) The human Y chromosome: an evolutionary marker comes of age. Nature Reviews Genetics, 4, 598-612.

information in addressing the issue of whether or not Thomas Jefferson fathered some of his slaves is presented below as an example of the power and the pitfalls of answering historical questions with DNA information from modern-day individuals. As in forensic casework, DNA information is only part of the evidence available in most investigations and should be considered carefully in the context of the 'case' without overstepping the bounds of conclusions that can be drawn.


In 1802, a year after becoming President of the United States, Thomas Jefferson was publicly accused by a Richmond, Virginia newspaper of fathering a child by his slave, Sally Hemings. While it is uncertain how this accusation arose, the connection between Thomas Jefferson and his slave Sally Hemings has been a source of controversy for almost 200 years.

Then, in November 1998, the prestigious scientific journal Nature published a report that introduced DNA evidence into this historical controversy (Foster et al. 1998). The report entitled 'Jefferson fathered slave's last child' used Y chromosome DNA markers to trace the Jefferson male line to a descendant of Sally Hemings's youngest son, Eston Hemings. The study involved 19 samples collected from living individuals who represented the Jefferson and Hemings line as well as other people who potentially could have been Jefferson's offspring or the father of Eston Hemings. These samples were tested at 19 different sites on the Y chromosome.

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