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Y Chromosome Consortium (YCC)

The Y Chromosome Consortium (aka YCC) is an organization founded in 1991 by University researchers (primarily University of Arizona) that continued up until the mid 2000’s with their web presence; finally disappearing completely by 2012. ISOGG formation was likely motivated by their decision to forgo updating the website and phylogenetic tree they had developed there.

They published a key, seminal paper in 2002 (see below) giving a common nomenclature for a yDNA phylogenetic tree. ISOGG, by its formation and citizen scientists, took over developing and maintaining a public yDNA tree on the web starting around 2006.

YCC Long or “lineage” format is based on the alternating letters and numbers to identify the path down the tree to a specific haplogroup. An example designation of Haplogroup R1b-P312 is R1b1a1a2a1a2

YCC Short or “mutation” format is based on simply defining an SNP (mutation) for that Haplogroup branch or leaf in the tree.

Early phylogenetic trees (and still the mitochondrial DNA tree of today) used letters to identify key Haplogroup branch points. As the tree grew they ran out of letters and started adding numbers below the first letters. The YCC Long nomenclature simply grew out of this form as the tree branching continued. They simply alternate labeling branches with letters and numbers. The long format is thus a path designation from the top level simple-single-letter early tree down to the current haplogroup branch or leaf to be designated.

An example of the different forms is taken from our Haplogroup R1b-P312 page:
  R      1      b        1        a      1      a      2     a     1              a               2    (YCC lineage)
M207 > M173 > M343 > L278/P25 > L754 > L388 > P297 > M269 > L23 > L51 > L151-L52-L11-P310-P311 > P312 (YCC mutation)

note: The mutation form is normally only shown with a single SNP that is unique to a Haplogroup (i.e. branch point or leaf node) in the phylogenetic tree. We have simply shown above the SNP name at each haplogroup branch point that corresponds to the lineage form letter or number above it. Unlike the lineage form, the mutation form is unique in each value at each branch point and uniquely identifies the Haplogroup. The mutation or short form does not indicate the lineage and thus is not susceptible to change when the order of haplogroups is changed.

Some cannot agree on the defining SNP to identify each haplogroup (i.e. branch point) and so we sometimes have to list more than one. Sometimes these are aliases for the same SNP. Other times they are different SNPs that are in the same haplogroup definition. Each haplogroup usually has many SNPs associated with it. Branch points (or Haplogroups) are commonly known by only one of the SNPs associated with it (often the first found to define it).

By strict definition, the use of a dash is only done in the mutation (or short) form and used to pre-pend an SNP by the major, “single letter” Haplogroup that comes before it in the tree. In the above example, R1b- is used as the major name before the SNP. The formal name should be simply R (a single letter). But most utilize R1b as a top level name due to its “weight” in the phylogenetic tree. That is, there are more in the current population below the R1b branch than above. This leads to a quasi long and short form, in a sense. You may see I1, I2, and R1a for similar reasons.

note: the pages of the old YCC website, previously located at http://ycc.biosci.arizona.edu/, were not captured by the InternetArchive as the YCC had a block for robot crawlers in their home folder.