An understanding of haplogroup naming systems and the phylogenetic tree is an essential foundation.

Phylogenetic Names

The haplogroup (and subclade) name indicates the exact position on the tree of Y-DNA.

All major haplogroups are designated by a capital letter, e.g., "R"; alternating numbers and lower-case letters denote subdivisions or "subclades". The longer the haplogroup name, the finer the divisions. For example, R1b1a2 is a subclade of R1b1a, which is in turn part of R1b1, which is part of R1b, and so on.

One advantage of this system is that heritage is immediately apparent. R1b1a2 comes out of R1b1a, R1b1a out of R1b1, etc. It's also theoretically possible to carry this subdividing system out to the place where the haplogroup describes only a single paternal lineage.

The disadvantage is that our understanding of origins is changing; what we "knew" about a sub-clade's origins yesterday isn't what we might know tomorrow. For example, yesterday's R1b1b is today's R1b1a2 and might be called something else in the future.

Shorthand Names (by SNP)

Recent scientific discoveries have led -- and continue to lead -- to revisions of the official phylogenetic tree by the Y Chromosome Consortium (YCC);

A more current, though less official tree, is kept by the International Society for Genetic Genealogy (ISOGG); for the latest version, see Subclades are being shifted around and renamed; the process isn't yet complete.

As a result of the frequent changes, it's becoming increasingly usual to refer to a subclade by its major haplogroup letter and its defining SNP. For example, R-M269 denotes R1b1a2.

An advantage of the shorthand system is that name revisions aren't necessary; R-M269 today will be R-M269 tomorrow. A disadvantage is that the place on the phylogenetic tree isn't immediately apparent.