I just added this to the DNA-Newbie forum at Groups.io, and thought it might be useful for WikiTreers. It isn't my usual squirrel-chasing, way-too-wordy, deep dive down a DNA rabbit hole, and instead is intended to provide a snapshot of how we arrived at the expansive yDNA haplotree that we have today.
Even though yDNA testing for consumers started in 2001 at Family Tree DNA, a decade before the first autosomal tests, many of us have a greater familiarity with autosomal testing and centiMorgans than we do with yDNA SNPs and STRs. It's a little different mindset, one where "genetic distance" doesn't mean "number of generations separated." But one of the huge advantages with yDNA is that it doesn't undergo recombination at meiosis and that it changes only via mutation...which means it can reach many centuries into the past.
Those time periods are defined by specific SNPs, single nucleotide polymorphisms, and while we really can't match an exact date to a mutation event, what we do have is a large tree, a haplotree, of discrete and hierarchical branches, or subclades. A test-taker may be 20 branches deep under a given top-level haplogroup--for example: R, I, G, or E--and for each branch there will be some coalescence point in time, some point when a mutation occurred and one subbranch split into two or more additional branches.
We've seen questions about what seem to be two different naming conventions for haplogroups, and occasionally some general confusion that arises from having so many branches in the tree, with new branches being added almost weekly. By contrast, the mtDNA phylotree hasn't been altered since February 2016, and is only 7% the size of the yDNA haplotree.
This is just a quick chronological rundown of where we started and how we got to where we are today.
1 February 2002: The Y Chromosome Consortium, now defunct, published in Genome Research an article titled, "A Nomenclature System for the Tree of Human Y-Chromosomal Binary Haplogroups." This was the proposal that launched the way we began naming haplogroups. The proposal showed two types of haplogroup naming systems, one described as "by lineage," which in some circles later came to be called the "YCC long-form" and that the International Society of Genetic Genealogy (ISOGG) continued to use while it maintained its own haplotree through 2020. This took the structure of the top-level, or basal haplogroup letter followed by a series of numbers and letters to help distinguish the branches, or subclades. For example, R1b1a1b and I1a1a1a1a.
The second nomenclature, called "by mutation" in the paper, came to be what we would shift to when the explosive growth of the haplotree meant that unwieldy strings of characters were no longer practical in defining branches of the tree. R1b1a1b became R-M269 and I1a1a1a1a became I-M227. Much more practical.
When the YCC paper was published, there were a total of 243 Y-SNPs known (single nucleotide polymorphisms, or mutations among the four DNA "letters" at a single position on the chromosome), and the haplotree had a proposed 153 branches.
2008: The haplotree, over the course of six years, had grown to 311 cataloged branches and approximately 600 identified SNPs.
2010: The tree now had 440 branches and included 800 SNPs.
2014: Family Tree DNA and the Genographic Project jointly released their new, combined yDNA haplotree. This impressive collaboration, housed at the FTDNA website, included at its launch over 1,200 branches and more than 6,200 SNPs. This represented the start of the yDNA haplogroup knowledge explosion because it was in 2014 that FTDNA introduced its first version of the Big Y sequencing test.
September 2018: It took a while for the more expensive Big Y test to be well understood and see greater sales volume, but in the intervening four years the new data had grown the haplotree over 13-fold, to 16,361 branches.
January 2019: FTDNA introduced the Big Y-700 test which, on average, provided 50% more SNP coverage and tested up up to 838 STRs (short tandem repeats, the type of markers examined in the original Y-12, Y-25, Y-37, Y-67, and Y-111 tests; SNPs define haplogroups, not STRs, but sets of STR values can reliably predict a high-level haplogroup).
March 2020: A little over one year after the Big Y-700 was first available for sale, the yDNA haplotree had grown to 26,862 branches.
9 February 2022: In a bit less than two years, the haplotree had doubled in size again and now counted 52,394 branches.
22 February 2023: A year later and we had added over 12,000 branches to the tree, which now numbered 64,638 distinct branches.
18 February 2024: This morning, the haplotree at FTDNA currently describes 76,626 branches.
Since the advent of FTDNA's Big Y test, the hierarchical "yDNA Tree of Humankind" has grown to identify almost 64 times as many discrete, chronological branches as we knew about as recently as 2014, just 10 years ago. And the authors of the original Y Chromosome Consortium paper in 2002 (for whom Michael Hammer of the University of Arizona, a foundational scientist for Family Tree DNA, was the corresponding author) likely never quite imagined that the 153 branches known at that time--and in need of a consistent and formal taxonomy with which to describe them--would be nearing 80,000 branches just 22 years later.
Edited: A particularly astute reader broke down one of my sentences in diagrammatic fashion and noted that, as described in Bill Bryson's book, Bryson's Dictionary of Troublesome Words (2002, page 114), I had incorrectly used the word "than" in a comparative construction when I should have used "as" because, strictly speaking, it was not a comparison of different things (e.g., X is larger than Y), but instead used a qualifier ("64 times as many") as a distinguishing factor between two of the same things that were simply in a different quantitative state of equality. Ahem. But the grammatical correction is proof that I may have as many as 14 people who actually read the stuff I write!
