Phylogenetic Tree Interpretation

Many in the genetic genealogy community are thrown into the world of phylogenetic trees with no history or background. Often because of interpretation of the few yDNA SNPs that happened to be returned with their microarray test. Sometimes with the high level haplogroup estimation coming from their yDNA STR test But what does it all mean? And what can you tell from it that helps in your genealogical search?

We attempt to delve into some of that here using an example prepared for someone we helped in a Facebook group who was lost. They happened to test at LivingDNA and were told they are now haplogroup R-S497. And they took the plunge ordering a BigY and are awaiting results. Which, we remind you, includes the y111 STR test now. Which often returns results weeks to months earlier than the BigY deep SNPs. So some of the analysis weaves in and out what you can tell from these various sources. Beside the linked terms here, you may also what to refresh your knowledge a bit by looking at one of our group pages like B10 Examining This Haplogroup With Various Test Services.

We will use yFulls tree throughout here as it still provides the most information and content that is also linkable. Let's start with going to the new "chart" form of their tree for S497. A copy from May 2020 which is captured and shown here. Restructured to only show 3 levels down. This chart form is more representative with what genealogists use to show family branches. A single patriarch at the top with branches of descendants down below.
While each block does represent one or more patriline descendants from the top; these block represent haplogroups. And thus groups of people who all descend from some single person who was the first to get a particular SNP change and then pass it down to all the descendants. When more than one SNP is in the block, it simply means that there have not been enough testers to break the branching out any further. SNP changes happen roughly every 80 to 100 years. So with S497 having 6 SNPs, the block represents roughly 500 years of ancestors. Only the SNP that names the block is shown. The others are visible in other charts. Which of the SNPs is used to name the block is arbitrary. There is not enough known at this point to decide which came first in time.

This top block of the clade represents about 500 years of male-line (patriline) descendants. There was some single, first person who exhibited a change in one of the 6 SNPs. And approximately 500 years, one of his descendants who had a 6th SNP change. We just do not know who these people are, how many were in between and similar. We do not yet know which SNPs changed in which order. All we really know is every ancestor above this haplogroup had none of the SNP changes appearing in this haplogroup and those below. And everyone below this haplogroup have all the SNP changes represented in this haplogroup. That would include anybody tested and placed below this haplogroup in the tree..

Sometimes, if the tree is more fully formed, the "Formed" date (in years before present or ybp) will represent when the first SNP in the haplogroup formed and the TMRCA will represent (roughly)) when the last SNP formed. But for most of the haplogroups in this "middle" section of the tree, that is not yet the case. There is just not enough information yet known. These trees are best-guess estimates based on very partial, vague information known so far. Phylogenetic trees for the yDNA are in a constant flux and state of refinement as more testers are added.