Phylogenetic Tree

A Phylogenetic Tree (often mis-named a Haplogroup tree) in genetic genealogy is a partial order of haplogroups based on the suspected time through history of SNP changes in the human population. Historically, in general biology, Phylogenetics is the study of the evolutionary history of a species or population and the tree is a representation of that current theory. In a phylogenetic tree, each node or branch point is a haplogroup. There is a separate patrilineal and matrilineal tree for humans that corresponds to the haplogroups defined by the non-recombining portion of the Y chromosome and the mitochondrial DNA; respectively.

As there are few SNPs in the mitochondrial DNA, the tree there is very small and not very useful for genealogy. The Y phylogenetic tree has been exploding in size and complexity with the advent of NGS testing allowing for a deep analysis of SNPs. Because of the recombining nature of the rest of the chromosomes (mainly the autosomes), no attempt to build a tree exists for those portions of the DNA (for genetic genealogy at least).

The nomenclature of the trees was standardized by the ad-hoc YCC group that introduced and maintained the most current Y Phylogenetic Tree from the early 1990’s to mid 2000’s. See the YCC page for information on the long and short format for naming the paths in a tree from the root to the leaf haplogroup.

The Mitochondrial PhyloTree founders (see the reference below) introduced a simplified, top-level Y Phylogenetic Tree that is now being adopted (in form) by others. It mimics the still-simple Mitochondrial PhyloTree at the top level and utilizes single letters and numbers.

Generally Phylogenetic Trees are used exclusively in population genetics and anthropology. For genetic genealogy and its matching analysis, it is generally enough to know if two tested individuals are in the same haplogroup or not. But as the depth of testing is constantly being refined, the accuracy of the haplogroup designation is different for different testers. Thus, the phylogenetic tree aids the genetic genealogy researcher in understanding if two testers could or definitely could not share the same leaf haplogroup in a tree if they were both tested to the same level. STR testing can be used to predict a likely haplogroup near the root in the Y Phylogenetic Tree.

Some have mistakenly taken Cladograms that are generated from comparing Haplotypes to be a type of Phylogenetic Tree.