mtDNA haplogroups

Haplogrep 3

Because mtDNA is inherited maternally and without recombination, its variants reveal a lineage. These lineages form a branching tree with regional main clades. Genome assigns the sample to a branch.

Key points

All lineages trace back to a common maternal ancestor (mitochondrial Eve).
Main clades such as L in Africa, M and N outside, and R with its European subgroups H, J, T, U, K structure the tree.
A haplogroup describes ancestry, not health; population-based statements need matching context.

# How the tree is built

Because mtDNA does not recombine, mutations accumulate along a lineage and are passed on. Shared mutations define common branches. PhyloTree captures this structure as a reference against which individual samples are placed. Variants are stated relative to the revised Cambridge Reference Sequence (rCRS), so each lineage is described as a list of differences from that anchor point.

# How Genome analyses

Genome runs Haplogrep 3 in classify mode on the sample's mitochondrial VCF, using the rCRS-anchored tree phylotree-rcrs@17.2 (PhyloTree 17). Haplogrep represents the observed variant profile as differences from the rCRS and compares it, rule- and distance-based, against the marker sets of the tree's branches. It returns the best-matching branch, a rank of the closest candidates, and a quality value between 0 and 1 that indicates how completely the branch's expected markers were found. The extended report additionally lists found, missing, and remaining private variants. The haplogroup report leads with a short conclusion, separates ancestry from disease and protection context, and explicitly marks population statements that are not supportable.

# Why the classification has limits

The quality value measures agreement with the reference tree, not the biological certainty of a lineage. Gaps in mtDNA coverage, heteroplasmy, or read errors can shift individual markers and thereby assign a sample to a neighbouring branch or lower the quality value. Because the tree is continually refined, the same sample may be placed more precisely or named differently under a newer PhyloTree version. Genome therefore reports haplogroup, quality, and remaining private variants as technical plausibility context and does not derive a diagnosis from them.

What Genome measures. The sample's mitochondrial haplogroup with a quality measure, determined from the pattern of mtDNA variants against the reference tree.

Sources

1Schönherr et al., 2023 Haplogrep 3 - an interactive haplogroup classification and analysis platform. Nucleic Acids Research 51(W1):W263-W268. doi.org/10.1093/nar/gkad284
2Weissensteiner et al., 2016 HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing. Nucleic Acids Research 44(W1):W58-W63. doi.org/10.1093/nar/gkw233
3van Oven & Kayser, 2009 Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Human Mutation 30(2):E386-E394. doi.org/10.1002/humu.20921