PhyloD3 — Interactive Human mtDNA Phylogenetic Tree Explorer

The human mtDNA phylogenetic tree, as PhyloTree publishes it

PhyloD3 draws the human mitochondrial DNA (mtDNA) phylogeny from PhyloTree Build 17 (van Oven & Kayser, 2009) as one collapsible tree. It starts at the mitochondrial most recent common ancestor (mt-MRCA) and ends at the terminal haplogroups. Build 17 publishes 5,400+ haplogroups. This tree holds 5,182 named clades of them.

What the tree shows

mtDNA passes from mother to child without recombination. A haplogroup is a clade that shares a set of mutations against the rCRS reference. The tree nests these clades: the African lineages L0 to L6 sit closest to the root, L3 forks into the macro-haplogroups M and N, and R hangs under N. The path from any clade back to mt-MRCA is that clade's maternal descent, and the tree draws it as one line.

What the instrument does

• Expand or collapse any clade. A collapsed clade shows how many descendants it hides.
• Search any haplogroup by name. The path from mt-MRCA to the result is drawn in the structure colour.
• Link to any node. The URL carries the haplogroup name, so a link opens the tree at that clade.
• Walk with the keyboard. Arrow keys move to the parent, a child, or a sibling.
• Light and dark themes. The page follows the system setting unless you choose one.

Where the major haplogroups sit

Under M: C and Z (via CZ), D, E, G, Q. Under N: A, I, S, W, X, Y, O, and R. Under R: R0 with HV, H and V; R2'JT with J and T; U with K; F (via R9); P. Every one of these can be expanded to its terminal clades.

Source and companion

Tree data: van Oven M, Kayser M. 2009. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Human Mutation 30(2):E386–E394. doi:10.1002/humu.20921. Build 17 is the last published build.

HaploFind is the companion instrument. It assigns a mitochondrial sequence to a haplogroup on the same Build 17 phylogeny, computed on your device, and links each call back into PhyloD3.