How haplogroups work

Most of the human genome shuffles every generation through recombination, so any given chromosomal segment carries information about many ancestors at once. Two regions are exceptions: the non-recombining portion of the Y chromosome and the mitochondrial DNA. The Y passes from father to son with no shuffling, and the mtDNA passes from mother to all of her children with no shuffling either. As a result, those two regions preserve uninterrupted genealogical lineages that can be reconstructed back through hundreds of generations.

A haplogroup is a named branch on one of those lineage trees, defined by a set of mutations that arose once in a common ancestor and were inherited by every descendant of that branch. The Y-DNA tree carries roughly 30 major haplogroups labelled A through T, each subdivided into hundreds of nested subclades. The mtDNA tree carries about 25 major haplogroups labelled L0 through L6 and a series of derived branches called M, N, R, H, V, J, T, U, K, I, W, X, and so on.

How Haeckel assigns your haplogroup

The platform carries a 140-node phylogenetic tree (75 nodes for Y-DNA, 65 for mtDNA), each node annotated with the SNPs that define it. Assignment uses recursive traversal from the root: at every branch, the analyser checks whether you carry all of the defining mutations for the most-derived child available. When you do, it descends one level and repeats. The traversal stops at the deepest node still consistent with your variants.

What the assignment can and cannot tell you

A Y-DNA assignment of R1b-M269 tells you that your patrilineal line, your father's father's father and so on, traces back through a series of male ancestors who ultimately share a common patriarch with most Western European men. It does not tell you about your mother, your father's mother, or any of the other dozens of ancestors who contributed to your autosomal genome.

Likewise, an mtDNA assignment of U5a1 tells you about your matrilineal line, your mother's mother's mother and so on. The two lineages are independent of each other, and both are independent of the rest of your genome. A useful mental model: imagine your full ancestry as a vast pedigree, and the haplogroups as two specific paths drawn from the bottom up through that pedigree, one entirely along female links and one entirely along male links.

Historical figures on the same tree

Ancient DNA studies have placed many historical individuals on the haplogroup tree, from Mitochondrial Eve at the root of the mtDNA L lineage through to better-known figures such as Genghis Khan (Y-DNA C2-M217), Niall of the Nine Hostages (R1b-M222), and Tutankhamun (R1b1a2). When you and a historical figure share the same haplogroup, you share an uninterrupted matrilineal or patrilineal ancestor, although that ancestor may live thousands of years upstream of either of you.