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What is a haplogroup?

Posted by Jean-Yves on Dec 5, 2023
graphic with people and a DNA strand

A haplogroup is a series of mutations found in a chromosome. It is therefore detectable in the DNA of an individual and may be different from one population to another, or even from one individual to another.

Haplogroups are identified by a code (for example: “T”, “H5a1”, “E1b1a1a1”) which simplifies genealogical tracing of these genetic mutations.

In human genetics, the haplogroups most commonly studied are:

• The patrilineal line haplogroup (Y-chromosome), passed from father to son (women don’t have it) ;
• The matrilineal line haplogroup (mitochondrial DNA), passed from mother to offspring of both sexes.

You can look at lists identifying the origin of your haplogroups or famous “cousins” (some quite distant).

Going further…

The generally accepted theory today is that all humans descend from a common ancestor who lived somewhere in Africa, several hundreds of thousands of years ago. Thus, all men alive today have a common ancestor, called Y-chromosomal Adam or patrilineal most recent common ancestor (MRCA), and all women have a common ancestor, called Mitochondrial Eve or matrilineal MCRA.

With the passage of time, a series of mutations have modified the genome of the decendants of the male MRCA and female MRCA, resulting in human populations with increased diversity. These populations have dispersed around the world, spreading their DNA and mutations. Haplogroups define human groups having a common male or female ancestor, and having the same series of mutations on the Y-chromosome or in mitochondrial DNA; it is therefore possible to date and trace these migrations.

Haplogroups are useful in genetic genealogy since they provide complementary information to autosomal DNA (atDNA) analysis.

What is a Y-chromosome (patrilineal line) haplogroup?

The Y-chromosome is transmitted only from father to son (via the patrilineal line). Women don’t have a Y-chromosome and therefore do not have a Y chromosome haplogroup in their genome.

Over generations and since the Y-chromosomal Adam MRCA, mutations have altered the Y-chromosome. Comparing the mutations between two males tells us how closely they are related (this relationship may be tens of thousands of years old, or may be much more recent in time). The higher the number of common mutations on the Y-chromosome, the more precise the paternal haplogroup and the closer the common ancestor is in time. On the contrary, the fewer common mutations there are, the older the common ancestor will be, having lived tens of thousands of years ago.

In our European societies where a family name is traditionally transmitted from father to son, the history of the last name generally coincides with the history of the Y-chromosome of a lineage. Studying this correlation thus allows scientific confirmation of links (recent or not) between two men theoretically sharing the same agnatic (male) lineage.

Phylogenetic tree of Y-chromosome DNA haplogroups

The phylogenetic tree can be read in the same way as a family tree: the further back one goes in the tree, the older the haplogroups are. To give an order of magnitude, the characteristic mutations of haplogroup P would have appeared 40,000 to 45,000 years ago, those of haplogroup R around 25,000 years ago. For each new haplogroup, new mutations are added to the previous ones. In concrete terms, haplogroup R therefore groups together individuals with the characteristic mutations of haplogroup P, to which new mutations are added.

What is a DNA mitochondrial (matrilineal line) haplogroup?

A mitochondrial DNA haplogroup is defined by analysis of the mitochondrial DNA (mtDNA) contained in the mitochondria and transmitted through mothers over generations. The study of matrilineal lineage is based on the detection of successive mutations that have occurred in this mitochondrial DNA since that of the MRCA of all present-day women, mitochondrial Eve, who is thought to have lived from 150,000 to 170,000 years ago.

In principle, it is far more difficult to find a common ancestor through the matrilineal line, since the family name changes from generation to generation, unlike the patrilineal line.

Phylogenetic tree of mitochondrial DNA haplogroups

This tree can be read in a similar way as the Y-chromosome haplogroups, like a family tree: the further back in the tree one goes, the older the haplogroups are. To give an order of magnitude, the characteristic mutations of the U haplogroup would have appeared between 43,000 and 50,000 years ago, those of haplogroup T about 30,000 years ago. These haplogroups are themselves subdivided into sub-clades. For haplogroup T, for example, there are the sub-clades T1 and T2, themselves divided into T1a and T1b, and T2a, T2b, T2c, etc.

To better understand how haplogroups work, let’s look at an example:

  • the C16294T mutation characterizes haplogroup T;
  • the C16294T and C16296T mutations characterize haplogroup T2;
  • the C16294T, C16296T, and G16153A mutations characterize haplogroup T2e.

About 30,000 years ago a mutation occurred in the mitochondrial DNA of your matrilineal ancestor, whom we will call Christine (mother of your mother’s mother… of your mother), the C16294T mutation (a cytosine became a thymine at position 16294 of her mitochondrial DNA) which characterizes haplogroup T. The haplogroup of Christine and her matrilineal descendants is therefore haplogroup T.

A few millennia later, a mutation appears in the mitochondrial DNA of one of her descendants, Anna, the C16296T mutation. Anna now has two mutations that characterize the T2 haplogroup, so she and her descendants have the T2 haplogroup.

A few more millennia after that, in the mitochondrial DNA of Mary, Anne’s descendant, a new mutation has appeared: the G16153A mutation. Mary thus has three mutations, this new mutation and the two previous ones inherited from her ancestors Christine and Anne. This series of three mutations corresponds to haplogroup T2e, to which Mary and her own descendants belong.

If your haplogroup is T2e and the haplogroup of your contact is also T2e, you will have Mary as your common ancestor.

If your haplogroup is T2 and your contact as well, you will have Anne as your common ancestor.

And if you are from haplogroup T and your contact is also from haplogroup T, you will have Christine as your common ancestor.

Your matrilineal relationship with this Geneanet user may therefore go back a few hundred years or a few millennia. The same principle applies for Y-chromosome haplogroups.

1 comment

Merci, very well explained

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