What is a Haplogroup?
To define what a haplogroup is, we have to start with the variants because they are fundamental to genetic analysis. A DNA sequence can be defined as base pairs that are illustrated by a series of letters like A, T, C and G.
In 1981, the mitochondrial DNA was sequenced, and the result is known as the Cambridge Reference Sequence. This is what is used as the baseline sequence in genetic analysis.
Each individual's DNA sequence is then compared to this reference sequence. There's nothing particularly special about this sequence. It is just used as the reference sequence.
In genetic analysis, every person's sequence is compared to this sequence and, if there are any differences between the sequences, it is known as a genetic variant. A genetic variant simply represents a change in the DNA.
For this person, they have A, where the Cambridge Reference Sequence has a T. That represents a change or a variant. The next one they have is a T where the Cambridge Reference Sequence has an A. Lastly, they have a C in a base pair position where the Cambridge Reference Sequence has a G.
A group of variants altogether are called a haplotype. A haplogroup is defined as a haplotype that is shared among a group of people who are similarly categorized. That categorization could mean they're from the same family, the same ethnic group, country, region, continent, etc.
Each haplogroup has a required set of variants. In our hypothetical example below, you'd need to have three of these required variants in order to be designated to the L3b1c haplogroup, (variants: 16001A, 16007T, 16013C). Any other variants that you have, if they don't fall into another haplogroup, are going to be discounted. These three are the only ones that will be considered when assigning haplogroups.
When you look at the way the haplogroup is written with the letters and the numbers, the first capitalized letter usually indicates the macro-haplogroup. That's the continental or regional origin of the haplogroup. "L" haplogroups are seen in Africa. The rest of the letters and numbers after that capital letter signify other variants along that capital group lineage, they don't have any specific meaning.
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