Understanding mtDNA Haplogroups

What are mitochondrial DNA (mtDNA) haplogroups?

Mitochondrial DNA (mtDNA) haplogroups are the major branches in our common maternal lineage. Your haplogroup traces your branch on the maternal tree of humanity back to our shared ancestor in Africa.

Are mtDNA haplogroups the same as Y-DNA haplogroups?

No, the names in the mitochondrial DNA (mtDNA) haplogroups do not correspond with the same names in the Y-chromosome DNA (Y-DNA) haplogroups.

How are mtDNA haplogroups named?

In general, scientists name mtDNA haplogroups according to their major branch with a capital letter. These are known as “root” haplogroups. Immediate subclades (branches) are known as “primary” haplogroups and are named with alternating numbers and letters: H, H1, H1a, H1a1, etc.

H
- H1
  - H1a
    - H1a1

Some root or primary haplogroups have so many subclades branching off from them that a second letter has been added.

For example, if H1a through H1z had already been named, the next discovered subclades might become H1aa, H1ab, etc.

Haplogroup Symbol Key

Certain punctuation marks and other special characters are used for some haplogroup names. Below is a key to their meaning:

SYMBOL	MEANING	EXAMPLE	NOTES
! (Exclamation Point)	Indicates a Back Mutation.
. (period)	Indicates an Insertion.		Only refers to mutation positions, not haplogroup names
d (lower-case letter)	Indicates a Deletion.		Only refers to mutation positions, not haplogroup names
0 (Zero)	Used when a new branch point needs to be inserted above a well-established branch point on the mitochondrial tree.	One of the best-known examples is the insertion of R0 between the R and HV branches. R R0 HV	In some older papers, the “pre” prefix is used instead of a 0 (zero.) This means you may see that R0 referred to as "Pre-HV" in these papers.
' (Apostrophe)	Used to create a common branch between two well-established (primary) branch points in the tree.	M1’20’51 is the common parent of the M1, M20, and M51 primary branches. M1’20’51 M1 M20 M51 Common branches may be formed from alphanumeric primary haplogroups as well. They also may exist above Primary Branches H1b’x’gm’gn H1b H1x H1gm H1gn	Some branches of the tree that were joined before the apostrophe was adopted are joined without the use of an apostrophe by historic convention. For example: HV is the parent of the H and V branches. JT is the parent of the J and the T branches.
" (Quotation Mark)	Indicates a common parent of a number of branches whose names span the range before and after the " (quotation mark.)	M1”60 might be the common parent of the M1, M20, M51, M55, and M60 branches: M1”60 M1 M20 M51 M55 M60 H1b”gx might be the common parent of the H1b, H1x, H1z, H1aa, H1gm, and H1gx branches: H1b”gn H1b H1x H1z H1aa H1gm H1gx	Using a " (quotation mark) does not imply that all numbers or alphanumeric characters within the range are immediate subclades of that common parent.
^ (Caret)	Used when a new tester has tested positive for most - but not all - of the variants common to that haplogroup, and the haplogroup therefore has split into two subgroups. In time, both the parent and the new subgroup will receive new names.	M1’20’51 M1 M1a Might become M1’20’51 M1^ - A new tester in the M1^ haplogroup for now) M1 - includes all prior testers in the previous M1 haplogroup M1a
( ) (Parentheses)	Indicates lower-quality variants. These are not generally used for branch determination.	One heteroplasmy or no call in a specific part of the tree could cause the exact location on the tree where the SNP happened to be uncertain.
+ (Plus Symbol)	Indicates the position or variant name of a lead variant for a new haplogroup. It is used in conjunction with the parent of that haplogroup.	Haplogroup H1+3915 indicates a new variant at position 3915 downstream of H1.

Types of mtDNA Haplogroups

TYPE	DEFINITION	EXAMPLE	NOTES
Upstream Haplogroup	Indicates that a haplogroup is older relative to another haplogroup.	H is upstream of H1, H2, etc. H H1 H2
Downstream Haplogroup	Indicates that a haplogroup is older relative to another haplogroup.	H1a is downstream of H1 and H. H H1 H1a H2
Root haplogroup	Applies only to major branches assigned a capital letter with no following numbers or letters.	A, B, C....Z	L0, L1, L2, L3, L4, L5, L6, L7 are also all "roots" even though they do not have "root haplogroup names" We also reserve AA and AB for Neanderthal and Denisovan samples
Primary Haplogroup	Has letters and numbers but no special characters.	H2, U5, X2, etc.
Inner Haplogroup	Has apostrophes (') or quotes (") and group haplogroups with primary names.
Interim Haplogroup	An upstream branch with a primary name that has been split and is expected to change to an inner name.	For now: K2a11^ - upstream of K2a11, split branch K2a11 Later: K2a11'23 - split branch (previously K2a11^) that includes the new daughter branch K2a11 K2a23 - when/if split sample forms a new daughter branch	There can be multiple interim haplogroup names for a branch if it splits multiple times. For example: K2a11^^^ K2a11^^ K2a11^ K2a11
Variant Haplogroup	Used for branches when there isn't sufficient scientific evidence to justify a new primary name, and creating an interim or inner name isn't practical either because there are no downstream primary names, or because there are so many downstream primary names that an inner classification would be too complex.	Haplogroup H1+3915 indicates a branch just downstream of H1 defined by a new variant at position 3915.