# Human mitochondrial DNA haplogroup

In human genetics, a human mitochondrial DNA haplogroup is a haplogroup defined by differences in human mitochondrial DNA. Haplogroups are used to represent the major branch points on the mitochondrial phylogenetic tree. Understanding the evolutionary path of the female lineage has helped population geneticists trace the matrilineal inheritance of modern humans back to human origins in Africa and the subsequent spread around the globe.
The letter names of the haplogroups (not just mitochondrial DNA haplogroups) run from A to Z. As haplogroups were named in the order of their discovery, the alphabetical ordering does not have any meaning in terms of actual genetic relationships.
The hypothetical woman at the root of all these groups (meaning just the mitochondrial DNA haplogroups) is the matrilineal most recent common ancestor (MRCA) for all currently living humans. She is commonly called Mitochondrial Eve.
The rate at which mitochondrial DNA mutates is known as the mitochondrial molecular clock. It is an area of ongoing research with one study reporting one mutation per 8000 years.

## Phylogeny

This phylogenetic tree is based Van Oven (2009). In June 2022, an alternative phylogeny for haplogroup L was suggested
* L (Mitochondrial Eve)
** L0
** L1-6
*** L1
*** L2-6
**** L5
**** L2'3'4'6
***** L2
***** L3'4'6
****** L6
****** L3'4
******* L4
******* L3
******** N
********* N1: I
********* N2: W
********* N9: Y
********* A
********* S
********* X
********* R
********** R0 (FMKA pre-HV)
*********** HV: (H, V)
********** pre-JT or R2'JT
*********** JT: (J, T)
********** R9: F
********** R11'B: B
********** P
********** U (formerly UK)
*********** U8: K
********* O
******** M
********* M9: E
********* M12'G: G
********* M29'Q: Q
********* D
********* M8: CZ (C, Z)

## Major mtDNA Haplogroups
### Macro-haplogroup L

Macro-haplogroup L is the most basal of human mtDNA haplogroups, from which all other haplogroups descend (specifically, from haplogroup L3). It is found mostly in Africa.
* Haplogroup L0
* L1-7
** Haplogroup L1
** L2-7
*** L3'4'6
**** Haplogroup L2
**** L346
***** L34
****** Haplogroup L3
****** Haplogroup L4
***** Haplogroup L6
*** L5'7
**** Haplogroup L5
**** Haplogroup L7

### Macro-haplogroup M

Macro-haplogroup M is found mostly in Asia and the Americas. Its descendants are haplogroup M, haplogroup C, haplogroup Z, haplogroup D, haplogroup E, haplogroup G and haplogroup Q.

### Macro-haplogroup N

Macro-haplogroup N is found mostly in Australia, the Americas and parts of Asia. Its descendants are haplogroup N, haplogroup O, haplogroup A, haplogroup S, haplogroup I, haplogroup W, haplogroup X and haplogroup Y, as well as macro-haplogroup R.

### Macro-haplogroup R

Macro-haplogroup R is found mostly in Europe, Northern Africa, the Pacific and parts of Asia and the Americas. Its descendants are haplogroup R, haplogroup B, haplogroup F, haplogroup H, haplogroup V, haplogroup J, haplogroup T, haplogroup U and haplogroup K

## Chronology

| Haplogroup | Est. time of origin (kya) | Possible place of origin |
| L | 200 | Africa |
| L1-6 | 170 | East Africa |
| L2-6 | 150 | East Africa |
| L0 | 150 | East Africa |
| L1 | 140 | Central Africa |
| L3-6 | 130 | |
| L5 | 120 | |
| L2 | 90 | |
| L3 | 70 | East Africa |
| N | 70 | East Africa or West Asia |
| M | 60 | East Africa, West Asia or South Asia |
| R | 60 | South Asia or Southeast Asia |
| U | 55 | North-East Africa or India (South Asia) |
| RT'JT | 55 | Middle East |
| JT | 50 | Middle East |
| U8 | 50 | Western Asia |
| R9 | 47 | |
| B4 | 44 | |
| F | 43 | |
| U4'9 | 42 | Central Asia |
| U5 | 35 | Western Asia |
| U6 | 35 | North Africa |
| J | 35 | |
| X | 30 | |
| K | 30 | |
| U5a | 27 | |
| HV | 27 | Near East |
| J1a | 27 | Near East |
| T | 27 | Mesopotamia |
| K1 | 27 | |
| I | 26 | |
| J1 | 24 | Near East |
| W | 20 | |
| U4 | 20 | Central Asia |
| X2 | 20 | |
| H | 20 | Western Asia |
| U5a1 | 18 | Europe |
| J1b | 11 | |
| V | 14 | |
| X2a | 13 | North America |
| H1 | 12 | |
| H3 | 12 | |
| X1 | 10 | |

## Geographical distribution

A 2004 paper suggested that the haplogroups most common in modern West Asian, North African and European populations were: H, J, K, N1, T, U4, U5, V, X and W.
African haplogroups: L0, L1, L2, L3, L4, L5, L6, T, U5a
Australian haplogroups: M42a, M42c, M14, M15, Q, S, O, N, P. (Refs 1, 2, 3, 4, 5, 6)
Asian haplogroups: F, C, W, M, D, N, K, U, T, A, B, C, Z, U many number variants to each section

## Research software
### Assignment

* mtHap: James Lick's tool (multiple input formats).
* YSEQ mt Clade Finder: FASTA based haplogroup tool. Replaced HAPLOFIND.
* HaploGrep: VCF based tool.
* Haplocheck: Mitoverse's tool for both WGS and WES.
* Haplotracker: A short fragment tool.
* Haplogroup Finder: Ian Logan's SNP to haplogroup tool.

### Dating

* mtDNA Mutation Computer Model: Ian Logan's mutation calculator.

### Phylogeny

* FTDNA's mtDNA Haplotree: Mostly based on PhyloTree Build 17 but with the addition of haplogroup L7.
* FTDNA's Mitotree BETA: The largest mtDNA tree.
* YFull's MTree: An mtDNA tree. Faster loading (simpler).
* PhyloTree$_{mt}$: A traditional mtDNA tree (last updated 2016-02-18).
* HIP: Haplogroup trees.

### Maps
#### Ancient

* HIP Haplomap: Ancient uniparental map.
* AH DNA: Nicky Rosenblatt's ancient uniparental map.
* Ancient DNA: An aDNA map made with Map Maker.

#### Modern

* HRAS mtDNA: A heatmap generator.

### Databases
#### Ancient

* AmtDB: An database of ancient mtDNA samples.
* All Ancient DNA Dataset: Carlos Quiles' uniparental database (with BAM).

#### Modern

* GenBank mtDNA Sequence Checker: Ian Logan's GenBank based accession matching tool.
* mitoYDNA: A uniparental database.
* MITOMAP: An mtDNA genome database.