Human mitochondrial DNA haplogroup

This article is about the human mtDNA haplogroup. For the human Y-DNA haplogroup, see Human Y-chromosome 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.

Contemporary human mtDNA haplogroup distribution, based on analysis of 2,054 individuals from 26 populations.^[1] (a) Pie charts on the map. (b) Counts of haplogroups in table format. For populations details, see 1000 Genomes Project#Human genome samples.

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.^[2]

Phylogeny

Further information: Molecular phylogeny

mtDNA haplogroup tree and distribution map.^[3] The numbers are haplogroup labels, reported according to the http://www.phylotree.org/ nomenclature,^[4] and give the location of one of the mutations leading to the derived haplotype. (Only a single branch defining marker, preferably from the coding region, is shown.) The main geographic features of haplogroup distribution are highlighted with colour.

Dispersal route of human mtDNA haplogroups

This phylogenetic tree is based Van Oven (2009).^[4] In June 2022, an alternative phylogeny for haplogroup L was suggested^[5]

• 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

Estimated world map of human migrations based on 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

Further information: Human mitochondrial molecular clock

Haplogroup	Est. time of origin (kya)[6]	Possible place of origin	Highest frequencies
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.^[7]

African haplogroups: L0, L1, L2, L3, L4, L5, L6, T, U5a

Australian and Oceanian haplogroups: M42a, M42c, M14, M15, Q, S, O, N, P. (Refs 1, 2, 3, 4, 5, 6)

Asian and native American 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.^[8]
• HaploGrep: VCF based tool.^[9][10]
• Haplocheck: Mitoverse's tool for both WGS and WES.^[11]
• Haplotracker: A short fragment tool.^[12]
• Haplogroup Finder: Ian Logan's SNP to haplogroup tool.

Dating

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

Phylogeny

• FTDNA's discover tool for browsing their new mtDNA Haplotree. (Released 2025-02-25)
• FTDNA's mtDNA Haplotree: Mostly based on PhyloTree Build 17 but with the addition of haplogroup L7.
• FTDNA's Mitotree: "Classic" view of FTDNA's mtDNA tree.
• YFull's MTree: An mtDNA tree. Faster loading (simpler).
• PhyloTree_mt: A traditional mtDNA tree (last updated 2016-02-18).^[13]
• HIP: Haplogroup trees.

Maps

Ancient

• HIP Haplomap: Ancient uniparental map.
• AH DNA: Nicky Rosenblatt's ancient uniparental map.^[14]
• Ancient DNA: An aDNA map made with Map Maker.

Modern

• HRAS mtDNA: A heatmap generator.

Databases

Ancient

• AmtDB: An database of ancient mtDNA samples.^[15]
• 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.^[16]

See also

• Human mitochondrial genetics
• Genetic genealogy
• Matrilineality
• Human Y-chromosome DNA haplogroups
• Population genetics