Human mitochondrial DNA haplogroup


Mitochondria are the primary energy generator of the cell and have unique organelles that maintain their own DNA. In human genetics, human mitochondrial DNA haplogroups are collections of similar haplotypes defined by combinations of single nuclear polymorphism in mtDNA inherited from a common ancestor. Mitochondrial DNA is passed down through cytoplasmic inheritance, where, upon fertilization, the paternal mitochondria are degraded, leaving only the maternal mitochondria regardless of the offspring’s sex. This characteristic of mitochondrial inheritance allows geneticists to track the movement and divergence of different haplogroups from female lineages. Haplogroups are used to represent the major branch points on the mitochondrial phylogenetic tree. Understanding this mechanism of inheritance 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 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 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.
Recent research has shown that mitochondrial DNA haplogroups can influence risk for various diseases and cancers.

Phylogeny

This phylogenetic tree is based Van Oven. In June 2022, an alternative phylogeny for haplogroup L was suggested

Major mtDNA haplogroups

Macro-haplogroup L

Macro-haplogroup L is the most basal of human mtDNA haplogroups, from which all other haplogroups descend. These haplogroups represent the majority of the typical sub-Saharan mtDNA variability. Approximately 65% of the European L lineages mostly likely arrived during the Arab conquest of Iberian Peninsula and Sicily and during the period of Atlantic slave trade. The remaining 35% of L mtDNAs form European-specific subclades, revealing that the gene flows from sub-Saharan Africa toward Europe from 11,000 years ago.

Macro-haplogroup H

Macro-haplogroup H is found mostly in European countries and forms ~40-45% of the European mitochondrial gene pool. Its focus has been an important aspect of human genetic diversity studies for more than a decade. It is estimated that the coalescence time for Hg H is ~21,000 years ago, which led to the proposal that the clade was involved in a post-glacial population re-expansion from southwestern Europe to the rest of the continent. Most of the population along the westernmost Mediterranean coasts, separated by a narrow body of water, shows the highest frequencies of mitochondrial haplogroup H. The most basal nodes of the most frequent H sub-haplogroup, H1 and H3, are found among many western Europeans origins.
A 2017 study published in BMC Genomic Data analyzed mitochondrial DNA haplogroup H in 750 individuals from southern Spain, finding 337 carriers primarily from the Andalusian provinces of Huelva and Granada. The research revealed that both populations exhibited a predominantly western European genetic profile, though Granada showed additional affinities with eastern Mediterranean populations, suggesting historical gene flow. Sub-haplogroups H1 and H3 were the most common, with molecular dating indicating origins around 16,000 and 13,000 years ago, respectively, and shared ancestry between Iberian and North African groups. Significant haplotype sharing between Andalusia and Morocco pointed to the Strait of Gibraltar as a corridor for maternal gene exchange rather than a genetic barrier. Overall, haplogroup H frequencies of about 39% in Huelva and 48% in Granada highlighted local diversity shaped by post-glacial expansions and later trans-Mediterranean interactions.

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 time of origin Possible place of originHighest frequencies
L200Africa
L1-6170East Africa
L2-6150East Africa
L0150East Africa
L1140Central Africa
L3-6130
L5120
L290
L370East Africa
N70East Africa or West Asia
M60East Africa, West Asia or South Asia
R60South Asia or Southeast Asia
U55North-East Africa or India
RT'JT55Middle East
JT50Middle East
U850Western Asia
R947
B444
F43
U4'942Central Asia
U535Western Asia
U635North Africa
J35
X30
K30
U5a27
HV27Near East
J1a27Near East
T27Mesopotamia
K127
I26
J124Near East
W20
U420Central Asia
X220
H20Western Asia
U5a118Europe
J1b11
V14
X2a13North America
H112
H312
X110

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 and Oceanian haplogroups: M42a, M42c, M14, M15, Q, S, O, N, P.
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

  • : James Lick's tool.
  • : FASTA based haplogroup tool. Replaced HAPLOFIND.
  • : VCF based tool.
  • : Mitoverse's tool for both WGS and WES.
  • : A short fragment tool.
  • : Ian Logan's SNP to haplogroup tool.

Dating

  • : Ian Logan's mutation calculator.

Phylogeny

  • for browsing their new mtDNA Haplotree.
  • : Mostly based on PhyloTree Build 17 but with the addition of haplogroup L7.
  • : "Classic" view of FTDNA's mtDNA tree.
  • : An mtDNA tree. Faster loading.
  • : A traditional mtDNA tree.
  • : Haplogroup trees.

Maps

Ancient

  • : Ancient uniparental map.
  • : Nicky Rosenblatt's ancient uniparental map.
  • : An aDNA map made with Map Maker.

Modern

  • : A heatmap generator.

Databases

Ancient

  • : An database of ancient mtDNA samples.
  • : Carlos Quiles' uniparental database.

Modern

  • : Ian Logan's GenBank based accession matching tool.
  • : A uniparental database.
  • : An mtDNA genome database.