Human mitochondrial DNA haplogroup

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

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.[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.
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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]

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.

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 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

Dating

Phylogeny

Maps

Ancient

Modern

Databases

Ancient

Modern

See also

References

  1. ^ Rishishwar L, Jordan IK (2017). "Implications of human evolution and admixture for mitochondrial replacement therapy". BMC Genomics. 18 (1): 140. doi:10.1186/s12864-017-3539-3. PMC 5299762. PMID 28178941.
  2. ^ Loogvali, Eva-Liis; Kivisild, Toomas; Margus, Tõnu; Villems, Richard (2009), O'Rourke, Dennis (ed.), "Explaining the Imperfection of the Molecular Clock of Hominid Mitochondria", PLOS ONE, 4 (12): e8260, Bibcode:2009PLoSO...4.8260L, doi:10.1371/journal.pone.0008260, PMC 2794369, PMID 20041137
  3. ^ Kivisild T (2015). "Maternal ancestry and population history from whole mitochondrial genomes". Investig Genet. 6: 3. doi:10.1186/s13323-015-0022-2. PMC 4367903. PMID 25798216.
  4. ^ a b van Oven M, Kayser M (February 2009). "Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation". Human Mutation. 30 (2): E386–94. doi:10.1002/humu.20921. PMID 18853457. S2CID 27566749.
  5. ^ Maier P, Runfeldt G, Estes R, Vilar M (2022). "African mitochondrial haplogroup L7: a 100,000-year-old maternal human lineage discovered through reassessment and new sequencing". Nature. 12 (1): 10747. Bibcode:2022NatSR..1210747M. doi:10.1038/s41598-022-13856-0. PMC 9232647. PMID 35750688. S2CID 250021505.
  6. ^ "Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock Supplementary" (PDF). Cell: 82–83 [89]. 2009. Archived from the original (PDF) on 2009-12-29.
  7. ^ Villems, Richard; Usanga, Esien; Mikerezi, Ilia; Gölge, Mukaddes; Claustres, Mireille; Michalodimitrakis, Emmanuel N.; Pappa, Kalliopi I.; Anagnou, Nicholas P.; Chaventré, André; Moisan, Jean-Paul; Richard, Christelle; Grechanina, Elena; Balanovska, Elena V.; Rudan, Pavao; Puzyrev, Valery; Stepanov, Vadim; Khusnutdinova, Elsa K.; Gusar, Vladislava; Balanovsky, Oleg P.; Peričić, Marijana; Barać, Lovorka; Golubenko, Maria; Lunkina, Arina; Laos, Sirle; Pennarun, Erwan; Parik, Jüri; Tolk, Helle-Viivi; Reidla, Maere; Tambets, Kristiina; Metspalu, Ene; Kivisild, Toomas; Derenko, Miroslava V.; Malyarchuk, Boris A.; Roostalu, Urmas; Loogväli, Eva-Liis (November 1, 2004). "Disuniting Uniformity: A Pied Cladistic Canvas of mtDNA Haplogroup H in Eurasia". Molecular Biology and Evolution. 21 (11): 2012–2021. doi:10.1093/molbev/msh209. PMID 15254257 – via academic.oup.com.
  8. ^ Capri, Miriam; Castellani, Gastone; Franceschi, Claudio; Lomartire, Laura; Sevini, Federica; Vianello, Dario (2013-06-12). "HAPLOFIND: a new method for high-throughput mtDNA haplogroup assignment". Human Mutation. 34 (9): 1189–1194. doi:10.1002/humu.22356. eISSN 1098-1004.
  9. ^ Binna, Robert; Kloss-Brandstätter, Anita; Kronenberg, Florian; Pacher, Dominic; Schönherr, Sebastian; Specht, Günther; Weissensteiner, Hansi (2010-10-19). "HaploGrep: a fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups". Human Mutaton: Variation, Informatics, and Disease. 32 (1): 25–32. doi:10.1002/humu.21382. eISSN 1098-1004.
  10. ^ Kronenberg, Florian; Forer, Lukas; Schönherr, Sebastian; Weissensteiner, Hansi (2023-04-23). "Haplogrep 3 - an interactive haplogroup classification and analysis platform". Nucleic Acids Research. 51 (1): 263–268. doi:10.1093/nar/gkad284. eISSN 1362-4962. PMC 10320078. PMID 37070190.
  11. ^ García-Olivares, Victor; et al. (2021-10-15) [received 2021-08-04]. "A benchmarking of human mitochondrial DNA haplogroup classifiers from whole-genome and whole-exome sequence data". Scientific Reports. 11 (20510): 20510. doi:10.1038/s41598-021-99895-5. eISSN 2045-2322. PMC 8519921. PMID 34654896.
  12. ^ Kim, Dong-han; Kim, Kijeong; Kim, Kyung-yong; Kim, Yoonyeong; Kwon, Chulhwan (2020-04-23). "Haplotracker: a web application for simple and accurate mitochondrial haplogrouping using short DNA fragments". bioRxiv 10.1101/2020.04.23.057646v1.
  13. ^ Kayser, Manfred; van Oven, Mannis (2008-10-13). "Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation". Human Mutation. 30 (2): 386–394. doi:10.1002/humu.20921. eISSN 1098-1004. PMID 18853457.
  14. ^ Various (2017-05-30). "Rosenblatt's ancient DNA map". Anthrogenica.
  15. ^ Chyleński, Maciej; Ehler, Edvard; Juras, Anna; Moravčík, Ondřej; Novotný, Jiří; Pačes, Jan (2018-09-24). "AmtDB: a database of ancient human mitochondrial genomes". Nucleic Acids Research. 47 (D1): 29–32. doi:10.1093/nar/gky843. eISSN 1362-4962.
  16. ^ Brown, Michael D.; Kogelnik, Andreas M.; Lott, Marie T.; Navathe, Shamkant B.; Wallace, Douglas C. (1996-01-01). "MITOMAP: A Human Mitochondrial Genome Database". Nucleic Acids Research. 24 (1): 177–179. doi:10.1093/nar/24.1.177. eISSN 1362-4962. PMC 145607.
Wikimedia Commons has media related to Human mtDNA haplogroups.

Phylogenetic tree of human mitochondrial DNA (mtDNA) haplogroups

  Mitochondrial Eve (L)    
L0 L1–6  
L1 L2   L3     L4 L5 L6
M N  
CZ D E G Q   O A S R   I W X Y
C Z B F R0   pre-JT   P   U
HV JT K
H V J T