Human mitochondrial DNA haplogroup
![](http://upload.wikimedia.org/wikipedia/commons/thumb/5/5e/MtDNA_haplogroup_distribution_among_2%2C054_individuals_across_26_populations_from_the_1000_Genomes_Project.png/350px-MtDNA_haplogroup_distribution_among_2%2C054_individuals_across_26_populations_from_the_1000_Genomes_Project.png)
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
[edit]![](http://upload.wikimedia.org/wikipedia/commons/thumb/8/80/MtDNA_haplogroup_tree_and_distribution_map.gif/350px-MtDNA_haplogroup_tree_and_distribution_map.gif)
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This phylogenetic tree is based Van Oven (2009).[4] In June 2022, an alternative phylogeny for haplogroup L was suggested[5]
Major mtDNA Haplogroups
[edit]Macro-haplogroup L
[edit]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
- L5'7
Macro-haplogroup M
[edit]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
[edit]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
[edit]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
[edit]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
[edit]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
[edit]Assignment
[edit]- 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
[edit]- mtDNA Mutation Computer Model: Ian Logan's mutation calculator.
Phylogeny
[edit]- FTDNA's mtDNA Haplotree: The largest mtDNA tree.
- YFull's MTree: An mtDNA tree. Faster loading (simpler).
- PhyloTreemt: A traditional mtDNA tree (last updated 2016-02-18).[13]
- HIP: Haplogroup trees.
Maps
[edit]Ancient
[edit]- HIP Haplomap: Ancient uniparental map.
- AH DNA: Nicky Rosenblatt's ancient uniparental map.[14]
- Ancient DNA: An aDNA map made with Map Maker.
Modern
[edit]- HRAS mtDNA: A heatmap generator.
Databases
[edit]Ancient
[edit]- AmtDB: An database of ancient mtDNA samples.[15]
- All Ancient DNA Dataset: Carlos Quiles' uniparental database (with BAM).
Modern
[edit]- GenBank mtDNA Sequence Checker: Ian Logan's GenBank based accession matching tool.
- mitoYDNA: A uniparental database.
- MITOMAP: An mtDNA genome database.[16]
See also
[edit]- Human mitochondrial genetics
- Genetic genealogy
- Matrilineality
- Human Y-chromosome DNA haplogroups
- Population genetics
References
[edit]- ^ 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.
- ^ 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
- ^ 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.
- ^ 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.
- ^ 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.
- ^ "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.
- ^ 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.
- ^ 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. eISSN 1098-1004.
- ^ 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. eISSN 1098-1004.
- ^ 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. eISSN 1362-4962.
- ^ 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). eISSN 2045-2322.
- ^ 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.
- ^ 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.
- ^ Various (2017-05-30). "Rosenblatt's ancient DNA map". Anthrogenica.
- ^ 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. eISSN 1362-4962.
- ^ 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. eISSN 1362-4962.
External links
[edit]- List of mtDNA haplogroup projects at ISOGG.
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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 |