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Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation
Open accessAbstract
Human mitochondrial DNA is widely used as tool in many fields including evolutionary anthropology and population history, medical genetics, genetic genealogy, and forensic science. Many applications require detailed knowledge about the phylogenetic relationship of mtDNA variants. Although the phylogenetic resolution of global human mtDNA diversity has greatly improved as a result of increasing sequencing efforts of complete mtDNA genomes, an updated overall mtDNA tree is currently not available. In order to facilitate a better use of known mtDNA variation, we have constructed an updated comprehensive phylogeny of global human mtDNA variation, based on both coding- and control region mutations. This complete mtDNA tree includes previously published as well as newly identified haplogroups, is easily navigable, will be continuously and regularly updated in the future, and is online available at http://www.phylotree.org.
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“the most recent revision of mtDNA haplogroups [87] clearly show an increase in the frequency of haplogroup B from Papua New Guinea and nearby islands at 60-40%, to over 80% in Fiji, and +90% among Polynesians (Figure 2).”
From Dispersal, Isolation, and Interaction in the Islands of Polynesia: A Critical Review of Archaeological and Genetic Evidence (2017) · cites this paper as [87]
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“Across all 160 Native Hawaiians, we identified 14 mtSNPs to have a minor allele frequency >1% (Table 1), of which 6 polymorphisms have not been previously identified by PhyloTree [46] to be a haplogroup identifying marker.”
From Population Genetic Structure and Origins of Native Hawaiians in the Multiethnic Cohort Study (2012) · cites this paper as [46]
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“MtDNA haplogroup assignment was performed on positions with a read depth > 1 (coverage filtered) using HaploGrep 2.0 (Kloss‐Brandstatter et al., 2011), followed by manual confirmation of haplogroup‐defining mutations provided in Phylotree mtDNA tree Build 16 (van Oven and Kayser, 2009).”
From Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus (2016) · cites this paper as van Oven and Kayser, 2009
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“It belongs to haplogroup HV18 [48], a rare lineage (five samples in EMPOP v4/R12, https://empop.online/)[49,50] that has been defined for the first time by analyzing modern Iranians [51] and that is nowadays present in Western Europe and the Middle East.”
From Resolving a 150-year-old paternity case in Mormon history using DTC autosomal DNA testing of distant relatives. (2019) · cites this paper as [48]
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“Both Gill et al. [7] and Ivanov et al. [13] evaluated the evidence in their investigations using a Bayesian approach to evaluate the weight of the evidence under two opposing hypotheses (likelihood ratio): (1) These are the remains of the Romanovs, and (2) these are not the remains of the Romanovs.”
From The identification of the Romanovs: Can we (finally) put the controversies to rest? (2011) · cites this paper as [13]
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“Nagai et al. [22] erroneously reported that Ivanov et al. [13] had observed a transition at nucleotide position 320 (C-T).”
From The identification of the Romanovs: Can we (finally) put the controversies to rest? (2011) · cites this paper as [13]
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“Although two sets of skeletal remains belonging to Alexei and one of his sisters were missing from the mass grave, the forensic results were very conclusive in identifying the Romanov family and their servants.”
From The identification of the Romanovs: Can we (finally) put the controversies to rest? (2011) · cites this paper as [13]
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In the citing paper
“Ivanov et al. [13] gave clear and convincing evidence that the 16,169 heteroplasmy found in the tsar was in fact authentic, since Georgii had the same point heteroplasmy, although at a ratio different from that of the tsar.”
From The identification of the Romanovs: Can we (finally) put the controversies to rest? (2011) · cites this paper as [13]
Experimental — accuracy not yet measuredThe check wasn’t confident either way, so it gives no verdict — never disputed.
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“The initial work from 1993 to 1996 [7,13] was a watershed moment for DNA testing, and despite the feeble attempts to discredit these studies with contaminated data, the results have withstood the test of time throughout scientific advances.”
From The identification of the Romanovs: Can we (finally) put the controversies to rest? (2011) · cites this paper as [13]
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In the citing paper
“The Anzick-1 D4h3a does not carry any of the polymorphisms that define the several sub-groups of the haplogroup13 and is thus placed at the root of D4h3a.”
From The genome of a Late Pleistocene human from a Clovis burial site in western Montana (2014) · cites this paper as [13]
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Self-citationThe saga of the many studies wrongly associating mitochondrial DNA with breast cancer
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Santorsola, M., Calabrese, C., Girolimetti, G., Diroma, M. A., Gasparre, G., & Attimonelli, M. (2015) · Human Genetics · doi:10.1007/s00439-015-1615-9 · Cited by 37
Cohen, T., Levin, L., & Mishmar, D. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1006407 · Cited by 36
Martin, F. N., Zhang, Y., Cooke, D. E. L., Coffey, M. D., Grünwald, N. J., & Fry, W. E. (2019) · PLoS ONE · doi:10.1371/journal.pone.0208606 · Cited by 37
Pérez-Amado, C. J., Tovar, H., Gómez-Romero, L., Beltrán‐Anaya, F. O., Bautista‐Piña, V., Domínguez-Reyes, C. A., Villegas‐Carlos, F., Tenorio‐Torres, A., Alfaro-Ruíz, L. A., Hidalgo‐Miranda, A., et al. (2020) · Frontiers in Oncology · doi:10.3389/fonc.2020.572954 · Cited by 37
Deciphering the Signature of Selective Constraints on Cancerous Mitochondrial Genome
Liu, J., Wang, L., Sun, Y., Li, E., Xu, L., Zhang, Y., Yao, Y., & Kong, Q. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr290 · Cited by 37
Genetic diversity and evidence for population admixture in Batak Negritos from Palawan
Scholes, C., Siddle, K. J., Ducourneau, A., Crivellaro, F., Järve, M., Rootsi, S., Bellatti, M., Tabbada, K. A., Mormina, M., Reidla, M., et al. (2011) · American Journal of Physical Anthropology · doi:10.1002/ajpa.21544 · Cited by 36
Ancient mitochondrial DNA sequences of Jomon teeth samples from Sanganji, Tohoku district, Japan
Kanzawa‐Kiriyama, H., Saso, A., Suwa, G., & Saitou, N. (2013) · Anthropological Science · doi:10.1537/ase.121113 · Cited by 36
Genetic evidence for the colonization of Australia
Pellekaan, S. V. H. (2011) · Quaternary International · doi:10.1016/j.quaint.2011.04.014 · Cited by 36
Updating the Y-chromosomal phylogenetic tree for forensic applications based on whole genome SNPs
Geystelen, A. V., Decorte, R., & Larmuseau, M. (2013) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2013.03.010 · Cited by 36
Intracellular evolution of mitochondrial DNA (mtDNA) and the tragedy of the cytoplasmic commons
Haig, D. (2016) · BioEssays · doi:10.1002/bies.201600003 · Cited by 36
A Comprehensive Characterization of Mitochondrial Genome in Papillary Thyroid Cancer
Su, X., Wang, W., Ruan, G., Liang, M., Zheng, J., Chen, Y., Wu, H., Fahey, T. J., Guan, M., & Teng, L. (2016) · International Journal of Molecular Sciences · doi:10.3390/ijms17101594 · Cited by 36
Entire Mitochondrial DNA Sequencing on Massively Parallel Sequencing for the Korean Population
Park, S., Cho, S., Seo, H. J., Lee, J. H., Kim, M., & Lee, S. D. (2017) · Journal of Korean Medical Science · doi:10.3346/jkms.2017.32.4.587 · Cited by 36
AQME: A forensic mitochondrial DNA analysis tool for next-generation sequencing data
Sturk‐Andreaggi, K., Peck, M. A., Boysen, C., Dekker, P., McMahon, T. P., & Marshall, C. K. (2017) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2017.09.010 · Cited by 36
An invasive Haemophilus influenzae serotype b infection in an Anglo-Saxon plague victim
Guellil, M., Keller, M., Dittmar, J. M., Inskip, S. A., Cessford, C., Solnik, A., Kivisild, T., Metspalu, M., Robb, J., & Scheib, C. L. (2022) · Genome biology · doi:10.1186/s13059-021-02580-z · Cited by 35
Parson, W., Strobl, C., Huber, G. E., Zimmermann, B., Gomes, S. M., Souto, L., Fendt, L., Delport, R., Langit, R., Wootton, S., et al. (2013) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2013.09.007 · Cited by 36
Zhang, P., Samuels, D. C., Lehmann, B. D., Stricker, T. P., Pietenpol, J. A., Shyr, Y., & Guo, Y. P. (2015) · Briefings in Bioinformatics · doi:10.1093/bib/bbv057 · Cited by 36
García, A., Pauro, M., Nores, R., Bravi, C. M., & Demarchi, D. A. (2012) · American Journal of Physical Anthropology · doi:10.1002/ajpa.22174 · Cited by 36
Holland, M. M., Makova, K. D., & McElhoe, J. A. (2018) · Genes · doi:10.3390/genes9030124 · Cited by 36
Santana, J., Fregel, R., Lightfoot, E., Morales, J., Alamón-Núñez, M., Guillén, J., Moreno, M., & Rodríguez, A. R. (2015) · American Journal of Physical Anthropology · doi:10.1002/ajpa.22879 · Cited by 35
Gorostiza, A., Acuña-Alonzo, V., Regalado-Liu, L., Tirado, S., Granados, J., Sámano, D., Rangel‐Villalobos, H., & González‐Martín, A. (2012) · PLoS ONE · doi:10.1371/journal.pone.0044666 · Cited by 35
Mitochondrial haplogroup N1a phylogeography, with implication to the origin of European farmers
Palanichamy, M. G., Zhang, C.-L., Mitra, B., Malyarchuk, B. А., Derenko, M. V., Chaudhuri, T. K., & Zhang, Y. (2010) · BMC Evolutionary Biology · doi:10.1186/1471-2148-10-304 · Cited by 36
Krzywanski, D. M., Moellering, D. R., Westbrook, D. G., Dunham‐Snary, K. J., Brown, J. A., Bray, A. W., Feeley, K. P., Sammy, M. J., Smith, M. R., Schurr, T. G., et al. (2016) · Circulation Cardiovascular Genetics · doi:10.1161/circgenetics.115.001308 · Cited by 35
MitoSuite: a graphical tool for human mitochondrial genome profiling in massive parallel sequencing
Ishiya, K., & Ueda, S. (2017) · PeerJ · doi:10.7717/peerj.3406 · Cited by 33
Batini, C., Hallast, P., Vågene, Å. J., Zadik, D., Eriksen, H. A., Pamjav, H., Sajantila, A., Wetton, J. H., & Jobling, M. A. (2017) · Scientific Reports · doi:10.1038/s41598-017-11307-9 · Cited by 34
Evolutionary analysis and lineage designation of SARS-CoV-2 genomes
Tang, X., Ying, R., Yao, X., Li, G., Wu, C., Tang, Y., Li, Z., Kuang, B., Wu, F. Y., Chi, C., et al. (2021) · 中国科学通报：英文版 · doi:10.1016/j.scib.2021.02.012 · Cited by 32
Bi, R., Zhang, A., Zhang, W., Kong, Q., Wu, B., Yang, X., Wang, D., Zou, Y., Zhang, Y., & Yao, Y. (2010) · Human Mutation · doi:10.1002/humu.21220 · Cited by 35
Continental influx and pervasive matrilocality in Iron Age Britain
Cassidy, L. M., Russell, M., Smith, M. J., Delbarre, G., Cheetham, P., Manley, H., Mattiangeli, V., Breslin, E. M., Jackson, I., McCann, M., et al. (2025) · Nature · doi:10.1038/s41586-024-08409-6 · Cited by 42
Prehistoric genomes from Yunnan reveal ancestry related to Tibetans and Austroasiatic speakers
Wang, T., Yang, M. A., Zhu, Z., Ma, M., Shi, H., Speidel, L., Min, R., Yuan, H., Jiang, Z., Hu, C., et al. (2025) · Science · doi:10.1126/science.adq9792 · Cited by 35
Chan, E. K. F., Hardie, R., Petersen, D. C., Beeson, K. Y., Bornman, R. M. S., Smith, A. B., & Hayes, V. M. (2015) · PLoS ONE · doi:10.1371/journal.pone.0121223 · Cited by 34
Mitochondrial DNA Variants in Obesity
Knoll, N., Jarick, I., Volckmar, A., Klingenspor, M., Illig, T., Grallert, H., Gieger, C., Wichmann, H. ‐., Peters, A., Wiegand, S., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0094882 · Cited by 34
Cardoso, S., Palencia-Madrid, L., Valverde, L., Alfonso‐Sánchez, M. Á., Gómez‐Pérez, L., Alfaro, E., Bravi, C. M., Dipierri, J. E., Peña, J. A., & de Pancorbo, M. M. (2013) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2013.01.007 · Cited by 34
Blein, S., Bardel, C., Danjean, V., McGuffog, L., Healey, S. C., Barrowdale, D., Lee, A., Dennis, J., Kuchenbaecker, K. B., Soucy, P., et al. (2015) · Breast Cancer Research · doi:10.1186/s13058-015-0567-2 · Cited by 34
RETRACTED ARTICLE: mtDNA structure: the women who formed the Brazilian Northeast
Schaan, A. P., Costa, L., Santos, D., Modesto, A. A. C., Amador, M. A. T., Lopes, C. B., Rabenhorst, S. H. B., Montenegro, R. C., Souza, B. D. A., Lopes, T. R., et al. (2017) · BMC Evolutionary Biology · doi:10.1186/s12862-017-1027-7 · Cited by 34
RetractedJiménez‐Morales, S., Pérez-Amado, C. J., Langley, E., & Hidalgo‐Miranda, A. (2018) · International Journal of Oncology · doi:10.3892/ijo.2018.4468 · Cited by 34
Mitonuclear interactions influence Alzheimer's disease risk
Andrews, S. J., Fulton‐Howard, B., Patterson, C., McFall, G. P., Gross, A. L., Michaelis, E. K., Goate, A., Swerdlow, R. H., Pa, J., & Initiative, F. T. A. D. N. (2019) · Neurobiology of Aging · doi:10.1016/j.neurobiolaging.2019.09.007 · Cited by 36
Андреева, Т. В., Manakhov, A. D., Gusev, F. E., Patrikeev, A. D., Golovanova, L. V., Doronichev, V. B., Shirobokov, I. G., & Rogaev, E. I. (2022) · Scientific Reports · doi:10.1038/s41598-022-16164-9 · Cited by 38
Complete Mitochondrial Genome Sequencing Reveals Novel Haplotypes in a Polynesian Population
Benton, M. C., Macartney-Coxson, D. P., Eccles, D., Griffiths, L. R., Chambers, G. K., & Lea, R. A. (2012) · PLoS ONE · doi:10.1371/journal.pone.0035026 · Cited by 35
Palencia-Madrid, L., Valverde, L., Álvarez, A. F., Cainé, L., Cardoso, S., Alfonso‐Sánchez, M. Á., Pinheiro, M. F., & de Pancorbo, M. M. (2010) · International Journal of Legal Medicine · doi:10.1007/s00414-010-0464-2 · Cited by 34
Metadata
- Authors
- van Oven, M., & Kayser, M.
- Affiliations
- Erasmus MC (NL)
- ORCID
- Kayser, Manfred
- Venue
- Human Mutation
- Publisher
- Wiley
- Published
- 2009-02
- Volume
- 30
- Issue
- 2
- Pages
- E386-E394
- ISSN
- 1059-7794 (ISSN-L)
- 1098-1004
- OpenAlex
- W2111668248
- Cited by
- 1,810
- References
- 90
- Citations by year
- 2026: 46 · 2025: 74 · 2024: 66 · 2023: 86 · 2022: 131 · 2021: 113 · 2020: 99 · 2019: 120 · 2018: 123 · 2017: 130 · 2016: 115 · 2015: 129 · 2014: 129 · 2013: 135 · 2012: 103
- FWCI
- 39.99
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Human Mutation (publishedVersion)
- PubMed (publishedVersion)
- EUR Research Repository (Erasmus University Rotterdam) (publishedVersion)
- EUR Research Repository (Erasmus University Rotterdam) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- human mitochondrial DNA, mtDNA phylogeny, mtDNA haplogroups
- MeSH terms
- DNA, Mitochondrial, Haplotypes, Humans, Phylogeny, Genetic Variation, Open Reading Frames, Locus Control Region
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