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 shows an increase in the frequency of haplogroup B from 60-40% in Papua New Guinea and nearby islands to over 80% in Fiji and over 90% among Polynesians.
“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]
The ‘UPDATED COMPLETE mtDNA TREE’ section describes an updated global mtDNA phylogenetic tree, supporting the identification of the source as a haplogroup revision. The ‘HAPLOGROUP NOMENCLATURE’ section identifies haplogroup B, but neither section reports its frequency in Papua New Guinea, Fiji, or Polynesia. Searches for those locations and the claimed percentages found no supporting passage; page numbers were not available in our copy. (LLM, conf=0.86)
Experimental — accuracy not yet measuredAcross 160 Native Hawaiians, 14 mtSNPs have minor allele frequency >1%, of which 6 have not been previously identified by PhyloTree as haplogroup-identifying markers.
“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]
MtDNA haplogroup assignment was performed on positions with a read depth > 1 (coverage filtered) using HaploGrep 2.0, followed by manual confirmation of haplogroup-defining mutations.
“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
Joseph Smith Jr.'s maternal line belongs to haplogroup HV18.
“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]
The Introduction describes a phylogenetic tree of human mitochondrial DNA, and the haplogroup-nomenclature section identifies HV as a lineage within R. Searches for “HV18” and “Joseph Smith maternal line” found no passage in our copy assigning Joseph Smith Jr.’s maternal line to HV18. (LLM, conf=0.75)
Experimental — accuracy not yet measuredBoth Gill et al. and Ivanov et al. evaluated the evidence using a Bayesian approach under two opposing hypotheses: the remains are the Romanovs versus they are not.
“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]
The cited paper’s ‘Coding versus Control Region’ section discusses mitochondrial DNA haplogroup assignment, not the Romanov remains. Searches for Gill, Ivanov, Romanovs, Bayesian analysis, and likelihood ratios found no passage addressing the claim in our copy. Page numbers were not provided. (LLM, conf=0.77)
Experimental — accuracy not yet measured
Nagai et al. erroneously reported that Ivanov et al. had observed a transition at nucleotide position 320 (C-T).
“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]
The cited paper’s ‘Coding Versus Control Region’ section discusses mtDNA nucleotide positions generally, but does not address the alleged transition at position 320. Searches for Nagai, Ivanov, and position 320 found no passage assessing whether Nagai misreported Ivanov’s observation. (LLM, conf=0.75)
Experimental — accuracy not yet measuredThe forensic DNA results were very conclusive in identifying the Romanov family and their servants, even though the remains of Alexei and one of his sisters were missing from the mass grave.
“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]
The supplied passages and searches for Romanov, Alexei, the mass grave, and forensic identification found no account of the remains or their identification. The cited paper’s retrieved passages concern mitochondrial DNA phylogeny and its references, so our copy does not substantiate this claim. (LLM, conf=0.76)
Experimental — accuracy not yet measuredIvanov et al. provided clear and convincing evidence that the 16,169 heteroplasmy in the tsar was authentic because Georgii had the same point heteroplasmy at a different ratio.
“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]
The paper’s ‘Coding versus Control Region’ section discusses mtDNA mutation rates and sites, but not the tsar, Georgii, or the authenticity of a 16,169 heteroplasmy. Searches for Ivanov, Georgii, and 16,169 found no passage addressing the claim; the cited paper’s authors are also not Ivanov et al. (LLM, conf=0.76)
Experimental — accuracy not yet measuredThe initial work from 1993 to 1996 was a watershed moment for DNA testing, and despite attempts to discredit these studies with contaminated data, the results have withstood the test of time throughout scientific advances.
“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]
The Introduction describes applications of mitochondrial DNA research, and the References list a 1993 study, but neither passage evaluates the 1993–1996 work as a watershed. Searches for contaminated data, attempts to discredit the studies, and whether their results endured found no passage addressing those claims in our copy. (LLM, conf=0.76)
Experimental — accuracy not yet measured
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- 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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