Haplogroup R (mtDNA)

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Haplogroup R
Haplogroup R (mtDNA) & subclades.PNG
Possible time of origin66.8±14.2 kya [1]
Possible place of origin Southeast Asia [2]
Ancestor N
Descendants R0, R1, R1b, R2'JT, R3, R5, R6'7, R8, R9, R11'B, R12'21, R14, R22, R23, R30, R31, P, U
Defining mutations12705, 16223 [3]

Haplogroup R is a widely distributed human mitochondrial DNA (mtDNA) haplogroup. Haplogroup R is associated with the peopling of Eurasia after about 70,000 years ago, and is distributed in modern populations throughout the world outside of sub-Saharan Africa. [4]

Contents

Haplogroup R is a descendant of the macro-haplogroup N. Among the R clade's descendant haplogroups are B, U (and thus K), F, R0 (and thus HV, H, and V), and JT (the ancestral haplogroup of J and T).

Origin

Soares et al. (2009) estimate the age of haplogroup R at roughly 50,000 to 70,000 years ago. [1]

This is consistent with an emergence in the course of the Coastal Migration out of East Africa to West, South and Southeast Asia. [5] It has been suggested that the early lineage of haplogroups M, N and R along the coastal route during the period of roughly 70,000 to 60,000 years ago. [6] The northern route out of Africa is another possibility, where the expansion of haplogroup R may originate from South East Asia. [7]

Haplogroup R has wide diversity and antiquity in the indigenous population of South Asia. Tribes and castes of Western and Southern India show higher diversity than the other regions, possibly suggesting their autochthonous status. [8] Larruga et al. (2017) found mtDNA R spread out to Eurasia and Australia from a core area along the Southeast Asian coast. [4]

Archaeogenetics

The Ust'-Ishim man fossil of Siberia, dated ca. 45,000 years old, belongs to haplogroup R* (formerly classified as U*). [9] [10]

Haplogroup R has also been observed among Egyptian mummies excavated at the Abusir el-Meleq archaeological site in Northern Egypt, which date from the Pre-Ptolemaic/late New Kingdom, Ptolemaic, and Roman periods. [11]

Subclade R2 was observed in the remains of a Neolithic human from western Iran in Tepe Abdul Hosein. [12]

Distribution

Haplogroup R and its descendants are distributed all over Australasia, Americas, Southeast Asia, South Asia, Central Asia, West Asia, East Asia, Europe, North Africa and Horn of Africa.

The basal R* clade is found among the Soqotri (1.2%), as well as in Northeast Africa (1.5%), the Middle East (0.8%), the Near East (0.8%), and the Arabian peninsula (0.3%). [13]

Subclades

Tree

This phylogenetic tree of haplogroup R subclades is based on the paper by Mannis van Oven and Manfred Kayser Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation [3] and subsequent published research.

Related Research Articles

<span class="mw-page-title-main">Haplogroup M (mtDNA)</span> Widespread human mitochondrial DNA grouping indicating common ancestry

Haplogroup M is a human mitochondrial DNA (mtDNA) haplogroup. An enormous haplogroup spanning all the continents, the macro-haplogroup M, like its sibling the macro-haplogroup N, is a descendant of the haplogroup L3.

Haplogroup T is a human mitochondrial DNA (mtDNA) haplogroup. It is believed to have originated around 25,100 years ago in the Near East.

Haplogroup U is a human mitochondrial DNA haplogroup (mtDNA). The clade arose from haplogroup R, likely during the early Upper Paleolithic. Its various subclades are found widely distributed across Northern and Eastern Europe, Central, Western and South Asia, as well as North Africa, the Horn of Africa, and the Canary Islands.

<span class="mw-page-title-main">Haplogroup F (mtDNA)</span> Human mitochondrial DNA haplogroup

Haplogroup F is a human mitochondrial DNA (mtDNA) haplogroup. The clade is most common in East Asia and Southeast Asia. It has not been found among Native Americans.

<span class="mw-page-title-main">Haplogroup N (mtDNA)</span> Widespread human mitochondrial DNA grouping indicating common ancestry

Haplogroup N is a human mitochondrial DNA (mtDNA) clade. A macrohaplogroup, its descendant lineages are distributed across many continents. Like its sibling macrohaplogroup M, macrohaplogroup N is a descendant of the haplogroup L3.

<span class="mw-page-title-main">Haplogroup L3</span> Widespread human mitochondrial DNA grouping indicating common ancestry

Haplogroup L3 is a human mitochondrial DNA (mtDNA) haplogroup. The clade has played a pivotal role in the early dispersal of anatomically modern humans.

Haplogroup I is a human mitochondrial DNA (mtDNA) haplogroup. It is believed to have originated about 21,000 years ago, during the Last Glacial Maximum (LGM) period in West Asia. The haplogroup is unusual in that it is now widely distributed geographically, but is common in only a few small areas of East Africa, West Asia and Europe. It is especially common among the El Molo and Rendille peoples of Kenya, various regions of Iran, the Lemko people of Slovakia, Poland and Ukraine, the island of Krk in Croatia, the department of Finistère in France and some parts of Scotland and Ireland.

Haplogroup E-M96 is a human Y-chromosome DNA haplogroup. It is one of the two main branches of the older and ancestral haplogroup DE, the other main branch being haplogroup D. The E-M96 clade is divided into two main subclades: the more common E-P147, and the less common E-M75.

In human mitochondrial genetics, Haplogroup G is a human mitochondrial DNA (mtDNA) haplogroup.

Haplogroup DE is a human Y-chromosome DNA haplogroup. It is defined by the single nucleotide polymorphism (SNP) mutations, or UEPs, M1(YAP), M145(P205), M203, P144, P153, P165, P167, P183. DE is unique because it is distributed in several geographically distinct clusters. An immediate subclade, haplogroup D, is mainly found in East Asia, parts of Central Asia, and the Andaman Islands, but also sporadically in West Africa and West Asia. The other immediate subclade, haplogroup E, is common in Africa, and to a lesser extent the Middle East and southern Europe.

<span class="mw-page-title-main">Haplogroup N1a (mtDNA)</span>

Haplogroup N1a is a human mitochondrial DNA (mtDNA) haplogroup.

<span class="mw-page-title-main">MT-ND3</span> Mitochondrial protein-coding gene whose product is involved in the respiratory chain

MT-ND3 is a gene of the mitochondrial genome coding for the NADH dehydrogenase 3 (ND3) protein. The ND3 protein is a subunit of NADH dehydrogenase (ubiquinone), which is located in the mitochondrial inner membrane and is the largest of the five complexes of the electron transport chain. Variants of MT-ND3 are associated with Mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS), Leigh's syndrome (LS) and Leber's hereditary optic neuropathy (LHON).

<span class="mw-page-title-main">Cytochrome c oxidase subunit III</span> Enzyme of the respiratory chain encoded by the mitochondrial genome

Cytochrome c oxidase subunit III (COX3) is an enzyme that in humans is encoded by the MT-CO3 gene. It is one of main transmembrane subunits of cytochrome c oxidase. It is also one of the three mitochondrial DNA (mtDNA) encoded subunits of respiratory complex IV. Variants of it have been associated with isolated myopathy, severe encephalomyopathy, Leber hereditary optic neuropathy, mitochondrial complex IV deficiency, and recurrent myoglobinuria.

<span class="mw-page-title-main">MT-CYB</span> A mitochondrial protein-coding gene whose product is involved in the respiratory chain

Cytochrome b is a protein that in humans is encoded by the MT-CYB gene. Its gene product is a subunit of the respiratory chain protein ubiquinol–cytochrome c reductase, which consists of the products of one mitochondrially encoded gene, MT-CYB, and ten nuclear genes—UQCRC1, UQCRC2, CYC1, UQCRFS1, UQCRB, "11kDa protein", UQCRH, Rieske protein presequence, "cyt c1 associated protein", and Rieske-associated protein.

In human mitochondrial genetics, Haplogroup M30 is a human mitochondrial DNA (mtDNA) haplogroup.

<span class="mw-page-title-main">Macro-haplogroup L</span> Human mitochondrial lineage

In human mitochondrial genetics, L is the mitochondrial DNA macro-haplogroup that is at the root of the anatomically modern human mtDNA phylogenetic tree. As such, it represents the most ancestral mitochondrial lineage of all currently living modern humans, also dubbed "Mitochondrial Eve".

<span class="mw-page-title-main">Genetic studies on Sinhalese</span>

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Listed here are notable ethnic groups and populations from Western Asia, Egypt and South Caucasus by human Y-chromosome DNA haplogroups based on relevant studies. The samples are taken from individuals identified with the ethnic and linguistic designations in the first two columns, the third column gives the sample size studied, and the other columns give the percentage of the particular haplogroup. Some old studies conducted in the early 2000s regarded several haplogroups as one haplogroup, e.g. I, G and sometimes J were haplogroup 2, so conversion sometimes may lead to unsubstantial frequencies below.

Y-DNA haplogroups in populations of South Asia are haplogroups of the male Y-chromosome found in South Asian populations.

In human mitochondrial genetics, haplogroup M18 is a human mitochondrial DNA (mtDNA) haplogroup. It is an India-specific lineage.

References

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  40. ↑ Haplogroup R14, Ian Logan's Mitochondrial DNA Site
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  46. ↑ Kayser, M.; Brauer, S; Cordaux, R; Casto, A; Lao, O; Zhivotovsky, LA; Moyse-Faurie, C; Rutledge, RB; Schiefenhoevel, W (2006). "Melanesian and Asian Origins of Polynesians: MtDNA and Y Chromosome Gradients Across the Pacific". Molecular Biology and Evolution. 23 (11): 2234–44. doi: 10.1093/molbev/msl093 . hdl: 11858/00-001M-0000-0010-0145-0 . PMID   16923821.
  47. ↑ Harding, Rosalind 2006, Gene tree analyses of Aboriginal Australians. Archived 2009-09-20 at the Wayback Machine University of Oxford
  48. ↑ Hudjashov, G.; Kivisild, T.; Underhill, P. A.; Endicott, P.; Sanchez, J. J.; Lin, A. A.; Shen, P.; Oefner, P.; Renfrew, C.; et al. (2007). "Revealing the prehistoric settlement of Australia by Y chromosome and mtDNA analysis". Proceedings of the National Academy of Sciences. 104 (21): 8726–30. Bibcode:2007PNAS..104.8726H. doi: 10.1073/pnas.0702928104 . JSTOR   25427741. PMC   1885570 . PMID   17496137.
  49. ↑ mtDNA Haplogroup U1a page at cagetti.com
  50. ↑ Karima Fadhlaoui-Zid; Laura Rodríguez-Botigué; Nejib Naoui; Amel Benammar-Elgaaied; Francesc Calafell; David Comas (May 2011). "Mitochondrial DNA structure in North Africa reveals a genetic discontinuity in the Nile Valley" (PDF). American Journal of Physical Anthropology. 145 (1): 107–117. doi:10.1002/ajpa.21472. hdl: 10261/42802 . PMID   21312180 . Retrieved 22 April 2016.
  51. ↑ Maca-Meyer, Nicole; González, Ana M; Pestano, José; Flores, Carlos; Larruga, José M; Cabrera, Vicente M (2003). "Mitochondrial DNA transit between West Asia and North Africa inferred from U6 phylogeography". BMC Genetics. 4: 15. doi: 10.1186/1471-2156-4-15 . PMC   270091 . PMID   14563219.
  52. ↑ Mohamed, Hisham Yousif Hassan. "Genetic Patterns of Y-chromosome and Mitochondrial DNA Variation, with Implications to the Peopling of the Sudan" (PDF). University of Khartoum. Retrieved 22 April 2016.
  53. ↑ Bernard Secher; Rosa Fregel; José M Larruga; Vicente M Cabrera; Phillip Endicott; José J Pestano; Ana M González (2014). "The history of the North African mitochondrial DNA haplogroup U6 gene flow into the African, Eurasian and American continents". BMC Evolutionary Biology. 14 (1): 109. Bibcode:2014BMCEE..14..109S. doi: 10.1186/1471-2148-14-109 . PMC   4062890 . PMID   24885141.
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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
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