Haplogroup J (mtDNA)

Haplogroup J is a human mitochondrial DNA (mtDNA) haplogroup. The clade derives from the haplogroup JT, which also gave rise to haplogroup T. In his book The Seven Daughters of Eve, Bryan Sykes named the originator of this mtDNA haplogroup Jasmine. Within the field of medical genetics, certain polymorphisms specific to haplogroup J have been associated with Leber's hereditary optic neuropathy.[2]

This article is about the human mtDNA haplogroup. For the human Y-DNA haplogroup, see Haplogroup J (Y-DNA).
Haplogroup J
Possible time of origin45,000 years before present
Possible place of originWestern Asia
AncestorJT
DescendantsJ1, J2
Defining mutations295 489 10398 12612 13708 16069[1]

Origin

Around 45,000 years before present, a mutation took place in the DNA of a woman who lived in the Near East or Caucasus. Further mutations occurred in the J line, which can be identified as the subclades J1a1, J1c1 (27,000 yrs ago), J2a (19,000 yrs ago), J2b2 (16,000 years ago), and J2b3 (5,800 yrs ago). Haplogroup J bearers along with persons carrying the T mtDNA clade settled in Europe from the Near East during the late Paleolithic and Mesolithic.

Coalescence time estimates for the subclades of mitochondrial haplogroup J
SubcladeEuropean coalescence time[2]Near East coalescence time[2]
J1a127,300 years (± 8,000 years)17,700 years (± 2,500 years)
J1a27,700 years (± 3,500 years)—
J1b5,000 years (± 2,200 years)23,300 years (± 4,300 years)
J2a19,200 years(± 6,900 years)—
J2b1—15,000 years (± 5,000 years)
J2b216,600* years (± 8,100 years)16,000 years (± 5,700 years)
J2b35,800 years (± 2,900 years)—

*Typographical error, was 161,600 years from original source material as per time table describing the spread of populations given in the same study.

However, any statements concerning the geographic origin of this or any other haplogroup are highly speculative and considered by most population geneticists to be 'story telling' and outside the domain of science. Furthermore, inferring close associations between a haplogroup and a specific archaeological culture can be equally problematic.

Age of younger branches of mtHG J
Subclade Alphanumeric assignationCalculated age via empirical spread and mutational drift rate ratio[3]
CI=95%
J228,259.7 ± 4,605.0 (Between 23,700 and 32,900 years old)
J2a24,051.5 ± 4,183.2 (Between 19,900 and 28,200 years old)
J2a121,186.1 ± 4,485.5 (Between 16,700 and 25,700 years old)
J2a1a12,986.1 ± 4,077.7 (Between 8,900 and 17,100 years old)
J2a1a18,949.8 ± 3,051.3 (Between 5,900 and 12,000 years old)
J2a1a1a7,591.6 ± 2,889.6 (Between 4,700 and 10,500 years old)
J2a1a1a23,618.9 ± 2,973.9 (Between 600 and 6,600 years old)

Distribution
Projected spatial frequency distribution for haplogroup J.

Basal haplogroup J* is found among the Soqotri (9.2%).[4]

Haplogroup J occurs in approximately 12% of native European populations.[5][6]

The average frequency of haplogroup J as a whole is today highest in the Near East (12%), followed by Europe (11%), the Caucasus (8%) and Northeast Africa (6%). Of the two main sub-groups, J1 takes up four-fifths of the total and is spread widely on the continent while J2 is more localised around the Mediterranean, Greece, Italy/Sardinia and Spain.

There is also limited evidence that the subclade J1 has long been present in Central Asia. For instance, perhaps the highest incidence of haplogroup J is the 19% of Polish Roma, who belong to J1 (although this has also been ascribed to a "founder effect" of some kind).[7] In Pakistan, where West Eurasian lineages occur at frequencies of up to 50% in some ethno-linguistic groups, the incidence of J1 averages around 5%, while J2 is very rare. However, J2 is found amongst 9% of the Kalash minority of north-west Pakistan.[8]

In the Arabian peninsula, mtDNA haplogroup J is found among Saudis (10.5–18.8% J1b) and Yemenis (0–20% J1b). The J1b subclade also occurs in the Near East among Iraqis (7.1%) and Palestinians (4%).[9]

In Africa, haplogroup J is concentrated in the northeast. It is found among Algerians (3.23–14.52%),[10] as well as Sudanese Copts (10.3% J1a; 10.3% J2),[11] Sudanese Fulani (10.7% J1b),[11] Meseria (6.7% J1b),[11] Arakien (5.9% J1b),[11] Egyptians (5.9%),[12] Mozabite Berbers (3.53%),[10] Sudanese Hausa (2.9% J1b),[11] Zenata Berbers (2.74%),[10] Beja (2.1% J1b),[11] and Reguibate Sahrawi (0.93%).[10]

Within Europe, >2% frequency distribution of mtDNA J is as follows:[13]

  • J* = Ireland — 12%, England-Wales — 11%, Scotland — 9%, Orkney — 8%, Germany — 7%, Russia (European) — 7%, Iceland — 7%, Austria-Switzerland — 5%, Finland-Estonia — 5%, Spain-Portugal — 4%, France-Italy — 3%
  • J1a = Austria-Switzerland — 3%
  • J1b1 = Scotland — 4%
  • J2 = France-Italy — 2%
  • J2a = Homogenously spread in Europe; absent in the nations around the Caucasus; not known to be found elsewhere.[2]
  • J2b1 = Virtually absent in Europe; found in diverse forms in the Near East.[2]
  • J2b1a = Found in Western Europe and Russia.[2]

Haplogroup J has also been found among ancient Egyptian mummies excavated at the Abusir el-Meleq archaeological site in Middle Egypt, which date from the Pre-Ptolemaic/late New Kingdom, Ptolemaic, and Roman periods.[14] Haplogroup J has been observed in ancient Guanche fossils excavated in Gran Canaria and Tenerife on the Canary Islands, which have been dardiocarbon-dated to between the 7th and 11th centuries CE. All of the clade-bearing individuals were inhumed at the Tenerife site, with one specimen found to belong to the J1c3 subclade (1/7; ~14%).[15] The J clade has also been found among Iberomaurusian specimens dating from the Epipaleolithic at the Afalou prehistoric site. Around 22% of the observed haplotypes belonged to various J subclades, including undifferentiated J (1/9; 11%) and J1c3f (1/9; 11%).[16]

In Eastern Siberia, haplogroup J1c5 has been observed in samples of Yakuts (3/111 = 2.7% Vilyuy Yakut,[17] 2/148 = 1.4% Northern Yakut,[17] 1/88 = 1.1% Central Yakut,[18] 1/164 = 0.6% Central Yakut[17]), Evenks in Yakutia (4/125 = 3.2%[17]), and Evens in Yakutia (1/105 = 1.0%[17]). Haplogroup J2a2b3 has been observed in a sample of Nyukzha Evenks (2/46 = 4.3%[18]). Haplogroup J2 also has been observed in a sample of Evenks collected in Olenyoksky District, Zhigansky District, and Ust-Maysky District of Yakutia (7/125 = 5.6%[17]). One instance of haplogroup J1c10a1 has been observed in the Human Genome Diversity Project's sample of ten Oroqen individuals from northernmost China.

Subclades
Schematic tree of mtDNA haplogroup J. Ages (in ka) indicated are maximum likelihood estimates obtained for the whole-mtDNA genome.

Tree

This phylogenetic tree of haplogroup J subclades is based on the paper by Mannis van Oven and Manfred Kayser Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation[1] and subsequent published research.

Genetic traits

It has been theorized that the uncoupling of oxidative phosphorylation related to SNPs which define mt-haplogroup J consequently produces higher body heat in the phenotype of mtDNA J individuals. This has been linked to selective pressure for the presence of the haplogroup in northern Europe, particularly Norway.[19] Individuals from haplogroups Uk, J1c and J2 were found to be more susceptible to Leber's hereditary optic neuropathy because they have reduced oxidative phosphorylation capacity, which results in part from lower mtDNA levels.[20] J mtDNA has also been associated with HIV infected individuals displaying accelerated progression to AIDS and death.[21] The T150C mutation, which is exclusive to but not definitive of, the J2 subclade of Haplogroup J may be part of a likely nuclearly controlled general machinery regarding the remodeling & replication of mtDNA. Controlling a remodeling which could accelerate mtDNA replication thus compensating for oxidative damage in mtDNA as well as functional deterioration occurring with old age related to it.[22] Haplogroup J was found to be a protective factor against ischemic cardiomyopathy.[23] It was also found that Haplogroup J was a protective factor among osteoarthritis patients from Spain[24] but not from UK,[25] and this was hypothesized to be due to a different genetic composition (polymorphisms) of the Haplogroup J in both populations. A study involving patients of European and West Asian origin or descent showed that individuals classified as haplogroup J or K demonstrated a significant decrease in risk of Parkinson's disease versus individuals carrying the most common haplogroup, H.[26]

gollark: I'm getting around your contracarcinization daemons by setting up ARMv5 VMs, of course.
gollark: Hmm. This needs "talloc" to build. I wonder what "talloc" is.
gollark: Time to execute exotic side-channel attacks!
gollark: I can read 5.3GB.
gollark: I'll check.

See also

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

References
  1. van Oven, Mannis; Manfred Kayser (13 Oct 2008). "Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation". Human Mutation. 30 (2): E386–94. doi:10.1002/humu.20921. PMID 18853457. Archived from the original on 4 December 2012.
  2. Piia Serk, Human Mitochondrial DNA Haplogroup J in Europe and Near East, Thesis, Tartu 2004 Archived 2008-09-08 at the Wayback Machine
  3. A “Copernican” reassessment of the human mitochondrial DNA tree from its root Behar, D.M., van Oven, M., Rosset, S., Metspalu, M., Loogväli, E.L., Silva, N.M., Kivisild, T., Torroni, A. and Villems, R., American Journal of Human Genetics, Vol. 90(4), pg. 675-684, 2012
  4. Černý, Viktor; et al. (2009). "Out of Arabia—the settlement of island Soqotra as revealed by mitochondrial and Y chromosome genetic diversity" (PDF). American Journal of Physical Anthropology. 138 (4): 439–447. doi:10.1002/ajpa.20960. PMID 19012329. Archived from the original (PDF) on 6 October 2016. Retrieved 13 June 2016.
  5. Bryan Sykes (2001). The Seven Daughters of Eve. London; New York: Bantam Press. ISBN 978-0393020182.
  6. "Maternal Ancestry". Oxford Ancestors. Archived from the original on 15 July 2017. Retrieved 7 February 2013.
  7. B.A. Malyarchuk, T. Grzybowski, M.V. Derenko, J. Czarny, and D. Miścicka-Śliwka, Mitochondrial DNA diversity in the Polish Roma, Annals of Human Genetics, vol. 70 (2006), pp. 195-206.
  8. Lluís Quintana-Murci, Raphaëlle Chaix, R. Spencer Wells, Doron M. Behar, Hamid Sayar, Rosaria Scozzari, Chiara Rengo, Nadia Al-Zahery, Ornella Semino, A. Silvana Santachiara-Benerecetti, Alfredo Coppa, Qasim Ayub, Aisha Mohyuddin, Chris Tyler-Smith, S. Qasim Mehdi, Antonio Torroni, and Ken McElreavey, Where west meets east: the complex mtDNA landscape of the southwest and Central Asian corridor, American Journal of Human Genetics, vol. 74 (2004), pp. 827–845.
  9. Non, Amy. "ANALYSES OF GENETIC DATA WITHIN AN INTERDISCIPLINARY FRAMEWORK TO INVESTIGATE RECENT HUMAN EVOLUTIONARY HISTORY AND COMPLEX DISEASE" (PDF). University of Florida. Retrieved 22 April 2016.
  10. Asmahan Bekada; Lara R. Arauna; Tahria Deba; Francesc Calafell; Soraya Benhamamouch; David Comas (September 24, 2015). "Genetic Heterogeneity in Algerian Human Populations". PLOS ONE. 10 (9): e0138453. doi:10.1371/journal.pone.0138453. PMC 4581715. PMID 26402429.; S5 Table
  11. 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.
  12. A. Stevanovitch; A. Gilles; E. Bouzaid; R. Kefi; F. Paris; R. P. Gayraud; J. L. Spadoni; F. El-Chenawi; E. Béraud-Colomb (January 2004). "Mitochondrial DNA Sequence Diversity in a Sedentary Population from Egypt". Annals of Human Genetics. 68 (1): 23–39. doi:10.1046/j.1529-8817.2003.00057.x. PMID 14748828.
  13. Lucia Simoni, Francesc Calafell, Davide Pettener, Jaume Bertranpetit, and Guido Barbujani, Geographic Patterns of mtDNA Diversity in Europe, American Journal of Human Genetics, vol. 66 (2000), pp. 262–278.
  14. Schuenemann, Verena J.; et al. (2017). "Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods". Nature Communications. 8: 15694. doi:10.1038/ncomms15694. PMC 5459999. PMID 28556824.
  15. Rodrı́guez-Varela; et al. (2017). "Genomic Analyses of Pre-European Conquest Human Remains from the Canary Islands Reveal Close Affinity to Modern North Africans". Current Biology. 27 (1–7): 3396–3402.e5. doi:10.1016/j.cub.2017.09.059. PMID 29107554. Retrieved 29 October 2017.
  16. Kefi, Rym; et al. (2018). "On the origin of Iberomaurusians: new data based on ancient mitochondrial DNA and phylogenetic analysis of Afalou and Taforalt populations". Mitochondrial DNA Part A. 29 (1): 147–157. doi:10.1080/24701394.2016.1258406. PMID 28034339. Retrieved 17 November 2017.
  17. Sardana A Fedorova, Maere Reidla, Ene Metspalu, et al., "Autosomal and uniparental portraits of the native populations of Sakha (Yakutia): implications for the peopling of Northeast Eurasia." BMC Evolutionary Biology 2013, 13:127. http://www.biomedcentral.com/1471-2148/13/127
  18. Duggan AT, Whitten M, Wiebe V, Crawford M, Butthof A, et al. (2013), "Investigating the Prehistory of Tungusic Peoples of Siberia and the Amur-Ussuri Region with Complete mtDNA Genome Sequences and Y-chromosomal Markers." PLoS ONE 8(12): e83570. doi:10.1371/journal.pone.0083570
  19. Different genetic components in the Norwegian population revealed by the analysis of mtDNA & Y chromosome polymorphisms Archived 2011-09-27 at the Wayback Machine
  20. Gómez-Durán, Aurora; Pacheu-Grau, David; Martínez-Romero, Íñigo; López-Gallardo, Ester; López-Pérez, Manuel J.; Montoya, Julio; Ruiz-Pesini, Eduardo (2012). "Oxidative phosphorylation differences between mitochondrial DNA haplogroups modify the risk of Leber's hereditary optic neuropathy". Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease. 1822 (8): 1216–1222. doi:10.1016/j.bbadis.2012.04.014. ISSN 0925-4439. PMID 22561905.
  21. Hendrickson SL, Hutcheson HB, Ruiz-Pesini E, et al. (November 2008). "Mitochondrial DNA haplogroups influence AIDS progression". AIDS. 22 (18): 2429–39. doi:10.1097/QAD.0b013e32831940bb. PMC 2699618. PMID 19005266.
  22. A Comprehensive Analysis of mtDNA Haplogroup J (Jim Logan. September, 2008)
  23. Fernández-Caggiano, Maria; Javier Barallobre-Barreiro; Ignacio Rego-Pérez; María G. Crespo-Leiro; María Jesus Paniagua; Zulaika Grillé; Francisco J. Blanco; Nieves Doménech (2012). "Mitochondrial Haplogroups H and J: Risk and Protective Factors for Ischemic Cardiomyopathy". PLOS ONE. 7 (8): e44128. doi:10.1371/journal.pone.0044128. PMC 3429437. PMID 22937160.
  24. Rego, I; Fernandez-Moreno, M; Fernandez-Lopez, C; Gomez-Reino, J J; Gonzalez, A; Arenas, J; Blanco, F J (2009). "Role of European mitochondrial DNA haplogroups in the prevalence of hip osteoarthritis in Galicia, Northern Spain". Annals of the Rheumatic Diseases. 69 (1): 210–213. doi:10.1136/ard.2008.105254. ISSN 0003-4967. PMID 19224903.
  25. Soto-Hermida, A.; Fernández-Moreno, M.; Oreiro, N.; Fernández-López, C.; Rego-Pérez, I.; Blanco, F.J. (2014). "mtDNA haplogroups and osteoarthritis in different geographic populations". Mitochondrion. 15: 18–23. doi:10.1016/j.mito.2014.03.001. ISSN 1567-7249. PMID 24632472.
  26. van der Walt, Joelle M.; Nicodemus, Kristin K.; Martin, Eden R.; Scott, William K.; Nance, Martha A.; Watts, Ray L.; Hubble, Jean P.; Haines, Jonathan L.; Koller, William C.; Lyons, Kelly; Pahwa, Rajesh; Stern, Matthew B.; Colcher, Amy; Hiner, Bradley C.; Jankovic, Joseph; Ondo, William G.; Allen Jr., Fred H.; Goetz, Christopher G.; Small, Gary W.; Mastaglia, Frank; Stajich, Jeffrey M.; McLaurin, Adam C.; Middleton, Lefkos T.; Scott, Burton L.; Schmechel, Donald E.; Pericak-Vance, Margaret A.; Vance, Jeffery M. (2003). "Mitochondrial Polymorphisms Significantly Reduce the Risk of Parkinson Disease". The American Journal of Human Genetics. 72 (4): 804–811. doi:10.1086/373937. ISSN 0002-9297. PMC 1180345. PMID 12618962.
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