Haplogroup J (Y-DNA)

Haplogroup J-M304
Possible time of origin	42900 years before present[1]
Possible place of origin	West Asia
Ancestor	IJ
Descendants	J-M267, J-M172
Defining mutations	M304/Page16/PF4609, 12f2.1

Haplogroup J-M304 ^{[Phylogenetics 1]} is a Y-chromosome DNA haplogroup. It is thought that J-M304 evolved in West Asia (a region known also as the Middle East or Near East).^[2] It expanded from there during the Neolithic Age, especially into North Africa, the Caucasus, Southeast Europe, Central Asia, Iran, Pakistan and western India.

J-M304 is divided into two main subclades (branches) J-M267 and J-M172.

Origins

Haplogroup J-M304is believed to have arisen roughly 42,900 years ago in West Asia (31,700±12,800 years ago according to Semino 2004). It is most closely related to Haplogroup I-M170, as both Haplogroup I-M170 and Haplogroup J-M304 are Haplogroup IJ subclades. Haplogroup IJ and haplogroup K derive from Haplogroup IJK, and only at this level of classification does haplogroup IJK join with Haplogroup G and Haplogroup H as immediate descendants of Haplogroup F. J-M304 is defined by the M304 genetic marker, or the equivalent 12f2.1 marker. According to a genetic study in China by Shou et al., J*-M304 is found among Xibo, Kazakh, Dongxiang and Uzbek people in Northwest China.^[3] The main current subgroups J-M267 and J-M172, which now comprise between them almost all of the population of the haplogroup, are both believed to have arisen very early, at least 10,000 years ago. Nonetheless, Y-chromosomes F-M89* and IJ-M429* were reported to have been observed in the Iranian plateau (Grugni et al. 2012).

On the other hand, it would seem to be that different episodes of populace movement had impacted southeast Europe, as well as the role of the Balkans as a long-standing corridor to Europe from the Near East is shown by the phylogenetic unification of Hgs I and J by the basal M429 mutation. This proof of common ancestry suggests that ancestral Hgs IJ-M429* probably would have entered Europe through the Balkan track sometime before the LGM. They then subsequently split into Hg J and Hg I in Middle East and Europe in a typical disjunctive phylogeographic pattern. Such a geographic hall is prone to have encountered extra consequent gene streams, including the horticultural settlers. Moreover, the unification of haplogroups IJK creates evolutionary distance from F–H delegates, as well as supporting the inference that both IJ-M429 and KT-M9 arose closer to the Middle East than central or eastern Asia.

Distribution

Haplogroup J-M304 is found in greatest concentration in Southwestern Arabian Peninsula. Outside of this region, haplogroup J-M304 has a presence in North Africa. It also has a moderate presence in Southern Europe (especially in central and southern Italy, Malta, Greece, and Albania), Central Asia, and South Asia, particularly in the form of its subclade J-M172. Haplogroup J-M304 is also found in north East Africa, particularly in the form of its J-M267 subclade. The J-M410 subclade is found mostly in Greece, Anatolia, and southern Italy.

Subclade distribution

J-M304*

Paragroup J-M304*^{[Phylogenetics 2]} includes all of J-M304 except for J-M267, J-M172 and their subclades. J-M304* is rarely found outside of the island of Socotra, off the coast of Yemen, where it is quite frequent at 71.4%.^[5] Haplogroup J-M304* also has been found with lower frequency in Oman (Giacomo 2004), Ashkenazi Jews,^[6] Saudi Arabia (Abu-Amero 2009), Greece (Giacomo 2004), the Czech Republic (Giacomo 2004 and Luca 2007), Uygurs ^[7] and several Turkic peoples.^[8] (Cinnioglu 2004 and Varzari 2006).

The following gives a summary of most of the studies which specifically tested for J-M267 and J-M172, showing its distribution in Europe, North Africa, the Middle East and Central Asia.

J-M267

Haplogroup J-M267^{[Phylogenetics 3]} defined by the M267 SNP is in modern times most frequent in the Arabian Peninsula: Yemen (up to 76%),^[9] Saudi (up to 64%) (Alshamali 2009), Qatar (58%),^[10] and Dagestan (up to 56%).^[11] J-M267 is generally frequent among Arab Bedouins (62%),^[12] Ashkenazi Jews (20%) (Semino 2004), Algeria (up to 35%) (Semino 2004), Iraq (up to 33%) (Semino 2004), Tunisia (up to 31%),^[13] Syria (up to 30%), Egypt (up to 20%) (Luis 2004), and the Sinai Peninsula. To some extent, the frequency of Haplogroup J-M267 collapses at the borders of Arabic/Semitic speaking territories with mainly non-Arabic/Semitic speaking territories, such as Turkey (9%), Iran (5%), Sunni Iraqi Biradari of North India (38%) and Northern Indian Shia (11%) (Eaaswarkhanth 2009). However, it should be noted that some figures above tend to be the larger ones obtained in some studies, while the smaller figures obtained in other studies are omitted. It is also highly frequent among Jews, especially the Kohanim line (46%) (Hammer 2009).

ISOGG states that J-M267 originated in the Middle East. It is found in parts of the Near East, Anatolia and North Africa, with a much sparser distribution in the southern Mediterranean flank of Europe, and in Ethiopia. But not all studies agree on the point of origin. The Levant has been proposed but a 2010 study concluded that the haplogroup had a more northern origin, possibly Asia Minor.

The origin of the J-P58 subclade is likely in the more northerly populations and then spreads southward into the Arabian Peninsula. The high Y-STR variance of J-P58 in ethnic groups in Turkey, as well as northern regions in Syria and Iraq, supports the inference of an origin of J-P58 in nearby eastern Anatolia. Moreover, the network analysis of J-P58 haplotypes shows that some of the populations with low diversity, such as Bedouins from Israel, Qatar, Sudan and UAE, are tightly clustered near high-frequency haplotypes suggesting founder effects with star burst expansion into the Arabian Desert (Chiaroni 2010).

J-M172

Haplogroup J-M172^{[Phylogenetics 4]} is found in the highest concentrations in the Caucasus and the Fertile Crescent/Iraq and is found throughout the Mediterranean (including the Italian, Balkan, Anatolian and Iberian peninsulas and North Africa) (Giacomo 2003).

The highest ever reported concentration of J-M172 was 72% in Northeastern Georgia (Nasidze 2004). Other high reports include Ingush 32% (Nasidze 2004), Cypriots 30-37% (Capelli 2005), Lebanese 30% (Wells et al. 2001), Assyrian, Mandean and Arab Iraqis 29.7% (Sanchez et al. 2005), Syrians and Syriacs 22.5%, Kurds 24%-28%, Iranians 23% (Aburto 2006), Ashkenazi Jews 24%, Palestinian Arabs 16.8%-25%, Sephardic Jews 29% and North Indian Shia Muslim 18%, Chechens 26%, Balkars 24%, Yaghnobis 32%, Armenians 21-24%, and Azerbaijanis 24%-48%.

Some J-M172 haplotypes (as well as some J-M267 ones) belong to the "Cohen Modal Haplotype".

In South Asia, J2-M172 was found to be significantly higher among Dravidian castes at 19% than among Indo-European castes at 11%. J2-M172 and J-M410 is found 21% among Dravidian middle castes, followed by upper castes, 18.6%, and lower castes 14%. (Sengupta 2006)^[14] Subclades of M172 such as M67 and M92 were not found in either Indian or Pakistani samples which also might hint at a partial common origin.(Sengupta 2006)^[14]

Phylogenetics

In Y-chromosome phylogenetics, subclades are the branches of haplogroups. These subclades are also defined by single nucleotide polymorphisms (SNPs) or unique event polymorphisms (UEPs).

Phylogenetic history

Prior to 2002, there were in academic literature at least seven naming systems for the Y-Chromosome Phylogenetic tree. This led to considerable confusion. In 2002, the major research groups came together and formed the Y-Chromosome Consortium (YCC). They published a joint paper that created a single new tree that all agreed to use. Later, a group of citizen scientists with an interest in population genetics and genetic genealogy formed a working group to create an amateur tree aiming at being above all timely. The table below brings together all of these works at the point of the landmark 2002 YCC Tree. This allows a researcher reviewing older published literature to quickly move between nomenclatures.

Research publications

The following research teams per their publications were represented in the creation of the YCC tree.

Phylogenetic trees

There are several confirmed and proposed phylogenetic trees available for haplogroup J-M304. The scientifically accepted one is the Y-Chromosome Consortium (YCC) one published in Karafet 2008 and subsequently updated. A draft tree that shows emerging science is provided by Thomas Krahn at the Genomic Research Center in Houston, Texas. The International Society of Genetic Genealogy (ISOGG) also provides an amateur tree.

The Genomic Research Center draft tree

This is Thomas Krahn at the Genomic Research Center's Draft tree Proposed Tree for haplogroup J-P209 (Krahn & FTDNA 2013). For brevity, only the first three levels of subclades are shown.

• J-M304 12f2a, 12f2.1, M304, P209, L60, L134
  • M267, L255, L321, L765, L814, L827, L1030
    • M62
    • M365.1
    • L136, L572, L620
      • M390
      • P56
      • P58, L815, L828
      • L256
    • Z1828, Z1829, Z1832, Z1833, Z1834, Z1836, Z1839, Z1840, Z1841, Z1843, Z1844
      • Z1842
      • L972
  • M172, L228
    • M410, L152, L212, L505, L532, L559
      • M289
      • L26, L27, L927
      • L581
    • M12, M102, M221, M314, L282
      • M205
      • M241

The Y-Chromosome Consortium tree

This is the official scientific tree produced by the Y-Chromosome Consortium (YCC). The last major update was in 2008 (Karafet 2008). Subsequent updates have been quarterly and biannual. The current version is a revision of the 2010 update.^[15]

See also

Genetics

Y-DNA J subclades

References

Works Cited

Journals

• Y Chromosome Consortium "YCC" (2002). "A Nomenclature System for the Tree of Human Y-Chromosomal Binary Haplogroups". Genome Research 12 (2): 339–48. doi:10.1101/gr.217602. PMC 155271. PMID 11827954. 

• Abu-Amero, Khaled K; Hellani, Ali; González, Ana M; Larruga, Jose M; Cabrera, Vicente M; Underhill, Peter A (2009). "Saudi Arabian Y-Chromosome diversity and its relationship with nearby regions". BMC Genetics 10: 59. doi:10.1186/1471-2156-10-59. PMC 2759955. PMID 19772609. 

• Alshamali, Farida; Pereira, LuÍsa; Budowle, Bruce; Poloni, Estella S.; Currat, Mathias (2009). "Local Population Structure in Arabian Peninsula Revealed by Y-STR diversity". Human Heredity 68 (1): 45–54. doi:10.1159/000210448. PMID 19339785. 

• Chiaroni, Jacques; King, Roy J; Myres, Natalie M; Henn, Brenna M; Ducourneau, Axel; Mitchell, Michael J; Boetsch, Gilles; Sheikha, Issa; et al. (2009). "The emergence of Y-chromosome haplogroup J1e among Arabic-speaking populations". European Journal of Human Genetics 18 (3): 348–53. doi:10.1038/ejhg.2009.166. PMC 2987219. PMID 19826455. 

• Chiaroni, Jacques; King, Roy J; Myres, Natalie M; Henn, Brenna M; Ducourneau, Axel; Mitchell, Michael J; Boetsch, Gilles; Sheikha, Issa; et al. (2010). "The emergence of Y-chromosome haplogroup J1e among Arabic-speaking populations". European Journal of Human Genetics 18 (3): 348–53. doi:10.1038/ejhg.2009.166. PMC 2987219. PMID 19826455. 

• Cinnioglu, Cengiz; King, Roy; Kivisild, Toomas; Kalfoglu, Ersi; Atasoy, Sevil; Cavalleri, Gianpiero L.; Lillie, Anita S.; Roseman, Charles C.; et al. (2004). "Excavating Y-chromosome haplotype strata in Anatolia". Human Genetics 114 (2): 127–48. doi:10.1007/s00439-003-1031-4. PMID 14586639. 

• Di Giacomo, F.; Luca, F.; Anagnou, N.; Ciavarella, G.; Corbo, R.M.; Cresta, M.; Cucci, F.; Di Stasi, L.; et al. (2003). "Clinal patterns of human Y chromosomal diversity in continental Italy and Greece are dominated by drift and founder effects". Molecular Phylogenetics and Evolution 28 (3): 387–95. doi:10.1016/S1055-7903(03)00016-2. PMID 12927125. 

• Di Giacomo, F.; Luca, F.; Popa, L. O.; Akar, N.; Anagnou, N.; Banyko, J.; Brdicka, R.; Barbujani, G.; et al. (2004). "Y chromosomal haplogroup J as a signature of the post-neolithic colonization of Europe". Human Genetics 115 (5): 357–71. doi:10.1007/s00439-004-1168-9. PMID 15322918. 

• Hammer, Michael F.; Behar, Doron M.; Karafet, Tatiana M.; Mendez, Fernando L.; Hallmark, Brian; Erez, Tamar; Zhivotovsky, Lev A.; Rosset, Saharon; Skorecki, Karl (2009). "Extended Y chromosome haplotypes resolve multiple and unique lineages of the Jewish priesthood". Human Genetics 126 (5): 707–17. doi:10.1007/s00439-009-0727-5. PMC 2771134. PMID 19669163. 

• Jobling, Mark A.; Tyler-Smith, Chris (2000). "New uses for new haplotypes". Trends in Genetics 16 (8): 356–62. doi:10.1016/S0168-9525(00)02057-6. PMID 10904265. 

• Karafet, T. M.; Mendez, F. L.; Meilerman, M. B.; Underhill, P. A.; Zegura, S. L.; Hammer, M. F. (2008). "New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree". Genome Research 18 (5): 830–8. doi:10.1101/gr.7172008. PMC 2336805. PMID 18385274. 

• Luca, F.; Di Giacomo, F.; Benincasa, T.; Popa, L.O.; Banyko, J.; Kracmarova, A.; Malaspina, P.; Novelletto, A.; Brdicka, R. (2007). "Y-chromosomal variation in the Czech Republic". American Journal of Physical Anthropology 132 (1): 132–9. doi:10.1002/ajpa.20500. PMID 17078035. 

• Luis, J; Rowold, D; Regueiro, M; Caeiro, B; Cinnioglu, C; Roseman, C; Underhill, P; Cavallisforza, L; Herrera, R (2004). "The Levant versus the Horn of Africa: Evidence for Bidirectional Corridors of Human Migrations". The American Journal of Human Genetics 74 (3): 532–44. doi:10.1086/382286. PMC 1182266. PMID 14973781. 

• Mirabal S; Varljen T; Gayden T; et al. (July 2010). "Human Y-chromosome short tandem repeats: A tale of acculturation and migrations as mechanisms for the diffusion of agriculture in the Balkan Peninsula". American Journal of Physical Anthropology 142 (3): 380–390. doi:10.1002/ajpa.21235. PMID 20091845. 

• Nasidze, I.; Ling, E. Y. S.; Quinque, D.; Dupanloup, I.; Cordaux, R.; Rychkov, S.; Naumova, O.; Zhukova, O.; et al. (2004). "Mitochondrial DNA and Y-Chromosome Variation in the Caucasus". Annals of Human Genetics 68 (3): 205–21. doi:10.1046/j.1529-8817.2004.00092.x. PMID 15180701. 

• Pericić M, Lauc LB, Klarić IM, et al. (October 2005). "High-resolution phylogenetic analysis of southeastern Europe traces major episodes of paternal gene flow among Slavic populations". Mol. Biol. Evol. 22 (10): 1964–75. doi:10.1093/molbev/msi185. PMID 15944443. 

• Shen, Peidong; Lavi, Tal; Kivisild, Toomas; Chou, Vivian; Sengun, Deniz; Gefel, Dov; Shpirer, Issac; Woolf, Eilon; et al. (2004). "Reconstruction of patrilineages and matrilineages of Samaritans and other Israeli populations from Y-Chromosome and mitochondrial DNA sequence Variation". Human Mutation 24 (3): 248–60. doi:10.1002/humu.20077. PMID 15300852. 

Thesis and Dissertations

• Varzari, Alexander (2006). Population History of the Dniester-Carpathians: Evidence from Alu Insertion and Y-Chromosome Polymorphisms (PDF) (Thesis). München, University. OCLC 180859661. 

Blogs

• Dienekes (2009). "Middle Eastern and Sub-Saharan lineages in Indian Muslim populations". 

Mailing Lists

• Aburto, Alfred A (2006). "Y haplogroup J in Iran" (Mailing list). Retrieved 3 January 2013. 

Further reading

• yJdb: the Y-haplogroup J database haplotypes of haplogroup J.
• Haplogroup J subclades at International Society of Genetic Genealogy
• Nebel et al. 2001, see Modal Haplotypes of "J1" (as Eu10)
• Sanchez, Juan J; Hallenberg, Charlotte; Børsting, Claus; Hernandez, Alexis; Gorlin, RJ (2005). "High frequencies of Y chromosome lineages characterized by E3b1, DYS19-11, DYS392-12 in Somali males". European Journal of Human Genetics 13 (7): 856–66. doi:10.1038/sj.ejhg.5201390. PMID 15756297. 
• Sengupta S, Zhivotovsky LA, King R, et al. (February 2006). "Polarity and temporality of high-resolution y-chromosome distributions in India identify both indigenous and exogenous expansions and reveal minor genetic influence of Central Asian pastoralists". Am. J. Hum. Genet. 78 (2): 202–21. doi:10.1086/499411. PMC 1380230. PMID 16400607. 

Phylogenetic Notes

External links

Phylogenetic tree and Distribution Maps of Y-DNA haplogroup J

• Y-DNA Haplogroup J and Its Subclades from ISOGG 2009

Other

• Youtube Haplogroup J2 Channel
• Spread of Haplogroup J, from National Geographic
• British Isles DNA Project