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In human genetics Haplogroup Q1a3a is a Y-chromosome DNA haplogroup (Y-DNA). Haplogroup Q1a3a' is a subclade of haplogroup Q. Haplogroup Q1a3a was previously known as haplogroup Q3. In 1996 Dr. Peter Underhill and his colleagues at Stanford Universitymarker first discovered the indigenous American clade or single nucleotide polymorphism (SNP) that was to become known as M3 (Q1a3aM3). Later studies completed the genetic bridge by determining that Q1a3a-M3 was related Q-M242-bearing populations found predominately in Central Asia. Within the parent Q clade, there is 13 haplogroups marked by 17 SNPs.

The "male" Y chromosome is one of the two sex chromosomes in humans. The Y chromosome spans about 58 million base pairs (the building blocks of DNA) and represents about 2 percent of the total DNA in all human cells. The Y chromosome differs from Human mitochondrial DNA haplogroups (mtDNA) in that the majority of the Y chromosome is unique and does not recombine during meiosis. Meaning the historical pattern of mutations can easily be studied.

Indigenous American subclade Q1a3a (Q3)

Haplogroup Q1a3aM3 is a Y Chromosome subclade haplo generally associated with the Indigenous peoples of the Americas. This haplogroup is defined by the presence of the rs3894 (Q1a3a-M3) single nucleotide polymorphism (SNP). The Q1a3a-M3 SNP is found "downstream" from the Q-M242 (SNP). Q-M242 is the defining (father-clade) single nucleotide polymorphism of the Q haplogroup.

The Q1a3a-M3 mutation is on the Q lineage roughly 10,000 to 15,000 years ago, as the migration throwout the Americas was underway by the early Paleo-Indians. The micro-satellite diversity and distribution of a Y lineage specific to South America "Q-M19" indicates that certain Amerind populations have been isolated since the initial colonization of the region approximately 5,000 to 10,000 years ago. The Na-Dené, Inuit and Indigenous Alaskan populations are distinct from other indigenous Americans. This suggests that the earliest migrants into the northern extremes of North America and Greenlandmarker derived from a much later populations along the Bering sea coast linemarker. This dates are in relative agreement with the age of well-established American archaeological evidence of widespread habitation of the continent.

Subclade M19

Populations carrying Q1a3a-M3 are widespread throughout the Americas. Since the discovery of M3 several subclades of M3 bearing populations have been discovered in the Americas. An example is in South America where some populations have a high prevalence of (SNP) M19 which defines subclade Q1a3a1-M19. M19 has been detected in (59%) of Amazonian Ticunamarker men and in (10%) of Wayuu men. Subclade Q1a3a1-M19 appears to be unique to South American Indigenous peoples and suggests that population isolation and perhaps even the establishment of tribes began soon after migration into the Americas.

Father clade Q

A migration from Asia into Alaska across the Bering Straitmarker (Beringia) was done by haplogroup Q-M2 populations approximately 22,000 to 17,000 years ago. A member of this initial founding population underwent a mutation, producing its descendant population defined by the Q1a3a-M3 single nucleotide polymorphism (SNP). In Eurasia haplogroup Q-M2 can still be found in Siberian populations and in particular within two populations, the Kets (93.8%) and the Selkups (66.4%). The Kets are thought to be the only survivors of ancient nomads living in Siberia. Their population size is very small; as of 2002, there were fewer than 1,500 Kets in Russiamarker. The Selkups have a slightly larger population size than the Kets, but it is still a relatively small population (approximately 4,250 in 2002).

F-haplo family tree

The Y-DNA F Haplogroup family tree
  • F-haplo - This ancient haplogroup may have first appeared in Indiamarker, the Levant, or the Arabian Peninsula - Possibly 50,000 to 55,000 years ago: 50,300±6500, Hammer and Zegura 2002; 48,000(38,700-55,700) The groups descending from haplogroup F are found in 90% of the world current male populations, however it appears most of the Sub-Saharan African and subregion of the Oceanias population is excluded.
    • IJK - Great-great-great-grandfather clade -Origin: Western Asia - 47,000 years ago
      • K - Great-great-grandfather clade -Origin: Western Asia - 42,000 years ago
        • MNOPS - Great-grandfather clade -Origin: Central Asia or Western Asia 34,000 - 40,000 years ago
          • P (92R7, M45, M74, N12, P27) - Grandfather clade. Origin: Hindu Kushmarker region in Siberiamarker, Kazakhstanmarker, or Uzbekistanmarker, approximately 34,000 to 38,000 years ago
            • P* Found in Hvarmarker
              • Q (M242) - Father clade. Origin: Siberia Sakha Republic the Altai Mountainsmarker or Verkhoyansk Rangemarker, approximately 17,000 to 22,000 years ago
              • Q* - Found at low frequencies in Indiamarker and Pakistanmarker
              • Q1 (P36.2)
              • Q1a2 (M25, M143) - Found at low to moderate frequency among some populations of Southwest Asia, Central Asia, and Siberia
                  • Q1a3 (M346)
                    • Q1a3* - Found at low frequency in Pakistanmarker, Indiamarker, and Tibet
                    • Q1a3a (M3) - Subclade associated with all Indigenous Americas. Origin: Americas 10,000 to 15,000 years ago - 10,000 year old human remains discovered in Alaska are part of this subclade
                    • Q1a3a2 (M194) - This is the defining mutation for Q1a3a2. It has only been found in South American populations.
                    • Q1a3a3 (M199, P106, P292) - They have only been found in South American populations
                • Q1a4 (P48)
                • Q1a5 (P89)
                • Q1a6 (M323) - Found in a significant minority of Yemenite Jews
              • Q1b (M378) - Found at low frequency among samples of Hazara and Sindhis

Y-DNA subclade C3b and Q*

Human Y-chromosome DNA haplogroup tree

Haplogroup C3 (M217, P44) is mainly found in indigenous Siberians, Mongoliansmarker and Oceanic populations. Haplogroup C3 is the most widespread and frequently occurring branch of the greater haplogroup C. Haplogroup C3 is believed to have originated approximately 20,000 years before present in eastern or central Asia. Haplogroup C3 decedent is commonly found among today's Na-Dené speakers as C3b (P39). The Na-Dené are also unusual among indigenous peoples of the Americas in having a relatively high frequency of (Q*). This distinct and isolated branch C3b (P39) includes almost all the Haplogroup C3 Y-chromosomes found among any indigenous peoples of the Americas.

* Note: (One particular haplotype within the Y-DNA Haplogroup C3 has received a great deal of attention for the possibility that it may represent direct patrilineal Descent from Genghis Khan. Genghis Y-chromosomal lineage is present in about 8% of the men in a large region of Asia and about 0.5% of the men in the world (Khan haplotype "C3c" is found lower on the C tree and is not found in Indigenous Americas. )


Human mitochondrial DNA haplogroup - X is one of the five mtDNA-haplogroups found in American indigenous peoples. However, unlike the four main American mtDNA-haplogroups (A, B, C and D) - X is not at all strongly associated with East Asia. The X genetic sequences subsequently further diverged about 20,000 to 30,000 years ago to give two sub-groups, X1 and X2. X2a occurs only at a frequency of about 3% for the total current indigenous population of the Americas. However, X2a is a major mtDNA (female) subclade in North America, where among the Algonquian peoples it comprises up to 25% of mtDNA types. It is also present in lesser percentages to the west and south of this area — among the Sioux (15%), the Nuu-Chah-Nulth (11%–13%), the Navajo (7%), and the Yakama (5%). The (mtDNA)X-haplo is more strongly present in the Near East, the Caucasus, and Mediterranean Europe; and somewhat less strongly present in the rest of Europe. Particular concentrations appear in Georgiamarker (8%), the Orkney Islandsmarker (in Scotlandmarker) (7%) and amongst the Israeli Druze community (26%). One theory for the haplogroup X (subclade X2a) appearance in North America; is it migrated along with A,B,C, and D mtDNA groups from a matrilineal (female) ancestral source originating in the Altai Regionmarker of central Asia.

Overlap between mtDNA and Y-DNA haplogroups

Populations that have a specific combination of Y-haplogroup and mt-haplogroup mutations can generally be seen in specific regional variations. Y mutations and mt mutations do not necessarily occur at a similar time and there are differential rates of sexual selection between the two. Combined with the founder effect and genetic drift this can alter the haplogroup composition of an isolated population making them very distinguishable.(i.e Taínos, Fuegians, Inuit and Yupik)

The rough overlaps between Y-DNA haplogroups and mtDNA haplogroups between the American and Siberia indigenous populations are:
Y-DNA haplogroup(s) mtDNA haplogroup(s) Geographical area(s)
Q, C3 A, X, Y, C, D (M types), (N types) Russian far east, Americas, Arctic

See also

  • Y-chromosomal Adam - most recent common ancestor for all currently living men (Y-DNA)
  • Mitochondrial Eve - most recent common ancestor for all currently living humans (mtDNA)
  • Lithic stage - 25,000 to 10,000 years ago in American Archaeology

Further reading

  1. Supplementary Table 2: NRY haplogroup distribution in Han populations, from the online supplementary material for the article by Bo Wen et al., "Genetic evidence supports demic diffusion of Han culture," Nature 431, 302-305. 16 September 2004 Retrieved 2009-11-27.
  2. Table 1: Y-chromosome haplotype frequencies in 49 Eurasian populations, listed according to geographic region, from The Eurasian Heartland: A continental perspective on Y-chromosome diversity, Proceedings of the National Academy of Sciences of the United States of America. R. Spencer Wells et al. August 28, 2001 Retrieved 2009-11-27.
  3. Michael F. Hammer, Tatiana M. Karafet, Hwayong Park, Keiichi Omoto, Shinji Harihara, Mark Stoneking and Satoshi Horai. Dual origins of the Japanese common ground for hunter-gatherer and farmer Y chromosomes," Journal of Human Genetics. Volume 51, Number 1 2006. Retrieved 2009-11-27.
  4. Yali Xue, Tatiana Zerjal, Weidong Bao, Suling Zhu, Qunfang Shu, Jiujin Xu, Ruofu Du, Songbin Fu, Pu Li, Matthew Hurles, Huanming Yang and Chris Tyler-Smith, Male demography in East Asia: a north-south contrast in human population expansion times," Genetics 172: 2431–2439 2006. Retrieved 2009-11-27.
  5. Atsushi Tajima, Masanori Hayami, Katsushi Tokunaga, Takeo Juji, Masafumi Matsuo, Sangkot Marzuki, Keiichi Omoto and Satoshi Horai, Genetic origins of the Ainu inferred from combined DNA analyses of maternal and paternal lineages," Journal of Human Genetics. Volume 49, Number 4. April, 2004. Retrieved 2009-11-27.
  6. R. Spencer Wells et al., The Eurasian Heartland: A continental perspective on Y-chromosome diversity," Proceedings of the National Academy of Sciences of the United States of America. 2001 August 28; 98(18): 10244–10249. Retrieved 2009-11-27.
  7. Ivan Nasidze, Dominique Quinque, Isabelle Dupanloup, Richard Cordaux, Lyudmila Kokshunova, and Mark Stoneking, Genetic Evidence for the Mongolian Ancestry of Kalmyks," American Journal of Physical Anthropology. 126:000–000. 2005. Retrieved 2009-11-27.
  8. Sanghamitra Sengupta, Lev A. Zhivotovsky, Roy King, S.Q. Mehdi, Christopher A. Edmonds, Cheryl-Emiliane T. Chow, Alice A. Lin, Mitashree Mitra, Samir K. Sil, A. Ramesh, M.V. Usha Rani, Chitra M. Thakur, L. Luca Cavalli-Sforza, Partha P. Majumder, and Peter A. Underhill, 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," The American Journal of Human Genetics. Volume 78, Issue 2, 202-221, 1 February 2006. Retrieved 2009-11-27.
  9. Peter A. Underhill, Peidong Shen, Alice A. Lin et al.. chromosome sequence variation and the history of human populations," Nature Genetics. Volume 26, November 2000. Retrieved 2009-11-27.
  10. Jeffrey T. Lell, Rem I. Sukernik, Yelena B. Starikovskaya, Bing Su, Li Jin, Theodore G. Schurr, Peter A. Underhill and Douglas C. Wallace, The Dual Origin and Siberian Affinities of Native American Y Chromosomes," The American Journal of Human Genetics. Volume 70, Issue 1, 192-206, 1 January 2002. Retrieved 2009-11-27.
  11. Brigitte Pakendorf, Innokentij Novgorodov, Vladimir Osakovskij, Albina Danilova, Artur Protodjakonov, and Mark Stoneking, "Investigating the effects of prehistoric migrations in Siberia: genetic variation and the origins of Yakuts," Human Genetics, Volume 120, Number 3, October 2006, pp. 334-353(20).
  12. V. N. Kharkov, V. A. Stepanov, O. F. Medvedeva, M. G. Spiridonova, N. R. Maksimova, A. N. Nogovitsina, and V. P. Puzyrev, The origin of Yakuts: Analysis of the Y-chromosome haplotypes," Molecular Biology. Volume 42, Number 2. April, 2008. Retrieved 2009-11-27.

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