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Haplogroup Q1a3a (Y-DNA): Wikis


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Haplogroup Y-DNA Q1a3a (Q-M3)

Y and C Haplogroups for NA.JPG

Time of origin 10 to 15 thousand years ago[1]
Place of origin Americas
Ancestor Q
Defining mutations rs3894 (M3)
Highest frequencies Indigenous Americas

In human genetics Haplogroup Q1a3a (phylogenetic name) and/or Q-M3 (mutational name) is a Y-chromosome DNA haplogroup (Y-DNA).[2] 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 University first discovered the indigenous American clade or single nucleotide polymorphism (SNP) that was to become known as Q1a3a and/or (Q-M3). Later studies completed the genetic bridge by determining that Q-M3 was related Q-M242-bearing populations found predominately in Central Asia.[3] Within the parent Q clade, there are 13 haplogroups marked by 17 SNPs.[4]

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.[5] The Y chromosome, like Human mitochondrial DNA haplogroups (mtDNA), differs from other nuclear chromosomes in that the majority of the Y chromosome is unique and does not recombine during meiosis. This has the effect that the historical pattern of mutations can easily be studied.[6]


Indigenous American subclade Q1a3a (Q-M3)

Y-DNA-based chart showing genetic clade Haplogroups 15,000 CE
Haplogroup "Q" is shown in purple and "C" is the other major color seen mainly in North America. The abbreviation "AM" stands for Amerinds.

Haplogroup Q1a3a is a Y Chromosome subclade haplo generally associated with the Indigenous peoples of the Americas.[1][7] This haplogroup is defined by the presence of the rs3894 (M3) single nucleotide polymorphism (SNP). The M3 SNP is found "downstream" from the Q-M242 (SNP).[1] Q-M242 is the defining (father-clade) single nucleotide polymorphism of the Q haplogroup.[1]

The Q-M3 mutation on the Q lineage is roughly 10,000 to 15,000 years ago,[1] as the migration throwout the Americas was underway by the early Paleo-Indians.[8] The micro-satellite diversity and distributions of the Y lineage specific to South America like Q-M19 and Q-M194 indicates that certain Amerind populations have been isolated since the initial colonization of the region approximately 5,000 to 10,000 years ago.[1] The Na-Dené, Inuit and Indigenous Alaskan populations exhibit Y-DNA Q-haplogroup mutations, however are distinct from other indigenous Americans with various mtDNA mutations.[9] This suggests that the earliest migrants into the northern extremes of North America and Greenland derived from a much later populations along the Bering sea coast line.[10] This dates are in relative agreement with the age of well-established American archaeological evidence of widespread habitation of the continent.[11]


Subclade Q1a3a1 (M19)

Populations carrying the Q haplo is 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 M19.[12] M19 has been detected in (59%) of Amazonian Ticuna men and in (10%) of Wayuu men.[12] Subclade 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.[12]

Father clade Q (M242)

A migration from Asia into Alaska across the Bering Strait (Beringia) was done by haplogroup Q-M2 populations approximately 22,000 to 17,000 years ago.[13] A member of this initial founding population underwent a mutation, producing its descendant population defined by the M3 single nucleotide polymorphism (SNP) mutation.[3] In Eurasia haplogroup Q-M2 is found in Siberian populations and in particular within two populations, the Kets (93.8%) and the Selkups (66.4%).[1] The Kets are thought to be the only survivors of ancient nomads living in Siberia.[3] Their population size is very small; as of 2002, there were fewer than 1,500 Kets in Russia.[3] The Selkups have a slightly larger population size than the Kets, but it is still a relatively small population (approximately 4,250 in 2002).[1]

F-haplo family tree

The Y-DNA F Haplogroup family tree
  • F-haplo - This ancient haplogroup may have first appeared in India, 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)[14] 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.[15]
    • IJK - Great-great-great-grandfather clade -Origin: Western Asia - 47,000 years ago[4]
      • K - Great-great-grandfather clade -Origin: Western Asia - 42,000 years ago[4]
        • MNOPS - Great-grandfather clade -Origin: Central Asia or Western Asia 34,000 - 40,000 years ago[4]

Y-DNA subclade C3b (P39) and Q*

Human Y-chromosome DNA haplogroup tree

Haplogroup C3 (M217, P44) is mainly found in indigenous Siberians, Mongolians and Oceanic populations. Haplogroup C3 is the most widespread and frequently occurring branch of the greater (Y-DNA) 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.[20]

* 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. [30])


(mtDNA) -Human mitochondrial DNA haplogroup world distribution map

Human mitochondrial DNA haplogroup - (mtDNA) 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.[3] 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.[3] However, X2a is a major mtDNA (female) subclade in North America, where among the Algonquian peoples it comprises up to 25% of mtDNA types.[31][2] 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%).[7] 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 Georgia (8%), the Orkney Islands (in Scotland) (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 Region of central Asia.[15]

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.[32] Combined with the founder effect and genetic drift this can alter the haplogroup composition of an isolated population making them very distinguishable.[33](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
Random sampling genetic drift.gif

See also

Human Y-chromosome DNA (Y-DNA) haplogroups (by ethnic groups · famous haplotypes)

most recent common Y-ancestor
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Further reading

  1. ^ a b c d e f g h "Summary of knowledge on the subclades of Haplogroup Q". Genebase Systems. 2009. Retrieved 2009-11-22.  
  2. ^ a b "Learn about Y-DNA Haplogroup Q" (Verbal tutorial possible). Wendy Tymchuk - Senior Technical Editor. Genebase Systems. 2008. Retrieved 2009-11-21. "Haplogroups are defined by unique mutation events such as single nucleotide polymorphisms, or SNPs. These SNPs mark the branch of a haplogroup, and indicate that all descendents of that haplogroup at one time shared a common ancestor. The Y-DNA SNP mutations were passed from father to son over thousands of years. Over time, additional SNPs occur within a haplogroup, leading to new lineages. These new lineages are considered subclades of the haplogroup. Each time a new mutation occurs, there is a new branch in the haplogroup, and therefore a new subclade. Haplogroup Q, possibly the youngest of the 20 Y-chromosome haplogroups, originated with the SNP mutation M242 in a man from Haplogroup P that likely lived in Siberia approximately 15,000 to 20,000 years before present"  
  3. ^ a b c d e f Wells, Spencer; Read, Mark (Digitised online by Google books). The Journey of Man - A Genetic Odyssey. Random House. ISBN 0812971469. Retrieved 2009-11-21.  
  4. ^ a b c d e f g h i "Y-DNA Haplogroup Tree". Genebase Systems. 2009. Retrieved 2009-11-21.  
  5. ^ Watson J.D. and Crick F.H.C. (1953). "A Structure for Deoxyribose Nucleic Acid" (PDF). Nature 171 (4356): 737–738. doi:10.1038/171737a0. PMID 13054692. Retrieved 2009-11-27.  
  6. ^ Orgel L (2004). "Prebiotic chemistry and the origin of the RNA world" (PDF). Crit Rev Biochem Mol Biol 39 (2): 99–123. doi:10.1080/10409230490460765. PMID 15217990. Retrieved 2009-11-27.  
  7. ^ a b Fagundes, Nelson J.R.; Ricardo Kanitz, Roberta Eckert, Ana C.S. Valls, Mauricio R. Bogo, Francisco M. Salzano, David Glenn Smith, Wilson A. Silva, Marco A. Zago, Andrea K. Ribeiro-dos-Santos, Sidney E.B. Santos, Maria Luiza Petzl-Erler, and Sandro L.Bonatto (2008). "Mitochondrial Population Genomics Supports a Single Pre-Clovis Origin with a Coastal Route for the Peopling of the Americas" (pdf). American Journal of Human Genetics 82 (3): 583-592. Retrieved 2009-11-19. "Since the first studies, it has been found that extant Native American populations exhibit almost exclusively five "mtDNA haplogroups" (A–D and X)6 classified in the autochthonous haplogroups A2, B2, C1, D1, and X2a.7 Haplogroups A–D are found all over the New World and are frequent in Asia, supporting a northeastern Asian origin of these lineages".  
  8. ^ "Genetic Variation and Population Structure in Native Americans". PLoS Genetics. 2007. p. 3(11). Retrieved 2009-11-18. "Comparing Native Americans to Siberian populations, both genetic diversity and similarity to Siberians decrease with geographic distance from the Bering Strait. The widespread distribution of a particular allele private to the Americas supports a view that much of Native American genetic ancestry may derive from a single wave of migration"  
  9. ^ "mtDNA Variation among Greenland Eskimos. The Edge of the Beringian Expansion". Laboratory of Biological Anthropology, Institute of Forensic Medicine, University of Copenhagen, Copenhagen, McDonald Institute for Archaeological Research,University of Cambridge, Cambridge, University of Hamburg, Hamburg. 2000. Retrieved 2009-11-22. "The relatively lower coalescence time of the entire haplogroup A2 including the shared sub-arctic branches A2b (Siberians and Inuit) and A2a (Eskimos and Na-Dené) is probably due to secondary expansions of haplogroup A2 from the Beringia area, which would have averaged the overall internal variation of haplogroup A2 in North America."  
  10. ^ "Native American Mitochondrial DNA Analysis Indicates That the Amerind and the Nadene Populations Were Founded by Two Independent Migrations". Center for Genetics and Molecular Medicine and Departments of Biochemistry and Anthropology, Emory University School of Medicine, Atlanta, Georgia. Genetics Society of America. Vol 130, 153-162. Retrieved 2009-11-28. "The divergence time for the Nadene portion of the HaeIII np 663 lineage was about 6,000-10,000 years. Hence, the ancestral Nadene migrated from Asia independently and considerably more recently than the progenitors of the Amerinds"  
  11. ^ First Americans Endured 20,000-Year Layover - Jennifer Viegas, Discovery News,, retrieved 2009-11-18, "Archaeological evidence, in fact, recognizes that people started to leave Beringia for the New World around 40,000 years ago, but rapid expansion into North America didn't occur until about 15,000 years ago, when the ice had literally broken"   page 2
  12. ^ a b c Bortolini MC, Salzano FM, Thomas MG, et al (September 2003). "Y-chromosome evidence for differing ancient demographic histories in the Americas". Am. J. Hum. Genet. 73 (3): 524–39. doi:10.1086/377588. PMID 12900798. PMC 1180678. Retrieved 2009-11-21.  
  13. ^ Zegura SL, Karafet TM, Zhivotovsky LA, Hammer MF (January 2004). "High-resolution SNPs and microsatellite haplotypes point to a single, recent entry of Native American Y chromosomes into the Americas". Mol. Biol. Evol. 21 (1): 164–75. doi:10.1093/molbev/msh009. PMID 14595095.  
  14. ^ Karafet TM, Mendez FL, Meilerman MB, Underhill PA, Zegura SL, Hammer MF (2008). "New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree". Genome Research 18: 830–8. doi:10.1101/gr.7172008.  
  15. ^ a b 73(5): 1178–119, Am J Hum Genet (3003). "Origin and Diffusion of mtDNA Haplogroup X". The American Society of Human Genetics. Retrieved 2009-11-22. "It is apparent that the Native American haplogroup X mtDNAs derive from X2 by a unique combination of five mutations. It is notable that X2 includes the two complete Native American X sequences that constitute the distinctive X2a clade, a clade that lacks close relatives in the entire Old World, including Siberia. The position of X2a in the phylogenetic tree suggests an early split from the other X2 clades, likely at the very beginning of their expansion and spread from the Near East northeast of the Altai area, haplogroup X sequences were detected in the Tungusic-speaking Evenks, of the Podkamennaya Tunguska basin (Central Siberia). In contrast to the Altaians, the Evenks did not harbor any West Eurasian mtDNA haplogroups other than X. However, neither of the two Evenk X haplotypes showed mutations characteristic of the Native American clade X2a. Instead, one sequence was a member of X2b and the other of X2. Thus, one possible scenario is that several X haplotypes arrived in Siberia from western Asia during the Palaeolithic, but only X2a crossed Beringia and survived in modern Native Americans."  
  16. ^ 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.
  17. ^ 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.
  18. ^ "On Your Knees Cave". Timothy H. Heaton. The University of South Dakota. 2002. Retrieved 2009-11-21. "The American Journal of Physical Anthropolog reports new DNA-based research that links the DNA retrieved from a 10,000-year-old fossilized tooth from an Alaskan island, with specific coastal tribes in Tierra del Fuego, Ecuador, Mexico and California. Unique markers found in DNA recovered from the Alaskan tooth were found in these specific coastal tribes, and were rare in any of the other indigenous peoples in the Americas. This finding lends substantial credence to a migration theory that at least one set of early peoples moved south along the west coast of the Americas in boats. A previous study showed that mtDNA (human mitochondrial DNA) from indigenous populations in coastal British Columbia showed similarities to coastal populations in Southern California, while inland populations in both localities differed markedly. Dates of 9,730 and 9,880 years BP were obtained on the human remains, making them the oldest ever found in Alaska or Canada. The associated bone tool was dated to 10,300 years old"  
  19. ^ "Reconstruction of Patrilineages and Matrilineages of Samaritans and Other Israeli Populations From Y-Chromosome and Mitochondrial DNA Sequence Variation," Human Mutation. 24:248-260 2004. Q-M323 in 3/20 = 15% of a sample of Yemenite Jews" (pdf). Peidong Shen, Tal Lavi, Toomas Kivisild, Vivian Chou, Deniz Sengun, Dov Gefel, Issac Shpirer, Eilon Woolf, Jossi Hillel, Marcus W. Feldman, and Peter J. Oefner. Retrieved 2009-11-27.  
  20. ^ a b 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.
  21. ^ 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.
  22. ^ 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.
  23. ^ a b 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.
  24. ^ 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.
  25. ^ 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.
  26. ^ a b c 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.
  27. ^ 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.
  28. ^ 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).
  29. ^ 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.
  30. ^ "The Genetic Legacy of the Mongols" (pdf). American Journal of Human Genetics. Zerjal et al. 2003. Retrieved 2009-11-27.  
  31. ^ "The peopling of the Americas: Genetic ancestry influences health". Scientific American. Retrieved 2009-11-27.  
  32. ^ "On the Probability of Fixation of Mutant Genes in a Population" (pdf). University of Wisconsin, Madison, Wisconsin. PubMed Central Genetics 47: 713–719. Retrieved 2009-11-27.  
  33. ^ "The peopling of the Americas: Genetic ancestry influences health". scientific journal American Journal of Physical Anthropology. University of Oklahoma. 2009. Retrieved 2009-11-21. "We cannot assume that all Native American populations will have similar trait frequencies nor will they have similar expectations for genetic risk or resistance to disease. Rather, the history of founder effects in the Americas, and around the world, contributes to the understanding of how well one local population might reflect a broader community"  
  34. ^ "Method and Theory in American Archaeology" (Digitised online by Questia Media). Gordon Willey and Philip Phillips. University of Chicago. 1958. Retrieved 2009-11-27.  

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