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Haplogroup Q-M242

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Haplogroup Q
Possible time of origin17,000 to 22,000 years ago[1][2]
Possible place of originCentral Asia,[3] the Indian Subcontinent,[4] Siberia[5]
AncestorP
DescendantsQ1 (P36.2), Q*
Defining mutationsM242
Highest frequenciesIndigenous Americans, Kets, and Selkups

In human genetics, Haplogroup Q (M242) is a Y-chromosome DNA haplogroup.

Origins

Haplogroup Q is one of the two branches of haplogroup P (M45). Haplogroup Q is believed to have arisen in Central Asia or South Asia approximately 17,000 to 22,000 years ago.[6] It has had multiple origins proposed. Much of the conflict may be attributed to limited sample sizes and early definitions that used a combination of M242, P36.2, and MEH2 as defining mutations.

This haplogroup has many diverse haplotypes despite its low frequency among most populations outside of the Americas. There also are over a dozen subclades that have been sampled and identified in modern populations.

Technical specification of mutation

The technical details of M242 are:

Nucleotide change: C to T
Position (base pair): 180
Total size (base pairs): 366
Forward 5′→ 3′: aactcttgataaaccgtgctg
Reverse 5′→ 3′: tccaatctcaattcatgcctc

Subclades

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). Haplogroup Q, according to the most recent available phylogenetics has between 15 and 21 subclades. The scientific understanding of these subclades has changed rapidly. Many key SNPs and corresponding subclades were unknown to researchers at the time of publication are excluded from even recent research. This makes understanding the meaning of individual migration paths challenging.

Haplogroup and Subclade Defining SNPs

Academic Name RS ID Position Change YCC 2008 rev ISOGG 2008 Parent Clade Publications Notes
P48 - 13006660-13006661 –>T Q1a4 Q1a4 MEH2 This is now considered a private SNP. The positive sample from Karafet 2008 was retested at the Family Tree DNA GRC and was found to be negative.
L57 rs34864948 14083496 A/G - - P36.2
L191 - 2947379 A>del - - L53, L54, L55, L213, L331, L475, L476 The L191 SNP has been observed in several paternal lineages which are thought to have originated in northern Mexico.
L213 rs34549365 8295033 C>G - - L56, L57, L528, M346
L245 - 5735090 C>G - - M378, L214, L215
M346 - 2947156 C>G Q1a3 Q1a3 MEH2
L215 rs34601266 13399368 C>T - - P36.2
L55 rs35768544 17922729 G>A - - L56, L57, L528, M346
L53 rs34724285 20101684 G>A - - L56, L57, L528, M346
L54 rs34954951 21702170 G>A - - L56, L57, L528, M346
L232 - 16025489 G>A - - M242 The SNP was found during WTY testing at the Family Tree DNA GRC.
L56 rs34703625 8208869 G>A - - P36.2
P36.2 - 13006449 G>T Q1 Q1 M242
MEH2 rs4252209 4985637 G>T Q1a Q1a P36.2
L214 rs34694026 20365995 T>C - - P36.2
M3 rs3894 17605757 C>T Q1a3a Q1a3a L53, L54, L55 The M3 SNP defines the dominant Y-DNA subclade of Haplogroup Q for the indigenous people of the Americas. This SNP is geographically widespread, occurring from the northeast tip of Siberia and throughout North America, the Caribbean, Central America, and South America.
M194 rs2032677 13523944 T>C Q1a3a2 Q1a3a2 M3
P292 rs13447374 13540161 –>G Q1a3a3 Q1a3a3 M3
P106 - 13932316 G>A Q1a3a3 Q1a3a3 M3
M19 rs3910 20192619 T>A Q1a3a1 Q1a3a1 M3
M199 rs2032589 13540505-13540504 –>G Q1a3a3 Q1a3a3 M3
M323 rs13447377 20327106 C>T Q1a6 Q1a6 M346
P89.1 - 13359859 G>T Q1a5 Q1a5 MEH2 Limited research indicates that this may be a private SNP. The P89 mutation is also found in R1b.
M265, N14 rs3212294 13540044 C>A Q1a1 Q1a1 MEH2
M242 rs8179021 13527976 C>T Q Q P SNPs
M378 - 13536901 A>G Q1b Q1b P36.2
M25 - 20326052 G>C Q1a2 Q1a2 P36.2
M143 - 20349206 G>T Q1a2 Q1a2 P36.2
M120 - 20366782 T>C Q1a1 Q1a1 P36.2

Phylogenetic Variants

The subclade proposed by Sharma 2007 (SS4bp, rs41352448) is not represented in any current trees because it is a value for the STR DYS435 with a value of 12.[4] Karafet 2008, dismissed it as unsuitable by not including it on the Y-Chromosome Consortium tree.[6] It has also been determined to be unsuitable for inclusion on the ISOGG Y-DNA tree.[7] Further, analysis of STR based haplotypes from Sharma 2007 indicates that the DYS435=12 variant, using online haplogroup prediction tools, may occur in multiple branches of the Q tree.

Phylogenetic Trees

There are several confirmed and proposed phylogenetic trees available for haplogroup Q. 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 Q.

  • P
    • Q M242
      • P36.2, L232, L273, L274
        • MEH2, L472, L528
          • M120, N14, M265
          • M25, M143
            • L697.2, L712, L713, L714, L715, L716, M365.3
          • M346, L56, L57, L474
            • L53, L54, L55, L213, L331
              • M3, L892
                • M19
                • M194
                • M199, P106, P292
                • PAGES00104, PAGES00126
                • PAGES00131
                • L663
                • SA01
                • L766, L767
                • L883, L884, L885, L886, L887
                • L888, L889, L890, L891
              • L191
              • L330, L334
                • L329, L332, L333
              • L400, L401
              • L456
              • L568, L569, L570, L571
                • L567
                • L619.1
              • L804, L805
                • L807
            • M323
            • L527, L529, L639
            • L717, L718
          • P89.1
        • L275, L314
          • M378, L214, L215
            • L245
              • L272.1
              • L315
              • L619.2
            • L301
            • L327

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.[6] Subsequent updates have been quarterly and biannual. The current version is a revision of the 2010 update.[8]

  • P
    • Q M242
      • Q1 P36.2
        • Q1a MEH2
          • Q1a1 M120, N14, M265
          • Q1a2 M25, M143
          • Q1a3 L213, L53, L54, L55
            • Q1a3a L56, L57, M346
              • Q1a3a1 M3
                • Q1a3a1a M19
                • Q1a3a1b M194
                • Q1a3a1c M199, P106, P292
              • Q1a3a2 L191
            • Q1a3b M323
          • Q1a4 P89.1
        • Q1b L275
          • Q1b1 L214, L215, M378
            • Q1b1a L272.1

The 2011 ISOGG Tree

The subclades of Haplogroup Q with their defining mutation(s), according to the 2011 ISOGG tree are provided below.

  • Q M242
    • Q1 P36.2, L232, L273, L274
      • Q1a MEH2
        • Q1a1 M120, M265/N14
        • Q1a2 M25, M143
        • Q1a3 L56, L57, M346, L528
          • Q1a3a L53, L54, L55, L213, L331
            • Q1a3a1 M3
              • Q1a3a1a M19
              • Q1a3a1b M194
              • Q1a3a1c M199, P106, P292
            • Q1a3a2 L191
            • Q1a3a3 L330, L334
              • Q1a3a3a L329, L332, L333
          • Q1a3b M323
          • Q1a3c L527, L529
      • Q1b L275, L314
        • Q1b1 M378/Page100, L214, L215/Page82
          • Q1b1a L245
            • Q1b1a1 L272.1

Distribution

Haplogroup Q may be one of the most widely distributed Y-chromosome lineages in the modern world. It is found in the Americas, North Africa, East Asia, South Asia, West Asia, and in Europe.

The Americas

Further information: Indigenous Amerindian genetics and Y-DNA haplogroups in Indigenous peoples of the Americas

Haplogroup Q is the predominant Y-chromosome haplogroup in indigenous peoples of the Americas.

Approximately 20,000 to 15,000 years ago, a group migrated from Asia into the Americas by crossing the Bering Strait.[2] Many of the men in this group must have belonged to haplogroup Q for it now accounts for the majority of non-European haplogroups in indigenous peoples of the Americas.

Indeed, haplogroup Q has been found in approximately 94% of Indigenous peoples of South America[9] and detected in Na-Dené speakers at a rate of 25-50%, and North American Eskimo–Aleut populations at about 46%.[10]

In more modern population groups from the Americas, all Q samples tested for M346 have been positive. This founding population spread throughout the Americas. In the Americas, a member of the founding population underwent a mutation, producing its descendant population defined by the M3 single nucleotide polymorphism (SNP).[2] Many members of haplogroup Q in the Americas belong to the Q-M3 subclade.[5]

However, a 4000-year-old Saqqaq individual belonging to Q-MEH2 haplogroup has been documented.[11]

Asia

Likely due to its origin in Central Asia, haplogroup Q may be found throughout Asia.[2] It has been reported that Q is found in the Altai people,[12] India,[13] Tibet,[14] Pakistan,[13] China,[15][16] Mongolia,[17] Tuvans,[18] and Uyghurs.[17] It is found at a frequency of more than 50% in the Pashtuns in Kabul the Capital of Afghanistan.[19]

East Asia

To the east, haplogroup Q has been found in approximately 4% of Southern Altaians and 32% of Northern Altaians.[12] It is found in 16% of Tuvans.[18]

The frequency of Q in northern China is about 4%, with many Chinese samples of haplogroup Q belonging to the subclade Q-M120.[15][16] Haplogroup Q is found in approximately 3% of males in Tibet[14] and Mongolia.[17] It is also found in 3% of Uyghurs.[17]

The highest frequencies of Q in Asia are found among the Selkups (~70%) and Kets (~95%), they live in western and middle Siberia and their populations are small in number, being just under 5,000 and 1,500, respectively.

South Asia

Some examples of Q* (negative for known subclades) have been reported in the Indian subcontinent in low frequency.[4] The same studies have found Q-M346* (negative for known subclades) restricted to the Indian subcontinent. The most plausible explanation for these observations could be an ancestral migration of individuals bearing ancestral lineage Q* to the Indian subcontinent followed by an autochthonous differentiation to Q-M346. However, these are from studies where all current branches of the Q tree have not been tested.

The problematic phylogeny sampling of early studies has been demonstrated by subsequent studies that have found Q-M346, Q-M378, and Q-M25 in South Asia.

West Asia

Two studies conducted Ivan Nasidze in 2004 and 2009, show that the frequency of Q in Iran, varies between approximately 2% to 6%, depending on region. Iranian samples of haplogroup Q belong primarily to the subclade Q-M25.[20]

In Pakistan, at the eastern end of the Iranian plateau, the frequency of haplogroup Q is about 2.2% (14/638)[21] or 3.4% (6/176).[22]

Approximately 2.5% of males in Saudi Arabia belong to haplogroup Q.[23]

According to Behar et al. 5% of Ashkenazi males belong to haplogroup Q.[24] This has subsequently been found to be entirely the Q-M378 subclade and may be restricted to Q-L245.

Haplogroup Q has also been found in Algerians, Arabians, Syrians, Lebanese[25] and the United Arab Emirates.,[26]

Approximately 2% of males in Turkey,[27] In a study by Gokcumen it was found that among Turks that belong to the Afshar tribe haplogroup Q is seen with a prevalence of 13%.[28] Further, the Q-M25 subclade has been found in Turkey[27]

Q-M346 is found among the Khanty.[29]

Europe

The frequency of haplogroup Q in Norway and Sweden is about 3%, while 2.5% of Slovak males are in haplogroup Q.

Population Frequencies from Studies

Population Paper N Percentage SNPs Tested
Austro-Asiatic (Khasi-Khmuic) Reddy 2009 353 5.40 P-M45(xM173) §
Austro-Asiatic (Mundari) Reddy 2009 64 10.90 P-M45(xM173) §
Nicobarese (Mon-Khmer) Reddy 2009 11 0.00 P-M45(xM173) §
Austro-Asiatic (Southeast Asia) Reddy 2009 257 1.60 P-M45(xM173) §
Garo (Tibeto-Burman) Reddy 2009 71 1.40 P-M45(xM173) §
Tibeto-Burman (India) Reddy 2009 226 3.10 P-M45(xM173) §
Tibeto-Burman (East Asia) Reddy 2009 214 0.00 P-M45(xM173) §
Indo-European (Eastern India) Reddy 2009 54 18.50 P-M45(xM173) §
Southern Talysh Iran Nasidze 2009 50 4.00 P-M45(xM124,xM173)
Northern Talysh Azerbaijan Nasidze 2009 40 5.00 P-M45(xM124,xM173)
Mazandarana Iran Nasidze 2009 50 4.00 P-M45(xM124,xM173)
Gilakia Iran Nasidze 2009 50 0.00 P-M45(xM124,xM173)
Iranians (Tehran) Iran Nasidze 2004 80 4.00 P-M45(xM124,xM173)
Iranians (Isfahan) Iran Nasidze 2004 50 6.00 P-M45(xM124,xM173)
Bakhtiari Iran Nasidze 2008 53 2.00 P-M45(xM124,xM173)
Iranian Arabs Iran Nasidze 2008 47 2.00 P-M45(xM124,xM173)
North Iran Iran Regueiro 2006 33 9.00 P-M45(xM124,xM173)
South Iran Iran Regueiro 2006 117 3.00 P-M45(xM124,xM173)
Georgians South Caucacus Nasidze and Stoneking 2001 77 3.00 P-M45(xM124,xM173)
Armenians South Caucacus Nasidze and Stoneking 2001 100 2.00 P-M45(xM124,xM173)
Azerbaijanis South Caucacus Nasidze and Stoneking 2001 72 0.00 P-M45(xM124,xM173)

§ These may include members of haplogroup R2.

Subclade Distribution

See also

References

Citations

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  2. ^ a b c d Zegura, S. L.; Karafet, TM; Zhivotovsky, LA; Hammer, MF (2003). "High-Resolution SNPs and Microsatellite Haplotypes Point to a Single, Recent Entry of Native American Y Chromosomes into the Americas" (PDF). Molecular Biology and Evolution. 21 (1): 164–75. doi:10.1093/molbev/msh009. PMID 14595095. Cite error: The named reference "Zegura" was defined multiple times with different content (see the help page).
  3. ^ Y-DNA Haplogroup Q and its Subclades - 2010
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Bibliography

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