Haplogroup CT

Haplogroup CT
Possible time of origin	c. 70,000 years ago[1]
Possible place of origin	Asia[2][3][4] or East Africa[5]
Ancestor	Haplogroup BT
Descendants	Haplogroup CF, Haplogroup DE
Defining mutations	P9.1, M168, M294, V9, V41, V54, V189, and V226

Haplogroup CT is a human Y chromosome haplogroup, defining one of the major paternal lineages of humanity.

Men who carry the CT clade have Y chromosomes with the SNP mutation M168, along with P9.1 and M294. These mutations are present in all modern human male lineages except A and B-M60, which are both found almost exclusively in Africa.

The most recent common male line ancestor (TMRCA) of all CT men today probably predated the recent African origin of modern humans, a migration in which some of his descendants participated. He is therefore thought to have lived in Africa before this proposed migration.^[1]^[5]^[6] In keeping with the concept of "Y-chromosomal Adam" given to the patrilineal ancestor of all living humans, CT-M168 has therefore also been referred to in popularized accounts as being the lineage of "Eurasian Adam" or "Out of Africa Adam".^[7]^[3]^[4]

No male in paragroup CT* has ever been discovered in modern populations. This means that all males carrying this haplogroup are also defined as being in one of the several major branch clades. All known surviving descendant lineages of CT are in one of two major subclades, CF and DE. In turn, DE is divided into an Asia-distributed haplogroup D-M174 and a now predominantly Africa-distributed haplogroup E-M96, while CF is divided into an East Asian, American, and Oceanian haplogroup C-M130 and haplogroup F-M89, which dominates most non-African populations.^[4]

Basal haplogroup CT* had been found in various prehistoric human fossils that were analysed for ancient DNA, including specimens associated with the Pre-Pottery Neolithic C (1/1; 100%), Neolithic Ganj Dareh Iran (1/2 50%), Natufian (2/5; 40%), Pre-Pottery Neolithic B (2/7; ~29%),^[8] Alföld Linear Pottery (1/1 at two ALP archaeological sites; 100%), Linearbandkeramik (1/2 at Karsdorf LBK archaeological site; 50%) cultures, and some Upper Paleolithic Europeans (Cioclovina1, Kostenki12, Vestonice13).^[9]^[10]

Subclades

Haplogroup CT (M168/PF1416)

CF (P143/PF2587, CTS3818/M3690/PF2668, CTS6376/M3711/PF2697)
- C (M130/Page51/RPS4Y711, M216) Asia, Oceania, and North America
  - C1 F3393/Z1426
    - C1a CTS11043
      - C1a1 formerly C1 (M8, M105, M131) Japan
      - C1a2 Very low frequency in Western Eurasia (including Kostenki 38 000 years ago) and North Africa
    - C1b
      - C1b1
        C1b1a
        C1b1a1 formerly C5 (M356) South Asia, Central Asia, and Southwest Asia
      - C1b2
        C1b2a formerly C2 (M38) Indonesia, New Guinea, Melanesia, Micronesia, and Polynesia
        
        C1b2b formerly C4 (M347) Indigenous Australians
  - C2 formerly C3 (M217, P44) Found throughout Eurasia and North America, but especially among Mongols, Kazakhs, Tungusic peoples, Paleosiberians, and Na-Dené-speaking peoples
- F (M89, M213) Found throughout Eurasia, Oceania, and the Americas
  - F1 (P91, P104)
  - F2 (M427, M428)
  - F3 (P96)
  - F4 (M481)
- GHIJK F1329/M3658/PF2622/YSC0001299, CTS2254/M3680/PF2657, FGC2045/Z12203 Throughout Eurasia; also The Americas; at low levels/among minorities in Africa and Oceania
  - G M201, P257 Primarily the Caucasus; also at low levels/among minorities in Europe, North Africa, South West Asia and Central Asia
  - HIJK Throughout Eurasia; also The Americas; at low levels/among minorities in Africa and Oceania
    - H M69, M370 South Asia, Central Asia, and Southwest Asia
    - IJK L15/S137, L16/S138 Eurasia, North Africa, Oceania, the Americas and East Africa
    - IJ M429/P125 Europe, Western Asia, North Africa and East Africa
      - I M170, M258, P19, P38, P212, U179 Europe
      - J 12f2.1, M304 Europe, Western Asia, South Asia, North Africa and East Africa
    - K M9 Found all over Eurasia; also significant in the Americas and Oceania; at lower levels in North Africa and East Africa
      - LT (K1) L298/P326
        L M11, M20, M22, M61, M185, M295 the Indian subcontinent
        
        T M70, M184/USP9Y+3178, M193, M272 (formerly K2) Southwestern Asia, South Asia, North Africa, the Horn of Africa, the Chad Basin, and Southern Europe
      - K2 M526 Eurasia, Oceania, The Americas, some indigenous Australians and some minorities in Africa
        NO (K2a) M214 Reportedly found in small numbers of Buyi and Japanese males.
        N M231 Eastern Europe, North Asia, and East Asia
        
        O M175 Oceania, Southeast Asia, and East Asia
        
        K2b formerly MPS P331 Eurasia, The Americas, Oceania and minorities in Africa
        K2b1 formerly MS P397/P399 Melanesians, Micronesians, indigenous Australians and Polynesians.
        M P256 Eastern Indonesia, Papua New Guinea, and Melanesia
        
        S M230, P202, P204 (formerly K5) Eastern Indonesia, Papua New Guinea, and Melanesia
        
        P (K2b2) 92R7, M45, M74/N12, P27.1/P207 Throughout Eurasia, The Americas and some minorities in Africa
        Q M242 The Americas and Eurasia
        
        R M207/UTY2, M306/S1 Europe, Near East, South Asia, Chad Basin, Canary Islands
        
        K2c P261 Low levels in Bali
        
        K2d P402/P403 Low levels in Java
        
        K2e M147 Low levels in South Asia
Haplogroup DE (M1/YAP, M145/P205, M203/Page36, P144, P153, P165, P167, P183) Asia, Africa, Southern and Eastern Europe; also at low levels in Oceania
- Haplogroup D (M174) Primarily Japan, Tibet and Andaman Islanders; also at low level/among minorities in East Asia, Central Asia, Micronesia and Melanesia
  - Haplogroup D1 (CTS11577) Mainly Tibet; minorities in Central Asia, East Asia, and South East Asia
    - Haplogroup D1a Z27276 East and Central Asia
      - D1a1 (M15) (ex-D1) Qiang people; also at low levels throughout East and Central Asia
      - Haplogroup D1a2 P99 (ex-D3) Tibet and Central Asia
    - Haplogroup D1b (ex-D2) (M64.1/Page44.1, M55, M57, M179/Page31, M359.1/P41.1, P37.1, P190, 12f2.2) Mainly Japan; also at lowel levels/among minorities in Korea, China, Micronesia and Melanesia
  - Haplogroup D2 L1366 (ex-D1a) Philippines
- Haplogroup E (M40, M96) Africa, Middle East, Southern and Eastern Europe
  - Haplogroup E1 (P147) At high levels throughout Africa; at lower levels in the Middle East and Europe
    - Haplogroup E1a (formerly E1) (M132) Primarily Africa
    - Haplogroup E1b (P177/PF1939)
      - Haplogroup E1b1 (formerly E3) (P2, DYS391p)
        Haplogroup E1b1a (V38)
        
        Haplogroup E1b1a1 (formerly E3a) (M2) West Africa, Central Africa, Southeast Africa and Southern Africa
        
        Haplogroup E1b1b (formerly E3b) (M215) Horn of Africa (Ethiopians, Somalis), North Africa (Berber speakers, Arabic speakers, Tuareg,^[11] Sahrawi), the Middle East, Europe (esp. areas near the Mediterranean Sea)
  - Haplogroup E2 (M75) East Africa

Sources

ISOGG:

References

1 2 Karafet et al. (2008) give "70,000", citing "68,500±6000 years" from Hammer and Zegura (2002). 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 (5): 830–8. doi:10.1101/gr.7172008. PMC 2336805. PMID 18385274. . The split between CF and DE (which in the absence of a paragroup CT* is equivalent to the age of CT) has been dated to 70,000–75,000 years ago in Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans, Nature 505, 87–91 (02 January 2014)
↑ Chuan-Chao Wang; Li Hui (2014-05-03). "Comparison of Y-chromosomal lineage dating using either evolutionary or genealogical Y-STR mutation rates". bioRxiv 004705.
1 2 Darwinian Detectives: Revealing the Natural History of Genes and Genomes, by Norman A. Johnson, 2007, ISBN 0-19-530675-9, ISBN 978-0-19-530675-0
1 2 3 Karafet et al. (2008), New Binary Polymorphisms Reshape and Increase Resolution of the Human Y-Chromosomal Haplogroup Tree, Genome Research, doi:10.1101/gr.7172008 PMID 18385274
1 2 Stone, Linda; Paul F. Lurquin; Luigi Luca Cavalli-Sforza (2007). "Voyages, Prehistoric Human Expansions". Genes, Culture, and Human Evolution. p. 187. ISBN 978-1-4051-5089-7.
↑ Underhill and Kivisild; Kivisild, T (2007). "Use of Y Chromosome and Mitochondrial DNA Population Structure in Tracing Human Migrations". Annu. Rev. Genet. 41 (1): 539–64. doi:10.1146/annurev.genet.41.110306.130407. PMID 18076332.
↑ Genes, Culture, and Human Evolution: A Synthesis, By Linda Stone, Paul F. Lurquin, 2007, ISBN 1-4051-5089-0, page 187
↑ Lazaridis, Iosif; et al. (17 June 2016). "The genetic structure of the world's first farmers". bioRxiv 059311. -- Table S6.1 - Y-chromosome haplogroups
↑ Mark Lipson et al. (2017). "Parallel palaeogenomic transects reveal complex genetic history of early European farmers". Nature. 551 (7680): 368–372. Bibcode:2017Natur.551..368L. doi:10.1038/nature24476. PMC 5973800. PMID 29144465. Retrieved 10 November 2017.
↑ Fu, Q; Posth, C; Hajdinjak, M; Petr, M; Mallick, S; Fernandes, D; Furtwängler, A; Haak, W; Meyer, M; Mittnik, A; Nickel, B; Peltzer, A; Rohland, N; Slon, V; Talamo, S; Lazaridis, I; Lipson, M; Mathieson, I; Schiffels, S; Skoglund, P; Derevianko, A. P; Drozdov, N; Slavinsky, V; Tsybankov, A; Cremonesi, R. G; Mallegni, F; Gély, B; Vacca, E; González Morales, M. R; et al. (2016). "The genetic history of Ice Age Europe". Nature. 534 (7606): 200–205. Bibcode:2016Natur.534..200F. doi:10.1038/nature17993. hdl:10211.3/198594. PMC 4943878. PMID 27135931.
↑ Pereira et al. (2010), Linking the sub-Saharan and West Eurasian gene pools: maternal and paternal heritage of the Tuareg nomads from the African Sahel, European Journal of Human Genetics (2010) 18, 915–923; doi:10.1038/ejhg.2010.21

Phylogenetic tree of human Y-chromosome DNA haplogroups ^{[χ 1]}^{[χ 2]}

A0-T ^{[χ 3]}

A1 ^{[χ 4]}

A1b

A1b1

F1

F2

F3

GHIJK

I

J

LT ^{[χ 5]}

K2 ^{[χ 6]}

L

T

K2a ^{[χ 7]}

K2b ^{[χ 8]}

K2c

K2d

K2e ^{[χ 9]}

K-M2313 ^{[χ 10]}

K2b1 ^{[χ 11]}

P ^{[χ 12]}

NO

S ^{[χ 13]}

M ^{[χ 14]}

P1

P2

Footnotes

↑ Van Oven M, Van Geystelen A, Kayser M, Decorte R, Larmuseau HD (2014). "Seeing the wood for the trees: a minimal reference phylogeny for the human Y chromosome". Human Mutation. 35 (2): 187–91. doi:10.1002/humu.22468. PMID 24166809.
↑ International Society of Genetic Genealogy (ISOGG; 2015), Y-DNA Haplogroup Tree 2015. (Access date: 1 February 2015.)
↑ Haplogroup A0-T is also known as A-L1085 (and previously as A0'1'2'3'4).
↑ Haplogroup A1 is also known as A1'2'3'4.
↑ Haplogroup LT (L298/P326) is also known as Haplogroup K1.
↑ Between 2002 and 2008, Haplogroup T-M184 was known as "Haplogroup K2". That name has since been re-assigned to K-M526, the sibling of Haplogroup LT.
↑ Haplogroup K2a (M2308) and its primary subclade K-M2313 were separated from Haplogroup NO (F549) in 2016. (This followed the publication of: Poznik GD, Xue Y, Mendez FL, et al. (2016). "Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences". Nature Genetics. 48 (6): 593–9. doi:10.1038/ng.3559. PMC 4884158. PMID 27111036. In the past, other haplogroups, including NO (M214) and K2e had also been identified with the name "K2a".
↑ Haplogroup K2b (M1221/P331/PF5911) is also known as Haplogroup MPS.
↑ Haplogroup K2e (K-M147) was previously known as "Haplogroup X" and "K2a" (but is a sibling subclade of the present K2a).
↑ K-M2313*, which as yet has no phylogenetic name, has been documented in two living individuals, who have ethnic ties to India and South East Asia. In addition, K-Y28299, which appears to be a primary branch of K-M2313, has been found in three living individuals from India. See: Poznik op. cit.; YFull YTree v5.08, 2017, "K-M2335", and; PhyloTree, 2017, "Details of the Y-SNP markers included in the minimal Y tree" (Access date of these pages: 9 December 2017)
↑ Haplogroup K2b1 (P397/P399) is also known as Haplogroup MS, but has a broader and more complex internal structure.
↑ Haplogroup P (P295) is also klnown as K2b2.
↑ Haplogroup S, as of 2017, is also known as K2b1a. (Previously the name Haplogroup S was assigned to K2b1a4.)
↑ Haplogroup M, as of 2017, is also known as K2b1b. (Previously the name Haplogroup M was assigned to K2b1d.)

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[Karafet-1] 1 2 Karafet et al. (2008) give "70,000", citing "68,500±6000 years" from Hammer and Zegura (2002). 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 (5): 830–8. doi:10.1101/gr.7172008. PMC 2336805. PMID 18385274. . The split between CF and DE (which in the absence of a paragroup CT* is equivalent to the age of CT) has been dated to 70,000–75,000 years ago in Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans, Nature 505, 87–91 (02 January 2014)

[2] Chuan-Chao Wang; Li Hui (2014-05-03). "Comparison of Y-chromosomal lineage dating using either evolutionary or genealogical Y-STR mutation rates". bioRxiv 004705.

[Johnson-3] 1 2 Darwinian Detectives: Revealing the Natural History of Genes and Genomes, by Norman A. Johnson, 2007, ISBN 0-19-530675-9, ISBN 978-0-19-530675-0

[Karafet1-4] 1 2 3 Karafet et al. (2008), New Binary Polymorphisms Reshape and Increase Resolution of the Human Y-Chromosomal Haplogroup Tree, Genome Research, doi:10.1101/gr.7172008 PMID 18385274

[stone-5] 1 2 Stone, Linda; Paul F. Lurquin; Luigi Luca Cavalli-Sforza (2007). "Voyages, Prehistoric Human Expansions". Genes, Culture, and Human Evolution. p. 187. ISBN 978-1-4051-5089-7.

[UnderhillandKivisild-6] Underhill and Kivisild; Kivisild, T (2007). "Use of Y Chromosome and Mitochondrial DNA Population Structure in Tracing Human Migrations". Annu. Rev. Genet. 41 (1): 539–64. doi:10.1146/annurev.genet.41.110306.130407. PMID 18076332.

[7] Genes, Culture, and Human Evolution: A Synthesis, By Linda Stone, Paul F. Lurquin, 2007, ISBN 1-4051-5089-0, page 187

[8] Lazaridis, Iosif; et al. (17 June 2016). "The genetic structure of the world's first farmers". bioRxiv 059311. -- Table S6.1 - Y-chromosome haplogroups

[9] Mark Lipson et al. (2017). "Parallel palaeogenomic transects reveal complex genetic history of early European farmers". Nature. 551 (7680): 368–372. Bibcode:2017Natur.551..368L. doi:10.1038/nature24476. PMC 5973800. PMID 29144465. Retrieved 10 November 2017.

[10] Fu, Q; Posth, C; Hajdinjak, M; Petr, M; Mallick, S; Fernandes, D; Furtwängler, A; Haak, W; Meyer, M; Mittnik, A; Nickel, B; Peltzer, A; Rohland, N; Slon, V; Talamo, S; Lazaridis, I; Lipson, M; Mathieson, I; Schiffels, S; Skoglund, P; Derevianko, A. P; Drozdov, N; Slavinsky, V; Tsybankov, A; Cremonesi, R. G; Mallegni, F; Gély, B; Vacca, E; González Morales, M. R; et al. (2016). "The genetic history of Ice Age Europe". Nature. 534 (7606): 200–205. Bibcode:2016Natur.534..200F. doi:10.1038/nature17993. hdl:10211.3/198594. PMC 4943878. PMID 27135931.

[Pereira2010-11] Pereira et al. (2010), Linking the sub-Saharan and West Eurasian gene pools: maternal and paternal heritage of the Tuareg nomads from the African Sahel, European Journal of Human Genetics (2010) 18, 915–923; doi:10.1038/ejhg.2010.21

[vanOven2014-12] Van Oven M, Van Geystelen A, Kayser M, Decorte R, Larmuseau HD (2014). "Seeing the wood for the trees: a minimal reference phylogeny for the human Y chromosome". Human Mutation. 35 (2): 187–91. doi:10.1002/humu.22468. PMID 24166809.

[ISOGG2015-13] International Society of Genetic Genealogy (ISOGG; 2015), Y-DNA Haplogroup Tree 2015. (Access date: 1 February 2015.)

[A0-T-14] Haplogroup A0-T is also known as A-L1085 (and previously as A0'1'2'3'4).

[A1-15] Haplogroup A1 is also known as A1'2'3'4.

[LT-16] Haplogroup LT (L298/P326) is also known as Haplogroup K1.

[K2-17] Between 2002 and 2008, Haplogroup T-M184 was known as "Haplogroup K2". That name has since been re-assigned to K-M526, the sibling of Haplogroup LT.

[K2a-18] Haplogroup K2a (M2308) and its primary subclade K-M2313 were separated from Haplogroup NO (F549) in 2016. (This followed the publication of: Poznik GD, Xue Y, Mendez FL, et al. (2016). "Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences". Nature Genetics. 48 (6): 593–9. doi:10.1038/ng.3559. PMC 4884158. PMID 27111036. In the past, other haplogroups, including NO (M214) and K2e had also been identified with the name "K2a".

[K2b-19] Haplogroup K2b (M1221/P331/PF5911) is also known as Haplogroup MPS.

[K2e-20] Haplogroup K2e (K-M147) was previously known as "Haplogroup X" and "K2a" (but is a sibling subclade of the present K2a).

[K-M2313-21] K-M2313*, which as yet has no phylogenetic name, has been documented in two living individuals, who have ethnic ties to India and South East Asia. In addition, K-Y28299, which appears to be a primary branch of K-M2313, has been found in three living individuals from India. See: Poznik op. cit.; YFull YTree v5.08, 2017, "K-M2335", and; PhyloTree, 2017, "Details of the Y-SNP markers included in the minimal Y tree" (Access date of these pages: 9 December 2017)

[K2b1-22] Haplogroup K2b1 (P397/P399) is also known as Haplogroup MS, but has a broader and more complex internal structure.

[P-23] Haplogroup P (P295) is also klnown as K2b2.

[S-24] Haplogroup S, as of 2017, is also known as K2b1a. (Previously the name Haplogroup S was assigned to K2b1a4.)

[M-25] Haplogroup M, as of 2017, is also known as K2b1b. (Previously the name Haplogroup M was assigned to K2b1d.)

Haplogroup CT

Possible time of origin	c. 70,000 years ago^[1]
Possible place of origin	Asia^[2]^[3]^[4] or East Africa^[5]
Ancestor	Haplogroup BT
Descendants	Haplogroup CF, Haplogroup DE
Defining mutations	P9.1, M168, M294, V9, V41, V54, V189, and V226

Haplogroup CT

Subclades

Sources

See also

Genetics

References