Haplogroup S1a (Y-DNA)

Haplogroup S1a
Possible place of origin	Maritime Southeast Asia or Oceania
Ancestor	S1 (S-B255)
Descendants	S-P405
Defining mutations	Z41335, Z41336, Z41337, Z41338, Z41339, Z41340, Z41341

Haplogroup S1a is a human Y-DNA haplogroup, defined by SNPs Z41335, Z41336, Z41337, Z41338, Z41339, Z41340, and Z41341.

S1a is found primarily in Melanesia (especially in Papua New Guinea), Micronesia, Maritime Southeast Asia and among indigenous Australians.^[1]

As of 2017, it includes an unnamed primary subclade referred to by ISOGG as "S1a~" (P405),^[1] ^[2]^[3] (which was previously known as K2b1a). The "~" symbol is ISOGG's way of indicating that an unverified and as-yet unnamed immediate ancestor may exist.

Its secondary subclades include: S1a1 (Z42413), S1a2~ (P79, P307) and S1a3 (P315).

Before 2016, S1a1b (M230, P202, P204) was known as Haplogroup S* (and before that as Haplogroup K5). (In 2016, haplogroup S-B254 was "promoted" to S*, from its previous position of S1.)

The "sibling" clades of S1a include: S1b (B275, Z33756, Z33757, Z33758, Z33759), S1c (Z41926, Z41927, Z41928, Z41929, Z41930) and S1d (SK1806).

Phylogeny

Haplogroup S1 (B255) includes the following subclades:
S1a Z41335

S1a1 Z42413
- S1a1a
  - S1a1a1 P60, P304, P308
  - S1a1a2
- S1a1b M230, P202, P204 – "demoted" from its previous position as the basal Haplogroup S* (and known before that as Haplogroup K5)
  - S1a1b1 M254 (previously known as K2b1a4a)
    - S1a1b1a P57
    - S1a1b1b P61
    - S1a1b1c P83
    - S1a1b1d SK1891
S1a2 P79, P307
S1a3 P315
- S1a3a Z41763
- S1a3b~ P401

S1b~ B275, Z33756, Z33757, Z33758, Z33759

S1c~ Z41926, Z41927, Z41928, Z41929, Z41930

S1d SK1806

(Based on the 2017 ISOGG tree and subsequent published research.^[1])

Distribution

Basal S1a* appears to be extremely rare or extinct in living males. The primary subclade S-P405* is also relatively rare, but is found at significant levels among various Micronesian populations: 5.6%. It is also found among males on the Indonesian island of Sumba at a rate of 0.2%.^[4]

According to ISOGG (2017), S1a1 (Z42413) has been found among the Lebbo' people of Indonesia and S1a1a1 (P60) among indigenous Australians.^[1] One study has reported finding S-M230 (S1a1b) in: 52% (16/31) of a sample from the Papua New Guinea (PNG) Highlands; 21% (7/34) of a sample from the Moluccas (Maluku); 16% (5/31) of a sample from the Papua New Guinea coast; 12.5% (2/16) of a sample of Tolai from New Britain; 10% (3/31) of a sample from Nusa Tenggara, and; 2% (2/89) of a sample from the West New Guinea lowlands/coast. One subclade, Haplogroup S1a1b1d1a (S-M226.1) has been found at low frequencies in the Admiralty Islands and along the coast of mainland PNG. ^[5] ^[6]

The distribution of the other major subclades of S1a according to ISOGG,^[1] is as follows:

S1a2 (P79) – Melanesia and Papua New Guinea, including the Admiralty Islands;
S1a3 (P315) – indigenous Australians and;
S1a3b (P401) – Vanuatu.

Footnotes

1 2 3 4 5 International Society of Genetic Genealogy (ISOGG; 2017), Y-DNA Haplogroup Tree 2015 (24 March 2017).
↑ http://www.phylotree.org/Y/tree/index.htm
↑ Karafet TM, Mendez FL, Sudoyo H, Lansing JS, Hammer MF (June 2014). "Improved phylogenetic resolution and rapid diversification of Y-chromosome haplogroup K-M526 in Southeast Asia". Eur J Hum Genet. 23: 369–373. doi:10.1038/ejhg.2014.106. PMC 4326703. PMID 24896152.
↑ Karafet TM, Mendez FL, Sudoyo H, Lansing JS, Hammer MF (2013). "Table 1 ("Improved phylogenetic resolution and rapid diversification of Y-chromosome haplogroup K-M526 in Southeast Asia")". European Journal of Human Genetics. 23. doi:10.1038/ejhg.2014.106. PMC 4326703.
↑ Kayser M, Choi Y, Van Oven M, Mona S, Brauer S, Trent RJ, Suarkia D, Schiefenhovel W, Stoneking M (2008). "The Impact of the Austronesian Expansion: Evidence from mtDNA and Y Chromosome Diversity in the Admiralty Islands of Melanesia". Molecular Biology and Evolution. 25 (7): 1362–74. doi:10.1093/molbev/msn078. PMID 18390477.
↑ Cox MP, Mirazón Lahr M (2006). "Y-chromosome diversity is inversely associated with language affiliation in paired Austronesian- and Papuan-speaking communities from Solomon Islands". American Journal of Human Biology. 18 (1): 35–50. doi:10.1002/ajhb.20459. PMID 16378340.

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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[isogg2017-1] 1 2 3 4 5 International Society of Genetic Genealogy (ISOGG; 2017), Y-DNA Haplogroup Tree 2015 (24 March 2017).

[2] ttp://www.phylotree.org/Y/tree/index.htm

[Karafet2014-3] Karafet TM, Mendez FL, Sudoyo H, Lansing JS, Hammer MF (June 2014). "Improved phylogenetic resolution and rapid diversification of Y-chromosome haplogroup K-M526 in Southeast Asia". Eur J Hum Genet. 23: 369–373. doi:10.1038/ejhg.2014.106. PMC 4326703. PMID 24896152.

[Karafet-4] Karafet TM, Mendez FL, Sudoyo H, Lansing JS, Hammer MF (2013). "Table 1 ("Improved phylogenetic resolution and rapid diversification of Y-chromosome haplogroup K-M526 in Southeast Asia")". European Journal of Human Genetics. 23. doi:10.1038/ejhg.2014.106. PMC 4326703.

[5] Kayser M, Choi Y, Van Oven M, Mona S, Brauer S, Trent RJ, Suarkia D, Schiefenhovel W, Stoneking M (2008). "The Impact of the Austronesian Expansion: Evidence from mtDNA and Y Chromosome Diversity in the Admiralty Islands of Melanesia". Molecular Biology and Evolution. 25 (7): 1362–74. doi:10.1093/molbev/msn078. PMID 18390477.

[6] Cox MP, Mirazón Lahr M (2006). "Y-chromosome diversity is inversely associated with language affiliation in paired Austronesian- and Papuan-speaking communities from Solomon Islands". American Journal of Human Biology. 18 (1): 35–50. doi:10.1002/ajhb.20459. PMID 16378340.

[vanOven2014-7] 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.

[ISOGG2015-8] International Society of Genetic Genealogy (ISOGG; 2015), Y-DNA Haplogroup Tree 2015. (Access date: 1 February 2015.)

[A0-T-9] Haplogroup A0-T is also known as A-L1085 (and previously as A0'1'2'3'4).

[A1-10] Haplogroup A1 is also known as A1'2'3'4.

[LT-11] Haplogroup LT (L298/P326) is also known as Haplogroup K1.

[K2-12] 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-13] 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-14] Haplogroup K2b (M1221/P331/PF5911) is also known as Haplogroup MPS.

[K2e-15] Haplogroup K2e (K-M147) was previously known as "Haplogroup X" and "K2a" (but is a sibling subclade of the present K2a).

[K-M2313-16] 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)

[K2b1-17] Haplogroup K2b1 (P397/P399) is also known as Haplogroup MS, but has a broader and more complex internal structure.

[P-18] Haplogroup P (P295) is also klnown as K2b2.

[S-19] Haplogroup S, as of 2017, is also known as K2b1a. (Previously the name Haplogroup S was assigned to K2b1a4.)

[M-20] Haplogroup M, as of 2017, is also known as K2b1b. (Previously the name Haplogroup M was assigned to K2b1d.)