Haplogroup S1a (Y-DNA)

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

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

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

Main article: Haplogroup S-B254

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. International Society of Genetic Genealogy (ISOGG; 2017), Y-DNA Haplogroup Tree 2015 (24 March 2017).
2. "PhyloTree y - Minimal y tree".
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 (3): 369–373. doi:10.1038/ejhg.2014.106. PMC 4326703. PMID 24896152.
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 (3): 369–373. doi:10.1038/ejhg.2014.106. PMC 4326703. PMID 24896152.
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. S2CID 4824401.