O   M175, P186, P191, P196
�     O*   -
�     O1   MSY2.2
�    �     O1*   -
�    �     O1a   M119, Page20
�    �     �     O1a*   -
�    �     �     O1a1   M307.1/P203.1
�    �     �    �     O1a1*   -
�    �     �    �     O1a1a   M101
�    �     �     O1a2   M50, M103, M110
�     O2   L463, L690, P31, M268
�    �     O2*   -
�    �     O2a   PK4
�    �     �     O2a*   -
�    �     �       O2a1   M95
�    �     �    �     O2a1*   -
�    �     �    �     O2a1a   M88, M111
�    �     �    �     O2a1b   M297
�    �     O2b   IMS-JST022454, L272.2, M176//Page63/SRY465, M302, P49, Page92
�    �     �     O2b*   -
�    �     �     O2b1   M312
�    �     �    �     O2b1*   -
�    �     �    �     O2b1a   47z
�    �     �    �     O2b1b   L682
�     O3   M122, P198
�    �     O3*   -
�    �     O3a   M324, P93/Page79, P197, P199, P200
�    �     �     O3a*   -
�    �     �     O3a1   L127.1, KL1/L465, KL2/L467
�    �     �    �     O3a1*   -
�    �     �    �     O3a1a   M121, DYS257_1/DYS257_2/P27.2_1/P27.2_2
�    �     �    �     O3a1b   M164
�    �     �    �     O3a1c   IMS-JST002611
�    �     �    �     �     O3a1c*   -
�    �     �    �     �     O3a1c1   P103
�    �     �     O3a2   IMS-JST021354/P201
�    �     �    �     O3a2*   -
�    �     �    �     O3a2a   M159/Page96
�    �     �    �     O3a2b   M7
�    �     �    �     �     O3a2b*   -
�    �     �    �     �     O3a2b1   M113, M188, M209
�    �     �    �     �    �     O3a2b1*   -
�    �     �    �     �    �     O3a2b1a   N4
�    �     �    �     �    �     O3a2b1b   N5
�    �     �    �     �     O3a2b2   P386
�    �     �    �     O3a2c   P164 (See Notes **)
�    �     �    �     �     O3a2c*   -
�    �     �    �     �     O3a2c1   M134
�    �     �    �     �    �     O3a2c1*   -
�    �     �    �     �    �     O3a2c1a   M117, M133, Page23
�    �     �    �     �    �     �     O3a2c1a*   -
�    �     �    �     �    �     �     O3a2c1a1   M162_1, M162_2
�    �     �    �     �    �     O3a2c1b   P101
�    �     �     O3a3   M300
�    �     �     O3a4   M333

Private SNPs - After having been investigated, these SNPs have not met the population distribution criteria for placement on the tree. Either too few confirmed positive testers have been found OR multiple confirmed testers were confined to either a single surname or to a small group of related males.

• N6, N7, N8, N9, N10, N11 were discovered downstream of M175. Listed 6 Apr 2006.

SNPs under Investigation - Additional testing is needed to confirm adequate positive samples and/or correct placement on the tree.

• L246, L247 and L466 have been found in O1-MSY2.2. Listed 26 Oct 2011.
• L387.1 has been found in O3a2-P201, Listed 26 Oct 2011.
• L681 has been found in O2b1b-L682. Listed 26 Oct 2011.
• Page109 has been found under O1a-M119, parallel to M50. Listed 26 Oct 2011.
• Page115 has been found downstream of O1a2-M50. Listed 26 Oct 2011.
• Page59 has been found under O2-M268, parallel to PK4. Listed 26 Oct 2011.
• Page103 has been found downstream of O2a1-M95. Listed 26 Oct 2011.
• Page90 has been found downstream of O2b-SRY465. Listed 26 Oct 2011.
• Page69 has been found downstream of O3a1c-IMS-JST002611. Listed 26 Oct 2011.
• Page127 has been found in O3, parallel to O3a1c-IMS-JST002611. Listed 26 Oct 2011.
• Page124 has been found in O3, downstream of Page 127. Listed 26 Oct 2011.
• Page130 has been found in O3, downstream of Page 124. Listed 26 Oct 2011.
• Page 125 has been found in O3, downstream of M134, Parallel to M117. Listed 26 Oct 2011.
• Page 101 has been found in O3, downstream of Page 125. Listed 26 Oct 2011.

NOTES:

• Identical SNPs that were discovered separately are listed in alphabetical order, not necessarily in the order of discovery, and separated by "/". Examples: M307.2/P203.2, M176/SRY465, DYS257,P27.2, P201/021354
• ** P164 is now defined to be an A to G mutation (rs17316007, Y-position 12511232) downstream of P201 and upstream of M134. P386 is now defined to be a T to C mutation downstream of M7. These snps were earlier confused. The tree is reorganized as of 24 June 2011.
• The L1 insertion (also known as LINE1) which appeared in previous versions of the tree is associated with subclades within sub-group O3 but has been observed to be absent due to recurrent deletions so is not included in the current version of the tree.
• The position of provisional snps M300 and M333 relative to L127.1, KL1/L465 and KL2/L467 is unknown.

Y-DNA haplogroup O probably originated in East Asia and later migrated into the South Pacific. The lineage expanded into Taiwan (high frequency in the aboriginal Taiwanese), Indonesia, Melanesia, Micronesia, and Polynesia.

O3 is the predominant sub-group in China. The O1 and O2a lineages are found in Southeast Asian populations of Malaysia, Vietnam, Indonesia and southern China. The O2b sub-group is of high frequency in the Japanese and Korean populations.

References:
Cinnioglu et al, Excavating Y-chromosome Haplotype Strata in Anatolia. (pdf) Human Genetics. 114:127-148, 2004.
Cox M P & Lahr M M, Y-Chromosome Diversity Is Inversely Associated with Language Affiliation in Paired Austronesian- and Papuan-Speaking Communities from Solomon Islands. (pdf) American Journal of Human Biology, 18:35-50, 2006.
Cruciani et al, A Back Migration from Asia to Sub-Saharan Africa Is Supported by High-Resolution Analysis of Human Y-Chromosome Haplotypes. American Journal of Human Genetics, 70:1197-1214, 2002.
Deng et al, Evolution and Migration History of the Chinese Population Inferred from the Chinese Y-chromosome Evidence. (pdf) Journal of Human Genetics, 49:339-348, 2004.
Hammer et al, Dual Origins of the Japanese: Common Ground for Hunter-gatherer and Farmer Y Chromosomes. (abstract) Journal of Human Genetics, 51:47-58, 2006.
Karafet et al, New Binary Polymorphisms Reshape and Increase Resolution of the Human Y-Chromosomal Haplogroup Tree. Abstract. Genome Research, published online April 2, 2008. Supplementary Material.
Karafet et al, Paternal Population History of East Asia: Sources, Patterns, and Microevolutionary Processes. (pdf) American Journal of Human Genetics, 69:615-628, 2001.
Kayser et al, Independent Histories of Human Y Chromosomes from Melanesia and Australia. American Journal of Human Genetics, 68:173-190, 2001.
Kayser et al, Melanesian and Asian Origins of Polynesians: mtDNA and Y-Chromosome Gradients across the Pacific. MBE Advance Access published August 21, 2006.
Kayser et al. Reduced Y-Chromosome, but Not Mitochondrial DNA, Diversity in Human Populations from West New Guinea. American Journal of Human Genetics, 72:281-302, 2003.
Mohyuddin et al, Detection of Novel Y SNPs Provides Further Insights into Y Chromosomal Variation in Pakistan. Journal of Human Genetics, 2006.
Mona et al, Patterns of Y-chromosome Diversity Intersect with the Trans-New Guinea Hypothesis. Mol Biol Evol. 2007 Sep 10; [Epub ahead of print]
Nonaka et al, Y Chromosomal Binary Haplogroups in the Japanese Population and their Relationship to 16 Y-STR Polymorphisms. (abstract) Annals of Human Genetics, 71:480-495, 2007.
Regueiro et al, Iran: Tricontinental Nexus for Y-Chromosome Driven Migration. (abstract) Human Heredity, Vol. 61, No 3, 132-143, 2006.
Rootsi S, Human Y Chromosomal Variations in European Populations. (dissertation) Council of the Institute of Molecular and Cell Biology, University of Tartu, Oct 2004.
Rozen et al, Remarkably Little Variation in Proteins Encoded by the Y Chromosome's Single-Copy Genes, Implying Effective Purifying Selection. American Journal of Human Genetics. 2009 December 11; 85(6): 923-928.
Scheinfeldt et al, Unexpected NRY Chromosome Variation in Northern Island Melanesia. (Link and comments from Dienekes' Anthropological Blog) Society for Molecular Biology, 2006.
Sengupta et al, 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. (pdf) American Journal of Human Genetics, 78:202-221, 2006.
Shen et al, Reconstruction of Patrilineages and Matrilineages of Samaritans and other Israeli Populations from Y-Chromosome and Mitochondrial DNA Sequence Variation. (pdf) Human Mutation, 24:248-260, 2004.
<Shi et al, Y-Chromosome Evidence of Southern Origin of the East Asian-Specific Haplogroup O3-M122. (abstract) American Journal of Human Genetics. 77:408-419, 2005.
Su et al, Y-chromosome Evidence for a Northward Migration of Modern Humans into Eastern Asia during the Last Ice Age. (pdf) American Journal of Human Genetics, 65:1718-1724, 1999.
Tan S, et al, Y-chromosome Polymorphisms Define the Origin of the Mang, an Isolated Population in China. Annals of Human Biology, Sep;34(5):573-581, 2007
Thangaraj et al, Genetic Affinities of the Andaman Islanders, a Vanishing Human Population. (pdf) Current Biology, 13:86-93, 2003.
Xue Y, et al, Male Demography in East Asia: A North-South Contrast in Human Population Expansion Times. (abstract) Genetics, 172:2431-2439, 2006
Shi Yan et al, An Updated Tree of Y-chromosome Haplogroup O and Revised Phylogenetic Positions of Mutations P164 and PK4. European Journal of Human Genetics advance online publication 20 April 2011; doi: 10.1038/ejhg.2011.64

Additional Resources:
ISOGG Wiki - What you need to know about Genetic Genealogy.
O...O3 Y-DNA Haplogroup Project, Denis Grigoriev.

Corrections/Additions made since 1 January 2011:

• Added haplogroup project to Additional Resources on 22 March 2011.
• Added Rozen et al (2009) on 24 March 2011.
• Added Page20, Page23, Page 92 on 29 March 2011.
• Added Page79, Page96 on 1 April 2011.
• Changed IMS-JST snps to full name instead of just using numbers on 3 April 2011.
• Added Kl1/L465, KL2/L467, L127.1 on 26 April 2011.
• Added Shi Yan et al (2011) on 26 April 2011.
• Corrected link for Rootsi's dissertation on 31 May 2011.
• Added note about P164 and its implications for the O tree on 31 May 2011.
• PK4 is no longer private on 31 May 2011.
• Determined correct placement for P164 and P386 (see note) on 24 June 2011.
• Corrected subclade name for P386 on 9 July 2011.
• Added L272.2 on 10 July 2011.
• Added extensions such as _1, _2, _3 to snps with multiple y-positions on 4 August 2011.
• Added L682, L690 on 11 September 2011.
• Added L246, L247, L387.1, L463, L466, L681, Page59, Page69, Page90, Page101, Page103, Page109, Page115, Page124, Page125, Page127, Page130 on 26 October 2011.

Contact Person for Haplogroup O: Gareth Henson

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