R   M207/UTY2, P224, P227, P229, P232, P280, P285, S4, S8, S9, V45
�       R*   -
�       R1   M173/P241, M306/S1,P225, P231, P233, P234, P236, P238, P242, P245, P286, P294
�      �       R1*   -
�      �       R1a   L62/M513, L63/M511, L145/M449, L146/M420
�      �       �       R1a*   -
�      �       �       R1a1   L120/M516, L122/M448, M459, SRY1532.2/SRY10831.2
�      �       �      �       R1a1*   -
�      �       �      �       R1a1a   M17, M198, M512, M514, M515
�      �       �      �       �       R1a1a*   -
�      �       �      �       �       R1a1a1   M417, Page07 (see Notes)
�      �       �      �       �      �       R1a1a1*   -
�      �       �      �       �      �       R1a1a1a   M56
�      �       �      �       �      �       R1a1a1b   M157
�      �       �      �       �      �       R1a1a1c   M64.2, M87, M204
�      �       �      �       �      �       R1a1a1d   P98
�      �       �      �       �      �       R1a1a1e   PK5
�      �       �      �       �      �       R1a1a1f   M434
�      �       �      �       �      �       R1a1a1g   M458
�      �       �      �       �      �       �       R1a1a1g*   -
�      �       �      �       �      �       �       R1a1a1g1   M334    (position relative to L260 uncertain)
�      �       �      �       �      �       �       R1a1a1g2   L260
�      �       R1b   M343
�      �       �       R1b*   -
�      �       �       R1b1   L278, M415, P25
�      �       �      �       R1b1*   -
�      �       �      �       R1b1a   V88
�      �       �      �       �      R1b1a*   -
�      �       �      �      �       R1b1a1   M18
�      �       �      �      �       R1b1a2   V8
�      �       �      �      �       R1b1a3   V35
�      �       �      �       �      �       R1b1a3*   -
�      �       �      �       �      �       R1b1a3a   V7
�      �       �      �      �       R1b1a4   V69
�      �       �      �       R1b1b   P297
�      �       �      �       �       R1b1b*   -
�      �       �      �       �       R1b1b1   M73, M478
�      �       �      �       �       R1b1b2   L265, M269, M520, S3, S10, S13, S17
�      �       �      �       �      �       R1b1b2*   -
�      �       �      �       �      �       R1b1b2a   L23/S141, L49, L150
�      �       �      �       �      �       �       R1b1b2a*   -
�      �       �      �       �      �       �       R1b1b2a1   L51/M412/S167
�      �       �      �       �      �       �      �       R1b1b2a1*   -
�      �       �      �       �      �       �      �       R1b1b2a1a   L11/S127, L52, L151, P310/S129, P311/S128
�      �       �      �       �      �       �      �       �       R1b1b2a1a*   -
�      �       �      �       �      �       �      �       �       R1b1b2a1a1   M405/S21/U106
�      �       �      �       �      �       �      �       �      �       R1b1b2a1a1*   -
�      �       �      �       �      �       �      �       �      �       R1b1b2a1a1a   M467/S29/U198
�      �       �      �       �      �       �      �       �      �       R1b1b2a1a1b   P107    (position relative to L48 uncertain)
�      �       �      �       �      �       �      �       �      �       R1b1b2a1a1c   DYS439(null)/L1/S26
�      �       �      �       �      �       �      �       �      �       R1b1b2a1a1d   L48/S162    
�      �       �      �       �      �       �      �       �      �       �       R1b1b2a1a1d*   -
�      �       �      �       �      �       �      �       �      �       �       R1b1b2a1a1d1   L47
�      �       �      �       �      �       �      �       �      �       �      �       R1b1b2a1a1d1*   -
�      �       �      �       �      �       �      �       �      �       �      �       R1b1b2a1a1d1a   L44
�      �       �      �       �      �       �      �       �      �       �      �       �       R1b1b2a1a1d1a*   -
�      �       �      �       �      �       �      �       �      �       �      �       �       R1b1b2a1a1d1a1   L45, L46, L164
�      �       �      �       �      �       �      �       �      �       �       R1b1b2a1a1d2   L148
�      �       �      �       �      �       �      �       �      �       R1b1b2a1a1e   L257/S186    
�      �       �      �       �      �       �      �       �       R1b1b2a1a2   P312/S116
�      �       �      �       �      �       �      �       �      �       R1b1b2a1a2*   -
�      �       �      �       �      �       �      �       �      �       R1b1b2a1a2a   M65
�      �       �      �       �      �       �      �       �      �       R1b1b2a1a2b   M153
�      �       �      �       �      �       �      �       �      �       R1b1b2a1a2c   M167/SRY2627
�      �       �      �       �      �       �      �       �      �       R1b1b2a1a2d   S28/U152
�      �       �      �       �      �       �      �       �      �      �       R1b1b2a1a2d*   -
�      �       �      �       �      �       �      �       �      �       �       R1b1b2a1a2d1   M126    (position relative to L2/S139 uncertain)
�      �       �      �       �      �       �      �       �      �       �       R1b1b2a1a2d2   M160    (position relative to L2/S139 uncertain)
�      �       �      �       �      �       �      �       �      �       �       R1b1b2a1a2d3   L2/S139
�      �       �      �       �      �       �      �       �      �       �      �       R1b1b2a1a2d3*   -
�      �       �      �       �      �       �      �       �      �       �      �       R1b1b2a1a2d3a   L20/S144
�      �       �      �       �      �       �      �       �      �       �       R1b1b2a1a2d4   L4/S178
�      �       �      �       �      �       �      �       �      �       R1b1b2a1a2e   L165/S68
�      �       �      �       �      �       �      �       �      �       R1b1b2a1a2f   L21/M529/S145
�      �       �      �       �      �       �      �       �      �       �       R1b1b2a1a2f*   -
�      �       �      �       �      �       �      �       �      �       �       R1b1b2a1a2f1   M37
�      �       �      �       �      �       �      �       �      �       �       R1b1b2a1a2f2   M222/USP9Y+3636
�      �       �      �       �      �       �      �       �      �       �       R1b1b2a1a2f3   P66
�      �       �      �       �      �       �      �       �      �       �       R1b1b2a1a2f4   L226/S168
�      �       �      �       �      �       �      �       �      �       �       R1b1b2a1a2f5   L193/S176
�      �       �      �       �      �       �      �       �      �       �       R1b1b2a1a2f6   L144/S175
�      �       �      �       R1b1c   M335
�       R2   M479
�      �       R2*   -
�      �       R2a   L266, M124, P249, P267

Private SNPs

• L3 is located under L2.
• L5, L6 and S69 are located under U106.
• L7, L8, L61, S121, S122, S123 and S124 are located under P312/S116.
• L9 and L10 are located under L21.
• L12 is located under M198.
• L50/S136 is located under L23.
• L196 is located under L2.
• L277 is located under L23.
• M228.2 is located under L20.
• P89.2 is located under U106.
• PK5 is located under M17.
• S44 is located under S28/U152.
• S50 is located under M269.

NOTES:

• P25 is an unreliable SNP with a 2% reversion rate within R1b1. It should not be used by itself to classify individuals. For further details see Adams et al (2006) and Discussion of P25
• Identical SNPs that were discovered separately are listed in alphabetical order, not necessarily in the order of discovery, and separated by "/". Examples: M207/UTY2, M306/S1, M173/P241, SRY1532.2/SRY10831.2, L23/S141, L48/S162, L11/S127, P310/S129, P311/S128, M405/S21/U106, M467/S29/U198, DYS439/L1/S26, P312/S116, M167/SRY2627, S28/U152, L2/S139, L20/S144, L21/S145, M222/USP9Y+3636.
• SNP SRY1532/SRY10831 appears twice on the Y-DNA Haplogroup tree. It is first seen as a mutation SRY1532.1/SRY10831.1 which is reported as a positive in BT and then reappears as a back mutation SRY1532.2/SRY10831.2 which is reported as a negative in R1a.
• Thanks to Jim Wilson, Thomas Krahn, and David F. Reynolds for their consultation on Haplogroup R.
• SNPS named Page are so named for their discoverer/developer David C. Page, Whitehead Institute for Biomedical Research. They are also written out such as PAGES00007 or PS7.

Y-DNA haplogroup R (M207) is believed to have arisen approximately 27,000 years ago in Asia. The two currently defined subclades are R1 and R2.

• Haplogroup R1 (M173) is estimated to have arisen during the height of the Last Glacial Maximum (LGM), about 18,500 years ago, most likely in southwestern Asia. The two most common descendant clades of haplogroup R1 are R1a and R1b.
• R1a (M420) is believed to have arisen on the Eurasian Steppe or the Indus Valley, and today is most frequently observed in eastern Europe and in western and central Asia. Haplogroup R1a1a7 (M458) is found at frequencies approaching or exceeding 30% in Eastern Europe.
• R1b (M343) is believed to have arisen in southwest Asia and today its sublcades are bound in various distributions across Eurasia and Africa.
• Paragroup R1b1* and haplogroup R1b1a (V88) are found most frequently in SW Asia and Africa. The African examples are almost entirely within R1b1a and are associated with the spread of Chadic languages.
• Haplogroup R1b1b (P297) is found throughout Eurasia.
• Haplogroup R1b1b1 (M73) is observed most frequently in Asia, with low frequency of observation in Europe.
• Haplogroup R1b1b2 (M269) is observed most frequently in Europe, especially western Europe, but with notable frequency in southwest Asia. R1b1b2 is estimated to have arisen approximately 4,000 to 8,000 years ago in southwest Asia and to have spread into Europe from there. The Atlantic Modal Haplotype, or AMH, is the most common STR haplotype in haplogroup R1b1b2a1a (P310/S129) and most European R1b1b2 belongs to haplogroups R1b1b2a1a1 (U106) or R1b1b2a1a2 (P312/S116).
• R2 is most often observed in Asia, especially on the Indian sub-continent and in central Asia.

References:

Adams et al, The Case of the Unreliable SNP: Recurrent Back-mutation of Y-chromosomal Marker P25 Through Gene Conversion. (abstract) Forensic Science International 159:14-20, 2006.
Alonso et al, The Place of the Basques in the European Y-chromosome Diversity Landscape. (available by subscription) European Journal of Human Genetics, 13:1293-1302, 2005.
Behar et al, Contrasting Patterns of Y Chromosome Variation in Ashkenazi Jewish and Host Non-Jewish European Populations. (pdf) Human Genetics 114:354-365, 2004.
Balaresque et al, A Predominantly Neolithic Origin for European Paternal Lineages. PLoS biology. 8(1):e1000285 2010.
Capelli et al, Population Structure in the Mediterranean Basin: A Y Chromosome Perspective. (pdf) Annals of Human Genetics, 2005.
Cinnioglu et al, Excavating Y-chromosome Haplotype Strata in Anatolia. (pdf) Human Genetics, 114:127-148, 2004.
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.
Cruciani et al, Human Y Chromosome Haplogroup R-V88: A Paternal Genetic Record of Early Mid Holocene Trans-Saharan Connections and the Spread of Chadic Languages. (abstract) (Epub ahead of print) European Journal of Human Genetics, January 6, 2010a.
Cruciani et al, Strong Intra- and Inter-continental Differentiation Revealed by Y chromosome SNPs M269, U106 and U152. Forensic Science International. Genetics,7-10, 2010b.
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.
Flores et al, Reduced Genetic Structure of the Iberian Peninsula Revealed by Y-chromosome Analysis: Implications for Population Demography. (pdf) European Journal of Human Genetics, 12:855-863, 2004.
Hinds et al, Whole-genome Patterns of Common DNA Variation in Three Human Populations. Science, 307:1072-1079, 2005.
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.
Karlsson et al, Y-chromosome Diversity in Sweden - A Long-time Perspective. (pdf) European Journal of Human Genetics, 14:963-970, 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.
Kivisild et al, The Genetic Heritage of the Earliest Settlers Persists in Both Indian Tribal and Caste Populations. (pdf) American Journal of Human Genetics, 72:313-332, 2003.
McEvoy et al, Y-chromosomes and the Extent of Patrilineal Ancestry in Irish Surnames (abstract) Human Genetics 2006 Jan 12;:1-8 (Epub ahead of print).
Mohyuddin et al, Detection of Novel Y SNPs Provides Further Insights into Y Chromosomal Variation in Pakistan. Journal of Human Genetics, 2006.
Moore et al, A Y-chromosome Signature of Hegemony in Gaelic Ireland. American Journal of Human Genetics, 78(2):334-338, 2006.
. Myres et al, A Major Y-chromosome Haplogroup R1b Holocene Era Founder Effect in Central and Western Europe. European journal of human genetics : EJHG. (July):1-7, 2010.
Myres et al, (2007), Y-chromosome Short Tandem Repeat DYS458.2 Non-concensus Alleles Occur Independently in Both Binary Haplogroups J1-M267 and R1b3-M405. Croatian Medical Journal, 48, 2007.
Nasidze et al, MtDNA and Y-chromosome Variation in Kurdish Groups. (abstract) Annals of Human Genetics, 69:401-412, 2005.
Regueiro et al, Iran: Tricontinental Nexus for Y-Chromosome Driven Migration. (abstract) Human Heredity, Vol. 61, No 3, 132-143, 2006.
Repping et al, High Mutation Rates Have Driven Extensive Structural Polymorphism among Human Y Chromosomes. (pdf) National Genetics, 38: 463-467, 2006.
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.
Semino et al, The Genetic Legacy of Paleolithic Homo Sapiens Sapiens in Extant Europeans. (pdf) Science, V290:1155-1159, 2000.
Semino et al, Ethiopians and Khoisan Share the Deepest Clades of the Human Y-Chromosome Phylogeny. (pdf) American Journal of Human Genetics, 70:265-268, 2002.
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. (available by subscription) 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.
Sims et al, Sub-Populations Within the Major European and African Derived Haplogroups R1b3 and E3a Are Differentiated by Previously Phylogenetically Undefined Y-SNPs. Human Mutation: Mutation in Brief #940, Online, 2007.
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.
Underhill et al, Separating the Post-Glacial Coancestry of European and Asian Y Chromosomes within Haplogroup R1a. (abstract) European Journal of Human Genetics, 1-6, 2009.
Valone et al, Y SNP Typing of African-American and Caucasian Samples Using Allele-Specific Hybridization and Primer Extension. (pdf) Journal of Forensic Science, 49:4, July 2004.
Wells et al, The Eurasian Heartland: A Continental Perspective on Y-chromosome Diversity. PNAS, Vol. 98; 18:10244-10249, 2001.

Additional Resources:

--, R1a International Y-DNA Project
Dan Draghici, YDNA Haplogroup R1b-U106/S21+ Research Group
David Faux, U152+/S28+ Data
Charles Kerchner, R1b and Subclades YDNA Haplogroup Project
John McEwan, Dal Riadic Migration Y Chromosome DNA Genealogy Page
Cyndi Rutledge, R1a and Subclades YDNA Haplogroup Project
Sean Silver, The Jewish R1b Project
Richard Stevens, R-P312 and Subclades Project.
David Wilson, R-M222 Haplogroup Project (Niall of the 9 Hostages, Ui Neill Clan)
Dennis Wright, The Irish Type III Website (L226) (Dalcassian Clans)

Corrections/Additions made since 1 January 2010:

• Added the following SNPs L165, L193, L196, L226, P89.2, V7, V8, V35, V45, V69, V88 and Cruciani et al (2010) on 12 January 2010.
• Revised Haplogroup description and removed links in Additional Resources that no longer exist or are outdated on 13 January 2010.
• Moved Ron Scott reference in additional resources to Tree Trunk on 13 January 2010.
• Added the following SNPs L120, L122 L145, L146, M417, M448, M449, M459, M511, M512, M513, M514, M515, M516, Page07 on 16 January 2010.
• Added Hinds et al (2005) and Repping (2006) on 16 January 2010.
• Changed position for L165 to identical with S68 and added L265 on 27 January 2010.
• Changed M306/S1 from R to R1; added P245 on 29 January 2010.
• Added S168 on 1 February 2010.
• Added L4 (no longer private), S167 and S176 on 3 March 2010.
• Added L150, L151, and L277 on 9 April 2010.
• Added L260; corrected typo of L222 to L122; changed M335 from private to confirmed on 25 April 2010.
• Reclassified L277 as private and added L278 on 26 April 2010.
• Added L257 on 12 May 2010.
• SNPs M17, M198, M512, M514, and M515 were removed from R1a1a and moved to R1a1a1 on 17 August 2010.
• SNPs for R1a1a and R1a1a1 were inadvertently reversed and are now in their proper order on 25 August 2010.
• Added L144, L266, M412, M415, M478, M479, M520, M529, S175, S178 and S186 on 9 September 2010.
• Added Cruciani et al (2010b), Myers et al (2010) on 9 September 2010.
• Added R1a International Y-DNA Project on 2 November 2010.
• Added more information on Notes about SNPs from David C. Page on 4 November 2010.

Contact person for Haplogroup R: Vincent Vizachero.

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