R   M207/UTY2, M306/S1, P224, P227, P229, P232, P280, P285, S4, S8, S9
�       R*   -
�       R1   M173/P241, P225, P231, P233, P234, P236, P238, P242, P286, P294
�      �       R1*   -
�      �       R1a   L62, L63
�      �       �       R1a*   -
�      �       �       R1a1   SRY1532.2/SRY10831.2
�      �       �      �       R1a1*   -
�      �       �      �       R1a1a   M17, M198
�      �       �      �       �       R1a1a*   -
�      �       �      �       �       R1a1a1   M56
�      �       �      �       �       R1a1a2   M157
�      �       �      �       �       R1a1a3   M64.2, M87, M204
�      �       �      �       �       R1a1a4   P98
�      �       �      �       �       R1a1a5   PK5
�      �       R1b   M343
�      �       �       R1b*   -
�      �       �       R1b1   P25
�      �       �      �       R1b1*   -
�      �       �      �       R1b1a   M18   (position relative to P297 uncertain)
�      �       �      �       R1b1b   P297
�      �       �      �       �       R1b1b*   -
�      �       �      �       �       R1b1b1   M73   
�      �       �      �       �       R1b1b2   M269, S3, S10, S13, S17   
�      �       �      �       �      �       R1b1b2*   -
�      �       �      �       �      �       R1b1b2a   L23/S141, L49
�      �       �      �       �      �       �       R1b1b2a*   -
�      �       �      �       �      �       �       R1b1b2a1   L11/S127, L51, L52, P310/S129, P311/S128
�      �       �      �       �      �       �      �       R1b1b2a1*   -
�      �       �      �       �      �       �      �       R1b1b2a1a   M405/S21/U106
�      �       �      �       �      �       �      �       �       R1b1b2a1a*   -
�      �       �      �       �      �       �      �       �       R1b1b2a1a1   M467/S29/U198
�      �       �      �       �      �       �      �       �       R1b1b2a1a2   P107
�      �       �      �       �      �       �      �       �       R1b1b2a1a3   DYS439(null)/L1/S26
�      �       �      �       �      �       �      �       �       R1b1b2a1a4   L48/S162    (position relative to P107 and L1/S26 uncertain)
�      �       �      �       �      �       �      �       �      �       R1b1b2a1a4*   -
�      �       �      �       �      �       �      �       �      �       R1b1b2a1a4a   L44, L45, L46, L47
�      �       �      �       �      �       �      �       R1b1b2a1b   P312/S116
�      �       �      �       �      �       �      �       �       R1b1b2a1b*   -
�      �       �      �       �      �       �      �       �       R1b1b2a1b1   M65
�      �       �      �       �      �       �      �       �       R1b1b2a1b2   M153
�      �       �      �       �      �       �      �       �       R1b1b2a1b3   M167/SRY2627
�      �       �      �       �      �       �      �       �       R1b1b2a1b4   S28/U152
�      �       �      �       �      �       �      �       �      �       R1b1b2a1b4*   -
�      �       �      �       �      �       �      �       �      �       R1b1b2a1b4a   M126    (position relative to L2/S139 uncertain)
�      �       �      �       �      �       �      �       �      �       R1b1b2a1b4b   M160    (position relative to L2/S139 uncertain)
�      �       �      �       �      �       �      �       �      �       R1b1b2a1b4c   L2/S139
�      �       �      �       �      �       �      �       �      �       �       R1b1b2a1b4c*   -
�      �       �      �       �      �       �      �       �      �       �       R1b1b2a1b4c1   L20/S144
�      �       �      �       �      �       �      �       �       R1b1b2a1b5   S68
�      �       �      �       �      �       �      �       �       R1b1b2a1b6   L21/S145
�      �       �      �       �      �       �      �       �      �       R1b1b2a1b6*   -
�      �       �      �       �      �       �      �       �      �       R1b1b2a1b6a   M37
�      �       �      �       �      �       �      �       �      �       R1b1b2a1b6b   M222/USP9Y+3636
�      �       �      �       �      �       �      �       �      �       R1b1b2a1b6c    P66
�      �       �      �       R1b1c   M335    (position relative to P297 uncertain)
�       R2   M124, P249, P267

Private SNPs

• L3 is located under L2.
• L4 and S44 are located under S28/U152.
• 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.
• M228.2 is located under L20.
• PK5 is located under M17.
• 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.

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

• Haplogroup R1 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 is believed to have arisen on the Eurasian Steppe, and today is most frequently observed in eastern Europe and in western and central Asia. R1b is believed to have arisen in southwest Asia and today is most frequently observed in Europe and especially in western Europe, which it entered after the LGM largely in the form of R1b1b2. The Atlantic Modal Haplotype, or AMH, is the most common STR haplotype in haplogroup R1b1b2a.
• 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.
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. (pdf) 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.
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.
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.
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.
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.
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:

David Faux, U152+/S28+ Data
A. A. Foster, Variations of R1b Ydna in Europe: Distribution and Origins
Dennis Garvey, Discussion on R1a
Dennis Garvey, Discussion on R1b
Proofer Joan, Major R1b Haplotypes in YHRD
Charles Kerchner, R1b and Subclades YDNA Haplogroup Project
John McEwan, Dal Riadic Migration Y Chromosome DNA Genealogy Page
Edward McKee, Y-DNA R1b1c7
National Geographic Genographic Project, Information on R1a
Cyndi Rutledge, R1a and Subclades YDNA Haplogroup Project
Ron Scott, R1a and R1b-R2: Frequency Distribution of Extended Haplotypes Gathered from YSearch
Sean Silver, The Jewish R1b Project
Vincent Vizachero, R1b Haplogroup Distribution Maps
David Weston et al, YDNA Haplogroup R1b-U106/S21+ Research Group
David Wilson, The Northwest Irish Variety of Y-DNA Haplogroup R
Dennis Wright, The Irish Type III Website

Corrections/Additions made since 31 December 2007:

• Karafet et al (2008) added on 4 May 2008.
• SNPs added on 4 May 2008: P98, P224, P225, P227, P229, P231, P232, P233, P234, P236, P238, P241, P242, P249, P267, P280, P285, P286, P294, P297, S116, S127, S128, S129
• Repaired spelling on Myres et al 2007 on 4 May 2008.
• Changed M18 from private to regular SNP on 4 May 2008.
• Added David Weston et al and Dennis Wright to Additional Resources on 4 May 2008.
• Added David Wilson and Vincent Vizachero as contacts for Haplogroup R on 4 May 2008.
• Added Charles Moore to Additional Resources on 6 May 2008.
• Notes added on uncertainty of location relative to P297 added to R1b1a and R1b1c on 7 May 2008.
• Haplogroup R description rewritten on 7 May 2008.
• The location of M37, M65 and P66 beneath S116 has been confirmed and the disclaimer removed on 9 May 2008.
• The location of S128 and S129 have been on confirmed on 9 May 2008 and are no longer marked provisional.
• SNPs L2/S139 were added on 26 September 2008.
• Notes for M126 and M160 added on 1 October 2008.
• Added L11, L20, L21, L23, L44, L45, L46, L47, L48, L49, L51, L52, P310, P311, P312, S144, S145 on 7 November 2008.
• Removed John McEwan and David Wilsons as contact people for Haplogroup R on 7 November 2008.
• SNPs L48, L61, L62, L63, S141, S162 were added on 15 Decenber 2008.
• Corrected subclades for L49 and L48/S162 on 21 December 2008.
• Changed location in Notes for L9 and L10 on 22 December 2008.

Contact person for Haplogroup R: Vincent Vizachero.

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