ISOGG 2009 Y-DNA Haplogroup R (original) (raw)

Y-DNA Haplogroup R and its Subclades - 2009
The entire work is identified by the Version Number and date given on theMain Page. Directions for citing the document are given at the bottom of the Main Page.
Version History Last revision date for this specific page: 24 November 2009

Because of continuing research, the structure of the Y-DNA Haplogroup Tree changes and ISOGG does its best to keep the tree updated with the latest developments in the field. The viewer may observe other versions of the tree on the Web. EmailAlice Fairhurst if the differences need clarification.

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, M420
� � � R1a* -
� � � R1a1 SRY1532.2/SRY10831.2
� � � � R1a1* -
� � � � R1a1a M17, M198
� � � � � R1a1a* -
� � � � � R1a1a1 M56
� � � � � R1a1a2 M157
� � � � � R1a1a3 M64.2, M87, M204
� � � � � R1a1a4 P98
� � � � � R1a1a5 PK5
� � � � � R1a1a6 M434
� � � � � R1a1a7 M458
� � � � � � R1a1a7* -
� � � � � � R1a1a7a M334
� � 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 L51
� � � � � � � � R1b1b2a1* -
� � � � � � � � R1b1b2a1a L11/S127, L52, 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
� � � � � � � � � 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
� � � � � � � � � � R1b1b2a1a2e S68
� � � � � � � � � � R1b1b2a1a2f L21/S145
� � � � � � � � � � � R1b1b2a1a2f* -
� � � � � � � � � � � R1b1b2a1a2f1 M37
� � � � � � � � � � � R1b1b2a1a2f2 M222/USP9Y+3636
� � � � � � � � � � � R1b1b2a1a2f3 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 andS69 are located under U106.
• L7, L8, L61,S121, S122, S123and 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) andDiscussion 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 subclades 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.
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, (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.
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:

Dan Draghici, YDNA Haplogroup R1b-U106/S21+ Research Group
David Faux, U152+/S28+ Data
A. A. Foster, Variations of R1b Ydna in Europe: Distribution and Origins
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
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
Richard Stevens, R-P312 and Subclades Project.
Vincent Vizachero, R1b Haplogroup Distribution Maps
David Wilson, R-M222 Haplogroup Project
Dennis Wright, The Irish Type III Website

Corrections/Additions made since 1 January 2009:

• Removed Garvey from Additional Resources on 22 January 2009.
• In Additional Resources: Changed from David Weston to Dan Draghici and added Richard Stevens on 9 March 2009.
• Added L51; in Additional Resources: deleted Edward McKee and changed project name and link for David Wilson on 10 March 2009.
• Removed note from L48 and added note to P107 on 17 March 2009.
• Repositioned L44, L45, L46 to underneath L47 on 9 April 2009.
• Added M434, M458 and M334 in R1a plus Underhill et al (2009) on 24 November 2009.

Contact person for Haplogroup R: Vincent Vizachero.