Summary of published results of the R subclade

Summary of published results in the R subclade

 

John McEwan

 

3rd January 2006 (updated 23rd October 2006)

 

Introduction

For those interested in genetic or anthro-genealogy perhaps one of the most confusing things, after you have grasped the basic concepts of Y-chromosome SNP based haplogroup, is the complexity of the available SNP and associated STR information within your haplogroup. The problems are varying names for haplogroups, SNPs with multiple names, and disparate sources of information, including papers that use common genotypes or samples or a combination of both.

 

This page attempts to summarize key aspects of the available literature for the R subclade, especially R1b. It is not definitive, does not cover the other haplogroups, and the reader is strongly recommended to actually read the articles. Its prime intention is to provide a clear road map to key data about individual SNPs. In particular it attempts to provide a list of key references with links where these are available, summarize what markers were genotyped, the numbers of individuals that were derived for each marker, and note availability of associated STR profiles.

 

Table 1. Summary of number of derived genotypes reported in the R haplogroup from the literature

Clade

SNP

Cinnoglu et al 2004

Brion et al edanp 2005

Vallone & Butler 2004

Underhill et al 1997

Bosch et al 2001

Brion et al (Spain) 2004

Underhill et al 2000

Rosser et al 2000

Hammer et al 2001

Karafet et al 2001

Cruciani et al 2002

Al-Zahery et al 2003

Flores et al 2004

Capelli et al 2003

Capelli et al 2005

Paracchini et al 2003

Sengupta et al 2006

Brion et al 2005

Nasidze et al 2004

Nasidze et al 2005

Moore et al 2006

Alonso et al 2005

Hammer et al 2006

Regueiro et al 2006

R pages Oct 23 2006

Total

total n

 

523

535

229

718x

353

453

1062

3616

2858

1383

608x

139

568

1775

656

2138

1432

1126

371

156

796

935

2517

150

353

24124

R

M207

126

 

105

 

 

 

 

 

 

113

63x

 

 

 

 

 

 

351

 

 

 

534

951

39

 

2219

R

S4

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

0

R

S8

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

0

R

S9

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

0

R*

 

 

 

 

 

 

 

 

 

 

15

 

 

 

 

 

 

 

 

 

 

 

2

4

 

 

21

R1

M306

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

37

 

 

R1

M173

121

 

 

 

75x

 

198

 

 

98

63x

24

334

1387

138

353

178

347

125

32

 

 

1053

 

 

4424

R1*

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

1

2

4

 

7

R1a

SRY10831.2

 

56

6

 

 

16

 

512

201

73

0

 

11

 

 

 

 

63

 

 

3

14

85

25

18

1083

R1a*

 

1?

4

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

1

 

5

R1a1

M17

36

52

 

36x

1

 

81

 

 

 

0

9

 

52

14

34

148

63

62

20

 

 

85

 

11

668

R1a1

M198

 

 

6

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

20

10

36

R1a1*

 

 

 

 

 

 

 

73

 

 

 

 

 

 

 

 

34

 

 

 

 

 

 

 

 

19

126

R1a1a

M56

 

 

 

 

 

 

1

 

 

 

 

 

 

 

 

0

 

 

 

 

 

 

 

 

0

1

R1a1b

M157

 

 

0

 

 

 

1

 

 

 

 

 

 

 

 

0

 

 

 

 

 

 

 

 

0

1

R1a1c

M64.2

 

 

 

 

 

 

3

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

0

3

R1a1c

M87

 

 

0

 

 

 

3

 

 

 

 

 

 

 

 

0

 

 

 

 

 

 

 

 

0

3

R1a1c

M204

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

1

 

1

R1b

M343

84

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

199

283

R1b*

 

1

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

1?

 

 

 

 

 

 

 

1

2

R1b1

P25

83

131

82

 

 

 

 

 

210

23

 

15

 

 

 

 

 

280

 

 

 

 

966

12

245

2047

R1b1*

 

2

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

15

 

 

17

R1b1a

M18

0

0

0

1x

0

 

2

 

 

 

0

 

 

 

 

0

 

 

 

 

 

 

 

 

0

2

R1b1b

M73

4

 

 

 

0

 

6

 

 

 

0

 

 

 

 

0

19

 

 

 

 

 

 

 

1

30

R1b1d

M335

1

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

1

R1b1c

M269

76

 

 

 

 

 

 

 

 

 

1

15

 

 

 

 

10

 

 

 

682

517

951

12

261

2525

R1b1c*

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

489

 

 

 

489

R1b1c1

M37

0

 

0

 

0

 

2

 

 

 

 

 

 

 

 

0

 

 

 

 

 

 

 

0

0

2

R1b1c2

M65

 

 

 

 

2x

 

2

 

 

 

 

 

 

 

 

0

 

 

 

 

 

 

 

0

0

2

R1b1c3

M126

 

 

 

 

0

 

1

 

 

 

 

 

 

 

 

0

 

 

 

 

 

 

 

 

0

1

R1b1c4

M153

 

0

1

 

8x1

 

7

 

 

 

 

 

6

 

 

5

 

 

 

 

 

18

 

0

1

39

R1b1c5

M160

 

 

 

 

0

 

3

 

 

 

 

 

 

 

 

0

 

 

 

 

 

 

 

 

0

3

R1b1c6

M167

 

2

 

 

11x2

8

5

23

 

 

 

 

23

 

 

1

 

 

 

 

1

10

 

0

12

85

R1b1c7

M222

0

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

0

65

65

R1b1c8

P66

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

0

0

R1b1c/P107+

P107

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

0

R1b1c/S50+

S50

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

1

1

R1b1c9

S21

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

34

34

R1b1c9*

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

20

20

R1b1c9a

S26

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

3

3

R1b1c9b

S29

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

3

3

R1b1c9/S69+

S69+

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

1

1

R1b1c10

S28

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

13

13

R1b1c10/S44+

S44

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

1

1

R2

M124

5

 

0

 

 

 

23

 

 

2?

 

 

 

 

 

0

81

 

10

18

 

 

 

2

5

144

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

STRs genotyped

10

na

na

na

8

6

na

 

na

 

8

 

na

6

6

na

9

0

na

9

17

5

11

na

37

 

NOTES

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

(1)Bosch et al had one novel M153

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

(2)Bosch had 5 novel SRY2627

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

(3)Bosch had 75-39 novel M173

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Other references examined but not icluded

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Bender et al 2003

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Underhill 2003

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Underhill 2001

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Wilson 2001

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Carvalho-Silva 2001

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Capelli 2003

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Shen 2001

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Semino 2000

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Hurles 1999

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Pacheo 2004

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Jarreta 2005

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Garcia 2003

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Khil et al 2005

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Maca-Meyer 2003

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Ke et al 2001

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

References

Alonso S, Flores C, Cabrera V, Alonso A, Martin P, Albarran C, Izagirre N, de la Rua C, Garcia O. 2005. The place of the Basques in the European Y-chromosome diversity landscape. Eur J Hum Genet. 2005 13:1293-302.

 

Al-Zahery N, Semino O, Benuzzi G, Magri C, Passarino G, Torroni A, Santachiara-Benerecetti AS. 2003 Y-chromosome and mtDNA polymorphisms in Iraq, a crossroad of the early human dispersal and of post-Neolithic migrations. Mol Phylogenet Evol. 28:458-72.

 

Bender, K., Stradmann-Bellinghausen, B., Rittner. C., Schneider, P.M. 2003. Comparative analysis of short tandem repeats and single nucleotide polymorphisms on the Y-chromosome in Germans, Chinese and Thais Legal Medicine 5:S164–S168

 

Bosch, E., Calafell, F., Comas, D., Oefner, P.J., Underhill, P.A. and Bertranpetit, J. 2001. High-resolution analysis of human Y-chromosome variation shows a sharp discontinuity and limited gene flow between Northwestern Africa and the Iberian Peninsula. Am. J. Hum. Genet. 68:1019-1029.

 

Brion M, Dupuy BM, Heinrich M, Hohoff C, Hoste B, Ludes B, Mevag B, Morling N, Niederstatter H, Parson W, Sanchez J, Bender K, Siebert N, Thacker C, Vide C, Carracedo A.  2005 A collaborative study of the EDNAP group regarding Y-chromosome binary polymorphism analysis. Forensic Sci Int. 153:103-8.

 

Brion M, Quintans B, Zarrabeitia M, Gonzalez-Neira A, Salas A, Lareu V, Tyler-Smith C, Carracedo A. 2004. Micro-geographical differentiation in Northern Iberia revealed by Y-chromosomal DNA analysis. Gene.329:17-25.

 

Brion M, Sanchez JJ, Balogh K, Thacker C, Blanco-Verea A, Borsting C, Stradmann-Bellinghausen B, Bogus M, Syndercombe-Court D, Schneider PM, Carracedo A, Morling N. 2005.  Introduction of an single nucleodite polymorphism-based "Major Y-chromosome haplogroup typing kit" suitable for predicting the geographical origin of male lineages. Electrophoresis. 26:4411-20.

 

Capelli, C., N. Redhead, J.K. Abernethy, F. Gratrix, J.F. Wilson, T. Moen, T. Hervig, M. Richards, M.P.H. Stumpf, P.A. Underhill et al. 2003. A Y chromosome census of the British Isles. Curr. Biol. 13:979-984.

 

Capelli C, Redhead, N, Romano V, Cali F, Lefranc, G, Delague V, Megarbane A, Felice A E, Pascali V L, Neophytou P I, Poulli Z, Novelletto A, Malaspina P, Terrenato L, Berebbi A, Fellous M, Thomas M G, Goldstein D B, (2005). Population Structure in the Mediterranean Basin: A Y Chromosome Perspective. Annals of Human Genetics.

 

Carvalho-Silva DR, Santos FR, Rocha J, Pena SD. 2001.  The phylogeography of Brazilian Y-chromosome lineages. Am J Hum Genet. 2001 Jan;68(1):281-6.

 

Cinnioglu C, King R, Kivisild T, Kalfoglu E, Atasoy S, Cavalleri GL, Lillie AS, Roseman CC, Lin AA, Prince K, Oefner PJ, Shen P, Semino O, Cavalli-Sforza LL, Underhill PA. 2004. Excavating Y-chromosome haplotype strata in Anatolia. Hum. Genet. 114:127-148.

 

Cruciani F, Santolamazza P, Shen P, Macaulay V, Moral P, Olckers A, Modiano D, Holmes S, Destro-Bisol G, Coia V, Wallace DC, Oefner PJ, Torroni A, Cavalli-Sforza LL, Scozzari R, Underhill PA. 2002  A back migration from Asia to sub-Saharan Africa is supported by high-resolution analysis of human Y-chromosome haplotypes. Am J Hum Genet. 70:1197-214.

 

Flores, C., N. Maca-Meyer, A.M. González, P.J. Oefner, P. Shen, J.A. Pérez, A. Rojas, J.M. Larruga and P.A. Underhill. 2004. Reduced genetic structure of the Iberian Peninsula revealed by Y-chromosome analysis: implications for population demography. Eur. J. Hum. Genet. 12:855-863

 

García, O., P. Martín, L. Gusmao et al. (13 co-authors). 2004. A Basque Country autochthonous population study of 11 Y-chromosome STR loci. Forensic Sci. Int. 145:65-68.

 

Hammer M F, Karafet T M, Redd A J, Jarjanazi H, Santachiara-Benerecetti A S, Soodyall H, Zegura S L. 2001. Hierarchical Patterns of Global Human Y-Chromosome Diversity.  Molecular Biology and Evolution, 18:1189-1203.

 

Hammer M F, Chamberlain V F, Kearney V F, Stover D, Zhang G, Karafet T, Walsh B, Redd A J. 2005. Population structure of Y chromosome SNP haplogroups in the United States and forensic implications for constructing Y chromosome STR databases. (in press) Forensic Science International.

 

Hurles, M.E., R. Veitia, E. Arroyo et al. (18 co-authors). 1999. Recent male-mediated gene flow over a linguistic barrier in Iberia, suggested by analysis of a Y-Chromosomal DNA polymorphism. Am. J. Hum. Genet. 65:1437-1448. (not included)

 

Martinez-Jarreta B, Nievas P, Abecia E, Hinojal R, Budowle B. 2003. Haplotype distribution of nine Y-chromosome STR-loci in two northern Spanish populations (Asturias and Aragon). J Forensic Sci. 48:204-5

 

Karafet T, Xu L, Du R, Wang W, Feng S, Wells RS, Redd AJ, Zegura SL, Hammer MF. 2001.  Paternal population history of East Asia: sources, patterns, and microevolutionary processes. Am J Hum Genet. 69:615-28.

 

Ke Y, Su B, Song X, Lu D, Chen L, Li H, Qi C, Marzuki S, Deka R, Underhill P, Xiao C, Shriver M, Lell J, Wallace D, Wells RS, Seielstad M, Oefner P, Zhu D, Jin J, Huang W, Chakraborty R, Chen Z, Jin L. 2001. African origin of modern humans in East Asia: a tale of 12,000 Y chromosomes. Science. 292:1151-3.

 

Khodjet El Khil H, Triki Marrakchi R, Yacoubi Loueslati B, Langaney A, Fellous M, Benammar Elgaaied A.  2005. Distribution of Y chromosome lineages in Jerba Island Population. Forensic Science International 148:211-218

 

Maca-Meyer N, Sanchez-Velasco P, Flores C, Larruga JM, Gonzalez AM, Oterino A, Leyva-Cobian F. 2003. Y chromosome and mitochondrial DNA characterization of Pasiegos, a human isolate from Cantabria (Spain). Ann Hum Genet. 67:329-39.

 

Moore, L.T., McEvoy, B., Cape, E.,  Simms, K., Bradley, D.G. 2006. A Y-Chromosome Signature of Hegemony in Gaelic Ireland. 78: 334-338

 

Nasidze, I., Quinque, D., Ozturk,  M., Bendukidze, N., and Stoneking, M. 2005. MtDNA and Y-chromosome Variation in Kurdish Groups. Annals of Human Genetics 69:401–412

 

Pacheco PR, Branco CC, Cabral R, Costa S, Araujo AL, Peixoto BR, Mendonca P, Mota-Vieira L. 2005. The Y-chromosomal heritage of the Azores Islands population. Ann Hum Genet. 69:145-56

 

Paracchini S, Pearce CL, Kolonel LN, Altshuler D, Henderson BE, Tyler-Smith C. 2003.   A Y chromosomal influence on prostate cancer risk: the multi-ethnic cohort study. J Med Genet. 40:815-9.

 

Regueiro M., Cadenas A.M., Gayden T., Underhill P.A., Herrera R.J. 2006. Iran: tricontinental nexus for Y-chromosome driven migration. Human Hered. 61: 132-142

 

 

Rosser, H.Z., T. Zerjal, M.E. Hurles et al. (63 co-authors). 2000. Y-Chromosomal diversity in Europe is clinal and influenced primarily by geography, rather than by language. Am. J. Hum. Genet. 67:1526-1543.

 

Semino, O., G. Passarino, P.J. Oefner et al (17 co-authors). 2000. The genetic legacy of Paleolithic Homo sapiens sapiens in extant Europeans: A Y chromosome perspective. Science 290:1155-1159. (not included)

 

Sengupta S, Zhivotovsky L A, King R, Mehdi S Q, Edmonds C A, Chow C-A T, Lin A A Mitra M, Sil S K, Ramesh A, Rani M V U, Thakur C M, Cavalli-Sforza L L, Majumder P P, Underhill P A. 2006. 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. American Journal of Human Genetics, 78:202-221.

 

Shen P, Lavi T, Kisivild T, Chou V, Sengun D, Gefel D, Shpirer I, Woolf E, Hillel J, Feldman M W, Oefner P J. 2004. Reconstruction of Patrilineages and Matrilineages of Samaritans and other Israeli Populations from Y-Chromosome and Mitochondrial DNA Sequence Variation. Human Mutation, 24:248-260

 

Underhill PA, Jin L, Lin AA, Mehdi SQ, Jenkins T, Vollrath D, Davis RW, Cavalli-Sforza LL, Oefner PJ. 1997. Detection of numerous Y chromosome biallelic polymorphisms by denaturing high-performance liquid chromatography. Genome Res. 7:996-1005

 

Underhill PA, Shen P, Lin AA, Jin L, Passarino G, Yang WH, Kauffman E, Bonne-Tamir B, Bertranpetit J, Francalacci P, Ibrahim M, Jenkins T, Kidd JR, Mehdi SQ, Seielstad MT, Wells RS, Piazza A, Davis RW, Feldman MW, Cavalli-Sforza LL, Oefner PJ. 2000. Y chromosome sequence variation and the history of human populations. Nat. Genet. 26:358-361

 

Underhill PA, Passarino G, Lin AA, Shen P, Mirazon Lahr M, Foley RA, Oefner PJ, Cavalli-Sforza LL. 2001. The phylogeography of Y chromosome binary haplotypes and the origins of modern human populations. Ann Hum Genet. 2001 65:43-62.

 

Underhill PA. 2003 Inferring human history: clues from Y-chromosome haplotypes. Cold Spring Harb Symp Quant Biol. 68:487-93.

 

Vallone PM, Butler JM. 2004 Y-SNP typing of U.S. African American and Caucasian samples using allele-specific hybridization and primer extension. J Forensic Sci. 49:723-32.

 

Wilson JF, Weiss DA, Richards M, Thomas MG, Bradman N, Goldstein DB. 2001. Genetic evidence for different male and female roles during cultural transitions in the British Isles. Proc Natl Acad Sci U S A. 98: 5078-5083

 

 

1