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. 2015 Jan;23(1):124-31.
doi: 10.1038/ejhg.2014.50. Epub 2014 Mar 26.

The phylogenetic and geographic structure of Y-chromosome haplogroup R1a

Peter A Underhill  1 , G David Poznik  2 , Siiri Rootsi  3 , Mari Järve  3 , Alice A Lin  4 , Jianbin Wang  5 , Ben Passarelli  5 , Jad Kanbar  5 , Natalie M Myres  6 , Roy J King  4 , Julie Di Cristofaro  7 , Hovhannes Sahakyan  8 , Doron M Behar  9 , Alena Kushniarevich  3 , Jelena Sarac  10 , Tena Saric  10 , Pavao Rudan  11 , Ajai Kumar Pathak  3 , Gyaneshwer Chaubey  3 , Viola Grugni  12 , Ornella Semino  13 , Levon Yepiskoposyan  14 , Ardeshir Bahmanimehr  15 , Shirin Farjadian  16 , Oleg Balanovsky  17 , Elza K Khusnutdinova  18 , Rene J Herrera  19 , Jacques Chiaroni  7 , Carlos D Bustamante  1 , Stephen R Quake  20 , Toomas Kivisild  21 , Richard Villems  22
Affiliations

The phylogenetic and geographic structure of Y-chromosome haplogroup R1a

Peter A Underhill et al. Eur J Hum Genet. 2015 Jan.

Abstract

R1a-M420 is one of the most widely spread Y-chromosome haplogroups; however, its substructure within Europe and Asia has remained poorly characterized. Using a panel of 16 244 male subjects from 126 populations sampled across Eurasia, we identified 2923 R1a-M420 Y-chromosomes and analyzed them to a highly granular phylogeographic resolution. Whole Y-chromosome sequence analysis of eight R1a and five R1b individuals suggests a divergence time of ∼25,000 (95% CI: 21,300-29,000) years ago and a coalescence time within R1a-M417 of ∼5800 (95% CI: 4800-6800) years. The spatial frequency distributions of R1a sub-haplogroups conclusively indicate two major groups, one found primarily in Europe and the other confined to Central and South Asia. Beyond the major European versus Asian dichotomy, we describe several younger sub-haplogroups. Based on spatial distributions and diversity patterns within the R1a-M420 clade, particularly rare basal branches detected primarily within Iran and eastern Turkey, we conclude that the initial episodes of haplogroup R1a diversification likely occurred in the vicinity of present-day Iran.

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Figures

Figure 1
Figure 1
Haplogroup (hg) R1a-M420 topology, shown within the context of hg R-M207. Common names of the SNPs discussed in this study are shown along the branches, with those genotyped presented in color and those for which phylogenetic placement was previously unknown in orange. Hg labels are assigned according to YCC nomenclature principles with an asterisk (*) denoting a paragroup. Dashed lines indicate lineages not observed in our sample. The marker Z280 was not used as it maps to duplicated ampliconic tracts.
Figure 2
Figure 2
(a–e) Spatial frequency distributions of Z282 affiliated haplogroups. Each map was generated using the frequencies from Supplementary Table 4 among 14 461 individuals, distributed across 119 population samples (references listed in Supplementary Table 4). Because of the known difference between the origin and present distribution of the Roma and Jewish populations, they were excluded from the plots. Additional populations from literature were used for the M458 map.
Figure 3
Figure 3
(a–d) Spatial frequency distributions of Z93 affiliated haplogroups. Maps were generated as described in Figure 2.
Figure 4
Figure 4
Principal component analysis of hg R1a subclades. The plot was obtained by collapsing the 126 populations into 49 regionally/culturally defined groups and calculating R1a subclade frequencies relative to R1a-M198. We excluded one population with small overall sample size and all populations in which fewer than 5 R1a Y-chromosomes were observed.
Figure 5
Figure 5
Y-chromosome phylogeny inferred from 13 ∼10-Mb sequences of hg R individuals. Branches are drawn proportional to the number of derived variants. Each of the 24 branches is labeled by an index, and the number of SNPs assigned to the branch is shown in brackets. The tips of the tree are labeled with sequencing coverage, population, ID, and the most derived commonly known SNP observed in the corresponding sample.
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