The phylogenetic and geographic structure of Y-chromosome haplogroup R1a

Abstract

,23R1a-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 B25 000 (95% CI: 21 300-29 000) years ago and a coalescence time within R1a-M417 of B5800 (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.

Ladakh, India: the land of high passes and genetic heterogeneity reveals a confluence of migrations

“…Also, most terminal West-Asian haplotypes germinate from other WestAsian collections. This is not surprising considering that the R1a1a-M198 mutation arose in either East Europe 8,21,22 or, alternately, a southern region of Central Asia 13,23 and is, today, very common in West Asia. As expected, and as we recently reported for Central and SouthAsian individuals, 23 the majority of the R1a1a-M198 Ladakh individuals (100% or 35/35) were R-Z93 (the Asian subclade).…”

Y‐Chromosomal Lineages of Latvians in the Context of the Genetic Variation of the Eastern‐Baltic Region

“…Hg R1a is frequent in North-Eastern Europe, with the highest frequencies (30%-50%) in Slavic-speaking populations (Underhill et al, 2010;Myres et al, 2011;Underhill et al, 2014) and moderate among populations of the VolgaUral basin, varying from 10.3% in Udmurts to 47.7% in Maris (Tambets et al, 2004). Recently, Underhill et al (2014) have studied phylogeography of European-specific R1a subclades of R1a-M458 and R1a-M558 lineages in details.…”

“…DNA samples were genotyped for 28 Y-chromosomal biallelic polymorphisms (SRY-1083.2, M168, YAP, M35, M78, M89, M201, M69, 12f2a, M172, M170, M253, P37.2, M223, M9, 92R7, M242, M207, M173, M17, M269, M124, LLY22g, Tat, M178, M458, M558, and P21), using PCR-RFLP and direct sequencing analysis. Detailed protocols for analysis using biallelic markers have been reported previously (Underhill et al, 2001;Y Chromosome Consortium, 2002;Sengupta et al, 2006;Karafet et al, 2008;Underhill et al, 2010;Underhill et al, 2014). NRY hgs were determined following the common guidelines of the Y Chromosome Consortium and subsequent updates (Karafet et al, 2008;Underhill et al, 2010;Myres et al, 2011;ISOGG).…”

“…Jobling &Tyler-Smith, 1995;Zerjal et al, 1997;Hammer et al, 2001;Jobling &Tyler-Smith, 2003;Rootsi et al, 2007;Tyler-Smith, 2008;Mirabal et al, 2009;Underhill et al, 2010;Underhill et al, 2014). The paternally inherited Y-chromosome is particularly sensitive to the influences of genetic drift, driving the haplogroup/haplotype frequency differentiation between different populations: therefore, the Y-chromosome markers are almost ideal for assessing the origins of contemporary population diversity and migration patterns Jobling & Tyler-Smith, 2003;Underhill, 2003).…”

“…For the first time, we have studied here the phylogeography of two recently described (Underhill et al, 2010(Underhill et al, , 2014 Y-chromosomal branches based on two SNPs (M458 and M558) within hg R1a1a among Latvians in the context of other Eastern European populations.…”