Discovery of Western European R1b1a2 Y Chromosome Variants in 1000 Genomes Project Data: An Online Community Approach

Rocca, Richard A.; Magoon, Gregory; Reynolds, David F.; Krahn, Thomas; Tilroe, Vincent O.; Boots, Peter M. Op den Velde; Grierson, Andrew J.

doi:10.1371/journal.pone.0041634

Cited by 35 publications

(28 citation statements)

References 25 publications

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“…[1][2][3][4][5] The International Society of Genetic Genealogy 10 has aggregated these variants and those discovered with previous technologies into a public resource that population surveys can leverage to further elucidate the geographic origins of and structure within haplogroups. [6][7][8][9][10][11][12][13] Y-chromosome haplogroup R (hg R) is one of 20 that comprise the standardized global phylogeny. 14 It consists of two main components: R1-M173 and R2-M479 15 (Figure 1).…”

Section: Introductionmentioning

confidence: 99%

The phylogenetic and geographic structure of Y-chromosome haplogroup R1a

Underhill¹,

Poznik²,

Rootsi³

et al. 2014

Eur J Hum Genet

141

137

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,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.

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Section: Introductionmentioning

confidence: 99%

The phylogenetic and geographic structure of Y-chromosome haplogroup R1a

Underhill¹,

Poznik²,

Rootsi³

et al. 2014

Eur J Hum Genet

141

137

View full text Add to dashboard Cite

show abstract

“…whole-genome sequencing studies produced thousands of singlenucleotide polymorphisms (SNPs) of the MSY from a large set of males (The 1000Genomes Project Consortium 2010. A refinement of the phylogenetic relationships in a portion of the MSY tree with these SNPs has been attempted, but due to the likely abundance of false negatives and biases resulting from low-depth sequencing, not all of these SNPs could be used to confidently reconstruct and date the MSY phylogeny (Rocca et al 2012). Highdepth, whole-genome sequences have been generated and made publicly available by Complete Genomics.…”

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confidence: 99%

An unbiased resource of novel SNP markers provides a new chronology for the human Y chromosome and reveals a deep phylogenetic structure in Africa

et al. 2014

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Sequence diversity and the ages of the deepest nodes of the MSY phylogeny remain largely unexplored due to the severely biased collection of SNPs available for study. We characterized 68 worldwide Y chromosomes by high-coverage nextgeneration sequencing, including 18 deep-rooting ones, and identified 2386 SNPs, 80% of which were novel. Many aspects of this pool of variants resembled the pattern observed among genome-wide de novo events, suggesting that in the MSY, a large proportion of newly arisen alleles has survived in the phylogeny. Some degree of purifying selection emerged in the form of an excess of private missense variants. Our tree recapitulated the previously known topology, but the relative lengths of major branches were drastically modified and the associated node ages were remarkably older. We found significantly different branch lengths when comparing the rare deep-rooted A1b African lineage with the rest of the tree. Our dating results and phylogeography led to the following main conclusions: (1) Patrilineal lineages with ages approaching those of early AMH fossils survive today only in central-western Africa; (2) only a few evolutionarily successful MSY lineages survived between 160 and 115 kya; and (3) an early exit out of Africa (before 70 kya), which fits recent western Asian archaeological evidence, should be considered. Our experimental design produced an unbiased resource of new MSY markers informative for the initial formation of the anatomically modern human gene pool, i.e., a period of our evolution that had been previously considered to be poorly accessible with paternally inherited markers.

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“…We reconstructed the phylogenetic relationships of the newly sequenced samples in the context of three other available high coverage sequences from this haplogroup using binary SNP data (Supplementary Data 1) from a total of 8.97 Mbp of sequence from the non-recombining region of nine Y-chromosomes28. For both sub-clades of R1, most Jewish sequences cluster separately from the clades that in previous studies have been shown to be common in Europe: in R1b where more than 90% of European lineages are within the L11/L52 clade29, three of the newly sequenced Jewish Y-chromosomes cluster within its copanion clade defined by the Z2105 mutation; in R1a where the majority of European individuals belong to the S198 (ref. 30) and M458 branches16, all four newly sequenced Jewish Y-chromosomes fall into the clade defined by Z94 mutation.…”

Section: Resultsmentioning

confidence: 99%

Phylogenetic applications of whole Y-chromosome sequences and the Near Eastern origin of Ashkenazi Levites

et al. 2013

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Previous Y-chromosome studies have demonstrated that Ashkenazi Levites, members of a paternally inherited Jewish priestly caste, display a distinctive founder event within R1a, the most prevalent Y-chromosome haplogroup in Eastern Europe. Here we report the analysis of 16 whole R1 sequences and show that a set of 19 unique nucleotide substitutions defines the Ashkenazi R1a lineage. While our survey of one of these, M582, in 2,834 R1a samples reveals its absence in 922 Eastern Europeans, we show it is present in all sampled R1a Ashkenazi Levites, as well as in 33.8% of other R1a Ashkenazi Jewish males and 5.9% of 303 R1a Near Eastern males, where it shows considerably higher diversity. Moreover, the M582 lineage also occurs at low frequencies in non-Ashkenazi Jewish populations. In contrast to the previously suggested Eastern European origin for Ashkenazi Levites, the current data are indicative of a geographic source of the Levite founder lineage in the Near East and its likely presence among pre-Diaspora Hebrews.

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Discovery of Western European R1b1a2 Y Chromosome Variants in 1000 Genomes Project Data: An Online Community Approach

Cited by 35 publications

References 25 publications

The phylogenetic and geographic structure of Y-chromosome haplogroup R1a

The phylogenetic and geographic structure of Y-chromosome haplogroup R1a

An unbiased resource of novel SNP markers provides a new chronology for the human Y chromosome and reveals a deep phylogenetic structure in Africa

Phylogenetic applications of whole Y-chromosome sequences and the Near Eastern origin of Ashkenazi Levites

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