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, 7 (7), e41634

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

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

Richard A Rocca et al. PLoS One.

Abstract

The authors have used an online community approach, and tools that were readily available via the Internet, to discover genealogically and therefore phylogenetically relevant Y-chromosome polymorphisms within core haplogroup R1b1a2-L11/S127 (rs9786076). Presented here is the analysis of 135 unrelated L11 derived samples from the 1000 Genomes Project. We were able to discover new variants and build a much more complex phylogenetic relationship for L11 sub-clades. Many of the variants were further validated using PCR amplification and Sanger sequencing. The identification of these new variants will help further the understanding of population history including patrilineal migrations in Western and Central Europe where R1b1a2 is the most frequent haplogroup. The fine-grained phylogenetic tree we present here will also help to refine historical genetic dating studies. Our findings demonstrate the power of citizen science for analysis of whole genome sequence data.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Proposed S116 (xU152, L21) Phylogenetic Tree.
Genetic variants are indicated on branches, and branch lengths are not proportional to the number of mutations or the age of the variant. Phylogenetically equivalent markers are shown in alphabetical and numerical order. Full details of these variants are shown in Table S1. The positions of 1000 Genomes samples are given at the tips of the branches.
Figure 2
Figure 2. Proposed L21 Phylogenetic Tree.
Genetic variants are indicated on branches, and branch lengths are not proportional to the number of mutations or the age of the variant. Phylogenetically equivalent markers are shown in alphabetical and numerical order. Full details of these variants are shown in Table S1. The positions of 1000 Genomes samples are given at the tips of the branches.
Figure 3
Figure 3. Proposed U152 Phylogenetic Tree.
Genetic variants are indicated on branches, and branch lengths are not proportional to the number of mutations or the age of the variant. Phylogenetically equivalent markers are shown in alphabetical and numerical order. Full details of these variants are shown in Table S1. The positions of 1000 Genomes samples are given at the tips of the branches.
Figure 4
Figure 4. Proposed U106 Phylogenetic Tree.
Genetic variants are indicated on branches, and branch lengths are not proportional to the number of mutations or the age of the variant. Phylogenetically equivalent markers are shown in alphabetical and numerical order. Full details of these variants are shown in Table S1. The positions of 1000 Genomes samples are given at the tips of the branches.
Figure 5
Figure 5. Validated L11 Phylogeny.
Genetic variants that have been validated by Sanger sequencing are indicated on branches, and branch lengths are not proportional to the number of mutations or the age of the variant. Phylogenetically equivalent markers are shown in alphabetical and numerical order. Full details of these variants are shown in Table S1.

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