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. 2013 Sep 12;9(9):e1003754. doi: 10.1371/journal.pgen.1003754

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© 2013 Brandvain et al

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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A) Pairwise nucleotide diversity () within and among C. rubella's founding haplotypes at synonymous sites (see Table S3 for values). B) Ratio of nucleotide diversity at non-synonymous relative to synonymous sites () within and among C. rubella's founding haplotypes. Error bars mark the upper and lower 2.5% tails and are generated by resampling blocks assigned to different (left hand side) or same (right hand side) founding haplotypes. In the top panel (A and B), orange, green, and blue horizontal lines are drawn for reference to interspecific comparisons, comparisons within C. grandiflora, and genome-wide C. rubella comparisons, respectively (taken from Table 1). C) Neighbor joining trees in Capsella, using all comparisons (C.1), comparisons within (C.2), or among (C.3) founding haplotypes to generate entries in the pairwise distance matrix for comparisons within C. rubella. All distances are generated from nucleotide diversity at synonymous sites.

Inline graphic — A) Pairwise nucleotide diversity () within and among C. rubella's founding haplotypes at synonymous sites (see Table S3 for values). B) Ratio of nucleotide diversity at non-synonymous relative to synonymous sites () within and among C. rubella's founding haplotypes. Error bars mark the upper and lower 2.5% tails and are generated by resampling blocks assigned to different (left hand side) or same (right hand side) founding haplotypes. In the top panel (A and B), orange, green, and blue horizontal lines are drawn for reference to interspecific comparisons, comparisons within C. grandiflora, and genome-wide C. rubella comparisons, respectively (taken from Table 1). C) Neighbor joining trees in Capsella, using all comparisons (C.1), comparisons within (C.2), or among (C.3) founding haplotypes to generate entries in the pairwise distance matrix for comparisons within C. rubella. All distances are generated from nucleotide diversity at synonymous sites.