Mutation Accumulation in an Asexual Relative of <i>Arabidopsis</i>

<div><p>Asexual populations experience weaker responses to natural selection, which causes deleterious mutations to accumulate over time. Additionally, stochastic loss of individuals free of deleterious mutations can lead to an irreversible increase in mutational load in asexuals (the “click” in Muller’s Ratchet). Here we report on the genomic divergence and distribution of mutations across eight sympatric pairs of sexual and apomictic (asexual) <i>Boechera</i> (Brassicaceae) genotypes. We show that apomicts harbor a greater number of derived mutations than sympatric sexual genotypes. Furthermore, in phylogenetically constrained sites that are subject to contemporary purifying selection, the ancestral, conserved allele is more likely to be retained in sexuals than apomicts. These results indicate that apomictic lineages accumulate mutations at otherwise conserved sites more often than sexuals, and support the conclusion that deleterious mutation accumulation can be a powerful force in the evolution of asexual higher plants.</p></div

Signatures of relaxed purifying selection in apomicts.

<p>We calculated <i>d</i>constrained/<i>d</i>neutral ratios for each population with bar colors following <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006550#pgen.1006550.g002" target="_blank">Fig 2A and 2B</a> (<b>A</b>). Additionally, <i>d</i>constrained/<i>d</i>neutral ratios were calculated from SNPs binned by their derived allele frequency among the 7 southern apomictic genotypes (<b>B</b>). For example <i>n</i> = 1 indicates a site where a single apomictic genotype has a derived allele, while <i>n</i> = 7 represents sites where all apomicts share a derived allele. Significance categories follow <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006550#pgen.1006550.g002" target="_blank">Fig 2A and 2B</a>.</p

Genomic distribution of SNP diversity.

<p>Observed heterozygosity (<i>H</i>_<i>0</i>, <b>A</b>) and substitution rate (<i>D</i>, <b>B</b>) were calculated for all populations across four SNP annotation categories. For each apomictic-sexual sympatric pair, the relative increase of the sympatric apomict to the sexual is plotted (colored by population, where the lightest populations are from the south and darkest are northern). Significance of the comparison is presented (Fisher’s test <i>P</i> ≤ 0.05*, <i>P</i> ≤ 0.1⁺). All comparisons are significant for <i>H</i>_<i>0</i>. <b>C</b> <i>H</i>_<i>0</i> of each apomictic genotype and proportion of pairwise differences between each sexual genotype (<i>d</i>_<i>ij</i>) were calculated for non-overlapping 20k SNP windows. Loess smoothed curves are plotted across these windows.</p

Classification of haplotype trees to infer the impact of hybridization.

<p>The ~22k trees generated from strictly filtered 5-sequence haplotype alignments were binned into six possible topologies. The relative abundance of each is plotted (for the distributions of all trees see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006550#pgen.1006550.s005" target="_blank">S3 Fig</a>). Those trees that present a hybrid evolutionary history are plotted on the left (<b>A</b>-<b>B</b>), while all other threes are on the right (<b>C</b>-<b>F</b>). Red branch tips indicate the apomictic haplotype, while blue branch tips depict the sexual ‘pseudohaplotype’. In the hybrid trees, the non-<i>B</i>. <i>spatifolia</i> sub-genome is represented by the most diverged terminal branch (dashed red edge), while the <i>B</i>. <i>spatifolia</i>-derived sub-genome (dashed black edge) is most closely related to the sexual <i>B</i>. <i>spatifolia</i> chromosomes. The <i>A</i>. <i>lyrata</i> rooted edges are not plotted. Branch lengths are averaged across all trees in each bin.</p

Classification of mutation accumulation within haplotype trees.

<p>We documented the types and number of mutations on the terminal branches of the two hybrid trees (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006550#pgen.1006550.g003" target="_blank">Fig 3A and 3B</a>). For both trees, the total numbers of coding SNPs along the terminal branches are plotted below the branch tips as vertical bars (<b>A</b>). The discrepancy in SNP numbers between trees is due to the presence of many more haplotypes belonging to the first (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006550#pgen.1006550.g004" target="_blank">Fig 4A</a>) topology. The sexual terminal branches were compared to the <i>B</i>. <i>spatifolia</i>-derived haplotype terminal branch directly. For the left tree, this involved three contrasts; however, since the sexual pseudo-haplotypes cluster together in the right tree, it was appropriate to group these and make only a single contrast. Fisher’s test odds ratios (± odds ratio SE) of the contrasts (labeled C₁ –C₄) are expanded as well as the overall Fisher’s test across all contrasts (<b>B</b>).</p

Linked neutral diversity and divergence as a function of distance from fixed substitutions across the <i>C. grandiflora</i> genome.

<p>A) Diversity at 4-fold degenerate sites, B) Divergence at 4-fold degenerate sites, and C) Diversity/divergence at 4-fold degenerate sites. In all figures, black lines represent measures surrounding fixed replacement substitutions and gray shading represents 95% confidence intervals, from bootstrapping, surrounding silent substitutions.</p

Estimates of negative and positive selection on coding and noncoding sites in <i>C. grandiflora</i>.

<p>A) The proportion of sites found in each bin of purifying selection strength, separated by site type, B) The proportion of divergent sites fixed by positive selection, and C) the rate of adaptive substitution relative to neutral divergence. Error bars represent 95% bootstrap confidence intervals.</p

Linked neutral diversity/divergence surrounding conserved noncoding sequences (CNSs).

<p>A) Diversity/divergence at 4-fold degenerate sites as a function of distance from fixed substitutions in CNSs (black lines) and fixed substitutions in non-conserved intergenic sequence (gray shading, 95% confidence interval). B) Diversity/divergence at 4-fold degenerate sites as a function of distance from CNSs containing fixed substitutions (black line) and CNSs without any fixed substitutions (gray shading, 95% confidence interval).</p