Plant community, related landscape data and GPS vegetation plot locations

Excel sheet with three tabs. First tab contains the presence absence of 122 grassland species for each of 134 2m x 2m vegetation plots across the fragmented grassland landscape in southern Sweden which acted as study area. The second tab contains the predictor variables used to describe the local and spatial processes associated with habitat fragmentation, calculated for each of the 134 grassland plots. The third and final tab are the exact GPS locations (latitude-longitude) for each of the 134 plots

A summary of our coalescent model of the history of <i>C. rubella.</i>

<p><i> A)</i> The relative composite log-likelihood surface as function of and . <i>B)</i> The probability that all individuals coalesce to the same founding haplotype () as a function of and three estimates of values (the MLE, lower and upper confidence intervals). The dotted red line indicates the value of () directly estimated from the data. <i>C)</i> A summary of simulation results (assuming ). <i>C1)</i> The frequency of singletons, doubletons, and tripletons observed in simulation (full lines), and estimated from our data (dashed lines) conditional on all four samples deriving from the same founding haplotype. <i>C2)</i> The frequency of one, two, three or four lineages surviving to the founding event. When is large, is the probability that all samples coalesce to the same founding haplotype. The dotted black line portrays the estimated frequency of all four samples residing on one founding haplotype . <i>D)</i> The estimated current effective number of chromosomes in <i>C. rubella</i> () as a function of the number of founding chromosomes (). We plot this for three different values of (the MLE, as well as the lower and upper confidence intervals). These results are robust to haplotype labeling criteria in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003754#pgen-1003754-g006" target="_blank">Figure 6</a> (see <i><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003754#pgen.1003754.s014" target="_blank">Text S1</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003754#pgen.1003754.s006" target="_blank">Figure S6</a></i>).</p

Percent sequence variation within and between <i>Capsella spp</i>.

<p>Neutral variation within and between <i>Capsella</i> populations. Percent sequence differences at synonymous sites averaged across pairs of individuals within and between <i>C. rubella</i> and <i>C. grandiflora</i>. This matrix is symmetric and comparisons between partially overlapping sets (e.g.<i>C. rubella</i> x Greek <i>C. rubella</i>) are noted as ‘NA’. Redundant cells above the main diagonal are intentionally left blank.</p

Variation within and among <i>C. rubella</i>'s founding haplotypes.

<p><i>A)</i> Pairwise nucleotide diversity () within and among <i>C. rubella</i>'s founding haplotypes at synonymous sites (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003754#pgen.1003754.s013" target="_blank">Table S3</a> for values). <i>B)</i> Ratio of nucleotide diversity at non-synonymous relative to synonymous sites () within and among <i>C. rubella</i>'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 <i>C. grandiflora</i>, and genome-wide <i>C. rubella</i> comparisons, respectively (taken from <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003754#pgen-1003754-t001" target="_blank">Table 1</a>). <i>C)</i> Neighbor joining trees in <i>Capsella</i>, using all comparisons (<i>C.1</i>), comparisons within (<i>C.2</i>), or among (<i>C.3</i>) founding haplotypes to generate entries in the pairwise distance matrix for comparisons within <i>C. rubella</i>. All distances are generated from nucleotide diversity at synonymous sites.</p

F2 data

This data file contains phenotype, genotype and linkage data for 550 F2 individuals resulting from an interspecific cross between C. grandiflora and C. rubella. The individuals were phenotyped in the greenhouse

Molecular response to reciprocal hybridizations of <i>C</i>. <i>rubella</i> × <i>C</i>. <i>grandiflora</i> is similar to interploidy hybridizations in Arabidopsis.

<p>(A) Genes up- and downregulated in <i>C</i>. <i>rubella</i> × <i>C</i>. <i>grandiflora</i> reciprocal hybrid seeds compared to both parents overlap with genes deregulated in Arabidopsis interploidy seeds. The Arabidopsis <i>osd1</i> mutant produces unreduced gametes, mimicking an interploidy hybridization when crossed with wild-type (WT). P values reflecting significance of overlap were calculated using a hypergeometric test. (B) Heatmap of expression log2 fold changes of selected <i>AGL</i> genes between samples. Capsella <i>AGLs</i> with several homologs in Arabidopsis are marked by small letters.</p

Ancestry probabilities for scaffold 7

This folder contains ancestry probabilities from MSG v0.3 for markers on scaffold 7. Each file contains ancestry probabilities for 7075 markers for each of 550 F2 individuals. File par1_sc7.tsv contains probabilities for being homozygous C. rubella, par12_sc7.tsv contains probabilities for being heterozygous and par2_sc7.tsv contains probabilities for being homozygous C. grandiflora. Individual order is as in the F2 data file, and these ancestry probabilities were used to fine-map self-compatibility

Cross direction-dependent incompatibility affects development of <i>Capsella rubella</i> and <i>C</i>. <i>grandiflora</i> hybrid seeds.

<p>Percentage (A) and phenotypes (B) of aborted and non-aborted seeds of <i>C</i>. <i>rubella</i>, <i>C</i>. <i>grandiflora</i> and reciprocal hybrids of both species. Scale bars reflect 1 mm. (C) Percentage of germinated seeds of indicated crosses. (D) Seedlings of indicated crosses 10 days after germination. Seed area (E) and seed weight (F) of indicated crosses. Error bars show standard deviation. Significance was determined by t test analysis. * P < 0.05, ** P < 0.01 ns, not significant. In all graphs numbers on top of the bars correspond to number of analyzed seeds.</p

Hybrid seed incompatibility between <i>C</i>. <i>rubella</i> and <i>C</i>. <i>grandiflora</i> correlates with endosperm cellularization defects.

<p>Sections of <i>C</i>. <i>rubella</i>, <i>C</i>. <i>grandiflora</i> and reciprocal hybrid seeds at 4–7 days after pollination (DAP). Scale bar 100μm.</p

<i>C</i>. <i>rubella</i> × <i>C</i>. <i>grandiflora</i> hybrid seed incompatibility involves multiple genetic loci.

<p>(A) Frequency of F2 plants derived from crosses of <i>C</i>. <i>grandiflora</i> × <i>C</i>. <i>rubella</i> producing defined rates of seed abortion when backcrossed to <i>C</i>. <i>rubella</i> maternal plants. (B) Theoretical distribution of F2 plants producing defined rates of seed abortion when assuming that one maternal locus from <i>C</i>. <i>rubella</i> negatively interacts with two or three paternal loci from <i>C</i>. <i>grandiflora</i>. Experimental data correspond to data shown in (A). Significance of the observed distributions with the predictions of the models has been tested by Chi-square and P>0.05 is marked by an asterisk. Ns, non significant. (C) LOD scores for paternal <i>C</i>. <i>grandiflora</i> QTLs affecting abortion of <i>C</i>. <i>rubella</i> × <i>C</i>. <i>grandiflora</i> hybrid seeds. The purple line (top) represents the LOD score of each marker and the purple line (bottom) represents the effects. The red line represents the significance threshold as estimated by 1,000 permutations.</p