Genetic variation among the 195 TOU-A accessions for disease index within each six micro-habitat.

The random effect ‘Accession’ is in italic. The model random term was tested with likelihood ratio tests of model with and without this effect. Bold P-values indicate significant effect after Bonferroni correction. LRT: Likelihood Ratio Test. ‘w/o’: absence of P. annua, ‘w.’: presence of P. annua. (DOCX)</p

A polygenic architecture underlying natural genetic variation of total seed production within each micro-habitat for which disease index was significantly heritable.

Manhattan plot of the Lindley process (local score method with a tuning parameter ξ = 2). The x-axis indicates the physical position of the 981,617 SNPs along the five chromosomes. The dashed lines indicate the minimum and maximum of the five chromosome-wide significance thresholds. (DOCX)</p

Comparison of the polygenic architecture underlying natural genetic variation of disease index and total seed production within each micro-habitat.

(A) soil A in absence of Poa annua. (B) soil A in presence Poa annua. (C) soil B in absence of Poa annua. (D) soil C in absence of Poa annua. (E) soil C in presence Poa annua. Manhattan plot of the Lindley process (local score method with a tuning parameter ξ = 2). The x-axis indicates the physical position of the 981,617 SNPs along the five chromosomes. The dashed lines indicate the minimum and maximum of the five chromosome-wide significance thresholds. (DOCX)</p

Genotypic values of the 48 accessions in response to six competition treatments.

'Treatment': A,C, P, S, T and V stand for intraspecific competition, absence of competition and interspecific competition with four species frequently associated with A. thaliana in natural plant communities (i.e. Poa annua, Stellaria media, Trifolium repens and Veronica arvensis). 'Accession': name of the 48 TOU-A1 accessions used in this study. 'ecotype_id' stands for the identity of the 48 accessions for running GWA mapping (see Horton et al. Nature Genetics 2012). FITTOT, BT, INT, RP, FT_diam, H1S, HD, RAMBB, RAMPB_S and COMP have been described in the main text

FITNESS_estimation

FITNESS_estimatio

Genotypic selection analysis with selection differentials (S), selection gradients (β), quadratic selection coefficients (γ) for phenological traits in each treatment.

<p>GERM: germination timing, BT: bolting time, INT: interval between bolting and anthesis, ANT: anthesis, FLO: flowering, RP: reproductive period duration, FRR: flowering-to-reproductive period ratio. Selection was stabilizing when γ<0 and disruptive when γ>0. Standard errors (SE) are in parentheses. Values in bold indicate significantly different selection coefficients compared to the ‘control’ treatment. Because ANT integrates BT and INT, ANT was not included in polynomial regressions.</p>*<p>0.05><i>P</i>>0.01,</p>**<p>0.01><i>P</i>>0.001,</p>***<p><i>P</i><0.001. NE: not estimated.</p

Relationship between bolting time and fitness for each treatment at both phenotypic and genotypic levels.

<p>For illustration purposes, a polynomial regression including both linear and quadratic terms described either in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032069#pone-0032069-t001" target="_blank">Table 1</a> (phenotypic level) or in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032069#pone-0032069-t002" target="_blank">Table 2</a> (genotypic level) was first performed including all traits but bolting time. Then, a second polynomial regression including the linear and quadratic terms associated with bolting time was run on the residual fitness of the first polynomial regression. The black lines were drawn using the parameters from this second polynomial regression. BT: bolting time. BT is expressed in standardized values.</p

Phenotypic selection analysis with selection differentials (S), selection gradients (β), quadratic selection coefficients (γ) for phenological traits in each treatment.

<p>GERM: germination timing, BT: bolting time, INT: interval between bolting and anthesis, ANT: anthesis, FLO: flowering, RP: reproductive period duration, FRR: flowering-to-reproductive period ratio. Selection is stabilizing when γ<0 and disruptive when γ>0. Standard errors (SE) are in parentheses. Values in bold indicate significantly different selection coefficients compared to the ‘control’ treatment. Because ANT integrates BT and INT, ANT was not included in polynomial regressions.</p>*<p>0.05><i>P</i>>0.01,</p>**<p>0.01><i>P</i>>0.001,</p>***<p><i>P</i><0.001. NE: not estimated.</p

Correlations among phenological traits in five treatments.

<p>Within each treatment, phenotypic and genetic Pearson correlations are given above and below the diagonal, respectively. GERM: germination timing, BT: bolting time, INT: interval between bolting and anthesis, FLO: flowering, RP: reproductive period duration, FRR: flowering-to-reproductive period ratio. The correlations between RP or FRR and the other phenological traits were not computed for the two water stress treatments (see Material and Methods section).</p>*<p>0.05><i>P</i>>0.01,</p>**<p>0.01><i>P</i>>0.001,</p>***<p><i>P</i><0.001. NA: not available.</p

Effect of water stress and competition on phenological traits and fitness.

<p>INT: interval between bolting and anthesis, ANT: anthesis, FLO: flowering, RP: reproductive period duration, FRR: flowering-to-reproductive period ratio, FITNESS: total silique length as a proxy of seed production. INT, FT, FP and RP are expressed in days. FITNESS is expressed in millimeters. Ctl: ‘control’ treatment. W−: ‘moderate water stress’ treatment. W+: ‘severe water stress’ treatment. C−: ‘moderate competition’ treatment. C+: ‘intense competition’ treatment. For each phenotypic trait, different letters indicate different phenotypic means among treatments after a Tukey's test of multiple comparisons of means (<i>P</i> = 0.05). Data are not available for RP and FRR in the two ‘water stress’ treatments (see Material and Methods).</p