Genome-wide effect of MRS-deficient hypermutability on the mutagenesis of mononucleotide SSRs.

<p>The bars show the fold increase in the mutations per year that occurred in mononucleotide G:C SSRs and A:T SSRs, and in other types of mutation after <i>P. aeruginosa</i> PACS2 became mutator<b>.</b></p

Mononucleotide SSRs in the <i>P. aeruginosa</i> PAO1 genome.

<p>The plots show the counts for mononucleotide SSRs (red circles) in the whole <i>P. aeruginosa</i> PAO1 genome and in random sequences generated by various predictive models (black symbols). b and m1: homogeneous models (Bernoulli and first-order Markov); b-b, b-bp, m1-m1, m1-m1p, m1-c and m1-c1: heterogeneous models (see Methods). Counts are shown of mononucleotide G:C and A:T SSRs in the coding and non-coding regions of the genome.</p

Involvement of mononucleotide SSRs in genes involved in <i>P. aeruginosa</i> adaptation during CF chronic infection.

<p>The bar graphs show (i) the percentages of the 60 genes mutated during CF lung chronic infection as reported by Smith <i>et al. </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080514#pone.0080514-Smith1" target="_blank">[1]</a> that harbor mononucleotide G:C SSRs (A) and A:T SSRs (B), relative to the length of the SSR (black bars); (ii) the percentages of those genes carrying mononucleotide SSRs that were mutated during the process of chronic infection, relative to the length of the SSR (gray bars).</p

Shade projection from the simulated horizontal and vertical structure of a given plot illustrative of each type.

<p>The simulations of structure were made with SExI-FS software and the shade projection simulations were made with Shademotion software. The four types were: complex diversified multistrata (CDM), low diversity with regular trees (LDR), low diversity with clustered trees (LDC), and high density of Musaceae (HDM).</p

List of tree species within the different shade layers in each type of the typology built.

<p>The types are: complex diversified multistrata (CDM), low diversity with regular trees (LDR), low diversity with clustered trees (LDC), and high density of Musaceae (HDM).</p

Representation of the types of our typology in a Cartesian plane made with the first two axes of the principal components analysis.

<p>The 4 types were: complex diversified multistrata (CDM), low diversity with regular trees (LDR), low diversity with clustered trees (LDC), and high density of Musaceae (HDM).</p

Representation of the hierarchical clustering on the factor map made on the selected principal components obtained from our matrix of 28 variables.

<p>The variables are for diversity (4 variables), composition (6), vertical spatial structure (9), horizontal spatial structure (3), and transmitted radiation (4). The cluster analysis defined 4 types: complex diversified multistrata (CDM), low diversity with regular trees (LDR), low diversity with clustered trees (LDC), and high density of Musaceae (HDM).</p

The 28 variables characterised in each parcel of the studied agroforest plots and their mean values in each type of the typology built.

<p>Values represent the mean ± standard deviation. P-value shows the differences between types of cacao agroforests in Colombian Amazonia.The four types are: complex diversified multistrata (CDM), low diversity with regular trees (LDR), low diversity with clustered trees (LDC), and high density of Musaceae (HDM). We have: 4 variables for diversity, 6 for composition, 9 for vertical spatial structure, 3 for horizontal spatial structure, and 4 for transmitted radiation. (LSD Fisher test significant at p <0.05).</p

Simulated representation of the structure (horizontal and vertical) of a given plot illustrative of each type.

<p>The simulations were made with SExI-FS software. The four types were: complex diversified multistrata (CDM), low diversity with regular trees (LDR), low diversity with clustered trees (LDC), and high density of Musaceae (HDM).</p

Importance value index (IVI) and physiognomic predominance index PPI for the tree species in the study plot, and within the different types of the typology built.

<p>The 4 types are: complex diversified multistrata (CDM), low diversity with regular trees (LDR), low diversity with clustered trees (LDC), and high density of Musaceae (HDM).</p