Linkage Disequilibrium (LD) for pairs of polymorphisms in the flanking regions.

<p>Dark cells contain LD values significantly different from zero. An asterisk next to a locus name indicates that the SSR repeat(s) is (are) located between that locus and the next. Colouring (shading) indicates the degree of significance of the test: green (light grey*), <i>P</i>>0.05; orange (grey*), 0.05<<i>P</i>>0.001; red (dark grey*), <i>P</i><0.001. * In shades-of-gray printouts.</p

Characteristics of simple sequence repeat (SSR) data sets of the three taxa, <i>Citrus</i> (C), <i>Jacaranda</i> (J) and <i>Quercus</i> (Q).

a<p>Total length of the amplicon consensus sequence in base pairs.</p>b<p>Total number of analysed alleles.</p

Glossary.

<p>Glossary.</p

Polymorphism at each simple sequence repeat (SSR) locus differentiated by segments of the DNA amplicon. SSR1, SSR2 and SSR3: respectively first, second and third SSR occurring in each amplicon (see figure S1 for details on each amplicon’s sequence); FR: flanking regions; <i>H_e</i>: Nei’s genetic diversity; A: number of alleles; h: number of haplotypes. Data sets: C, <i>Citrus</i>; J, <i>Jacaranda</i>; Q, <i>Quercus</i>.

<p>Polymorphism at each simple sequence repeat (SSR) locus differentiated by segments of the DNA amplicon. SSR1, SSR2 and SSR3: respectively first, second and third SSR occurring in each amplicon (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040699#pone.0040699.s001" target="_blank">figure S1</a> for details on each amplicon’s sequence); FR: flanking regions; <i>H_e</i>: Nei’s genetic diversity; A: number of alleles; h: number of haplotypes. Data sets: C, <i>Citrus</i>; J, <i>Jacaranda</i>; Q, <i>Quercus</i>.</p

Alignment of a subset of DNA fragments at simple sequence repeat (SSR) loci Jc3H10 (<i>Jacaranda copaia</i>) (A) and QrZAG30 (<i>Quercus robur</i>) (B).

<p>Numbers in the top line indicate positions relative to the consensus sequence of (A) 190 bp and (B) 247 bp. Bold nucleotides in brackets indicate SSR motifs and their number of repeats. Dashes indicate gaps, highlighted nucleotides in green (light grey*) indicate indels of one to three bases, highlighted nucleotides in red (dark grey*) mark mutations from one base to another, and yellow (light grey*) boxes indicate groups of insertion/deletions longer than three bases and considered as a single mutational event. * In shades-of-gray printouts.</p

Phylogenetic trees of <i>Jacaranda</i> populations based on different components of simple sequence repeat (SSR) data.

<p>SSR variation (A), amplicon size variation (B), flanking region (FR) sequence variation (C) and amplicon sequence variation (D). Each type of data was analysed according to a pair of suitable genetic distance estimators: F_ST, suitable for loci following the infinite allele model (IAM); R_ST, for loci following the stepwise mutation model (SMM); and N_ST, for loci following the infinite site model (ISM) model. There are four geographic populations: Counami (<i>C</i>), Paracou (<i>P</i>) and Saint-Laurent (<i>S</i>) in French Guiana; Tapajos (<i>T</i>) in Brazil. Note that scales are not the same among trees.</p

Two alternative genealogies for simple sequence repeat (SSR) alleles containing the same number of repeats.

<p>SSR alleles are indicated by their number of repeats (n, n+1). The A/C letters indicate a SNP in the flanking regions. Red bars correspond to mutational events in the flanking region sequence or in the number of SSR repeats. (A) No sequence information: deduced genealogy of observed data (third line) groups alleles together according to their number of repeats and involves a single SSR mutation. Genealogy is recent. (B) Consideration of sequence information: deduced genealogy involves a SNP mutation and two SSR mutations (alternative topology will involve two identical and independent substitutions at the same nucleotide site and a unique SSR mutation, which is less likely). Genealogy is ancient and SSR alleles do not group according to their numbers of repeats.</p

Distance-based Redundancy Analysis (dbRDA) ordination of the distance-based linear model (distLM) relating the (A) bacterial and (B) fungal communities to the floristic composition.

<p>Cuno.mac = <i>Cunonia macrophylla</i>, Tabe.cer = <i>Tabernaemontana cerifera</i>, Cten.las = <i>Ctenopteris lasiostipes</i>, Poly.pan = <i>Polyscias pancheri</i>, <i>Ptis</i>. <i>att = Ptisana attenuata</i>, Tris. gla = <i>Tristaniopsis glauca</i>, Grev. Gil.var.gil = <i>Grevillea gillivrayi var</i>. <i>gillivrayi</i>, Bass. Gra = <i>Basselinia gracilis</i> and Cost. com = <i>Costularia comosa</i>, Mela cf. gni = <i>Melaleuca cf</i>. <i>gnioides</i>, Glei dic = <i>Gleichenia dicarpa</i> and Myrs obl = <i>Myrsine oblanceolata</i>.</p

Scatter plots and trending curves between the bacterial and fungal communities at the (A) Kopéto site and (B) Rivière Blanche site.

<p>Scatter plots and trending curves between the bacterial and fungal communities at the (A) Kopéto site and (B) Rivière Blanche site.</p

Nonmetric Multi-Dimensional Scaling (NMDS) ordination of Bray-Curtis dissimilarity for (A) the bacterial community and (B) the fungal community.

<p>K = Kopéto, RB = Rivière Blanche, S = sedge-dominated formation (in black), Mq = <i>Tristaniopsis</i> spp maquis (in yellow), Na = <i>N</i>. <i>aequilateralis</i> monodominant rainforest (in red), and M = mixed rainforest (in purple). The ellipses represent the 0.95 standard error calculated for each plant formation at each site.</p