Spatial coordinates and genotypes (8 microsatellites) of individuals (adults, saplings, seeds) used in the study

Column A: Individual ID; Column B: Country of origin; Column C: Location of origin; Columns D and E: Spatial coordinates of the individuals (degree decimals); Column F: Cohort of the individuals (adult, sapling, seed); Column G: Number of seeds per adult tree; Column H: Diameter at breast height (DBH in cm); Column I: Individuals collected in the 400 ha plot; Columns J to Y: Genotypes of the individuals at the 8 nuclear SSR (PEcCir12, PEcCir22, PEcCir227, PEcCir244, PEcCir247, PEcCir84, PEcCir103 and PEcCir271

Cluster richness, i.e. the number of different clusters shown in <b>figure 5</b> that occur in a given area.

<p>Cluster richness, i.e. the number of different clusters shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0047676#pone-0047676-g005" target="_blank"><b>figure 5</b></a> that occur in a given area.</p

Observed locally common alleles compared to past and current modeled distribution of cacao.

<p>Upper: distribution of areas with modeled habitat suitability of cacao during the LGM; red dashed polygons show potential relatively isolated refugia associated with areas holding high levels of locally common alleles. Lower: changes in cacao habitat suitability from the LGM until present; red areas represent potential habitat suitability during LGM but no longer at present (high impact or restriction areas); green indicates areas with continued habitat suitability from LGM until present (low impact or stable areas); and blue indicates areas that were probably not suitable for cacao at the LGM, but are suitable at present (new or expansion areas).</p

Averages of genetic parameters per locus for trees from coastal Ecuador (Nacional cultivar) and the remaining trees from cluster 6 (Contamana + Nacional (+Purus)), based on 1,000 bootstrap samples of 20 trees (i.e. the number of trees from coastal Ecuador).

<p>Averages of genetic parameters per locus for trees from coastal Ecuador (Nacional cultivar) and the remaining trees from cluster 6 (Contamana + Nacional (+Purus)), based on 1,000 bootstrap samples of 20 trees (i.e. the number of trees from coastal Ecuador).</p

Species richness of genus <i>Theobroma</i>.

<p>Left: observed species richness in 10 minute grid cells and a circular neighborhood of 1 decimal degree; Right: modeled species richness in 2.5 minute grid cells.</p

Averages of genetic parameters per locus for clusters 1 to 10, based on 1,000 bootstrap samples of 35 trees (i.e. the size of the smallest cluster).

<p>Four highest values for each of the parameters are underlined.</p

Complete linkage clustering based on Nei’s distance (cophenetic correlation = 0.92).

<p>Complete linkage clustering based on Nei’s distance (cophenetic correlation = 0.92).</p

Overview of the different locations of the ten clusters identified by k-means clustering.

<p>The three subclusters of cluster 6 are highlighted with different colours, clearly distinguishing the group that is largely composed of the Nacional cultivar of the Ecuadorean coastal plains (red colour).</p

Scores of sampled trees as projected on the first ordination axis of the biplot of a Spatial Analysis of Principal Components.

<p>Location of the genetic cline coincides with the bean-shaped area (and particularly the southern part of it) where the highest values of the measured genetic parameters were observed (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0047676#pone-0047676-g002" target="_blank">figure 2</a>).</p

Genotypes (9 microsatellites) and coordinates of individuals (adults, seedlings, seeds) used in the study

Column A: Individual ID; Colum B: Country of origin; Colum C: cohort of the individual (adult, seedling, seed); Columns D and E: coordinates of the individuals (degree decimals); Colmums F to W: genotypes of the individuals at the 9 nuclear SSR (23, 4, 3, 18, 14, 6, 17, 7 and 1)