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

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

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

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

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

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

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

The distribution of cultivated (<i>Bactris gasipaes</i> var. <i>gasipaes</i>, triangles) and wild (var. <i>chichagui</i>, dots) peach palm observation points.

<p>The points used only for modelling and gathered from sources other than this study are reported in blue and green, whereas the points referring to samples used in this study are shown in red or yellow, depending on the additional analyses carried out on each (genetic or phenotypic characterization). The red, blue and green polygons show the approximate distribution of <i>Bactris</i> wild types [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144644#pone.0144644.ref020" target="_blank">20</a>]; the grey lines divide the different regions of Amazonia (NWA: north-western Amazonia, GS: Guyana shield, EA: eastern Amazonia, CA: central Amazonia, SA: southern Amazonia, SWA: south-western Amazonia; after [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144644#pone.0144644.ref034" target="_blank">34</a>]).</p

Spatial distribution of allelic richness (A) and locally common alleles (B) based on the cultivated samples (~20 individuals per population) from the <i>Bactris gasipaes</i> var. <i>gasipaes</i> dataset of Hernández <i>et al</i> [37].

<p>Spatial distribution of allelic richness (A) and locally common alleles (B) based on the cultivated samples (~20 individuals per population) from the <i>Bactris gasipaes</i> var. <i>gasipaes</i> dataset of Hernández <i>et al</i> [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144644#pone.0144644.ref037" target="_blank">37</a>].</p