Spatial variation of different genetic parameters, represented at a resolution of ten minute grid cells and a circular neighborhood of 1 degree.

<p>Highest values are consistently observed in the extensive bean-shaped Amazonian area covering both the Peruvian-Brazilian border, and the southern part of the Colombian-Brazilian border, as well as Amazonian Ecuador.</p

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

<p>Upper: predicted changes in cacao habitat suitability from present until 2050; red areas represent potential habitat suitability at present but no longer by 2050 (high impact or restriction areas); green indicates areas with continued habitat suitability from present until 2050 (low impact or stable areas); and blue indicates areas which are currently unsuitable for cacao, but may become suitable by 2050 (new or expansion areas) Lower: distribution of areas with modeled habitat suitability of cacao by 2050, overlaid with the location of currently existing protected areas.</p

Ordination diagram of a Principal Coordinate Analysis applied on the cacao dataset, using Nei’s distance.

<p>The first two axes show 69% of the variation in data. Environmental variables were added <i>a posteriori</i> through vector fitting. Arrows point in the direction of most rapid change in the variable and their length is proportional to the correlation between ordination and variable. According to the classification used by <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0047676#pone.0047676-Motamayor2" target="_blank">[9]</a>, Cluster1 = Purus; Cluster2 = Criollo; Cluster3 = Guiana; Cluster4 = Marañon-Amazon River; Cluster5 = Amelonado; Cluster6 = Contamana + Nacional (+Purus); Cluster7 = Marañon-Rondônia; Cluster8 = Iquitos (+Purus); Cluster9 = Nanay; Cluster10 = Curaray (alt = altitude; BIO1 = Annual mean temperature; BIO2 = Mean diurnal range (max temp – min temp) (monthly average); BIO3 = Isothermality (BIO1/BIO7) * 100; BIO4 = Temperature Seasonality (Coefficient of Variation); BIO5 = Max Temperature of Warmest Period; BIO6 = Min Temperature of Coldest Period; BIO7 = Temperature Annual Range (BIO5–BIO6); BIO8 = Mean Temperature of Wettest Quarter; BIO9 = Mean Temperature of Driest Quarter; BIO10 = Mean Temperature of Warmest Quarter; BIO11 = Mean Temperature of Coldest Quarter; BIO12 = Annual Precipitation; BIO13 = Precipitation of Wettest Period; BIO14 = Precipitation of Driest Period; BIO15 = Precipitation Seasonality (Coefficient of Variation); BIO16 = Precipitation of Wettest Quarter; BIO17 = Precipitation of Driest Quarter; BIO18 = Precipitation of Warmest Quarter; BIO19 = Precipitation of Coldest Quarter).</p

Deviance of individual positive deviants that were visited for qualitative follow-up research, practices identified with them, and numbers of resource homologue households per positive deviant.

Deviance of individual positive deviants that were visited for qualitative follow-up research, practices identified with them, and numbers of resource homologue households per positive deviant.</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

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 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

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