Fig. 3
Population Demographics of T. cacao. a Maximum likelihood tree generated by TreeMix using intergenic regions of whole-genome sequencing data from individuals belonging to each one of the 10 main genetic groups. b Maximum likelihood tree allowing for admixture, as generated by TreeMix, showing some of the most significant ancestral contributions (migrations) from and to other groups. c Changes in effective population sizes over time, inferred under the coalescent with PSMC, for each on the 10 genetic groups in cacao. Each line represents the within-population median estimate, smoothed by fitting a cubic spline. d Detail of PSMC effective population size reconstruction for Criollo cacao, represented at a different scale to better represent the population decline. e Changes in effective population sizes over time, inferred under the coalescent with SMC + + , for each on the 10 genetic groups in cacao. Different color lines correspond to each population. A similar trend of historical population reduction (albeit different magnitudes) was observed with the two methods. f Observed two-dimensional site frequency spectrum (SFS, left panel) for the Criollo/Curaray population pair and expected SFS (right panel) under the inferred demographic model depicted in g The colors correspond to magnitudes (number of SNPs in each minor allele frequency bins). Anscombe residuals (difference between observed and expected) per frequency bin (left panel) and as an overall distribution (right panel). h Diagram for the proposed demographic model to explain Criollo/Curaray divergence, a model of isolation with migration. The time progresses from top to bottom and horizontal size of the boxes are relative to the relative effective population size. The estimated migration is relatively higher going from Curaray to Criollo, yet the scale of recombination estimated from the model is small
