Impact Of Selfing On The Inference Of Demographic History From Whole Genomes In Theobroma cacao L.

Theobroma cacao L (cacao: Malvaceae) is a small tree found naturally in the Amazonian rain forest.  An interesting feature of cacao is that it persists in populations of naturally outcrossing and inbreeding plants, as it is a species with a complex system of self-incompatibility, where a fraction of the population is able to undergo the most extreme form of inbreeding: self-fertilization. The theoretical consequences of inbreeding have been well characterized by theoretical population genetic studies; in particular the reduction in heterozygosity caused by self-fertilization and the fitness decrease in highly inbreed individuals in the population. A less trivial result, also derived from theoretical analyses, is the impact of selfing on the inference of demographic history from genetic data. Theoretical results have shown that inbreeding only increases the probability of coalescence between alleles found within a single diploid individual; with little impact on the estimation of the coalescent process as a whole. In this work, we show improved estimates of the demographic history of cacao, by including a larger number of sequenced accessions, and evaluate the impact of selfing in the estimation of the demographic history of cacao. Our estimates of inbreeding, from microsatellite data, suggest that different populations undergo different selfing rates that vary from 0.25 to 0.9, consistent with the range of inbreeding coefficients (F) estimated from individually sequenced genomes. We use forward simulations to estimate in a maximum likelihood framework the demographic history of cacao, and evaluate with the aid of simulations the impact of selfing on our estimations.