This thesis entails the results of three research projects. These have focused on the influence of diversity, demography and structure in the divergence (i.e. the speciation process) of four wild tomato species. In the first project, using coalescent simulations, we studied the impact of three different sampling schemes on patterns of neutral diversity in structured populations. Specifically, we evaluated two summary statistics based on the site frequency spectrum (Tajima’s D and Fu and Li’s D) as a function of migration rate, demographic history of the entire metapopulation and the sampling scheme. Using simulations, we demonstrate strong effects of the sampling scheme on Tajima’s D and Fu and Li’s D statistics, particularly under specieswide expansions. Under such scenarios, the effects of spatial sampling may persist up to very high levels of gene flow (Nm > 25). This suggests that validating the assumption of panmixia is crucial if robust demographic inferences are to be made from local or pooled samples. For the second project, we investigated how selection acts in four species of wild tomatoes (S. habrochaites, S. arcanum, S. peruvianum, and S. chilense) using sequence data from eight housekeeping genes. Our analysis quantified the number of adaptive and deleterious mutations, and the distribution of fitness effects of new mutations (its mean and variance) taking into account the demography of the species. We found no evidence for adaptive mutations but very strong purifying selection in coding regions of the four species. More interestingly, the four species exhibit different strength of purifying selection in non-coding regions (introns). Taking into account the results from the first project, we also highlighted the utility of analyzing pooled samples and local samples from a metapopulation in order to measure selection and the distribution of fitness effects. Finally, the third project deals with the estimation of nucleotide diversity and population structure in S. habrochaites and S. arcanum. We also compared these results to those of S. peruvianum and S. chilense. We found that S. arcanum and S. habrochaites present lower diversity levels than S. peruvianum and S. chilense. Our neutrality tests have not revealed any particular pattern, leading us to conclude that the loci sequenced for the present study have not evolved under strong positive selection, although they show a distinctive pattern of purifying selection (second project). We also tested the demography of all four species and found a strong expansion after a bottleneck in the recent past for S. peruvianum and a similar statistically significant pattern for S. arcanum, even though the signal seemed weaker in this case. Additionally, we found moderate levels of population sub-structure in these species, similar to previous results found in S. peruvianum and S. chilense. Still, regardless of the levels of population structure, we found at least two (Rupe and San Juan from S. arcanum) populations collected in the field that could actually be considered as a single deme. We also expanded these population structure analyses to gain insight into the phylogenetic relations between the four species in order to contribute to the taxonomical treatment of the Solanum section Lycopersicon from a population genetics perspective. Thus, we found a clear differentiation between S. arcanum and S. peruvianum based on all polymorphic sites.