Variation in recombination rate is expected to have profound consequences for molecular evolution, mediating the genomic footprints of both positive and purifying selection along chromosomes. Due to the availability of abundant genomic resources and several closely related species with different effective population size and mating system, wild tomatoes (Solanum section Lycopersicon) provide a good plant model system to assess genome-wide effects of variation in recombination rate. Based on range-wide geographic sampling and estimates of nucleotide diversity obtained from transcriptome sequencing, we found evidence for pervasive effects of recombinational environment on both levels and patterns of diversity. In particular, despite having much less functional site density, the heterochromatic regions characterized by very low recombination harbor less synonymous diversity and weaker signatures of purifying selection, compared to high-recombination euchromatic regions, consistent with signatures of linked selection. We are also interested in the evolution of reproductive isolation and have started to exploit the variable levels of hybrid seed failure (HSF) among wild tomato lineages. HSF can evolve fairly quickly and appears to be mediated by endosperm defects early in seed development, similar to published cases in Arabidopsis, Capsella, and Mimulus. Using a series of intraspecific and hybrid crosses, we have obtained transcriptomes from developing endosperms after laser-assisted endosperm capture. These genome-wide data have revealed maternal expression proportions of 7,700–13,200 transcripts, including candidate imprinted genes identified in intraspecific crosses. A consistent pattern is a shift toward higher maternal expression proportions in strongly-abortive crosses, concomitant with largely biparental expression of normally Paternally Expressed Genes (PEGs). Moreover, there are strong parallels between phenotypic asymmetries regarding seed size and overall expression perturbation in strongly abortive crosses, which can be interpreted as reflecting different ‘genetic strengths’ of the interacting taxa.