Reticulate Evolution in Eucalypts: Evidence of Whole Chloroplast Capture Among Sections of Corymbia

As eucalypts represent the widest planted hardwood tree in the world, a greater understanding of their biology, genetics and evolution is paramount. Within the eucalypt taxa, the relationships between genera Eucalyptus, Corymbia and Angophora have been difficult to describe due to their complex evolutionary past. Using a combination of reference-based read mapping and de novo assembly of whole genome Illumina data, we assembled the complete chloroplast genomes of four previously undescribed Corymbia species, as represented by nine distinct genotypes.Comparison and phylogenetic analysis among the chloroplast genomes and nuclear external transcribed spacer sequences revealed evidence that reticulate evolution, a well-described phenomenon within the evolutionary past of Tasmanian populations of Eucalyptus, is widespread and extends into Corymbia as evidenced by whole chloroplast sharing and incongruent phylogenies.  This is the first evidence of reticulate evolution based on whole chloroplast genome sequencing. It also provides the first documentation of chloroplast capture between sections of Corymbia, suggesting the importance of hybridization and introgression during the adaptive radiation of eucalypts.