Disentangling serial chloroplast captures in willows.

Chloroplast capture is a process through which the chloroplast of a focal species is replaced by the chloroplast from another species during repeated backcrossing of an initial hybrid. Here we investigated serial chloroplast capture from Salix nigra in willows during sequential hybridization events that led to the capture of the same chloroplast lineage across multiple Salix species. Previously generated sequences of nuclear and chloroplast regions from several Salix species were used to identify cases of cytonuclear phylogenetic discordance, a pattern indicating chloroplast capture. Serial chloroplast captures were identified by comparing phylogenetic topologies of the chloroplast trees to discriminate among (1) a single chloroplast capture and subsequent speciation of the lineage with the captured chloroplast, (2) multiple chloroplast captures from the same parent species, and (3) serial chloroplast captures. We also looked for hybridization in genes involved in cytonuclear interactions and in photosynthesis. We identified cases of serial chloroplast capture and speciation after chloroplast capture in Salix. Although these chloroplast capture events were accompanied by signals of hybridization in the nuclear genomes, nuclear genes that functionally interact with chloroplast genes and nuclear genes involved in photosynthesis were no more likely to introgress in species with chloroplast captures than in species without chloroplast captures. This study illuminates the complex evolution of the chloroplast genomes in Salix and the potential for hybridization and introgression to influence genomic evolution.