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 through a process of repeated backcrossing of an initial hybrid. Using whole genome sequences of nuclear and chloroplast from several species of willows (Salix spp.), we identify multiple chloroplast captures, and identify the phylogenetic relationships among these events. We present a phylogenetic strategy 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, which we define as the sequential capturing of the same chloroplast lineage across multiple species. Using this method, we identify cases of both serial chloroplast capture and speciation after chloroplast capture in Salix. We also show that although these chloroplast capture events are 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.