Data from: 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.