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 th..., , , # Data from: Disentangling serial chloroplast captures in willows [https://doi.org/10.5061/dryad.r4xgxd2qh](https://doi.org/10.5061/dryad.r4xgxd2qh) ## Description of the data and file structure  This dataset contains information for the final sequence alignment file and the initial maximum likelihood tree for 77 chloroplast samples for willows. ### Files and variables #### File: chloroplast\_sequences\_final\_alignment.fasta **Description:** final alignment file for chloroplast sequences #### File: chloroplast\_tree\_initial.iqtree **Description:** maximum likelihood tree for chloroplast sequences ## Access information Other publicly accessible locations of the data: The raw sequences are uploaded to NCBI under bioproject number PRJNA1230114 ,