Data for "DNA-based Identification of Plants and the Genomic Nature of Plant Species Differences"

We compiled studies to assess the extent of plant species monophyly, with the criteria that they were published after 2013, sequenced three or more unlinked nuclear loci, included at least three individuals from multiple congeneric species and had a phylogenetic tree where species monophyly could be inferred. The average number of multiple-sampled species per study was 12 (range from 2 - 53). A total of 151 plant groups from the published literature or from collaborators were included. Studies were categorised by sequencing techniques, namely 1) Restriction site‐Associated DNA sequencing (RAD‐seq) and its derivatives, (e.g., GBS, ddRAD‐seq, 2b‐RAD); 2) Target Capture; 3) Genome skimming; 4) Transcriptome or exon sequencing. For full criteria for inclusion see this protocol http://dx.doi.org/dx.doi.org/10.17504/protocols.io.kxygx3z9og8j/v1. Among these studies, 27 datasets were selected to further assess genomic differences between plant species. They were chosen because they have relevant metadata that link sequences of individuals to their species identities, a sequence alignment file in .fasta, .phylip, or .nex format or SNP matrix in .vcf or .fasta format, and a phylogenetic tree.