Data recovery and phylogenomic results
Target capture data recovery for 76 samples of the Tamus clade ofDioscorea and the four outgroup samples included in this study are summarized in Table 1. Sequence data are available at SRA repository, PRJNA525269. An average of 2,240,287 quality filtered paired-end reads were retrieved per sample, ranging between 43,612 and 16,196,619 reads. While the samples from herbarium specimens dated from 1788 to recently collected material, the differences in number of retrieved reads were not related to the age of the specimens. On average, the proportion of reads on target (enrichment efficiency) was 0.33 (0.09–0.60), and although sequences were assigned on average to 258 genes per sample, assemblies at 50% of the expected size of each gene were retrieved on average for 215 genes per sample.
Our target capture approach allowed us to recover an average of 326,149 bp (45,171–394,977) of nuclear data per sample, which corresponds to a recovery rate of 76.9% (10.6–93.1%), while the off-target reads contained plastid data that permitted the assembly of 131,543 bp on average (30,666–151,239) of the plastome per sample. No differences were observed in recovery rates between the clades reconstructed in our analysis (see below); the overall sequencing and target capture data obtained for the four outgroup samples were in the range of the remaining samples.
Both nuclear- and plastid-based phylogenomic reconstructions support the monophyly of the Tamus clade in Dioscorea (Figure 1), with two highly supported clades that corresponded to the two currently recognized species (D. communis and D. orientalis ). Three highly supported subclades were reconstructed in the D. communiss.l. clade in the nuclear tree (Figure 1). A first split separated the samples of D. communis from Macaronesia (clade DC1). The remaining samples of D. communis fell into two sister subclades corresponding to samples of D. communis from the eastern Mediterranean (clade DC2) and Mediterranean and Europe (clade DC3), respectively. The latter clade DC3 was subsequently further subdivided into (eastern Mediterranean, (central Mediterranean, western Europe)) subclades. Overall bootstrap support was >90% for most of the nodes (Figure 1).