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).