Fig. 1

Phylogenetic estimations based on the intron-set and exon-set. a Coalescent and concatenated species trees inferred from the intron-set show the same topology (only the MP-EST species tree is shown here). b–d Coalescent (b and c, generated with MP-EST and ASTRAL, respectively) and concatenated phylogenies (d, generated with IQ-TREE) derived from the exon-set. All four trees support monophyly of the subgenera Prunella (shaded by light green) and Laiscopus (shaded by light blue). Within Prunella, the four phylogenetic trees also support the basal splits of P. immaculata and P. rubeculoides. However, the relationships among the remaining species differ between the concatenated and coalescent trees inferred from the exon-set and intron-set (indicated by red box). Bootstrap supports exceed 90% at all nodes except those marked by red arrows