Abstract
Recently developed computational tools in ITS2 sequence-structure phylogenetics are improving tree robustness by exploitation of the added information content of the secondary structure. Despite this strength, however, their adoption for species-level clarifications in angiosperms has been slow. We investigate the utility of combining ITS2 sequence and secondary structure to separate species of southern African
Strychnos
, and assess correlation between compensatory base changes (CBCs) and currently recognised species boundaries. Combined phylogenetic analysis of sequence and secondary structure datasets performed better, in terms of robustness and species resolution, than analysis involving primary sequences only, achieving 100 and 88.2 % taxa discriminations respectively. Further, the
Strychnos madagascariensis
complex is well-resolved by sequence-structure phylogenetic analysis. The 17
Strychnos
species corresponded to 14 ITS2 CBC clades. Four of the five taxa in section
Densiflorae
belong to a single CBC clade, whose members tend to form natural hybrids. Our finding supports the application of ITS2 as a complementary barcoding marker for species identification. It also highlights the potential of comparative studies of ITS2 CBC features among prospective parental pairs in breeding experiments as a rapid proxy for cross compatibility assessment. This could save valuable time in crop improvement. Patterns of CBC evolution and species boundaries in
Strychnos
suggests a positive correlation. We conclude that the CBC pattern coupled with observed ITS2 sequence paraphyly in section
Densiflorae
points to a speciation work-in-progress.