Phylogenomics of the <i>Callicarpa rubella</i> complex: implications for species delimitation in a morphologically homogenous group

Abstract The Callicarpa rubella complex, including C. rubella var. rubella, C. rubella var. subglabra, C. rubella f. angustata, C. rubella f. crenata, C. longipes var. longipes, and C. longipes var. mixiensis, is a highly homogenous group and suffers from longstanding taxonomic confusion. Clearly defined species boundaries are essential and this study sequenced and analysed the complete chloroplast (cp) genomes and two nrDNA sequences of the C. rubella complex to clarify their phylogenetic relationships. Comparative analyses of their cp genomes reveal highly similar characteristics. Phylogenetic inference based on the concatenated cp genomes and nrDNA sequences shows improved resolution, demonstrating that all members of the C. rubella complex are embedded together. They form a monophyletic clade with strong support, indicating that these taxa are conspecific. On the basis of morphological similarities and the phylogenetic relationship within the C. rubella complex, we propose treating C. rubella f. angustata, C. rubella f. crenata, C. longipes var. longipes, and C. longipes var. mixiensis as synonyms of C. rubella var. rubella. It is advisable to retain C. rubella var. subglabra as a variety of C. rubella var. rubella due to the unknown mechanism of hairlessness observed throughout the entire plant. This study is expected to provide an insight for resolution of phylogenetic relationships in highly homogenous taxa.