Reconciling Phylogenetic Incongruence: Insights from Chloroplast Genomes and Nuclear Data

These conflicts between different datasets may arise from a variety of reasons. On the one hand, the incongruence could be caused by recombination and incomplete lineage sorting present in the biparentally inherited nuclear sequences. On the other hand, the hypothesis of hybridization and introgression cannot be disregarded as indicated by the strong cytonuclear discordance. The future direction of systematic research in this taxon should include more comprehensive data from single-copy nuclear genomes and a larger sample size to further investigate the potential mechanisms and evolutionary history that result in inconsistent phylogenetic relationships between sections.