Tracing the Maternal Lineages and Historical Biogeography of southern South American Hollies (Ilex, Aquifoliaceae)

This study aims to clarify the evolutionary history of maternal lineages of southern South American Ilex taxa and their divergence times and dispersal patterns. Through comprehensive phylogenetic analyses of complete plastomes, a core phylogenetic structure was established and subsequently employed 11 plastid markers as its proxy, allowing the inclusion of species lacking plastomic data. Robust clades, consistently supported by maximum likelihood and Bayesian analyses, were identified across datasets, suggesting that the markers retain phylogenetic signal. Four distinct maternal lineages were discerned within southern South America, alongside with five from North America and seven from Asia. Notably, Ilex paraguariensis-the yerba mate tree- demonstrates an ancestral relationship to northern American plastid lineages during the early Eocene to early Oligocene, indicating a separate dispersal event from other South American lineages, which originated in Asia in the early Eocene and likely diversified within South America. Furthermore, findings suggest that Ilex chloroplast genomes originated in the late Cretaceous, earlier than previously reported, supporting a scenario of extensive Neogene radiation. The utility of plastome data in resolving hybrid origins is also validated. This study underscores the necessity for further research on taxa from South, Central, and North America to comprehensively understand Ilex evolution.