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Background and Aims The genus Buxus has high levels of endemism in the Caribbean flora, with ~ 50 taxa. In Cuba, 82 % grow on ultramafic substrates and 59 % are nickel (Ni) accumulators or Ni hyperaccumulators. Hence it is an ideal model group to study if this diversification could be related to adaptation to ultramafic substrates and to Ni hyperaccumulation. Methods We generated a well-resolved molecular phylogeny, including nearly all of the Neotropical and Caribbean Buxus taxa. To obtain robust divergence times we tested for the effects of different calibration scenarios, and we reconstructed ancestral areas and ancestral character states. Phylogenetic trees were examined for trait-independent shifts in diversification rates and we used multi-state models to test for state-dependent speciation and extinction rates. Storms could have contributed to Cuba acting as a species pump and to Buxus reaching other Caribbean islands and northern South America'. Key Results We found a Caribbean Buxus clade with Mexican ancestors, encompassing three major subclades, which started to radiate during the middle Miocene (13.25 Mya). Other Caribbean islands and northern South America were reached from ~3 Mya onwards. Conclusions An evolutionary scenario is evident in which Buxus plants able to grow on ultramafic substrates by exaptation became ultramafic substrate endemics and evolved stepwise from Ni tolerance through Ni accumulation to Ni hyperaccumulation, which has triggered species diversification of Buxus in Cuba. Storms could have contributed to Cuba acting as a species pump and to Buxus reaching other Caribbean islands and northern South America'. [ABSTRACT FROM AUTHOR]

Premise: The genus Gynoxys and relatives form a species‐rich lineage of Andean shrubs and trees with low genetic distances within the sunflower subtribe Tussilaginineae. Previous molecular phylogenetic investigations of the Tussilaginineae have included few, if any, representatives of this Gynoxoid group or reconstructed ambiguous patterns of relationships for it. Methods: We sequenced complete plastid genomes of 21 species of the Gynoxoid group and related Tussilaginineae and conducted detailed comparisons of the phylogenetic relationships supported by the gene, intron, and intergenic spacer partitions of these genomes. We also evaluated the impact of manual, motif‐based adjustments of automatic DNA sequence alignments on phylogenetic tree inference. Results: Our results indicate that the inclusion of all plastid genome partitions is needed to infer well‐supported phylogenetic trees of the Gynoxoid group. Whole plastome‐based tree inference suggests that the genera Gynoxys and Nordenstamia are polyphyletic and form the core clade of the Gynoxoid group. This clade is sister to a clade of Aequatorium and Paragynoxys and also includes some but not all representatives of Paracalia. Conclusions: The concatenation and combined analysis of all plastid genome partitions and the construction of manually‐curated, motif‐based DNA sequence alignments are found to be instrumental in the recovery of well‐supported relationships of the Gynoxoid group. We demonstrate that the correct assessment of homology in genome‐level plastid sequence data sets is crucial for subsequent phylogeny reconstruction and that the manual post‐processing of multiple sequence alignments improves the reliability of such reconstructions amid low genetic distances between taxa. [ABSTRACT FROM AUTHOR]