Data from: Resolution, conflict and rate shifts: Insights from a densely sampled plastome phylogeny for Rhododendron (Ericaceae)

Background and Aims Rhododendron is a species-rich and taxonomically
challenging genus due to recent adaptive radiation and frequent
hybridization. A well-resolved phylogenetic tree would help to understand
the diverse history of Rhododendron in the Himalaya–Hengduan
Mountains where the genus is most diverse. Methods We reconstructed the
phylogeny based on plastid genomes with broad taxon sampling,
covering 161 species representing all eight subgenera and all 12
sections, including ~45 % of the Rhododendron species native to
the Himalaya–Hengduan Mountains. We compared this phylogeny with nuclear
phylogenies to elucidate reticulate evolutionary events and
clarify relationships at all levels within the genus. We
also estimated the timing and diversification history of
Rhododendron, especially the two species-rich
subgenera Rhododendron and Hymenanthes that comprise >90 %
of Rhododendron species in the Himalaya–Hengduan Mountains. Key
Results The full plastid dataset produced a well-resolved and supported
phylogeny of Rhododendron. We identified 13 clades that were almost always
monophyletic across all published phylogenies. The conflicts between
nuclear and plastid phylogenies strongly suggested that reticulation
events may have occurred in the deep lineage history of the
genus. Within Rhododendron, subgenus Therorhodion diverged first at 56
Mya, then a burst of diversification occurred from 23.8 to 17.6 Mya,
generating ten lineages among the component 12 clades of
core Rhododendron. Diversification in subgenus Rhododendron
accelerated c. 16.6 Mya and then became fairly
continuous. Conversely, Hymenanthes diversification was slow at
first, then accelerated very rapidly around 5 Mya. In the
Himalaya–Hengduan Mountains, subgenus Rhododendron contained one major
clade adapted to high altitudes and another to low altitudes,
whereas most clades in Hymenanthes contained both low- and high-altitude
species, indicating greater ecological plasticity during its
diversification. Conclusions The 13 clades proposed here may help to
identify specific ancient hybridization events. This study will
help to establish a stable and reliable taxonomic framework for
Rhododendron, and provides insight into what drove its
diversification and ecological adaption. Denser sampling of taxa,
examining both organelle and nuclear genomes, is needed to better
understand the divergence and diversification history
of Rhododendron.