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

• <strong>Background and Aims</strong> <em>Rhododendron </em>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 <em>Rhododendron </em>in the Himalaya–Hengduan Mountains where the genus is most diverse.
• <strong>Methods </strong>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 <em>Rhododendron </em>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 <em>Rhododendron</em>, especially the two species-rich subgenera <em>Rhododendron </em>and <em>Hymenanthes </em>that comprise &gt;90 % of <em>Rhododendron </em>species in the Himalaya–Hengduan Mountains.
• <strong>Key Results </strong>The full plastid dataset produced a well-resolved and supported phylogeny of <em>Rhododendron</em>. We identified 13 clades that were almost always monophyletic across all published phylogenies. The conflicts between nuclear and plastid phylogenies suggested strongly that reticulation events may have occurred in the deep lineage history of the genus. Within <em>Rhododendron</em>, subgenus <em>Therorhodion </em>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 <em>Rhododendron</em>. Diversification in subgenus <em>Rhododendron </em>accelerated c. 16.6 Mya and then became fairly continuous. Conversely, <em>Hymenanthes </em>diversification was slow at first, then accelerated very rapidly around 5 Mya. In the Himalaya–Hengduan Mountains, subgenus <em>Rhododendron </em>contained one major clade adapted to high altitudes and another to low altitudes, whereas most clades in <em>Hymenanthes </em>contained both low- and high-altitude species, indicating greater ecological plasticity during its diversification.
• <strong>Conclusions </strong>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 <em>Rhododendron</em>, 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 <em>Rhododendron</em>.

• **研究背景与研究目的**：杜鹃花属（Rhododendron）是一个物种丰富且分类学极具挑战性的类群，其成因在于近期发生的适应性辐射与频繁的杂交事件。分辨率优异的系统发育树将有助于理解该属在物种多样性最为丰富的喜马拉雅-横断山区的复杂演化历史。
• **研究方法**：本研究基于质体基因组（plastid genomes）开展系统发育重建，类群采样覆盖广泛，包含隶属于全部8个亚属与全部12个组的161个物种，其中约45%的物种为喜马拉雅-横断山区原生的杜鹃花属物种。我们将本次构建的质体系统发育树与核系统发育树进行比对，以阐明网状进化事件，并厘清该属内各级分类单元间的系统发育关系。此外，本研究还估算了杜鹃花属的演化时间与分化历史，尤其聚焦于占喜马拉雅-横断山区杜鹃花属物种总量90%以上的两个物种丰富亚属：杜鹃花亚属（Rhododendron）与常绿杜鹃亚属（Hymenanthes）。
• **主要研究结果**：完整的质体数据集成功构建了分辨率高、支持度优良的杜鹃花属系统发育树。我们共鉴定出13个支系，这些支系在所有已发表的系统发育树中几乎均为单系类群。核系统发育树与质体系统发育树之间的显著冲突，强烈表明该属的深层谱系演化历史中可能发生过网状演化事件。在杜鹃花属内，越橘杜鹃亚属（Therorhodion）于56百万年前（Mya）率先分化，随后在23.8至17.6百万年前发生了一次演化辐射爆发，在核心杜鹃花属的12个支系中衍生出10个演化支。杜鹃花亚属的分化速率在约16.6百万年前开始加速，之后趋于相对平稳。与之相反，常绿杜鹃亚属的分化初期较为缓慢，随后在约5百万年前出现了极速的分化加速。在喜马拉雅-横断山区，杜鹃花亚属包含两个主要支系，分别适应高海拔与低海拔生境；而常绿杜鹃亚属的多数支系同时涵盖低海拔与高海拔物种，表明其在分化过程中具备更强的生态可塑性。
• **研究结论**：本次研究提出的13个支系将有助于针对性地识别古老杂交事件。本研究可为建立稳定可靠的杜鹃花属分类框架提供重要支撑，并为揭示其分化与生态适应的驱动机制提供新的研究视角。未来仍需开展更为密集的类群采样，并同时分析细胞器基因组与核基因组，以更深入地解析杜鹃花属的谱系分化与演化历史。