Stachyuraceae, an East Asian endemic family of shrubs or small trees, comprises a single genus, Stachyurus (c. 11 spp.). Despite previous extensive studies based on both morphology and molecular data, species relationships within Stachyurus are still unresolved. Here, we employed transcriptome data aiming to elucidate the evolutionary history of Stachyurus and investigate possible causes of phylogenetic incongruence among individual gene trees in this genus. Our transcriptome phylogeny strongly supports four major clades of Stachyurus, with S. praecox from Japan being resolved as sister to the remainder of the genus on the Asian mainland. The deciduous S. praecox in Japan appears to have originated in the late Miocene, while the remainder diversified and expanded on the mainland over late Miocene to Pliocene/early Pleistocene times. These latter episodes of diversification and expansion were likely promoted by changes in paleoclimate and orogeny (e.g., late Miocene uplift of the Hengduan Mts. and/or enforcement of the East Asian summer monsoon). Species of this genus evolved from a deciduous ancestor, followed by multiple and independent transitions in leaf habit, possibly reflecting climate-related adaptations. Phylogenetic incongruence observed among individual gene trees may be attributable to incomplete lineage sorting following ancient rapid diversification and frequent interspecific gene flow caused by hybridization events. In sum, this study demonstrates the potential usefulness of genome-wide phylogenetic incongruence and network analyses for reconstructing complex evolutionary histories in rapidly diversifying and naturally hybridizing species groups.

旌节花，灌木或小乔木的东亚特有的家庭，包括一个属，旌（角11种）。尽管先前已经根据形态学和分子数据进行了广泛的研究，但仍未确定水苏属内部的物种关系。在这里，我们使用转录组数据，旨在阐明的进化史旌并调查该属个体基因树间的系统发育不一致的可能原因。我们的系统发育转录强烈支持的四大分支旌，与S.雷竹从日本被解析为妹妹到在亚洲大陆属的剩余部分。落叶S. praecox在日本，它似乎起源于中新世晚期，而其余部分则在中新世晚期至上新世/早更新世时期在大陆多样化并扩展。后来这些多样化和扩张的事件可能是由于古气候和造山运动的变化而引起的（例如，横断山的中新世晚期隆起和/或东亚夏季风的实施）。该属的物种是从落叶祖先演变而来的，随后是叶片习性的多次独立转变，这可能反映了与气候有关的适应。在各个基因树之间观察到的系统发育不一致性可能归因于古老的快速多样化和杂交事件引起的频繁种间基因流动之后的不完整谱系排序。总共，