Phylogenomic insights into the temporal-spatial divergence history, evolution of leaf habit and hybridization in...

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.