A transcriptome-based study on the phylogeny and evolution of the taxonomically controversial subfamily Apioideae (Apiaceae)

BACKGROUND AND AIMS: A long-standing controversy in the subfamily Apioideae concerns relationships among the major lineages, which has prevented a comprehensive study of their fruits and evolutionary history. Here we use single copy genes (SCGs) generated from transcriptome datasets to generate a reliable species tree and explore the evolutionary history of Apioideae. METHODS: In total, 3351 SCGs were generated from 27 transcriptome datasets and one genome, and further used for phylogenetic analysis using coalescent-based methods. Fruit morphology and anatomy were studied in combination with the species tree. Eleven SCGs were screened out for dating analysis with two fossils selected for calibration. KEY RESULTS: A well-supported species tree was generated with a topology [Chamaesieae, (Bupleureae, (Pleurospermeae, (Physospermopsis Clade, (Group C, (Group A, Group B)))))] that differed from previous trees. Daucinae and Torilidinae were not in the tribe Scandiceae and existed as sister groups to the Acronema Clade. Five branches (I-V) of the species tree showed low quartet support but strong local posterior probabilities. Dating analysis suggested that Apioideae originated around 56.64 Mya (95 % highest posterior density interval, 45.18-73.53 Mya). CONCLUSIONS: This study resolves a controversial phylogenetic relationship in Apioideae based on 3351 SCGs and coalescent-based species tree estimation methods. Gene trees that contributed to the species tree may undergoing rapid evolutionary divergence and incomplete lineage sorting. Fruits of Apioideae might have evolved in two directions, anemochorous and hydrochorous, with epizoochorous as a derived mode. Molecular and morphological evidence suggests that Daucinae and Torilidinae should be restored to the tribe level. Our results provide new insights into the morphological evolution of this subfamily, which may contribute to a better understanding of species diversification in Apioideae. Molecular dating analysis suggests that uplift of the Qinghai-Tibetan Plateau (QTP) and climate changes probably drove rapid speciation and diversification of Apioideae in the QTP region.