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A transcriptome-based study on the phylogeny and evolution for taxonomic controversial subfamily Apioideae (Apiaceae).

J. Wen,Yan Yu,D. Xie,C. Peng,Qing Liu,Songdong Zhou,Xingjin He

Published 2020 in Annals of Botany

ABSTRACT

BACKGROUND AND AIMS The long-standing controversy in Apioideae concerns relationships among the major lineages of this subfamily, which led to comprehensive study for fruits and evolutionary history of the whole subfamily cannot be implemented accurately. Here we attempt to use single copy genes (SCGs) generated from transcriptome datasets to generate a reliable species tree and explore the evolutionary history of Apioideae. METHODS Total of 3351 SCGs were generated from 27 transcriptome datasets and one genome, and further used for phylogenetic analysis using coalescent-based methods. Morphology and anatomy of the fruits 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 highly supported species tree were generated with topology [Chamaesieae, (Bupleureae, (Pleurospermeae, (Physospermopsis Clade, (Group C, (Group A, Group B)))))] differing from the previous. Daucinae and Torilidinae skipped out of tribe Scandiceae and existed as sister groups to Acronema Clade. Five branches (I~V) of species tree showed low quartet supports but strong local posterior probabilities. Dating analysis suggested that Apioideae originated around 56.64 Ma (95 % HPD, 45.18~73.53 Ma). CONCLUSIONS This study resolves a controversial phylogenetic relationship in Apioideae based on 3351 SCGs and coalescent-based species tree estimate methods. Gene trees that contributed to the species tree may undergoing rapid evolutionary divergence and incomplete lineage sorting. Fruits of the Apioideae might evolve in two directions, anemochorous and hydrochorous, with epizoochorous as a derived mode. Molecular and morphological evidence suggested Daucinae and Torilidinae should be restored as tribe. 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 QTP and climate changes probably drive rapid radiation speciation and diversification of Apioideae in the QTP region.

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