Plastome phylogenomics of Cephalotaxus (Cephalotaxaceae) and allied genera

Abstract

Background and aims: Cephalotaxus is a paleo-endemic genus in East Asia that consists of about 7-9 conifer species. Despite its great economic and ecological importance, the relationships between Cephalotaxus and related genera, as well as the interspecific relationships within Cephalotaxus, have long been controversial, resulting in contrasting taxonomic proposals in delimitation of Cephalotaxaceae and Taxaceae. Based on plastome data, this study aims to reconstruct a robust phylogeny to infer the systematic placement and the evolutionary history of Cephalotaxus.

Methods: A total of 11 plastomes, representing all species currently recognized in Cephalotaxus and two Torreya species, were sequenced and assembled. Combining these with previously published plastomes, we reconstructed a phylogeny of Cephalotaxaceae and Taxaceae with nearly full taxonomic sampling. Under a phylogenetic framework and molecular dating, the diversification history of Cephalotaxus and allied genera was explored.

Key results: Phylogenetic analyses of 81 plastid protein-coding genes recovered robust relationships between Cephalotaxus and related genera, as well as providing a well-supported resolution of interspecific relationships within Cephalotaxus, Taxus, Torreya and Amentotaxus. Divergence time estimation indicated that most extant species of these genera are relatively young, although fossil and other molecular evidence consistently show that these genera are ancient plant lineages.

Conclusions: Our results justify the taxonomic proposal that recognizes Cephalotaxaceae as a monotypic family, and contribute to a clear-cut delineation between Cephalotaxaceae and Taxaceae. Given that extant species of Cephalotaxus are derived from recent divergence events associated with the establishment of monsoonal climates in East Asia and Pleistocene climatic fluctuations, they are not evolutionary relics.

Keywords: Cephalotaxaceae; Gymnosperm; Taxaceae; molecular dating; phylogeny; recent speciation; taxonomic delineation.

Fig. 1.

Map of Cephalotaxus plastomes. Genes shown outside the circle are transcribed clockwise, and those inside are transcribed counterclockwise. The dark grey area in the inner circle indicates the CG content of the plastome.

Fig. 2.

Multiple alignment resulted from Mauve showing genic arrangements detected in plastomes of Cephalotaxus and allied genera. Colour bars indicate syntenic blocks, and connecting lines indicate correspondence of blocks across plastomes.

Fig. 3.

Alignment of Cephalotaxus plastomes using mVISTA, showing the percentages of sequence identity (y-axis).

Fig. 4.

Phylogenetic relationships between Cephalotaxus and allied genera reconstructed by analyses of 81 plastid protein-coding genes using maximum likelihood (ML) and Bayesian inference (BI) methods. Numbers above branches indicated ML bootstrap percentage (BS) and BI posterior probability (PP).

Fig. 5.

Divergence time estimation based on 81 plastid protein-coding genes. Numbers above and under the branches represent mean divergent ages and 95 % confidence interval of each node, respectively. Red arrows show the calibrating points for molecular dating. Divergence time and the timeline are indicated in million years ago (Mya).