Phylogeny and Historical Biogeography of the East Asian Clematis Group, Sect. Tubulosae, Inferred from Phylogenomic Data

Abstract

The evolutionary history of Clematis section Tubulosae, an East Asian endemic lineage, has not been comprehensively studied. In this study, we reconstruct the phylogeny of this section with a complete sampling using a phylogenomic approach. The genome skimming method was applied to obtain the complete plastome sequence, the nuclear ribosomal DNA (nrDNA), and the nuclear SNPs data for phylogenetic reconstruction. Using a Bayesian molecular clock approach and ancestral range reconstruction, we reconstruct biogeographical history and discuss the biotic and abiotic factors that may have shaped the distribution patterns of the section. Both nuclear datasets better resolved the phylogeny of the sect. Tubulosae than the plastome sequence. Sect. Tubulosae was resolved as a monophyletic group sister to a clade mainly containing species from the sect. Clematis and sect. Aspidanthera. Within sect. Tubulosae, two major clades were resolved by both nuclear datasets. Two continental taxa, C. heracleifolia and C. tubulosa var. ichangensis, formed one clade. One continental taxon, C. tubulosa, and all the other species from Taiwan island, the Korean peninsula, and the Japanese archipelago formed the other clade. Molecular dating results showed that sect. Tubulosae diverged from its sister clade in the Pliocene, and all the current species diversified during the Pleistocene. Our biogeographical reconstruction suggested that sect. Tubulosae evolved and began species diversification, most likely in mainland China, then dispersed to the Korean peninsula, and then expanded its range through the Japanese archipelago to Taiwan island. Island species diversity may arise through allopatric speciation by vicariance events following the range fragmentation triggered by the climatic oscillation and sea level change during the Pleistocene epoch. Our results highlight the importance of climatic oscillation during the Pleistocene to the spatial-temporal diversification patterns of the sect. Tubulosae.

Phylogenomic Analysis and Dynamic Evolution of Chloroplast Genomes of Clematis nannophylla

“…However, the complexity and high morphological diversity of Clematis make it di cult to classify this genus systematically [4]. Currently, most studies have mainly focused on morphology, physiology, ecology, and pharmacological activity [7][8][9], whereas there are few basic molecular studies on germplasm resource identi cation, genetic breeding, resource conservation, and phylogeny. Furthermore, the chloroplast genome data of Clematis previously tested were submitted directly without detailed analysis, thus limiting our overall understanding of their phylogeny and genome evolution.…”

Characterization of Angraecum (Angraecinae, Orchidaceae) Plastomes and Utility of Sequence Variability Hotspots

“…Advancements in next-generation sequencing (NGS) technology have greatly facilitated the acquisition of complete plastomes, which can provide more loci to clarify the phylogenetic relationships of complex taxa [ 15 , 16 , 17 ]. Plastomes are suitable for phylogenetic analysis due to their uniparental inheritance, abundance of informative loci and moderate mutation rate [ 18 ].…”