Phylogeny of Leontopodium (Asteraceae) in China-with a reference to plastid genome and nuclear ribosomal DNA

Phylogeny, biogeography, and character evolution of Anaphalis (Gnaphalieae, Asteraceae)

The HAP clade, mainly including Helichrysum Mill, Anaphalis DC., and Pseudognaphalium Kirp., is a major component of tribe Gnaphalieae (Asteraceae). In this clade, Anaphalis represents the largest genus of Asian Gnaphalieae. The intergeneric relationships among Anaphalis and its related genera and the infrageneric taxonomy of this genus are complex and remain controversial. However, there are few studies that have focused on these issues. Herein, based on the current most comprehensive sampling of the HAP clade, especially Anaphalis, we conducted phylogenetic analyses using chloroplast (cp) genome and nuclear ribosomal DNA (nrDNA) to evaluate the relationships within HAP clade, test the monophyly of Anaphalis, and examine the infrageneric taxonomy of this genus. Meanwhile, the morphological characters were verified to determine the circumscription and infrageneric taxonomy system of Anaphalis. Additionally, the biogeographical history, diversification processes, and evolution of crucial morphological characters were estimated and inferred. Our phylogenetic analyses suggested that Anaphalis is polyphyletic because it nested with Helichrysum and Pseudognaphalium. Two and four main clades of Anaphalis were identified in cp genome and nrDNA trees, respectively. Compared with nrDNA trees, the cp genome trees were more effective for phylogenetic resolution. After comprehensively analyzing morphological and phylogenetic evidence, it was concluded that the achene surface ornamentation and leaf base showed less homoplasy and supported the two Anaphalis lineages that were inferred from cp genome. Our biogeographical analyses based on cp genome indicated that HAP clade underwent rapid diversification from late Miocene to Pliocene. The two Anaphalis lineages appeared to have originated in Africa, then spread to Western and Southern Asia, and subsequently moved into Southwestern China forming a diversity center. The dispersal patterns of the two Anaphalis lineages were different. One dispersed around the world, except in Africa and South America. The other one dispersed to Eastern and Southeastern Asia from the ancestral origin region.

Comparative analyses of complete chloroplast genomes reveal interspecific difference and intraspecific variation of Tripterygium genus

The genus Tripterygium was of great medicinal value and attracted much attention on the taxonomic study using morphological and molecular methods. In this study, we assembled 12 chloroplast genomes of Tripterygium to reveal interspecific difference and intraspecific variation. The sequence length (156,692-157,061 bp) and structure of Tripterygium were conserved. Comparative analyses presented abundant variable regions for further study. Meanwhile, we determined the ndhB gene under positive selection through adaptive evolution analysis. And the phylogenetic analyses based on 15 chloroplast genomes supported the monophyly of Tripterygium hypoglaucum and the potential sister relationship between Tripterygium wilfordii and Tripterygium regelii. Molecular dating analysis indicated that the divergence time within Tripterygium was approximately 5.99 Ma (95% HPD = 3.11-8.68 Ma). The results in our study provided new insights into the taxonomy, evolution process, and phylogenetic construction of Tripterygium using complete plastid genomes.