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

Abstract

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.

Keywords: Anaphalis; Asteraceae; Gnaphalieae; biogeography; molecular phylogenetic.

Figure 1

Comparison of phylogenetic trees inferred from the complete chloroplast genomes and the concatenated sequences of ITS and ETS. The skeletal phylogenetic trees of the HAP clade and its closely related genera are showed emphasizing the mainly clades: (A) ML tree, inferred from the complete chloroplast genomes, with bootstrap values of ML and posterior probabilities of BI shown at each node. Bootstrap values higher than 70 and posterior probabilities higher than 0.90 are indicated on branches. “-” means that the bootstrap; (B) ML tree, inferred from the concatenated sequences of ITS and ETS, with bootstrap values of ML shown at each node.

Figure 2

The complete phylogenetic trees of the HAP clade and its closely related genera are inferred from the concatenated sequences of ITS and ETS. (A) Topology of the ML tree. (B) Topology of the BI tree. (C) ML tree, with bootstrap values of ML shown at each node. Bootstrap values higher than 70 are indicated on branches.

Figure 3

Divergence times estimation and BAMM analysis of HAP clade based on complete plastome sequences. (A) Time-calibrated phylogenetic tree of the HAP clade and its closely related genera, inferred with BEAST from the 127 represent samples plastid dataset. Bars on the nodes indicate the 95% HPD intervals, numbers on the bars indicate the mean age (Mya). The calibrated nodes are indicated by red asterisk. (B) Speciation rate dynamics of HAP clade estimated by BAMM. Branch color reflects the mean of the marginal posterior density of speciation rates for each segment of the branches, with rates increasing from blue to red. (C) The diversification rates from the origin of the HAP clade to the present obtained using BAMM. (D) LTT plots show the cumulative number of lineages over time of HAP clade. The red line shows the maximum clade credibility tree.

Figure 4

Ancestral area reconstruction of the HAP clade under the S-DIVA model in RASP v4.2 and using the phylogenetic tree from the BEAST analysis. Pie charts denote the ancestral areas with probability values. The map shows the coding areas in different colors.

Figure 5

The ancestral state reconstruction and stochastic character mapping of morphological characters performed in R v4.1, using the make.simmap commands under ER model in phytools package. (A) Achene surface ornamentation (B) Leaf base.