Phylogenomics and comparative transcriptomics of selected clades in the early divergent angiosperm family Annonaceae : unlocking patterns of floral evolution, pollination ecology and evolutionary diversification

Abstract

The Annonaceae is a species-rich family within the Magnoliales. Subfam. Ambavioideae, as the second-divergent clade of Annonaceae, consists of nine genera with approximately 56 species. Previous phylogenetic studies have been based on insufficient taxon sampling and limited DNA information, hindering a robust reconstruction of relationships within the Ambavioideae. To clarify phylogenetic relationships, biogeographical history, diversification processes, and species evolution and adaptation mechanisms, I employed genome skimming sequencing methods to generate data for the entire chloroplast (cp) genome in order to reconstruct a more robust, better-resolved phylogeny of the Ambavioideae.

The use of newly assembled chloroplast genomes enables reconstruction of the phylogenetic relationships among 39 species within subfam. Ambavioideae based on 70 protein-coding genes. The results indicate that Meiocarpidium remains sister to other genera, while Cyathocalyx and Drepananthus form distinct monophyletic groups. Drepananthus emerged as the basal lineage of the sister clade Cyathocalyx-Cananga, and two African genera, Ambavia and Cleistopholis, were identified as sister genera. Character evolution supports the fusion hypothesis regarding solitary carpel formation in Cyathocalyx. Significant structure variations contribute to genome size evolution. Rpl20 was detected to undergo positive selection.

The molecular adaptation of Annonaceae species to limestone conditions has not previously been explored. I address this gap by using transcriptome data of two facultative limestone species and one obligate limestone species to investigate these adaptive changes. The common adaptive strategies of the two facultative species include up-regulation of genes related to light stimuli, water deprivation and ion transportation. Specific genes related to cytokinin response, ethylene response and chloroplast organization were differentially enriched in each species. The enrichment of differentially expressed genes in hormone signaling and glycolysis pathways contributes to hormone levels and drought resistance.

Recent research has identified biotic traits that are positively correlated with diversification rates in Annonaceae; however, the impacts of abiotic traits on diversification in Annonaceae are unclear. I explore the abiotic factors driving Annonaceae diversification based on a dated phylogenetic tree comprising 835 taxa using eight cpDNA regions. The results show that global temperature provide a better explanation for accelerated diversification in Annonaceae. There is no direct link between range evolution and species diversification in Annonaceae, and changes in niche evolution do not align with shifts in diversification rates. Annonaceae species tend to diversify in tropical regions first and then disperse to more temperate areas to escape interspecific competition, leading to later niche acceleration.

No study has comprehensively explored the relationship between biotic and abiotic factors and diversification rates in Annonaceae. This study focuses on Drepananthus, which has been found to possess a diversification rate shift, to investigate the interrelationships among biogeographical events, fruit traits and net diversification rates. The results suggest that global temperature influences the diversification of the Ambavioideae clade, and a dispersal-related trait (monocarp attachment) promotes diversification. Although the crossing of Huxley's Line alone cannot fully explain the diversification of subfam. Ambavioideae, it is possible that other factors contribute synergistically.