Phylogenomic analyses of the diverse desert-alpine plant lineage Cistantheae

Desert and alpine environments, although ecologically distinct, often share similar environmental stressors, such as drought and high radiation. Various plant lineages traverse both biomes, which is often associated with transitions in life-history strategy, whereby annuality is more often associated with drier desert habitats and perenniality is more common in higher elevations. One such lineage is Cistantheae (Montiaceae), a morphologically diverse herbaceous clade in western North and South America. We aimed to infer a robust phylogeny of the clade as a foundation for taxonomic and comparative work.

We used double-digest restriction site-associated DNA sequencing to generate reduced-representation genomic data from >160 samples representing 48 putative species in Cistantheae. Maximum likelihood and coalescent-based phylogenetic methods were used to infer evolutionary relationships across the full clade and within major subclades. We tested for signatures of admixture and introgressive gene flow, and we reconstructed ancestral life history and climatic niche to identify patterns of correlated evolution.

We inferred a well-resolved phylogeny of Cistantheae, providing strong support for relationships among subclades within Cistantheae. Although many species relationships were clarified, we also found evidence of rampant gene flow and incomplete lineage sorting, particularly within the annual Cistanthe clade from the Atacama Desert. Life history is evolutionarily labile across the clade and strongly correlated with temperature and precipitation-related bioclimatic variables: annuals tend to occur in hotter and drier environments, whereas perennials tend to occur in cooler and wetter habitats. Elevational range is also evolutionarily labile, with several species occupying broad elevational gradients.

We present the first densely sampled phylogenomic analysis of Cistantheae, providing key insights into species relationships in the clade. Repeated transitions in life history and climatic niche, alongside wide elevational ranges, suggest that many Cistantheae species might be pre-adapted to both arid and montane habitats. This phylogeny will underpin further comparative, taxonomic and phylogenomic studies in this ecologically important lineage.