Phylogenetic Endemism and Ancestral Area Inference Reveal Historical Refugia in the Greater Cape Floristic Region

ABSTRACT Aim Refugial areas and habitats are thought to have played a key role in facilitating both the emergence and persistence of floristic diversity in the Greater Cape Floristic Region (GCFR) of South Africa. While refugial areas may be identified using a diversity of biological proxies (e.g., narrow‐range endemism; paleoendemism), there is a shortage of studies in the GCFR that apply these approaches at the species level and in a comparative manner across multiple clades. Location GCFR, South Africa. Time Period Cenozoic. Major Taxa Studied Protea, Leucadendron, Pentameris, Restionoideae. Methods We quantify and compare the spatial distribution of phylogenetic endemism (PE) in four Cape‐centric plant clades, two clades of shallow‐rooted graminoids (Poales) and two of deep‐rooted shrubs (Proteales). For each clade, we also quantify the phylogenetic effect on PE (PPE), a metric describing the contribution of evolutionarily distinctive species (paleoendemics) to PE. Spatial moving average regression models are used to assess the influence of climate stability and topography on the distributions of PE and PPE. Finally, we use ancestral area inference to complement these analyses, on the premise that refugial areas are more likely to be resolved as ancestral. Results Both PE and PPE are concentrated in the southwestern GCFR, a pattern consistent with the long‐term climate stability and steep relief of this mountainous region. In addition, ancestral area inference resolves the southwestern GCFR as a likely area of origin for all clades examined. Spatial patterns of PE and PPE nevertheless vary between clades, with PE centres more diffusely and broadly distributed in Proteales than in Poales. Main Conclusions Our study indicates that stable climate and topography have played an important refugial role in shaping patterns of diversity and endemism in the GCFR, but that functionally distinct clades (i.e., shallow‐rooted graminoids versus deep‐rooted shrubs) differ in terms of the location and dispersion of areas that have served as historical refugia. We attribute this variation to trait‐dependent differences in their climate sensitivity.