Spatial phylogenetic diversity in Africa – a case study of the Cyperaceae (Poales)

Biogeography is increasingly adopting evolutionary approaches that integrate spatial phylogenetics and functional diversity to better understand patterns of biodiversity beyond species counts. Here, we use Cyperaceae as a model clade to investigate spatial phylogenetic and functional diversity across Africa, where the family is widespread, ecologically versatile, and highly diversified. Despite their relevance, fine-scale phylogenetic patterns and the functional traits shaping habitat occupancy in African vegetation remain poorly understood. This study addresses these gaps by assessing spatial phylogenetic structure and key functional traits across African biomes. We test four hypotheses, including: (1) paleo-endemism is more pronounced in regions dominated by open habitats than in regions dominated by closed habitats (2) Mixed- and super-endemism is likely to be more pronounced in the Cape region and Madagascar than in the rest of Africa. (3) The Sahara and Kalahari regions will show lower species richness, PD and PE than the rest of Africa. We extracted 261,029 Cyperaceae records from the Global Biodiversity Information Facility (GBIF) and the Bolus Herbarium (BOL), refining them to 144,001 records of 643 species occurring in Africa to match the phylogenetic tips. Diversity analyses were performed using a grid of 1° × 1° cells across Africa, calculating standard indices including species richness (SR), weighted endemism (WE), phylogenetic diversity (PD), and phylogenetic endemism (PE). Phylogenetic regionalization was also constructed using K-means and elbow methods, followed by hierarchical dendrogram clustering.The datasets submitted here represent the cleaned 144,001 occurrence records of 643 species occurring in Africa and the dated phylogeny used for the diversity analyses. The dataset tagged as "cleaned records" consists of 60 columns. The first 49 columns represent the collection details of the species from GBIF and BOL. The latter 11 columns represent grid information from the geodetic datum used. The dated phylogeny consists of all tips in the order Poales from Elliott et al. (2024) paper published in the New Phytologist journal.The occurrence dataset was collected from 1894 to 2023 on sedges in Africa and adjacent oceanic islands. The sequences used for the phylogeny were retrieved from GenBank between 2021 and 2023.