Data and code from: Plant phylogenetic history, not diversity, drives insect biodiversity across South Africa’s biomes

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Abstract Aim: Insects provide essential ecosystem services, but there is a concern that insect abundance is in rapid decline. Identifying trends in insect biodiversity is challenging because we lack baseline data for most biogeographic regions, and most insect species remain undescribed. Here, we aim to report the first nationwide inventory of insect biodiversity in South Africa. Location: Eleven National Botanical Gardens representing four major South African biomes: Savanna, Grassland, Fynbos, and Albany Thicket. Time period: Sampling from 1 February 2022 to 31 January 2023. Major taxa studied: Insects (Arthropods) and vascular plants. Methods: We deployed two Malaise traps per botanical garden and used DNA barcoding to identify insect specimens. We reconstructed phylogenies for insect molecular clusters (BINs) and (12,149) vascular plant species. Insect and plant community structure were compared using dissimilarity metrics and Mantel tests. Results: We generated DNA barcodes for 337,809 specimens, representing 29,919 unique molecular clusters, as species proxies. We estimated that the true richness of insect biodiversity in South Africa may be closer to 100,000 species, yet 97% of barcoded taxa could not be assigned to species level. At current rates of taxonomic description, formally cataloguing this dark diversity would take more than 200 years. Estimated insect species richness varied strongly among biomes, with higher insect diversity in the Savanna biome than the floristically rich Fynbos. Turnover in plant lineages was associated with insect community turnover, particularly insect herbivores and predators. Main conclusions: We show that plant species richness alone is a poor predictor of insect species richness, with biome-specific factors playing an important role in shaping insect richness gradients. However, turnover in plant lineages was a strong predictor of insect compositional differences between gardens. Our study provides both critical baseline data on insect diversity in South Africa and new insights into the ecological and evolutionary drivers of insect biodiversity gradients.