Climatic Refugia, Phylogeographic Breaks, and Functional Turnover Across a Macaronesian Island Gradient: An integrative biogeographic assessment of endemic shrub assemblages under contemporary and late-Holocene climate change

Abstract

Oceanic archipelagos concentrate endemic lineages, steep environmental gradients, and high extinction risk, making them ideal systems for testing how climatic stability, dispersal limitation, and lineage history jointly shape biodiversity patterns. Yet integrative studies linking phylogeographic structure to functional turnover across entire island networks remain uncommon. We evaluated whether climatically stable upland refugia predict contemporary endemic richness, phylogeographic partitioning, and functional beta diversity across the Macaronesian archipelagos, with particular attention to endemic shrub assemblages spanning the Azores, Madeira, Selvagens, Canary Islands, and Cabo Verde. We assembled 412 georeferenced occurrence records for 37 endemic shrub taxa, generated species distribution models under contemporary and late-Holocene climate layers, summarized trait space using leaf area, seed mass, wood density, and maximum height, and reconstructed chloroplast haplotype networks for 18 focal taxa. We then linked local assemblage composition to island area, topographic complexity, refugial persistence, and inter-island isolation using generalized linear mixed models, variation partitioning, and distance-based redundancy analyses. Refugial persistence was the strongest predictor of endemic richness and unique haplotype occurrence, exceeding the explanatory power of island area alone. Functional turnover increased sharply along aridity and elevational contrasts, whereas taxonomic turnover saturated with geographic distance. Several islands retained deep phylogeographic splits despite modest present-day richness, indicating a decoupling between lineage history and contemporary species counts. Conservation prioritization based only on richness overlooked islands harboring disproportionately high evolutionary and functional uniqueness. Macaronesian endemic shrub assemblages reflect the combined influence of climatic microrefugia, historical isolation, and trait-mediated environmental filtering. Biogeographic prioritization should therefore integrate taxonomic, functional, and phylogeographic information rather than relying on richness metrics alone.