Unlocking the Forgotten Dimension of Biodiversity: A Scalable Genetic Diversity Index for Multi-Species Analysis

Conservation strategies and biodiversity assessments have long prioritized taxonomic metrics such as species richness and endemism, often neglecting intraspecific genetic diversity, a key driver of population adaptability and long-term resilience. Here, we present a scalable framework for quantifying and mapping multi-species genetic diversity using publicly available DNA sequence data. By calculating nucleotide diversity ({pi}) across taxa and aggregating values spatially, we define the Genetic Diversity Index (GDI): a site-level metric capturing geographic patterns of intraspecific genetic variation. Using simulations under different scenarios, we assessed the robustness of the GDI and implemented three corrective measures to address sampling bias and the additive effects of species richness. We queried over 25 million accessions from public databases representing 9,409 European vascular plant species and applied this approach to [~]630,000 georeferenced sequences across 1,860 species. Our results reveal distinct genetic diversity hotspots in the Anatolian Peninsula, Southern Iberia, and Eastern Alps regions corresponding to historical glacial refugia and ecological transition zones. GDI values were largely uncorrelated with species richness or phylogenetic diversity, confirming that the index captures a unique and independent dimension of biodiversity. Our indices performed extremely well and showed that fewer than 1% of studied sites exhibited a significant effect of sampling bias, validating the methods reliability under uneven data coverage. By integrating genetic diversity into spatial biodiversity analyses, the GDI detects large-scale patterns of evolutionary significance and fills a critical methodological gap, providing a reproducible tool to support conservation prioritization and policy at regional and global scales. SignificanceGenetic diversity is a fundamental component of biodiversity and critical to species resilience, yet it remains absent from most biodiversity assessments. We present a scalable framework for evaluating multi-species genetic diversity across landscapes, introducing three complementary Genetic Diversity Indices (GDI) designed for different scenarios in biodiversity assessment and conservation planning. Applying this approach to European vascular plants, we reveal that genetic diversity patterns are largely decoupled from taxonomic and phylogenetic diversity, highlighting a fundamental yet overlooked dimension of biodiversity. Our framework charts a clear path for global assessments of genetic diversity in vascular plants and beyond. Incorporating GDI into conservation strategies is critical to complement traditional metrics and better safeguard evolutionary potential of biodiversity in a rapidly changing world.