Saving the locals: a conservation genomics approach to the Endangered Spanish Toothcarp, Aphanius iberus (Valenciennes, 1846)

Understanding the genetic structure and evolutionary history of endangered species is crucial for effective conservation planning. The Spanish toothcarp, Aphanius iberus (Valenciennes, 1846), an endemic and euryhaline fish of the Mediterranean coast of the Iberian Peninsula, is currently threatened by habitat destruction, climate change, and anthropogenic translocations. Here, we employed genome-wide SNP data from medium- to low-coverage whole genomes to investigate the population structure, genetic diversity, and demographic history of A. iberus , especially focussing on its northern distribution, which has remained poorly studied.Our analyses revealed a well-structured genetic pattern across the species’ range, with four main genetic lineages: Northern Catalonia, Southern Catalonia, Levantine, and Murcian. Genomic indicators, including heterozygosity, ROHs, and migration analyses, suggest higher inbreeding and genetic erosion in the northernmost populations, likely due to long-term isolation, whereas southern populations maintain healthier genetic diversity. We also identified several admixed and potentially introduced populations.These findings underscore the importance of accurately determining the origin of populations before any translocation or reintroduction, as misguided management may compromise the genetic integrity of natural lineages. This work provides essential genomic insights to guide conservation strategies and emphasizes the need for lineage-aware management of endemic species like A. iberus .