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

## TL;DR

This study uses conservation genomics to understand the genetic structure of the endangered Spanish toothcarp, revealing distinct lineages and guiding conservation efforts.

## Contribution

The study identifies four genetic lineages and highlights the need for lineage-aware conservation strategies in endangered fish species.

## Key findings

- Four main genetic lineages were identified across the species' range.
- Northern populations show higher inbreeding and lower genetic diversity.
- Admixed and translocated populations were detected, emphasizing the need for careful management.

## Abstract

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 both a single genetic marker (cytochrome b) and genome-wide SNP data from medium-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 higher genetic diversity. We also identified several admixed and potentially translocated 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 native 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.

The online version contains supplementary material available at 10.1038/s41598-025-31909-y.