Future Climate Change Threatens the Genetic Diversity and Distribution of Some South American Freshwater Crustaceans of the Genus <i>Aegla</i>

ABSTRACT Climate change significantly threatens biodiversity, particularly in freshwater ecosystems, which host many endemic and threatened species. Among them, aeglids stand out as strictly endemic, ecologically important and highly threatened crustaceans, making them a relevant model for investigating the impacts of climate change on aquatic environments. Here, we assess the impacts of climate change on the geographical distribution, genetic and phylogenetic diversity of four Aegla species ( Aegla alacalufi , Aegla neuquensis , Aegla platensis and Aegla uruguayana ), using ecological niche models (ENMs) and genetic simulations. ENMs incorporated bioclimatic variables and altitude under two Shared Socio‐economic Pathways (SSP2–4.5 and SSP5–8.5) for 2060 and 2100. Genetic and phylogenetic diversities were estimated from mitochondrial and nuclear DNA sequences. Projected impacts varied significantly among the Aegla species, with the most contrasting results observed between A. platensis and A. uruguayana . Although we projected an increase in the suitable habitat areas of A. platensis across all future climate scenarios, A. uruguayana may experience a substantial loss of suitable habitat, particularly under the SSP5–8.5 scenario, along with a marked reduction in genetic and phylogenetic diversity, with losses of up to 53.13% in unique haplotypes and 49.27% in phylogenetic diversity. These findings reinforce the complexity of species responses to climate change and emphasize the need for species‐specific conservation strategies, particularly for those, like A. uruguayana , at risk of significant habitat loss. By reinforcing the critical impact of climate change, our results provide a foundation for effective conservation efforts, benefiting both Aegla and other freshwater crustaceans facing similar threats in vulnerable ecosystems.