Genomic Connectivity and Adaptation Signals of the Freshwater Sponge <i>Ephydatia muelleri</i> Across Its Distribution

ABSTRACT Aim Genetic connectivity and local adaptation were examined across the distribution of the freshwater sponge Ephydatia muelleri . Because it occupies an exceptional breadth of freshwater environments across a broad geographic range, this species offers key insights into biogeographic processes shaping genetic structure and adaptation in inland waters. Location Freshwater habitats across North America, Europe and Asia. Taxon Freshwater sponges (Porifera, order Spongillida). Methods A total of 106 individuals were sampled from 11 localities across three continents. Double‐digest RADseq was used to generate genome‐wide SNP data, resulting in 3114 putatively neutral SNPs for analyses of population structure and connectivity and 115 candidate SNPs potentially under selection for assessing signatures of local adaptation to environmental variables such as light and temperature. Results Neutral loci revealed low connectivity and strong genetic differentiation among regions, with two major genetic clusters corresponding to North America and Eurasia. Loci under selection indicated polygenic adaptation to environmental gradients of light and temperature and evidence of selection on gene regulatory processes. Patterns of genetic structure are consistent with the monopolisation hypothesis, suggesting that historical processes, particularly range shifts and barriers associated with the Last Glacial Maximum, have had a stronger influence on current genetic structure than ongoing gene flow. Main Conclusions Ephydatia muelleri populations show limited dispersal and strong historical imprints on genetic structure but also exhibit adaptive responses to local environmental variation. These findings highlight how monopolisation and historical climatic events shape freshwater invertebrate biogeography. Our study provides new insights into dispersal pathways, genetic plasticity and the resilience of freshwater sponges, with implications for the conservation of freshwater ecosystems.