Refugia, but Not for Everyone: Genetic Structure Differentiates Shallow and Mesophotic Populations of the Brooder...

Understanding how gene-flow and selection interact across environmental gradients is essential for assessing population resilience and evaluating the deep-refugia potential of mesophotic habitats under rapid climate change. In the context of depth, genetic connectivity patterns have been documented for broadcast-spawning species, but that of brooding marine invertebrates remains largely unexplored, leaving the role of mesophotic habitats as potential refugia uncertain. Here, we investigated the genetic structure of the brooder sponge Ircinia variabilis across shallow and mesophotic habitats in the Eastern Mediterranean and across shallow sites spanning multiple Mediterranean basins (i.e., Mallorca, Ionian-Sea and Israel). By quantifying depth and distance-related connectivity, and assessing the relative roles of neutral processes and temperature-driven selection, we evaluated the genetic connectivity of I. variabilis and the potential of mesophotic habitats to function as refugia. Using ddRADseq, we obtained 957 SNPs, to characterize gene-flow patterns, genetic structure, and environmental influences on differentiation. Ircinia variabilis exhibited pronounced vertical and geographic genetic structure, consistent with limited larval dispersal. Notably, Ionian-Sea populations were genetically closer to Mallorca than to the geographically closer Israeli populations, suggesting influence of oceanographic barriers. Analyses of selection-associated loci indicate that environmental variability contributes to population divergence, supporting local adaptation. Along the Israeli coast, pronounced differentiation between shallow and mesophotic populations highlights depth as a key axis of evolutionary divergence. Limited vertical connectivity challenges a central assumption of the deep refugia hypothesis, suggesting mesophotic populations may not sustain shallow populations under climate change.