Connectivity and population structure of Northeast Pacific squat lobsters across chemosynthetic and non-chemosynthetic deep-sea habitats: a museomics approach

The eastern Pacific is characterized by intense chemosynthetic activity along active mid-ocean ridges, including numerous hydrothermal vents and cold seeps. Genetic connectivity among organic-rich deep-sea environments is influenced by habitat instability, physical oceanographic processes, and species-specific biological traits. Squat lobsters are among the most abundant and diverse macrofaunal groups in deep-sea ecosystems, with several endemic species found in eastern Pacific chemosynthetic environments, making them an ideal model for investigating deep-sea eco-evolutionary dynamics. Here, we examine intraspecific genetic variation in closely related squat lobster species from the Northeast Pacific that differ in ecological and life-history traits, using a combined approach based on ultraconserved elements (UCEs) and mitochondrial cytochrome c oxidase subunit I (COI) sequences. Our results reveal overall weak geographic population structure across large spatial scales, despite ecological differences among species and the limited sample sizes inherent to deep-sea sampling. Both mitochondrial and genomic data show high haplotypic and nucleotide diversity, consistent with large effective population sizes and ongoing connectivity. This study represents the first comparative population genomic assessment of Northeast Pacific squat lobsters across contrasting habitats and depths. Despite limited sampling, we demonstrate the utility of UCEs for population genomic analyses using museum specimens and for characterizing associated bacterial communities, highlighting the value of natural history collections for deep-sea evolutionary research. More broadly, our results provide a practical framework for investigating population connectivity in deep-sea taxa when fresh material and dense geographic sampling are difficult to obtain.