Geological opportunity and symbiotic flexibility drive the evolutionary radiation of deep-sea mussels

Deep-sea mussels of the subfamily Bathymodiolinae dominate hydrothermal vent and cold seep ecosystems through partnerships with chemosynthetic bacteria. However, the timing of their diversification and the evolutionary dynamics of host-symbiont associations remain unclear. Here, we integrate mitochondrial phylogenomics, molecular dating, and cophylogenetic analyses to reconstruct their evolutionary history. We generated 10 new mitochondrial genomes and analyzed them with 22 published Mytilidae mitochondrial genomes. Phylogenetic analyses recovered two major mussel lineages, a deep-sea clade (Bathymodiolinae) and a shallow water clade. Notably, Bathymodiolinae is most closely related to the shallow water subfamily Modiolinae, as supported by mitogenome architecture. Molecular dating placed the Bathymodiolinae-Modiolinae split in the Early Jurassic (~ 186.6 Ma). However, the main diversification within Bathymodiolinae occurred much later in the Paleocene (~ 59.1 Ma). This temporal gap indicates a primarily Cenozoic radiation. Symbiont community analyses revealed dominance by SUP05 sulfur-oxidizing bacteria and Methyloprofundus methanotrophs, with marked variation among hosts. Cophylogenetic tests detected significant host-symbiont phylogenetic congruence for both methane-oxidizing and sulfur-oxidizing symbionts, but the signal was stronger and more consistently supported across individual associations in methane-oxidizing symbionts. These results suggest that bathymodioline diversification was shaped by geological opportunity and symbiotic flexibility, with environmentally acquired symbionts nevertheless retaining detectable host-associated phylogenetic structure.