Phylogenomic analyses of Pliocardiinae (Bivalvia: Vesicomyidae) update genus‐level taxonomy and shed light on trait evolution

Abstract Vesicomyid clams in the subfamily Pliocardiinae are chemosymbiotic and specific to deep‐sea chemosynthetic ecosystems with wide bathymetric and geographic ranges, making them a suitable model to study molecular adaptation and biogeography. Its phylogeny, however, still remains contentious due to limited molecular markers. Here, we elucidate the evolutionary relationships among pliocardiines based on phylogenomics data. By testing a wide range of matrices with methods including maximum likelihood, maximum parsimony, Bayesian inference, and a coalescent approach, we present a robust phylogenomic tree at the genus level supported by AU‐test and GLS analyses. We revise the genus‐level taxonomy of pliocardiines updating from Johnson et al. ( Syst. Biodivers. 2017, 15, 346) synonymising a number of species in the “ gigas ‐group” with Archivesica —also supported by a mitogenome phylogeny. Our fossil‐calibrated tree based on the phylogenomic backbone reveals that Pliocardiinae originated earlier than [41.06, 42.00] Ma in the middle Eocene, while its diversification has been concurrent with global climatic cooling events. Ancestral state reconstruction analyses found two independent invasions into the abyssal zone, and a shift from harbouring the Ca . Ruthia symbionts to Ca. Vesicomyosocius symbionts. Our results present a solid backbone for future investigations into molecular adaptation, biogeography and symbiosis in this fascinating group of molluscs.