High connectivity at abyssal depths: Genomic and proteomic insights into population structure of the pan-Atlantic deep-sea bivalve Ledella ultima (E. A. Smith, 1885)

The bivalve Ledella ultima is one of the most abundant protobranchs in the abyssal Atlantic, making it a valuable model organism for studying phylogeographic patterns and population connectivity. To examine the population structure of L. ultima across seven Atlantic basins spanning over 10000 km in latitude, we used single-nucleotide polymorphisms (SNPs) from 2b-RAD and proteomic fingerprinting by MALDI-TOF MS. Despite overall low genetic divergence, subtle genetic structure was detected by admixture analyses, supporting two source populations: one in the north and central Atlantic, and a second in the south Atlantic, with moderate admixture in the Brazil and Cape basins. Proteomic fingerprinting revealed two basin-separated groups with patterns distinct from the nuclear data, suggesting environmentally driven shifts in protein expression. Our findings underscore the value of integrating nuclear genomic and proteomic tools to decipher population connectivity at abyssal depths, where minimal genetic differentiation necessitates fine-scale analyses.