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.