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)

Phylogeographic analyses have advanced our understanding of evolutionary processes in the deep sea, yet patterns of genetic variation and population divergence at abyssal depths remain poorly understood. 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. However, evidence for sex-specific heteroplasmic mtDNA challenges the assessment of genetic structure using mitochondrial markers alone. To address this, we used mtDNA (COI, 16S), single-nucleotide polymorphisms (SNPs) from 2b-RAD, and proteomic profiles to examine the population structure of L. ultima across seven Atlantic basins spanning over 10,000 km in latitude. Five mitochondrial lineages with a lack of geographic structure were consistently identified by COI and 16S. Conversely, SNP and proteomic data did not mirror these findings, denoting that heteroplasmic mtDNA inflates intraspecific genetic divergence in this gonochoric species. Despite the SNP data revealing 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.