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 min..., , # 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)

Dataset DOI: [10.5061/dryad.t1g1jwtdr](10.5061/dryad.t1g1jwtdr)

The following help file is in regards to the manuscript:

\"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)\"

[[e-mail]](mailto:[e-mail])

## Description of the 2b-RAD data and file structure

Restriction site–associated DNA genotyping with type IIB restriction endonucleases (2b-RAD; restriction enzyme BgcI) was carried out using 93 samples of *Ledella ultima*. Raw reads of 50-bp paired-end sequence strands are deposited as fastq.gz files to the NCBI Sequence Read Archive (SRA) under accession numbers SAMN47739826–SAMN47739903 (BioProjectPRJNA1245090). Raw reads were demultiplexed by internal barcodes a...,