How the interplay of biotic and abiotic factors shapes current genetic diversity at the community level remains an open question, particularly in the deep sea. Comparative phylogeography of multiple species can reveal the influence of past climatic events, geographic barriers, and species life history traits on spatial patterns of genetic structure across lineages.

Here, we conducted a comparative population genomic study on seven hydrothermal vent species co-distributed in the Back-arc Basins of the Southwest Pacific region. Using ddRAD-seq, we compared distribution range-wide genomic diversity patterns across species and discovered a shared zone of phylogeographic break. Although species exhibit congruent patterns of spatial structure, they also show variation in the degree of divergence among lineages across the suture zone. Additionally, two species have a sympatric contact zone in the Woodlark Basin.

Demogenetic inference revealed shared histories of lineage divergence and secondary contact. Low levels of asymmetric gene flow probably occurred in most species between the Woodlark and North Fiji basins, but the exact location of contact zones varied from species to species. Results show that gene flow is heterogeneous across the genome, indicating possible partial reproductive isolation between lineages and early speciation.

Our comparative study sheds light on the factors that shape genetic variation at the community level, and our findings enrich our understanding of deep-sea biogeography patterns. Emphasizing the pivotal role of historical and contemporary factors, our research underscores the necessity for a holistic approach, and in particular filling in the gaps regarding life history traits of deep-sea species (generation time, development type, duration of the larval phase).