Combining population genomics, larval dispersal modelling and graph theory to reveal connectivity patterns of the black-lipped pearl oyster in French Polynesia.

Unravelling the mechanisms driving marine connectivity in open ocean environments remains a challenge, particularly for bentho-pelagic species, where larval dispersal further complicates analysis. Integrating currentology with population genomics provides a powerful framework for inferring population connectivity and guiding conservation strategies. In this study, we combined population genomics (26,080 SNPs on 872 individuals), multigeneration connectivity estimates from larval dispersal modelling, and graph theory to assess the connectivity patterns of the pearl oyster (Pinctada margaritifera) across French Polynesia. We identified unprecedented fine-scale population structure with genetically distinct populations among four of the five archipelagos (excluding the Austral Archipelago), revealing a unique genetic signature of these archipelago. Global population structure aligns with coalescent connectivity estimates (R2 = 0.6), but discrepancies between the two approaches highlighted the influence of both historical and contemporary processes on present-day population structure. The Last Glacial Maximum may have played a role in shaping the genetic structure of P. margaritifera in French Polynesia, while modern pearl farming practices appear to have contributed to genetic homogenization. These results provide crucial insights for delineating management units to ensure the sustainable exploitation and diversity conservation of pearl oysters in French Polynesia. They also show the value of combining approaches to study connectivity.