Distinct lineages and population genomic structure of the coral Pachyseris speciosa in the small equatorial reef system of Singapore

Genetic population patterns in coral reefs are important for understanding biodiversity and forecasting recovery following disturbance. Studying gene flow between small and disrupted marine ecosystems, such as the reefs along the Singapore Strait, is especially crucial due to their fragile nature. Here we sampled the ubiquitous coral species complex Pachyseris speciosa from seven sites in Singapore and applied genotyping-by-sequencing (nextRAD) for a fine-scale population genomic assessment. Our results confirm the existence of two clearly distinct, possibly cryptic, lineages that occur sympatrically at each of the seven sampling sites and are related to the “blue” and “green” lineages found in other parts of the Indo-Pacific. The closely related lineages show contrasting patterns characterised by panmixia and substantial (but unexplained) substructuring, respectively. Analysis of barriers and corridors to gene flow reveals limited connectivity between the two largest clusters of reefs at the eastern and western sectors of Singapore’s southern coastal waters. Our results extend the geographic range of the two recently uncovered P. speciosa species, further confirming their status as distinct and widespread species. More broadly, our findings highlight how conservation and management strategies may maximise connectivity among Singapore’s urbanised reef ecosystems.