Weak Structure and Environment‐Associated Loci Across a Eutrophication Gradient in a Resilient Coral Species

ABSTRACT In marine species, large effective population sizes and high connectivity minimise drift and maintain genetic diversity. However, it is uncertain how this influences their ability to adapt to projected environmental changes from anthropogenic effects. Scleractinian corals are keystone species that face increasing threats from coastal pollution and climate change. Here we used RADseq to examine the population structure of Oulastrea crispata , an encrusting coral native to the Indo‐Pacific that inhabits a large geographic range and exhibits high tolerance to environmental stress. To assess potential adaptive differences in O. crispata , we sampled individuals from across a spatially small but pronounced eutrophication gradient (Dissolved inorganic nitrogen: 1.6–9.0 μM) within Hong Kong. A set of 39,527 genome‐wide single nucleotide polymorphisms (SNPs) revealed no broad neutral population structure within our dataset of 90 individuals despite variation in environmental conditions. The level of diversity estimates and low inbreeding coefficient suggest no loss of diversity in coral population despite the challenging environment. While F ST outlier analyses failed to reveal any clear signature of selection across sites, genotype‐environment association analyses identified 137 outlier SNPs associated with several water quality parameters. The transcriptome‐based annotation of these outlier loci indicates that their potential roles in environmental response. We also find that across the eutrophication gradient we sampled, O. crispata was consistently associated with the environmental stress‐tolerant symbiont genus Durusdinium sp. The presence of environment‐associated alleles, despite panmixia at nuclear loci, is compatible with adaptive responses driven by local environmental conditions. The detection of a stress‐tolerant Symbiodiniaceae species suggests a complementary holobiont‐level mechanism. Phenotypic plasticity of O. crispata could be another mechanism for stress resilience. Future additional studies using whole genome sequencing and transcriptome analyses will be needed to clarify the genetic architecture of host resilience in O. crispata and the relative contributions from host genetics and holobiont‐mediated effects.