Environmental heterogeneity contributes to population genetic diversity and spatial genetic structure of coral-algal symbiosis of Platygyra daedalea in the northern South China Sea

•Environmental heterogeneity affected the genetic structure of coral-algal symbiosis.•Very low amounts of nutrients significantly affect genetic diversity of coral.•In the South China Sea, coral genetic diversity is proportional to phosphate content.•Coral hosts with different genotypes prefer different Symbiodiniaceae types.