Seascape Genomics Reveal Contrasting Population Structure in Sympatric and Congeneric Corals Across Thermal Clines

ABSTRACT Aim Understanding local adaptation in species along environmental gradients provides insight for how species can and will adapt to increasing climate‐driven marine heatwaves. Here, the population structure of two closely related Pocillopora corals was evaluated across environmentally heterogeneous reef gradients to understand spatially variable adaptive potential of vulnerable species. Location Australia's Coral Sea and Great Barrier Reef Marine Parks span a ca. 1300 km latitudinal gradient across a 1.6°C range in Maximum Monthly Mean temperatures. Method A total of 255 colonies of Pocillopora verrucosa and 188 colonies of Pocillopora cf. meandrina were prepared and genotyped by sequencing using Illumina NovaSeq. Initial filtering and population statistics were conducted for each species. Correlations between genetic structure and environmental variables were assessed using partial redundancy analyses. The specific effects of environmental (including temperature, which was also analysed separately) and spatial variables were quantified to understand the drivers of local adaptation and how this varies across taxa and regions. Results Both species exhibited gene flow between the two reef systems (Coral Sea and Great Barrier Reef), indicating connectivity across ~12° of latitude and longitude. Population structure differed between species: P. cf. meandrina displayed pronounced genetic subdivision with two ancestral lineages partitioned along a north–south axis, while P. verrucosa maintained one dominant lineage across most reefs. In both species, population structure was shaped by ancestral lineage and thermal history. Additionally, P. cf. meandrina showed genetic structure correlated with sea current velocity, whereas P. verrucosa correlated with sea surface temperature. Main Conclusions Closely related taxa can exhibit distinct population genetic patterns and environmental responses, reflecting different capacities for local adaptation. These results highlight the importance of incorporating multiple taxa and environmental variables when predicting responses to environmental change. Conservation strategies relying solely on environmental data may suffice for some species but not others.