Microgeographic differentiation in the genetic structure of catch bowl coral, Isopora cf. palifera (Scleractinia; Acroporidae), in Kenting National Park, Taiwan

With coral reefs increasingly threatened by rapid environmental changes, understanding genetic diversity at microgeographic scale is critical for assessing their capacity to respond to local stress regimes. Theory for continuous populations predicts that brooding corals with restricted dispersal should exhibit fine-scale genetic structure and isolation-by-distance, yet such patterns remain poorly resolved in marginal and environmentally extreme reef ecosystems. Here, we investigated the genetic structure of the catch bowl coral, Isopora cf. palifera, across 11 sites within ~ 14 km in Kenting National Park (KNP), southern Taiwan, a reefscape characterized by strong small-scale environmental heterogeneity, including chronic thermal influence from a nuclear power plant and tidally driven upwelling. We genotyped 466 colonies (six microsatellite loci yielding 302 unique multilocus genotypes) and sequenced nuclear PaxC 46/47-intron from 322 colonies of I. cf. palifera. Microsatellite data revealed strong genetic structure (K = 2, K = 5): principal coordinate analyses identified four geographic groupings, and Bayesian clustering (STRUCTURE) supported two major clusters separating Nanwan (plus Tantzei Bay) from the remaining coastal sites, with one site (Shiaowan) showing admixture. The PaxC marker resolved ten haplotypes, with H1 widespread, H2 concentrated along Nanwan, and H3 dominant at thermally influenced sites near the nuclear power plant outfall. Overall, populations showed high site differentiation, significant isolation-by-distance, and high self-recruitment (68-92%), indicating limited effective dispersal. A temporal comparison (2000-2015) at Tantzei Bay indicated stable genetic structure through time despite repeated regional disturbances. Generalized estimating equation (GEE) models showed that site-level seawater temperature was positively associated with both host haplotype composition (GEE; coefficient = 0.0479, p < 0.001) and Symbiodiniaceae genera (GEE; coefficient = 0.0462, p < 0.001, symbiont data from a previous work in KNP), suggesting non-random host-symbiont-environment associations at microgeographic scale. Together, these results indicate that I. cf. palifera in KNP exhibits pronounced fine-scale genetic structure consistent with restricted dispersal and possible microgeographic adaptation of the holobiont to local thermal regimes. While such structuring may enhance local resilience by maintaining diverse, site-specific host-symbiont combinations, it also implies limited scope for rescue via gene flow if future warming pushes populations beyond their adapted tolerances. Our findings underscore the importance of accounting for microgeographic genetic structure and local adaptation when designing management and conservation strategies for reefscape such as those in KNP.