Causal modelling reveals lower coral genetic diversity in more heterogenous reef environments

Conserving genetic diversity is crucial for maintaining species evolutionary potential and resilience to environmental change. Yet, directly measuring genetic diversity across large spatial scales remains resource-intensive and impractical for conservation planning. Identifying reliable, accessible, and cost-effective spatial predictors of genetic diversity would significantly enhance our ability to incorporate genetic diversity into conservation efforts. Caribbean coral reefs represent a compelling system for investigating such predictors, as these ecosystems face unprecedented threats from disease outbreaks and climate change. Here, we investigate the utility of several environmental proxies as surrogates for genetic diversity, which may be useful for conservation planning in resource- or data-poor regions. To achieve this goal, we used reduced-representation genomic sequencing to estimate intraspecific genetic diversity, and in doing so, identified two genetically distinct and sympatric cryptic coral species in the Agaricia tenuifolia species complex. We employed a causal inference approach to assess the relationships between genetic alpha diversity and habitat area and connectivity, habitat heterogeneity, and temperature. Statistical investigations revealed that increased habitat heterogeneity, derived from remotely sensed habitat maps, was associated with lower genetic diversity within coral populations, suggesting that habitat characteristics promoting species diversity may not maintain high genetic diversity within a single species. Habitat area and connectivity, and temperature have predominantly negative effects on genetic diversity with coral habitat area and connectivity showing markedly contrasting responses in two cryptic taxa. Thus, our findings reveal that context matters greatly, as results differ between cryptic species, across variables, and among spatial scales.