This study analyzed 46 high-coverage genomes of the staghorn coral Acropora cervicornis sampled from 10 locations across the tropical western Atlantic. The authors used these genomes to evaluate both neutral and adaptive population structure, genomic diversity, demographic history, inbreeding, and connectivity. They also generated a regional haplotype reference panel intended to support future genomic monitoring efforts for this critically endangered reef-builder.
Genome-wide analyses recovered recurring regional substructure among sampled sites, but differentiation across the range was modest. The patterns observed do not indicate deeply divergent evolutionary lineages within the sampled Caribbean populations. Instead, the genomic signal is consistent with weak to moderate partitioning of variation across space, with subpopulations sharing substantial genetic similarity.
Part of the observed structure was explained by isolation-by-distance. In addition, spatial variation in effective migration rates contributed to regional differences. Together these processes account for much of the modest differentiation seen, rather than long-term isolation or strong historical barriers to gene flow.
Subpopulations across sampled sites exhibited similar levels of genomic diversity and a shared demographic history. The authors report retained genetic variation and low levels of current inbreeding, which indicate that, at present, populations retain measurable genetic resources. Despite this, estimates of contemporary effective population size (Ne) were small. A small Ne increases vulnerability to the stochastic loss of variation by genetic drift as demographic collapse continues, particularly if management actions inadvertently isolate groups further.
Analyses found limited evidence for local adaptation across the sampled range. Adaptive divergence appeared weak relative to neutral patterns, suggesting that standing adaptive variation is not strongly partitioned among regions sampled in this study. The limited adaptive differentiation supports a management view that emphasizes maintaining connectivity and preserving overall genetic diversity rather than treating many deeply divergent adaptive units separately.
Based on the combined results, the authors recommend interpreting sampled Caribbean populations of Acropora cervicornis as a single evolutionarily significant unit (ESU) that contains multiple regional management units (MUs). This framing reflects modest differentiation, shared demographic history, similar diversity levels among subpopulations, and limited local adaptation. The data do not support recognition of deeply divergent evolutionary lineages across the sampled range.
Given the modest neutral and adaptive divergence and the species’ small contemporary effective population size, the authors emphasize the urgent need for interventions that preserve and enhance genomic diversity. Key recommendations include coordinated, risk-managed assisted gene flow and other strategies designed to maintain connectivity and genetic variation across the range. The study warns that isolated or uncoordinated management, which could reinforce structure and reduce effective migration, may increase the influence of drift and heighten extinction risk.
Coordinated efforts across regional conservation entities are framed as essential for the long-term conservation and restoration of A. cervicornis as a jointly managed, single ESU. The authors present the haplotype reference panel developed in this study as a tool to support these coordinated genomic monitoring and management actions.
The authors developed a regional haplotype reference panel from the sampled genomes to facilitate future genomic monitoring of the species. This resource is intended to enable ongoing assessment of genetic diversity, population structure, and the effects of restoration or assisted gene flow interventions. Use of a common reference and coordinated monitoring can help ensure management actions preserve adaptive potential while minimizing unintended consequences of fragmenting the species’ genetic landscape.
Collectively, the genomic data indicate that management of Acropora cervicornis at the scale of a single ESU, with attention to multiple regional MUs and actions to sustain or restore connectivity and diversity (including assisted gene flow), is supported by current evidence from these 46 genomes sampled across 10 locations in the tropical western Atlantic. The authors stress urgency: despite retained variation and low inbreeding now, the small contemporary Ne signals elevated risk of drift-driven loss of diversity as demographic declines continue, underscoring the need for coordinated conservation interventions.