Genetic connectivity of the metapopulation of the coral Pocillopora verrucosa (Scleractinia: Pocilloporidae) in multi-use marine protected areas of the Gulf of California, and management implications

Introduction: Estimates of contemporary connectivity of the broadcast spawning coral Pocillopora verrucosa between multi-use marine protected areas (MUMPAs) are required to assess MUMPA effectiveness and their ability to enhance resilience against disturbances. Objective: To determine the genetic structure and connectivity patterns between P. verrucosa demes inside the Gulf of California and evaluate the role and effectiveness of established MUMPAS in their protection and resilience. Methods: We assessed P. verrucosa connectivity along its peninsular range (∼350 km), including five locations and three MUMPAs in the Gulf of California using six microsatellite genetic markers. Results: Population structure was significant (FST = 0.108***) when demes included clonal replicates; however, when these clones were removed from the analysis, the sexual individuals comprised a metapopulation panmixia (FST = 0.0007 NS). To further understand connectivity patterns, an assignment test was carried out which identified ten recent between-deme migrants with a mean dispersal distance of 116.6 km (± 80.5 SE). No long-distance dispersal was detected. These results highlight the ecological importance of the Bahía de La Paz region, including Archipiélago de Espíritu Santo MUMPA. This region, located at the center of the species peninsular range, exports larva to downstream sink demes such as the Loreto (northwardly) and Cabo Pulmo (southwardly) MUMPAs. Of importance, inter-MUMPA spacing was larger than the mean larval dispersal by ~56 km, suggesting thar the designation of intermediate ‘no-take’ zones would enhance short-distance connectivity. Conclusion: This study contributes as a baseline for policymakers and authorities to provide robust strategies for coral ecosystem protection and suggest that protection efforts must be increased towards peninsular intermediate reefs to promote metapopulation resilience from natural and anthropogenic factors.

Strong horizontal and vertical connectivity in the coral Pocillopora verrucosa from Ludao, Taiwan, a small oceanic island

Mesophotic habitats could be sheltered from natural and anthropogenic disturbances and act as reproductive refuges, providing propagules to replenish shallower populations. Molecular markers can be used as proxies evaluating the connectivity and inferring population structure and larval dispersal. This study characterizes population structure as well as horizontal and vertical genetic connectivity of the broadcasting coral Pocillopora verrucosa from Ludao, a small oceanic island off the eastern coast of Taiwan. We genotyped 75 P. verrucosa specimens from three sites (Gongguan, Dabaisha, and Guiwan) at three depth ranges (Shallow: 7–15 m, Mid-depth: 23–30 m, and Deep: 38–45 m), spanning shallow to upper mesophotic coral reefs, with eight microsatellite markers. F-statistics showed a moderate differentiation (FST = 0.106, p<0.05) between two adjacent locations (Dabaisha 23–30 and Dabaisha 38–45 m), but no differentiation elsewhere, suggesting high levels of connectivity among sites and depths. STRUCTURE analysis showed no genetic clustering among sites or depths, indicating that all Pocillopora individuals could be drawn from a single panmictic population. Simulations of recent migration assigned 30 individuals (40%) to a different location from where they were collected. Among them, 1/3 were assigned to deeper locations, 1/3 to shallower populations and 1/3 were assigned to the right depth but a different site. These results suggest high levels of vertical and horizontal connectivity, which could enhance the recovery of P. verrucosa following disturbances around Ludao, a feature that agrees with demographic studies portraying this species as an opportunistic scleractinian.

The Genome of the Cauliflower Coral Pocillopora verrucosa

Climate change and ocean warming threaten the persistence of corals worldwide. Genomic resources are critical to study the evolutionary trajectory, adaptive potential, and genetic distinctiveness of coral species. Here, we provide a reference genome of the cauliflower coral Pocillopora verrucosa, a broadly prevalent reef-building coral with important ecological roles in the maintenance of reefs across the Red Sea, the Indian Ocean, and the Pacific Ocean. The genome has an assembly size of 380,505,698 bp with a scaffold N50 of 333,696 bp and a contig N50 of 75,704 bp. The annotation of the assembled genome returned 27,439 gene models of which 89.88% have evidence of transcription from RNA-Seq data and 97.87% show homology to known genes. A high proportion of the genome (41.22%) comprised repetitive elements in comparison to other cnidarian genomes, in particular in relation to the small genome size of P. verrucosa.