Publicaciones

@article{Suleimán-Ramos2025,

title = {Integrating 3D-Printed and Natural Staghorn Coral (\textit{Acropora cervicornis}) Restoration Enhances Fish Assemblages and Their Ecological Functions},

author = {Edwin A. Hernández-Delgado and Jaime S. Fonseca-Miranda and Alex E. Mercado-Molina

and Samuel E. Suleimán-Ramos},

editor = {Bert W. Hoeksema

},

url = {https://www.mdpi.com/1424-2818/17/7/445

https://sampr.org/diversity-17-00445-v2/},

doi = {https://doi.org/10.3390/d17070445},

year  = {2025},

date = {2025-06-23},

urldate = {2025-06-23},

journal = {Diversity},

volume = {17},

issue = {445},

pages = {1-50},

abstract = {Coral restoration is essential for recovering depleted populations and reef ecological functions. However, its effect on enhancing fish assemblages remains understudied. This study investigated the integration of 3D-printed and natural Staghorn coral (Acropora cervicornis) out-planting to assess their role in enhancing benthic spatial complexity and attracting fish communities. Conducted between 2021 and 2023 at Culebra Island, Puerto Rico, we employed a before-after-control-impact (BACI) design to test four treatments: natural A. cervicornis, 3D-printed corals, mixed stands of 3D-printed and natural corals, and non-restored controls. Fish assemblages were monitored through stationary counts.



Results showed that integrating 3D-printed and natural corals enhanced fish assemblages and their ecological functions. Significant temporal changes in fish community structure and biodiversity metrics were observed, influenced by treatment and location. Herbivore abundance and biomass increased over time, especially in live coral and 3D-printed plots. Reefs with higher rugosity exhibited greater Scarid abundance and biomass post-restoration. Piscivore abundance also rose significantly over time, notably at Tampico site. Fishery-targeted species density and biomass increased, particularly in areas with live and 3D-printed coral out-plants. Fish assemblages became more complex and diverse post-restoration, especially at Tampico, which supported greater habitat complexity.



Before restoration, fish assemblages showed a disturbed status, with biomass k-dominance curves above abundance curves. Post-out-planting, this trend reversed. Control sites showed no significant changes. The study demonstrates that restoring fast-growing branching corals, alongside 3D-printed structures, leads to rapid increases in abundance and biomass of key fishery species, suggesting its potential role promoting faster ecosystem recovery and enhanced coral demographic performance.},

keywords = {biodiversity, coral 3D printing, coral restoration, fish community, fishery target species, phylogenetic diversity, taxonomic distinctness, trophic functional groups},

pubstate = {published},

tppubtype = {article}

}

@article{Hernández-Delgado2025,

title = {Climate extremes across the Caribbean and Eastern Pacific in the Anthropocene: Threats to coral reef conservation, restoration, and regional socio-economic resilience.},

author = {Edwin A. Hernández-Delgado and Yanina M. Rodríguez-González},

url = {https://sampr.org/atmosphere-16-00575/

https://www.mdpi.com/2073-4433/16/5/575},

doi = {https://doi.org/10.3390/atmos16050575},

year  = {2025},

date = {2025-05-11},

urldate = {2025-05-11},

journal = {Atmosphere},

volume = {16},

number = {575},

issue = {5},

pages = {1- 45},

abstract = {Marine heatwaves (MHWs) are increasingly affecting tropical seas, causing mass coral bleaching and mortality in the wider Caribbean (WC) and eastern tropical Pacific (ETP). This leads to significant coral loss, reduced biodiversity, and impaired ecological functions. Climate models forecast a troubling future for Latin American coral reefs, but downscaled projections for the WC and ETP remain limited. Understanding regional temperature thresholds that threaten coral reef futures and restoration efforts is critical. Our goals included analyzing historical trends in July–August–September–October (JASO) temperature anomalies and exploring future projections at subregional and country levels. From 1940 to 2023, JASO air and ocean temperature anomalies showed significant increases. Projections indicate that even under optimistic scenario 4.5, temperatures may exceed the +1.5 °C air threshold beyond pre-industrial levels by the 2040s and the +1.0 °C ocean threshold beyond historical annual maximums by the 2030s, resulting in severe coral bleaching and mortality. Business-as-usual scenario 8.5 suggests conditions will become intolerable for coral conservation and restoration by the 2030s, with decadal warming trends largely surpassing historical rates, under unbearable conditions for corals. The immediate development of regional and local adaptive coral reef conservation and restoration plans, along with climate change adaptation and mitigation strategies, is essential to provide time for optimistic scenarios to materialize.},

keywords = {Anthropocene, Caribbean, Coral Reef, eastern tropical Pacific, runaway climate, sea surface temperature, surface (2 m) temperature},

pubstate = {published},

tppubtype = {article}

}

@article{Ruiz-Barrionuevo2024,

title = {Shifts in the gut microbiota of sea urchin \textit{Diadema antillarum} associated with the 2022 disease outbreak},

author = {Juliana M. Ruiz-Barrionuevo and Elif Kardas and Ruber Rodríguez-Barreras and Marcos A. Quiñones-Otero and Claudia P. Ruiz-Diaz and Carlos Toledo-Hernández and Filipa Godoy-Vitorino},

editor = {Eria Alaide Rebollar and Mirna Vázquez-Rosas-Landa and Emanuel Martinez},

url = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2024.1409729/full



https://sampr.org/shifts-in-the-gut-microbiota-of-sea-urchin-diadema-antillarum-associated-with-the-2022-disease-outbreak/



},

doi = {doi: 10.3389/fmicb.2024.1409729},

year  = {2024},

date = {2024-07-29},

urldate = {2024-07-29},

journal = {Frontiers},

volume = {15},

pages = {1-11},

abstract = {In recent decades, Caribbean coral reefs have lost many vital marine species due to diseases. The well-documented mass mortality event of the long-spined black sea urchin \textit{Diadema antillarum} in the early 1980s stands out among these collapses. This die-off killed over 90% of \textit{D. antillarum} changing the reefscape from coral to algal-dominated. Nearly 40 years later, \textit{D. antillarum} populations have yet to recover. In early 2022, a new mortality event of \textit{D. antillarum} was reported along the Caribbean, including Puerto Rico.},

keywords = {165 rRNA, Diadema antillarum, gut microbiota, outbreak, Puerto Rico, Sea urchin},

pubstate = {published},

tppubtype = {article}

}

@article{Hernández-Delgado2024c,

title = {Bringing Back Reef Fish: Sustainable Impacts of Community-Based Restoration of Elkhorn Coral (\textit{Acropora palmata}) in Vega Baja, Puerto Rico (2008–2023)},

author = {Edwin A. Hernández-Delgado and Ricardo Laureano},

url = {https://www.mdpi.com/2071-1050/16/14/5985

https://sampr.org/sustainability-16-05985-v2/},

doi = { https://doi.org/10.3390/su16145985},

year  = {2024},

date = {2024-07-12},

urldate = {2024-07-12},

journal = {Sustainability},

volume = {16},

number = {5985},

issue = {14},

pages = {1-80},

abstract = {In response to the severe fragmentation of Elkhorn coral, Acropora palmata (Lamarck, 1816), stands caused by a major winter swell (“Holy Swell”) in March 2008, an emergency community-based low-tech restoration was initiated in Vega Baja, Puerto Rico. Over a 15-year period, coral demographic performance and fish assemblages were monitored across four restored and four control (non-restored) 100 m² plots. The restoration effort proved to be highly successful, leading to successful coral survival and growth, and to sustained recovery of fish assemblages, particularly herbivore guilds. Significantly increased abundance, biomass, and diversity were observed across all trophic functional groups, fishery target species, and geo-ecological functional groups in both restored and control plots. These positive outcomes were attributed to enhanced spatial complexity by long-term coral growth, “nutrient hotspots” within restored plots, the refugia effect from enhanced benthic spatial complexity, and the recovery of fish dispersal paths promoting spillover effects from restored to adjacent non-restored areas. Restoring herbivore guilds and geo-ecological functional groups played a crucial role in restoring vital ecological processes promoting reef ecosystem resilience. Recommendations include integrating fish assemblage recovery into coral restoration strategies, establishing natural coral nursery plots for future coral sourcing, and incorporating the concept of nursery seascapes for a holistic and ecosystem-based approach to restoration.},

keywords = {Acropora palmata, Caribbean Coral Reefs, coral restoration, Fish Assemblages, fishery target species, geo-ecological functional group, taxonomic distinctness, trophic functional groups},

pubstate = {published},

tppubtype = {article}

}

@article{Schopmeyer2024,

title = {An evaluation tool for assessing coral restoration efforts},

author = {Stephanie Schopmeyer and Victor Galvan and Edwin Hernandez-Delgado and Gabriela Nava and Martine D’Alessandro and Lisa Carne and Elizabeth Goergen and Shay Viehman and Alison Moulding and Diego Lirman},

editor = {Baruch Rinkevich},

url = {https://sampr.org/wp-content/uploads/2024/06/fmars-11-1404336.pdf},

doi = {https://doi.org/10.3389/fmars.2024.1404336},

year  = {2024},

date = {2024-06-10},

urldate = {2024-06-10},

journal = {Frontiers in Marine Science},

volume = {11},

pages = {1-13},

abstract = {The ever-increasing need for coral restoration as a tool available to mitigate reef declines and aid in the recovery of lost ecosystem services requires improving restoration performance over time through an adaptive management framework to evaluate the status of restoration programs using uniform, consistent metrics. An evaluation tool, presented herein, allows restoration practitioners and managers to self-evaluate the robustness of each project and identify successful metrics, those metrics that need special attention, and changes to restoration strategies that can improve performance and aid recovery. This tool is designed to allow programs to track the progress of each key metric over time to assist in improving upon successes and learning from failures. The metrics within this restoration evaluation tool focus on published best-management practices and have resulted from extensive research conducted by restoration experts over the past 20 years. Common metrics of growth and survival are included, in addition to parameters vital to the operational success of restoration programs, such as coral reproduction, recruitment of associated reef taxa, increasing habitat for reef fisheries, and improving overall reef habitat. Five Caribbean restoration programs, each with at least 15 years of restoration experience, are presented as case studies. Each program was evaluated based on six restoration categories including: field-based nurseries, outplantings, programmatic management, education and outreach, event-driven restoration, and socioeconomic restoration. Category-specific metrics were scored with a binary scoring system and summarized using a stop-light indicator framework, where the resulting color/score indicates the operations tatus of the different program components (Scores >75% = green/successful; 50–74.9% = light green > yellow > orange/intermediate; <49.9% = red/sub-optimal). Composite scores may be used to evaluate individual projects, overall restoration programs, or even large-scale state of regional restoration plans. Overall, four of the five programs scored >75% indicating most of these programs are performing well, are versatile, well managed, and sustainable. Outside of environmental factors and large-scale disturbance events, many programs described resource limitations, including funding and staffing, as reasons for scoring low on some metrics. A holistic evaluation rubric incorporated into programmatic self-assessment can ensure that restoration projects and programs are working towards success and sustainability.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hernández-Delgado2024,

title = {Coastal Restoration Challenges and Strategies for Small Island Developing States in the Face of Sea Level Rise and Climate Change},

author = {Edwin A. Hernández-Delgado},

editor = {Donald C. Barber},

url = {https://www.mdpi.com/2673-964X/4/2/14

https://sampr.org/wp-content/uploads/2024/04/coastal-restoration-challenges-and-strategies-for-small-island-developing-states-in-the-face-of-sea-level-rise-and-climate-change.pdf

},

doi = { https://doi.org/10.3390/coasts4020014},

year  = {2024},

date = {2024-04-01},

urldate = {2024-04-01},

journal = {Coasts},

volume = {4},

issue = {2},

pages = {235-286},

abstract = {The climate crisis poses a grave threat to numerous small island developing states (SIDS), intensifying risks from extreme weather events and sea level rise (SLR). This vulnerability heightens the dangers of coastal erosion, chronic water quality degradation, and dwindling coastal resources, demanding global attention. The resultant loss of ecological persistence, functional services, and ecosystem resilience jeopardizes protection against wave action and SLR, endangering coastal habitats’ economic value, food security, infrastructure, and livelihoods. Implementing integrated strategies is imperative. A thorough discussion of available strategies and best management practices for coastal ecosystem restoration is presented in the context of SIDS needs, threats, and major constraints. Solutions must encompass enhanced green infrastructure restoration (coral reefs, seagrass meadows, mangroves/wetlands, urban shorelines), sustainable development practices, circular economy principles, and the adoption of ecological restoration policies. This requires securing creative and sustainable funding, promoting green job creation, and fostering local stakeholder engagement. Tailored to each island’s reality, solutions must overcome numerous socio-economic, logistical, and political obstacles. Despite challenges, timely opportunities exist for coastal habitat restoration and climate change adaptation policies. Integrated strategies spanning disciplines and stakeholders necessitate significant political will.},

keywords = {climate change adaptation; coral reefs; ecological restoration; seagrass meadows; mangroves; sand beaches; green infrastructure; hybrid infrastructure; small island developing states; urban coastal habitats},

pubstate = {published},

tppubtype = {article}

}

@article{Ruiz-Diaz2024,

title = {A successful method to restore seagrass habitats in coastal areas affected by consecutive natural events},

author = {Claudia Patricia Ruiz-Diaz and Carlos Toledo-Hernández and Juan Luis Sánchez-González and Alex E. Mercado-Molina},

editor = {Haider Mahmood},

url = {https://peerj.com/articles/16700/

},

doi = {https://doi.org/10.7717/peerj.16700},

year  = {2024},

date = {2024-01-02},

journal = {PeerJ},

pages = {1-17},

abstract = {Seagrass meadows, known for providing essential ecosystem services like supporting fishing, coastline protection from erosion, and acting as carbon sinks to mitigate climate change effects, are facing severe degradation. The current deteriorating state can be attributed to the combination of anthropogenic activities, biological factors (i.e., invasive species), and natural forces (i.e., hurricanes). Indeed, the global seagrass cover is diminishing at an alarming mean rate of 7% annually, jeopardizing the health of these vital ecosystems. However, in the Island Municipality of Culebra, Puerto Rico, losses are occurring at a faster pace. For instance, hurricanes have caused over 10% of cover seagrass losses, and the natural recovery of seagrasses across Culebra’s coast has been slow due to the low growth rates of native seagrasses (Thalassia testudinum and Syringodium filiforme) and the invasion of the invasive species Halophila stipulacea. Restoration programs are, thus, necessary to revitalize the native seagrass communities and associated fauna while limiting the spread of the invasive species.},

keywords = {Carbon storage, Caribbean, Halophila stipulacea, Hurricanes, Plug propagation units (PUS), restoration, Syringodium filiforme, Thalassia testudinum},

pubstate = {published},

tppubtype = {article}

}

@article{Rodríguez-Barreras​2023,

title = {Uneven demographic consequences of the 2022 disease outbreak for the sea urchin \textit{Diadema antillarum} in Puerto Rico},

author = {Ruber Rodríguez-Barreras​ and Claudia Patricia Ruiz-Diaz and Marcos A. Quiñones-Otero and Carlos Toledo-Hernández},

editor = {Anastazia Banaszak},

url = {https://peerj.com/articles/16675/

https://sampr.org/wp-content/uploads/2024/01/Uneven-demographic-consequences-of-the-2022-disease-outbreak-for-the-sea-urchin-Diadema-antillarum-in-Puerto-Rico-peerj-16675.pdf},

doi = {https://doi.org/10.7717/peerj.16675},

year  = {2023},

date = {2023-12-20},

urldate = {2023-12-20},

journal = {PeerJ},

volume = {11},

number = {e16675},

pages = {1-16},

abstract = {Pervasive epizootic events have had a significant impact on marine invertebrates throughout the Caribbean, leading to severe population declines and consequential ecological implications. One such event was the regional collapse of herbivory, partly caused by the Diadema antillarum mortality event in 1983–84, resulting in a trophic cascade and altering the structure of reef communities. Consequently, there was a notable decrease in coral recruitment and an increase in the coverage of macroalgae. Nearly four decades later, in early 2022, the Caribbean basin experienced another widespread mass mortality event, further reducing the populations of D. antillarum. To assess the effects of this recent mortality event on the current demographics of D. antillarum, we surveyed eight populations along the eastern, northeastern, northern, and northwestern coast of Puerto Rico from May to July 2022, estimating their population density, size distribution, and disease prevalence. Additionally, the study compared these population parameters with data from four sites previously surveyed in 2012 and 2017 to understand the impact of the recent mortality event. The survey conducted in 2022 showed varying population densities at the surveyed reefs. Some populations exhibited mean densities of nearly one individual per square meter, while others had extremely low or no living individuals per square meter. The four populations with the highest density showed no evidence of disease, whereas the four populations with the lowest D. antillarum densities exhibited moderate to high disease prevalence. However, when considering all sites, the estimated disease prevalence remained below 5%. Nevertheless, the comparison with data from 2012 and 2017 indicated that the recent mortality event had a negative impact on D. antillarum demographics at multiple sites, as the densities in 2022 were reduced by 60.19% compared to those from the previous years. However, it is still too early to determine the severity of this new mortality event compared to the 1983–84 mortality event. Therefore, it is imperative to continue monitoring these populations.},

keywords = {demography, Diadema antillarum, Mass mortality, Puerto Rico, Sea urchin},

pubstate = {published},

tppubtype = {article}

}

@article{Rodriguez-Casariego2023,

title = {Multi-omic characterization of mechanisms contributing to rapid phenotypic plasticity in the coral \textit{Acropora cervicornis} under divergent environments},

author = {Javier A. Rodriguez-Casariego and Alex Mercado-Molina and Leila Soledade Lemos and Natalia Soares Quinete and Anthony Bellantuono and Mauricio Rodriguez-Lanetty and Alberto Sabat and Jose M. Eirin-Lopez},

url = {https://link.springer.com/article/10.1007/s00338-023-02446-9#author-information},

doi = {https://doi.org/10.1007/s00338-023-02446-9},

year  = {2023},

date = {2023-12-09},

urldate = {2023-12-09},

journal = {Coral Reefs},

abstract = {Phenotypic plasticity is defined as a property of individual genotypes to produce different phenotypes when exposed to different environmental conditions. This ability may be expressed at behavioral, biochemical, physiological, and/or developmental levels, exerting direct influence over species' demographic performance. In reef-building corals, a group critically threatened by global change in the Anthropocene, non-genetic mechanisms (i.e., epigenetic and  microbiome variation) have been shown to participate in plastic 

 hysiological responses to environmental change. Yet, the precise way in which these mechanisms interact, contribute to such responses, and their adaptive potential is still obscure. The present work aims to fill this gap by using a multi-omics approach to elucidate the contribution and interconnection of the mechanisms modulating phenotypic plasticity in staghorn coral (Acropora cervicornis) clones subject to different depth conditions. Results show changes in lipidome, epigenome and transcriptome, but not in symbiotic and microbial communities. In addition, a potential shift toward a more heterotrophic feeding behavior was evidenced in corals at the deeper site. These observations are consistent with a multi-mechanism modulation of rapid acclimation in corals, underscoring the complexity of this process and the importance of a multifactorial approach to inform potential intervention to enhance coral adaptive capacity.},

keywords = {epigenetics, Lipidome, Microbiome, Phenotypic plasticity, staghorn coral, Symbiodiniaceae, Transcriptome, WGBS},

pubstate = {published},

tppubtype = {article}

}

@article{Mercado-Molina2023,

title = {Outplants of the Threatened Coral \textit{Acropora cervicornis} Promote Coral Recruitment in a Shallow-Water Coral Reef, Culebra, Puerto Rico},

author = {Alex E. Mercado-Molina and Samuel E. Suleimán-Ramos },

url = {https://www.mdpi.com/2071-1050/15/24/16548

https://sampr.org/wp-content/uploads/2024/01/Outplants-of-the-Threatened-Coral-Acropora-cervicornis-Promote-Coral-Recruitment-in-a-Shallow-Water-Coral-Reef-CulebraPuerto-Rico-sustainability-15-16548.pdf},

doi = {https://doi.org/10.3390/su152416548},

year  = {2023},

date = {2023-12-05},

urldate = {2023-12-05},

journal = {Sustainability},

volume = {15},

number = {16548},

issue = {24},

pages = {1-13},

abstract = {The numerous socioeconomic and ecological challenges that coral reef degradation poses in the Greater Caribbean have led to a surge in restoration efforts. In this context, outplanting nursery-reared coral colonies has emerged as one of the most common strategies used to rejuvenate degraded reefs and reinstate critical ecosystem processes such as coral recruitment. However, the extent to which coral outplanting promotes the recruitment of coral species remains a subject of ongoing debate. This study tested the hypothesis that reintroducing the threatened coral Acropora cervicornis to a degraded coral reef promotes coral recruitment. To test our hypothesis, a series of recruitment

quadrats were established in an area populated with A. cervicornis outplants and in a reference location devoid of the coral. To further investigate the relationship between A. cervicornis and coral recruitment, an experiment was implemented in which half of the quadrats in the restored area received a coral outplant, while the other half were left undisturbed. After one year, all coral recruits located within the quadrats were counted and identified. It was found that in the restored area the mean recruit density exceeded that of the reference location by a factor of 2.15. Results also unveiled a positive association between coral recruitment and the presence of A. cervicornis. Specifically,

the mean recruit density in quadrats that received an A. cervicornis colony was 2.21 to 4.65-times higher than in the quadrats without coral outplants. This intriguing observation underscores the pivotal role of A. cervicornis in shaping the recruitment dynamics of corals within degraded reef areas, highlighting the potential of active coral outplanting to enhance the resilience of deteriorating coral reef ecosystems.},

keywords = {Acropora cervicornis, Caribbean, coral outplans, coral recruitment, coral reef degradation, coral reefs restauration},

pubstate = {published},

tppubtype = {article}

}

@article{Hernández-Delgado2023,

title = {Long-Term Persistence of Propeller and Anchor Damage to Seagrass Canopy and Demersal Biodiversity in Puerto Rico},

author = {Edwin A. Hernández-Delgado},

url = {https://www.scirp.org/journal/paperinformation?paperid=128458

https://sampr.org/wp-content/uploads/2024/01/Long-Term-Persistence-of-Propeller-and-Anchor-Damage-to-Seagrass-Canopy-and-Demersal-Biodiversity-in-Puerto-Rico.pdf},

doi = {https://doi.org/10.4236/oje.2023.1310042},

issn = {2162-1993},

year  = {2023},

date = {2023-10-24},

urldate = {2023-10-24},

journal = {Open Journal of Ecology},

volume = {13},

number = {10},

pages = {671-710},

abstract = {Seagrass ecosystems support high biodiversity and productivity and constitute critical links to adjacent ecosystems. However, there is a growing concern that increasing recreational navigation may affect its ecological processes and functions, which may affect its recreational and tourism values, compromising local economies and livelihoods. The long-term impacts (1996-2011) of recreational navigation on seagrass benthic community structure were assessed by addressing the question of whether long-term effects of recreational navigation had a significant impact on seagrass community structure and on its benthic faunal assemblages. Findings evidenced: 1) a consistent spatio-temporal gradient in the ecological conditions of seagrasses across the scoured areas, with increased percent seagrass cover, density and canopy height, and seagrass benthic biodiversity with increasing distance from disturbed areas; 2) a decline in percent seagrass cover, and an increased macroalgal and cyanobacterial percent cover through time around the disturbed areas; 3) a significant shift in seagrass assemblage biodiversity as a response to boating that followed the intermediate disturbance hypothesis; 4) an adverse effect on the spatial distribution and survival of multiple benthic invertebrate taxa; and 5) a significant decline in cnidarians, echinoids, ophiuroids, holothurians, and gastro-pods, and an increase in polychaetes, platyhelminths, and hermit crabs, particularly in areas exposed to boating. Spatio-temporal variation in seagrass community structure explained the observed variation in benthic faunal assemblages. The long-term consequences on ecosystem functions and management needs are discussed to foster the conservation of seagrasses.},

keywords = {Benthic Faunal Communities, community trajectory, Ecological Disturbance, Fish Assemblages, Recreational Navigation, Seagrass Ecosystems},

pubstate = {published},

tppubtype = {article}

}

@article{Aponte-Marcano12023,

title = {Effectiveness of different nursery designs for the restoration of the threatened coral \textit{Acropora cervicornis} in Culebra, Puerto Rico},

author = {Aponte-Marcano Patria I. and Suleimán-Ramos Samuel E. and Mercado-Molina Alex E.},

url = {https://www.conservationevidence.com/individual-study/12254

https://sampr.org/wp-content/uploads/2024/01/Effectiveness-of-different-nursery-designs-for-the-restoration-of-the-threatened-coral-Acropora-cervicornis-in-Culebra-Puerto-Rico.pdf},

doi = {https://doi.org/10.52201/CEJ20/PNCI5011},

issn = {1758-2067},

year  = {2023},

date = {2023-09-01},

urldate = {2023-09-01},

journal = {Conservation Evidence Journal},

volume = {20},

pages = {30-39},

abstract = {The threatened staghorn coral Acropora cervicornis is an important reef-builder species in the Caribbean. Its ecological importance and critical status have prompted efforts to restore degraded populations. In this respect, nursery-based programmes have effectively propagated A. cervicornis and helped to increase population sizes. Despite many advances in low-cost coral nursery designs, there is still a need to increase productivity while reducing costs. This study evaluates A. cervicornis demographic performance in two propagation structures: floating trees (FT) and floating horizontal frames (HF). Two equal-sized fragments were collected from 50 healthy staghorn coral colonies. Each fragment was placed into an FT or HF design. Survival, growth, branching, and productivity were recorded for seven months. To address the cost-effectiveness of the coral propagation techniques, we compared the total cost of producing corals between the two designs. Survival was similar, with 91% and 92% of the coral fragments surviving in the FT and HF, respectively. Although colonies in HF nurseries grew faster and produced more branches than those in FT nurseries, these differences were not statistically significant. Likewise, productivity did not differ statistically between nursery designs despite fragments in HF nurseries being 1.5 times more productive than those in FT nurseries. Because of the similarity in demographic performance, the selection of nursery designs could be based solely on their cost-effectiveness. In this respect, the cost-effectiveness analysis shows that producing corals using HF costs about 70% less than FT. Thus, we conclude that floating horizontal frame (HF) nurseries are better for propagating A. cervicornis and accelerating coral restoration activities.},

keywords = {Acropora cervicornis, Caribbean Coral Reefs, coral restoration, Puerto Rico},

pubstate = {published},

tppubtype = {article}

}

@article{Santiago-Padua2023,

title = {Demographic and population response of the threatened coral \textit{Acropora cervicornis} (\textit{Scleractinia}, \textit{Acroporidae}) to fireworm corallivory},

author = {Paola Santiago-Padua and Jeremy Velázquez-Alvarado and Arelys Del Mar López-Pérez and Julimar Nevárez-Mélendez and Lemuel E. Díaz-Druet and Samuel E. Suleimán-Ramos and Alex E. Mercado-Molina},

url = {https://revistas.ucr.ac.cr/index.php/rbt/article/view/54912

https://sampr.org/wp-content/uploads/2024/01/Demographic-and-population-response-of-the-threatened-coral-Acropora-cervicornis-Scleractinia-Acroporidae-to-fireworm-corallivory.pdf},

doi = {https://doi.org/10.15517/rev.biol.trop..v71iS1.54912},

issn = {2215-2075 Vol. 71 (S1): e54912},

year  = {2023},

date = {2023-04-30},

urldate = {2023-04-30},

journal = {Revista de Biología Tropical},

volume = {71},

issue = {1},

pages = {1-15},

abstract = {Introduction: The fireworm Hermodice carunculata is a widespread polychaete that can prey upon many coral species. However, few studies have examined the effect of fireworm predation on coral demographics during non-outbreak periods.



Objective: To determine whether predation by H. carunculata compromised the growth, survival, and population performance of the threatened coral Acropora cervicornis.



Methods: Nursery-reared coral fragments (n = 99) were fixed to the bottom of Punta Melones reef in the Island Municipality of Culebra, Puerto Rico. Predation activity and its demographic consequences on coral outplants were assessed from December 2020 to August 2022. Susceptibility to predation was compared between colonies collected directly from the reef and those originating from outside sources (e.g., coral nurseries). With the demographic data, simple size-based population matrix models were developed to 1) examine whether fireworm predation led to a significant decline in population growth rate (λ), 2) determine the demographic transition(s) that contribute the most to λ, and 3) determining the demographic transition(s) that accounted for differences in λ when comparing scenarios that considered either only predated colonies or both predated and non-predated outplants.



Results: Predation increased over time, being more frequently observed in the area with the highest topographic relief and on colonies foreign to the study site. Outplants that were partially consumed grew significantly slower than non-predated colonies; however, predation did not threaten their survival. The likelihood of being attacked by the fireworm increased with branching complexity. The estimated λ for a scenario considering only predated colonies was 0.99, whereas, for a scenario where both predated and non-predated colonies were considered, λ was 0.91. Population growth, under the two scenarios, was mainly influenced by the probability of a large colony surviving and remaining at the largest size.



Conclusions: Although predation can negatively impact coral growth, the relatively high survival rate of predated colonies compensates for the adverse effect. Since survival is the demographic transition that contributes most to population growth, it could be concluded that under a non-outbreak scenario, fireworm predation may not be the primary cause of A. cervicornis population decline.



Keywords: coral demographics; coral outplants; elasticity analysis; Hermodice carunculata; population matrix model; predation; restored population.},

keywords = {Acropora cervicornis, Caribbean, coral demographics, coral outplants, elasticity analysis, Hermodice carunculata, population matrix model, predation, restored population},

pubstate = {published},

tppubtype = {article}

}

@article{Toledo-Hernández12023,

title = {Uncovering the link between environmental factors and coral immunity: A study of fluorescent protein expression and phenoloxidase activity in \textit{Acropora cervicornis}},

author = {Carlos Toledo-Hernández and Claudia Patricia Ruiz-Diaz and Juan Sebastian Ramírez-Lugo and Marielys Torres-Díaz and Lisby Santiago-Pagán and Andrea Bruno-Chardón and Liz M. Díaz-Vázquez},

editor = {Virginia M. Weis and Nicholas MacKnight and Bradford Dimos

},

url = {https://www.frontiersin.org/articles/10.3389/fmars.2023.1133486/full

https://sampr.org/wp-content/uploads/2024/01/Uncovering-the-link-between-environmental-factors-and-coral-immunity-A-study-of-fluorescent-protein-expression-and-phenoloxidase-activity-in-Acropora-cervicornisfmars-10-1133486.pdf},

doi = {https://doi.org/10.3389/fmars.2023.1133486},

year  = {2023},

date = {2023-03-02},

urldate = {2023-03-02},

journal = {Frontiers in Marine Science},

volume = {10},

pages = {1-11},

abstract = {Worsening environmental conditions due to climate change have profoundly affected the health of coral reefs worldwide. Thus, understanding how corals respond to fluctuating and/or extreme levels of temperature and solar irradiation will guide future protection and restoration efforts of this valuable ecosystem. Herein, we present a study of the immune responses of the endangered coral Acropora cervicornis to seasonal fluctuations in water temperature (WT), light intensity (LI), and water depth. Immune responses were observed by measuring the concentration of green and cyan fluorescent proteins (GFP and CyFP) and the activity of phenoloxidase (PO), an enzyme involved in the biosynthesis of the photoprotective protein melanin. To study these responses, visually healthy A. cervicornis fragments were placed at 8, and 12 m depth, and GFP, CyPF, and PO activity were measured at three-month intervals over a 12-month period. Seawater temperature and light intensity were also measured at each depth during this period. A general linear mixed model was used to determine the effects of seasonal variations of WT, LI, and water depth on the immune proteins. GFP, CyFP, and PO activity varied significantly across time – all higher in late summer/early fall and lower in late winter/early spring. Likewise, WT and LI significantly affected GFP, CyFP, and PO activity. On the other hand, water depth only had a significant effect on fluorescent protein concentrations but not PO activity. Our study demonstrates that corals can modulate these key immune-related proteins throughout natural seasonal fluctuations. That is, increasing in months of higher thermal and light conditions while decreasing in months with mild thermal and light conditions. The phenotypic plasticity of A. cervicornis in adapting to a changing environment underscores the importance that in future studies time of the year should be a meaningful consideration when evaluating the responses of A. cervicornis to the environment.},

keywords = {Acropora cervicornis, Coral immunity, coral reefs, coral reefs restauration},

pubstate = {published},

tppubtype = {article}

}

@article{Hernández-Delgado2022,

title = {The Long and Winding Road of Coral Reef Recovery in the Anthropocene: A Case Study from Puerto Rico},

author = {Edwin A. Hernández-Delgado and María F. Ortiz-Flores},

url = {https://www.mdpi.com/1424-2818/14/10/804

https://sampr.org/hernandez-ortiz-2022-coral-recruitment-pr-final/

},

doi = {https://doi.org/10.3390/d14100804},

year  = {2022},

date = {2022-09-27},

journal = {Diversity},

volume = {14},

issue = {804},

pages = {1-25},

abstract = {The persistence and resilience of marginal shallow coral reefs at their limits of environmental tolerance have declined due to chronic environmental degradation and climate change. However, the consequences for the natural recovery ability of reefs after disturbance remain poorly understood. This study considered the potential for natural recovery through coral recruitment on fringing reefs across different geographic regions under contrasting environmental conditions in Puerto Rico. Reefs in areas with significant water quality degradation and more severe physical impacts of hurricanes were expected to have lower coral recruit density and diversity, and therefore less potential for recovery.



Sixteen reefs were assessed across three geographic regions. Degraded reefs sustained a lower percentage of live coral cover and had higher macroalgae and turf algae abundance. Locations affected by high PO₄, NH₃, and optical brightness concentrations, high turbidity, and high sea surface temperature anomalies, chlorophyll-a concentration, and light attenuation Kd490 evidenced significantly lower coral recruit density and diversity. Hurricane-decimated reefs also exhibited impoverished coral recruit assemblages.



Low coral recruitment could have important long-term implications under projected climate change and sea level rise, particularly in coastal urban habitats. There is a need to implement effective environmental conservation, ecological restoration, and community participation strategies that facilitate enhanced coral recruitment success and assisted recovery processes.},

keywords = {Assisted Recovery, Chlorophyll-a Concentration, Climate change, Coastal Urban Habitats, Community Participation, Coral Recruit Density, Coral Recruit Diversity, coral recruitment, Ecological Restoration, Environmental Conservation, Environmental Degradation, Environmental Tolerance, Fringing Reefs, Geographic Regions, Hurricane Impact, Hurricane-Decimated Reefs, Light Attenuation Kd490, Live Coral Cover, Long-term Implications, Macroalgae Abundance, Marginal Shallow Coral Reefs, Natural Recovery, NH3, Optical Brightness, PO4, Projected Climate Change, Puerto Rico, Sea Level Rise, Sea Surface Temperature Anomalies, Turbidity, Turf Algae Abundance, Water Quality Degradation},

pubstate = {published},

tppubtype = {article}

}

@article{Bayraktarov2022,

title = {Joining global efforts to halt coral reef decline: a call for more diversity, equity, and inclusion at international scientific meetings  },

author = {Elisa Bayraktarov and Edwin A. Hernández-Delgado and Valeria Pizarro and Phanor H Montoya-Maya and Claudia Patricia Ruiz-Diaz and Stuart R Phinn and Chris Roelfsema and Sarah Frías-Torres},

editor = {Rupert Ormond and Caroline Rogers Beatriz Casareto and Douglas Fenner and Edwin Hernandez-Delgado and Dennis Hubbard and Nicolas Pascal and William Precht and Silas Principe and Brian Rosen and Sue Wells},

url = {http://coralreefs.org/wp-content/uploads/2022/06/Reef_Encounter_51_lores.pdf

https://sampr.org/wp-content/uploads/2024/01/Joining-global-efforts-to-halt-coral-Reef_Encounter_51_lores.pdf},

issn = {0225-27987},

year  = {2022},

date = {2022-06-01},

urldate = {2022-06-01},

journal = {Reef Ecounter},

volume = {37},

issue = {1},

pages = {28-35},

abstract = {Finding solutions to the global coral reef crisis will require active adaptive management, where scientific results on successes vs failures at local field sites are used to inform conservation interventions and natural resource management. Any scientific progress and solution-focused innovation starts with the exchange of knowledge. Scientific conferences can quickly disseminate major research findings and encourage public debates to push the boundaries of science.},

keywords = {Caribbean Coral Reefs, Coral Reef Decline, coral reefs, halt coral reef},

pubstate = {published},

tppubtype = {article}

}

@article{Arias-González2022,

title = {Editorial:  Coral Reef Restoration in a Changing World: Science-Based Solutions},

author = {Arias-Gonzalez, J.E. and I.B. Baums and A.T. Banaszak and C. Prada, S. Rossi and E.A. Hernandez-Delgado, and B. Rinkevich.},

editor = {Raquel Peixoto},

url = {https://www.frontiersin.org/journals/marine-science/articles/10.3389/fmars.2022.919603/full},

doi = {https://doi.org/10.3389/fmars.2022.919603},

year  = {2022},

date = {2022-05-23},

urldate = {2022-05-23},

journal = {Frontiers in marine Science},

volume = {9},

abstract = {The collection explores diverse themes, including propagation and husbandry, improved outplanting success, microfragmentation techniques, assisted evolution, larval recruitment, species ecology, and advanced monitoring and modeling tools. Key findings highlight innovative approaches such as universal and goal-based performance metrics for assessing restoration success, the role of sea urchins and fish assemblages in reef recovery, and selective breeding for heat-tolerant corals. Studies also emphasize the importance of genetic diversity, substrate selection, and regional environmental gradients to enhance restoration outcomes. Advanced technologies, like 3D scanning and imaging spectroscopy, alongside data management tools such as the Coral Sample Registry, are showcased as critical for improving restoration scalability and effectiveness. This comprehensive effort underscores the rapid evolution of coral reef restoration as a vital field to preserve ecosystem functionality amidst climate change challenges, offering both general and region-specific solutions to foster resilient reefs worldwide.},

keywords = {adaptive evolution, Climate change, Coastal Resilience, husbandry, Management, modeling, monitoring, propagation, restauration},

pubstate = {published},

tppubtype = {article}

}

@article{Ruiz-Diaz2022b,

title = {The Effects of Depth-Related Environmental Factors on Traits in Acropora cervicornis Raised in Nurseries.},

author = {Claudia Patricia Ruiz-Diaz and Carlos Toledo-Hernández and Juan Luis Sánchez-González and Brenda Betancourt},

editor = {Kevin B. Strychar},

url = {https://www.mdpi.com/2073-4441/14/2/212

https://www.researchgate.net/publication/357778397_The_Effects_of_Depth-Related_Environmental_Factors_on_Traits_in_Acropora_cervicornis_Raised_in_Nurseries

https://sampr.org/wp-content/uploads/2024/01/The-Effects-of-Depth-Related-Environmental-Factors-on-Traits-in-Acropora-cervicornis-Raised-in-Nurseries-water-14-00212.pdf},

doi = {https://doi.org/10.3390/w14020212},

year  = {2022},

date = {2022-01-12},

urldate = {2022-01-12},

journal = {Water},

volume = { 14},

issue = {2},

pages = {212},

abstract = {Populations of Acropora cervicornis, one of the most important reef-building corals in the Caribbean, have been declining due to human activities and global climate change. This has prompted the development of strategies such as coral farms, aimed at improving the long-term viability of this coral across its geographical range. This study focuses on comprehending how seawater temperature (ST), and light levels (LL) affect the survival and growth of A. cervicornis fragments collected from three reefs in Culebra, Puerto Rico. These individuals were fragmented into three pieces of the similar sizes and placed in farms at 5, 8, and 12 m depth. The fragments, ST and LL were monitored for 11 months. Results show that fragments from shallow farms exhibit significantly higher mortalities when compared to the other two depths. Yet, growth at shallow farms was nearly 24% higher than at the other two depths. Corals grew fastest during winter, when temperature and LL were lowest, regardless of the water depth. Fragment mortality and growth origin were also influenced by reef origin. We conclude that under the current conditions, shallow farms may offer a slight advantage over deep ones provided the higher growth rate at shallow farms and the high fragment survival at all depths.},

keywords = {Acropora cervicornis, coral farm, light levels, restauration, sea temperature},

pubstate = {published},

tppubtype = {article}

}

@article{Vardi2021,

title = {Six priorities to advance the science and practice of coral reef restoration worldwide},

author = {Tali Vardi and Whitney C. Hoot and Jessica Levy and Elizabeth Shaver and R. Scott Winters and Anastazia T. Banaszak and Iliana B. Baums and Valérie F. Chamberland and Nathan Cook and David Gulko and Margaux Y. Hein and Les Kaufman and Michelle Loewe and Petra Lundgren and Caitlin Lustic and Petra MacGowan and Mikhail V. Matz and Miles McGonigle and Ian McLeod and Jennifer Moore and Tom Moore and Sandrine Pivard and F. Joseph Pollock and Baruch Rinkevich and David J. Suggett and Samuel Suleiman and T. Shay Viehman and Tatiana Villalobos and Virginia M. Weis and Chelsea Wolke and Phanor H. Montoya-Maya},

url = {https://onlinelibrary.wiley.com/doi/epdf/10.1111/rec.13498

https://sampr.org/wp-content/uploads/2024/01/Restoration-Ecology-2021-Vardi-Six-priorities-to-advance-the-science-and-practice-of-coral-reef-restoration-worldwide.pdf},

doi = {https://doi.org/10.1111/rec.13498},

issn = {1061-2971},

year  = {2021},

date = {2021-11-29},

urldate = {2021-11-29},

journal = {Restoration Ecology},

volume = {29},

number = {e13498},

issue = {8},

pages = {1-7},

abstract = {Coral reef restoration is a rapidly growing movement galvanized by the accelerating degradation of the world's tropical coral reefs. The need for concerted and collaborative action focused on the recovery of coral reef ecosystems coalesced in the creation of the Coral Restoration Consortium (CRC) in 2017. In March 2020, the CRC leadership team met for a biennial review of international coral reef restoration efforts and a discussion of perceived knowledge and implementation bottlenecks that may impair scalability and efficacy. Herein we present six priorities wherein the CRC will foster scientific advancement and collaboration to: (1) increase restoration efficiency, focusing on scale and cost-effectiveness of deployment; (2) scale up larval-based coral restoration efforts, emphasizing recruit health, growth, and survival; (3) ensure restoration of threatened coral species proceeds within a population-genetics management context; (4) support a holistic approach to coral reef ecosystem restoration; (5) develop and promote the use of standardized terms and metrics for coral reef restoration; and (6) support coral reef restoration practitioners working in diverse geographic locations. These priorities are not exhaustive nor do we imply that accomplishing these tasks alone will be sufficient to restore coral reefs globally; rather these are topics where we feel the CRC community of practice can make timely and significant contributions to facilitate the growth of coral reef restoration as a practical conservation strategy. The goal for these collective actions is to provide tangible, local-scale advancements in reef condition that offset declines resulting from local and global stressors including climate change.},

keywords = {coral interventions, coral reefs, coral restoration, Corals, reefs, restoration},

pubstate = {published},

tppubtype = {article}

}

@article{Ramírez-Lugo2021,

title = {CREARE: A Course-Based Undergraduate Research Experience To Study the Responses of the Endangered Coral \textit{Acropora cervicornis} to a Changing Environment.},

author = {Juan S. Ramírez-Lugo and Carlos Toledo-Hernández and Ivonne Vélez-González and Claudia P. Ruiz-Diaz},

url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8060141/

https://sampr.org/wp-content/uploads/2024/01/ramirez-lugo-et-al-2021-creare-a-course-based-undergraduate-research-experience-to-study-the-responses-of-the.pdf},

doi = {https://doi.org/10.1128/jmbe.v22i1.2253c},

year  = {2021},

date = {2021-03-31},

urldate = {2021-03-31},

journal = {Journal of Microbiology & Biology Education},

volume = {22},

number = {1},

pages = {1-12},

abstract = {There is mounting evidence to support that students who participate in scientific research experiences are more likely to continue on to advanced degrees and careers in science, technology, engineering, and mathematics (STEM). To introduce more students to the benefits of research, we have drawn on an ongoing project aimed at understanding how the Caribbean staghorn coral Acropora cervicornis responds to environmental fluctuations to develop a semester-long course-based undergraduate research experience (CURE), entitled CREARE (Coral Response to Environment Authentic Research Experience). The main mode of instruction in CREARE is through topic modules, and course evaluation is achieved through writing assignments. Students in CREARE perform experiments in the laboratory to measure the abundance of photo-protective proteins in coral tissue from samples collected at different depths and at different times of the year and analyze environmental data using the R programming language. CREARE participants have contributed to the progress of the research project by generating novel data and making improvements to experimental protocols. Furthermore, pre- and post-course assessment of content knowledge revealed that students perform significantly better on a written exam after participating in CREARE, while also displaying appreciable shifts in attitudes towards science in student perception surveys. In addition, through qualitative analysis of focus group interviews, we gathered evidence to suggest that mediating variables that predict students’ persistence in science are bolstered through our application of the CURE modality. Overall, CREARE can serve as a model for developing more research-based courses that successfully engage students in scientific research.},

keywords = {Acropora cervicornis, coral reefs, CORAL SPECIES LISTING, Endangered Coral},

pubstate = {published},

tppubtype = {article}

}

@article{Cortés-Useche2021,

title = {Conservation actions and ecological context: optimizing coral reef local management in the Dominican Republic},

author = {Camilo Cortés-Useche​ and Edwin A. Hernández-Delgado and Johanna Calle-Triviño and Rita Sellares Blasco and Victor Galván and Jesús E. Arias-González},

editor = {Ida Kubiszewski and Jonathan Colville},

url = {https://peerj.com/articles/10925/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7953877/

https://sampr.org/wp-content/uploads/2024/01/Conservation-actions-and-ecological-context-optimizing-coral-reef-local-management-in-the-Dominican-Republic-peerj-10925.pdf},

doi = {https://doi.org/10.7717/peerj.10925},

year  = {2021},

date = {2021-03-09},

urldate = {2021-03-09},

journal = {Peerj},

volume = {9},

number = { e10925},

pages = {1-28},

abstract = {Over the past few decades, coral reef ecosystems have been lost at accelerated rates as a result of global climate change and local stressors. Local management schemes can help improve the condition of coral reefs by enhancing their ecosystem recovery capacity. Caribbean conservation efforts include mitigation of local anthropogenic stressors, and integrating social participation. Here, we analyzed the case of the Bayahibe reefs in the Southeastern (SE) Dominican Republic to identify conservation actions and illustrate a conceptual example of local seascape management. We assessed reef health indicators from 2011 to 2016. Overall, our results show increases in total fish biomass, in both commercial and herbivorous fishes. Mean live coral cover was 31% and fleshy macroalgae was 23% after multiple disturbances such as Hurricanes Sandy and Isaac (2012), Mathew (2016) and heat stress presented in the study area in 2015. We also described actions taken by stakeholders and government institutions, including the implementation of a policy declaring an area of 869,000 ha as a marine protected area (MPA), enhanced water quality treatment, local restrictions to vessel traffic, enforcement of fishing regulations, and the removal of invasive lionfish (Pterois spp.). In addition, a restoration program for the threatened staghorn coral (Acropora cervicornis) was established in 2011, and currently has eight coral nurseries and six outplanting sites. Considering the biology and ecology of these reefs, we observed good results for these indicators (live coral cover, fish biomass, and water quality) in contrast with severely degraded Caribbean reefs, suggesting that optimizing local management may be a useful example for improving reef condition. Our results provide an overview of trends in reef condition in the SE Dominican Republic and could support current strategies to better protect reefs in the region. Given that Caribbean coral reefs face extreme challenges from global climate change, management measures may improve reef conditions across the region but stronger policy processes and increased scientific knowledge are needed for the successful management of coral reefs.},

keywords = {biodiversity, Caribbean, Coastal health, coral reefs, coral restoration, Dominican Republic, Management, Marine protected area, Tropical coastal ecosystems, Water quality},

pubstate = {published},

tppubtype = {article}

}

@article{Gómez-Andújar2020,

title = {Spatial benthic community analysis of shallow coral reefs to support coastal management in Culebra Island, Puerto Rico.},

author = {Nicolás X Gómez-Andújar and Edwin A Hernandez-Delgado },

editor = {Gregory Verutes},

url = {https://pubmed.ncbi.nlm.nih.gov/33088617/

https://sampr.org/wp-content/uploads/2024/01/Spatial-benthic-community-analysis-of-shallow-coral-reefs-to-support-coastal-management-in-Culebra-Island-Puerto-Rico.pdf},

doi = {https://doi.org/10.7717/peerj.10080},

year  = {2020},

date = {2020-10-14},

urldate = {2020-10-14},

journal = {PeerJ},

pages = {1-27},

abstract = {Caribbean coral reefs provide essential ecosystem services to society, including fisheries, tourism and shoreline protection from coastal erosion. However, these reefs are also exhibiting major declining trends, leading to the evolution of novel ecosystems dominated by non-reef building taxa, with potentially altered ecological functions. In the search for effective management strategies, this study characterized coral reefs in front of a touristic beach which provides economic benefits to the surrounding coastal communities yet faces increasing anthropogenic pressures and conservation challenges. Haphazard photo-transects were used to address spatial variation patterns in the reef’s benthic community structure in eight locations. Statistically significant differences were found with increasing distance from the shoreline, reef rugosity, Diadema antillarum density, among reef locations, and as a function of recreational use. Nearshore reefs reflected higher percent macroalgal cover, likely due to increased exposure from both recreational activities and nearby unsustainable land-use practices. However, nearshore reefs still support a high abundance of the endangered reef-building coral Orbicella annularis, highlighting the need to conserve these natural shoreline protectors. There is an opportunity for local stakeholders and regulatory institutions to collaboratively implement sea-urchin propagation, restoration of endangered Acroporid coral populations, and zoning of recreational densities across reefs. Our results illustrate vulnerable reef hotspots where these management interventions are needed and recommend guidelines to address them.},

keywords = {Benthic community structure, Caribbean Coral Reefs, Coastal spatial variability, Ecosystem-based management, GIS, Mapping, Marine biology},

pubstate = {published},

tppubtype = {article}

}

@article{Zimmerman2020b,

title = {Resistance, resilience, and vulnerability of social‐ecological systems to hurricanes in Puerto Rico.},

author = {Jess K. Zimmerman and Michael R. Willig and Edwin A. Hernández-Delgado},

url = {https://esajournals.onlinelibrary.wiley.com/doi/10.1002/ecs2.3159

https://sampr.org/wp-content/uploads/2024/01/Ecosphere-2020-Zimmerman-Resistance-resilience-and-vulnerability-of-social‐ecological-systems-to-hurricanes-in.pdf},

doi = {https://doi.org/10.1002/ecs2.3159},

year  = {2020},

date = {2020-10-09},

urldate = {2020-10-09},

journal = {Ecosphere},

volume = {11},

issue = {10},

pages = {e03159},

abstract = {Subject to hurricane disturbance for millennia, natural ecosystems of Puerto Rico exhibit clear patterns of resistance (e.g., many tree species have little immediate storm-related mortality) and resilience (e.g., leaf litterfall and stream chemistry returned to pre-hurricane levels in as little as five years). Contemporaneous studies of near-shore areas also suggested no long-term impacts of hurricanes; however, anthropogenic effects (coral bleaching, sedimentation) dominate the long-term condition of marine systems in Puerto Rico, many of which have slowly evolved into novel ecosystems. A key characteristic of novel marine ecosystems is their long-term loss of benefits and resilience, coupled to declining biodiversity and loss of structural or functional redundancy, signaling increased vulnerability to subsequent hurricanes. Human systems are also strongly affected by cyclonic storms, as evidenced by the recent impacts of Hurricanes Irma and Maria in the Caribbean. The lack of short-term recovery from disturbance by coral reef ecosystems, coupled with an increasing recurrence of anthropogenic impacts, increasing hurricane frequency or severity, and sea-level rise, may have irreversible long-term socioeconomic consequences for coastal social–ecological systems and for community livelihoods. A comprehensive social–ecological understanding of hurricane effects in Puerto Rico is lacking in part because hurricane effects on human populations are not comprehensively followed. Although some studies suggest a path forward, finding effective methods to link measurements of storm intensity to the diverse components of tropical social–ecological systems remains a challenge.},

keywords = {anthropogenic effects, coastal ecosystems, cyclonic storms, forested ecosystems, Hurricane Irma, Hurricane Maria, marine ecosystems, novel ecosystems, ridge to reef},

pubstate = {published},

tppubtype = {article}

}

@article{Precht2020b,

title = {The timing and causality of ecological shifts on Caribbean coral reefs},

author = {William F Precht and Richard B Aronson and Toby A Gardner and Jennifer A Gill and Julie P Hawkins and Edwin A Hernández-Delgado and Walter C Jaap and Tim R McClanahan and Melanie D McField and Thaddeus J T Murdoch and Maggy M Nugues and Callum M Roberts and Christiane K Schelten and Andrew R Watkinson and Isabelle M Côté},

url = {https://pubmed.ncbi.nlm.nih.gov/33293016/},

doi = {https://doi.org/10.1016/bs.amb.2020.08.008},

year  = {2020},

date = {2020-10-08},

urldate = {2020-10-08},

journal = {Advances in Marine Biology},

volume = {87},

number = {1},

pages = {331-360},

abstract = {Caribbean reefs have experienced unprecedented changes in the past four decades. Of great concern is the perceived widespread shift from coral to macroalgal dominance and the question of whether it represents a new, stable equilibrium for coral-reef communities. The primary causes of the shift—grazing pressure (top-down), nutrient loading (bottom-up) or direct coral mortality (side-in)—still remain somewhat controversial in the coral-reef literature. We have attempted to tease out the relative importance of each of these causes. Four insights emerge from our analysis of an early regional dataset of information on the benthic composition of Caribbean reefs spanning the years 1977–2001. First, although three-quarters of reef sites have experienced coral declines concomitant with macroalgal increases, fewer than 10% of the more than 200 sites studied were dominated by macroalgae in 2001, by even the most conservative definition of dominance. Using relative dominance as the threshold, a total of 49 coral-to-macroalgae shifts were detected. This total represents ~ 35% of all sites that were dominated by coral at the start of their monitoring periods. Four shifts (8.2%) occurred because of coral loss with no change in macroalgal cover, 15 (30.6%) occurred because of macroalgal gain without coral loss, and 30 (61.2%) occurred owing to concomitant coral decline and macroalgal increase. Second, the timing of shifts at the regional scale is most consistent with the side-in model of reef degradation, which invokes coral mortality as a precursor to macroalgal takeover, because more shifts occurred after regional coral-mortality events than expected by chance. Third, instantaneous observations taken at the start and end of the time-series for individual sites showed these reefs existed along a continuum of coral and macroalgal cover. The continuous, broadly negative relationship between coral and macroalgal cover suggests that in some cases coral-to-macroalgae phase shifts may be reversed by removing sources of perturbation or restoring critical components such as the herbivorous sea urchin Diadema antillarum to the system. The five instances in which macroalgal dominance was reversed corroborate the conclusion that macroalgal dominance is not a stable, alternative community state as has been commonly assumed. Fourth, the fact that the loss in regional coral cover and concomitant changes to the benthic community are related to punctuated, discrete events with known causes (i.e. coral disease and bleaching), lends credence to the hypothesis that coral reefs of the Caribbean have been under assault from climate-change-related maladies since the 1970s.},

keywords = {Bleaching; Coral reefs; Disease; Macroalgae; Mortality; Phase shift},

pubstate = {published},

tppubtype = {article}

}

@article{Sabat2020,

title = {Population dynamics of diseased corals: Effects of a Shut Down Reaction outbreak in Puerto Rican \textit{Acropora cervicornis}.},

author = {Alex E Mercado-Molina and Alberto M Sabat and Edwin A Hernández-Delgado},

url = {https://pubmed.ncbi.nlm.nih.gov/33293020/

https://www.sciencedirect.com/science/article/abs/pii/S006528812030033X?via%3Dihub},

doi = {https://doi.org/10.1016/bs.amb.2020.08.001},

year  = {2020},

date = {2020-10-07},

urldate = {2020-10-07},

journal = {Advance in Marine Biology},

volume = {87},

issue = {1},

pages = {61-82},

abstract = {Chronic coral reef degradation has been characterized by a significant decline in the population abundance and live tissue cover of scleractinian corals across the wider Caribbean. Acropora cervicornis is among the species whose populations have suffered an unprecedented collapse throughout the region. This species, which once dominated the shallow-water reef communities, is susceptible to a wide range of stressors, resulting in a general lack of recovery following disturbances. A. cervicornis is a critical contributor to the structure, function, and resilience of Caribbean coral reefs. Therefore, it is essential to identify the factors that influence their demographic and population performance. Diseases are one of the factors that are compromising the recovery of coral populations. In this chapter, we use size-based population matrix models to evaluate the population-level effect of a Shut Down Reaction Disease},

keywords = {Acropora cervicornis; Coral demography; Coral diseases; Coral reefs; Matrix population models; Shut Down Reaction, coral reefs},

pubstate = {published},

tppubtype = {article}

}

@article{Rodríguez-Casariego2020,

title = {Genome-wide DNA methylation analysis reveals a conserved epigenetic response to seasonal environmental variation in the staghorn coral \textit{Acropora cervicornis}.},

author = {Javier A. Rodríguez-Casariego and Alex E. Mercado-Molina and Daniel Garcia-Souto and Ivanna M. Ortiz-Rivera and Christian Lopes and Iliana B. Baums and Alberto M. Sabat and Jose M. Eirin-Lopez},

editor = {Yong Wang and Mikhail V. Matz and Alexandre Fellous and Hui Huang},

url = {https://www.frontiersin.org/articles/10.3389/fmars.2020.560424/full

https://sampr.org/wp-content/uploads/2024/01/Genome-wide-DNA-methylation-analysis-reveals-a-conserved-epigenetic-response-to-seasonal-environmental-variation-in-the-staghorn-coral-Acropora-cervicornis.pdf},

doi = {https://doi.org/10.3389/fmars.2020.560424},

year  = {2020},

date = {2020-09-30},

urldate = {2020-09-30},

journal = {Frontiers in Marine Science},

volume = {7},

abstract = {Epigenetic modifications such as DNA methylation have been shown to participate in plastic responses to environmental change in a wide range of organisms, including scleractinian corals. Unfortunately, the current understanding of the links between environmental signals, epigenetic modifications, and the subsequent consequences for acclimatory phenotypic changes remain obscure. Such a knowledge gap extends also to the dynamic nature of epigenetic changes, hampering our ability to ascertain the magnitude and extent of these responses under natural conditions. The present work aims to shed light on these subjects by examining temporal changes in genome-wide patterns of DNA methylation in the staghorn coral Acropora cervicornis in the island of Culebra, PR. During a 17-month period, a total of 162 polymorphic loci were identified using Methylation-Sensitive Amplified Polymorphism (MSAP). Among them, 83 of these restriction fragments displayed changes in DNA methylation that were significantly correlated to seasonal variation as determined mostly by changes in sea water temperature. Remarkably, the observed time-dependent variation in DNA methylation patterns is consistent across coral genets, coral source sites and site-specific conditions studied. Overall, these results are consistent with a conserved epigenetic response to seasonal environmental variation. These findings highlight the importance of including seasonal variability into experimental designs investigating the role of epigenetic mechanisms such as DNA methylation in responses to stress.},

keywords = {Acropora cervicornis, coral reefs, DNA methylation, epigenetics, MSAP, seasonality, staghorn coral, stress response, temperature},

pubstate = {published},

tppubtype = {article}

}

@article{Bayraktarov2020,

title = {Review of coral reef restoration efforts in Latin American countries and territories},

author = {Elisa Bayraktarov and Anastazia T. Banaszak and Phanor Montoya Maya and Joanie Kleypas and Jesús E. Arias-González and Macarena Blanco and Johanna Calle-Triviño and Nufar Charuvi and Camilo Cortés-Useche and Victor Galván and Miguel A. García Salgado and Mariana Gnecco and Sergio D. Guendulain-García and Edwin A. Hernández Delgado and José A. Marín Moraga and María Fernanda Maya and Sandra Mendoza Quiroz and Samantha Mercado Cervantes and Megan Morikawa and Gabriela Nava and Valeria Pizarro and Rita I. Sellares-Blasco and Samuel E. Suleimán Ramos and Tatiana Villalobos Cubero and María F. Villalpando and Sarah Frías-Torres},

editor = {Shashank Keshavmurthy},

url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0228477

https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0228477&type=printable

https://sampr.org/wp-content/uploads/2024/01/Coral-reef-restoration-efforts-in-Latin-American-countries-and-territories.pdf},

doi = {https://doi.org/10.1371/journal.pone.0228477},

year  = {2020},

date = {2020-08-05},

urldate = {2020-08-05},

journal = {Plos ONE},

volume = {15},

number = {8},

abstract = {Coral reefs worldwide are degrading due to climate change, overfishing, pollution, coastal development, coral bleaching, and diseases. In areas where the natural recovery of an ecosystem is negligible or protection through management interventions insufficient, active restoration becomes critical. The Reef Futures symposium in 2018 brought together over 400 reef restoration experts, businesses, and civil organizations, and galvanized them to save coral reefs through restoration or identify alternative solutions. The symposium highlighted that solutions and discoveries from long-term and ongoing coral reef restoration projects in Spanish-speaking countries in the Caribbean and Eastern Tropical Pacific were not well known internationally. Therefore, a meeting of scientists and practitioners working in these locations was held to compile the data on the extent of coral reef restoration efforts, advances and challenges. Here, we present unpublished data from 12 coral reef restoration case studies from five Latin American countries, describe their motivations and techniques used, and provide estimates on total annual project cost per unit area of reef intervened, spatial extent as well as project duration. We found that most projects used direct transplantation, the coral gardening method, micro-fragmentation or larval propagation, and aimed to optimize or scale-up restoration approaches (51%) or provide alternative, sustainable livelihood opportunities (15%) followed by promoting coral reef conservation stewardship and re-establishing a self-sustaining, functioning reef ecosystems (both 13%). Reasons for restoring coral reefs were mainly biotic and experimental (both 42%), followed by idealistic and pragmatic motivations (both 8%). The median annual total cost from all projects was $93,000 USD (range: $10,000 USD—$331,802 USD) (2018 dollars) and intervened a median spatial area of 1 ha (range: 0.06 ha—8.39 ha). The median project duration was 3 years; however, projects have lasted up to 17 years. Project feasibility was high with a median of 0.7 (range: 0.5–0.8). This study closes the knowledge gap between academia and practitioners and overcomes the language barrier by providing the first comprehensive compilation of data from ongoing coral reef restoration efforts in Latin America.},

keywords = {Caribbean, coral reefs, coral reefs restauration},

pubstate = {published},

tppubtype = {article}

}

@article{Hernández-Delgado2020,

title = {Hurricane Impacts and the Resilience of the Invasive Sea Vine, \textit{Halophila stipulacea}: a Case Study from Puerto Rico.},

author = {E. A. Hernández-Delgado and C. Toledo-Hernández and C. P. Ruíz-Díaz and N. Gómez-Andújar and J. L. Medina-Muñiz and M. F. Canals-Silander and S. E. Suleimán-Ramos},

url = {https://link.springer.com/article/10.1007/s12237-019-00673-4

},

doi = {https://doi.org/10.1007/s12237-019-00673-4},

year  = {2020},

date = {2020-01-08},

urldate = {2020-01-08},

journal = {Estuaries and Coasts},

volume = {43},

pages = {1263–1283},

abstract = {Category five hurricanes Irma and María (September 2017) caused significant damage to shallow seagrass communities across Puerto Rico. The magnitude and spatial extent of hurricane impacts on representative seagrass habitats of Culebra Island were addressed using a combination of random photo-quadrats and before–after hurricanes GIS-based imagery analyses. There was a significant loss of shallow seagrasses across all nine surveyed locations. Most of the documented impacts were associated with sediment bedload (horizontal transport), which resulted in burial and suffocation. There was also localized physical disruption of the seagrass habitat matrix across locations exposed to stronger wave action, creating major scars and exposing below-ground structure to further disintegration by future storm events. Displaced coral rubble also caused seagrass burial. Aerial imagery analyses (2007, 2010, 2017) showed a significant decline in seagrass percent cover. Seagrass decline was positively correlated with wave exposure (p < 0.05). Seagrass cover, density, and changes in benthic community structure were documented across five of the surveyed locations during 2018, and these data were further compared to data collected in 2004 at these same sites. There was a decline in percent seagrass cover and density and a change in benthic community structure favoring habitat homogenization. A remarkable finding was the rapid recovery, expansion, and increased localized dominance of the invasive seagrass, Halophila stipulacea. This was particularly evident in areas impacted by recurrent land-based runoff pulses, anchoring, sediment resuspension due to navigation, trampling or by the accumulation of decaying Sargassum mats. Hurricanes triggered a localized shift in marine vegetation, favoring the invasion of H. stipulacea, with potentially significant consequences on ecosystem resilience and on the ability of native in seagrasses to persist and adapt to projected climate change impacts.},

keywords = {Coast, Coastal Erosion, Coastal Resilience, Halophila stipulacea, Hurricane Impacts, Hurricane Irma, Hurricane Maria, Hurricanes, Puerto Rico, Resilience},

pubstate = {published},

tppubtype = {article}

}

@article{Weil2019,

title = {Spread of the new coral disease “SCTLD” into the Caribbean: implications for Puerto Rico.},

author = {E Weil and EA Hernández-Delgado and M Gonzalez and S Williams and S Suleimán-Ramos and M Figuerola and T Metz-Estrella},

url = {https://www.researchgate.net/publication/342477916_REEF_ENCOUNTER_Spread_of_the_new_coral_disease_SCTLD_into_the_Caribbean_implications_for_Puerto_Rico

https://www.agrra.org/wp-content/uploads/2020/08/Weil-et-al.-2020-Reef-Encounter.pdf

https://sampr.org/wp-content/uploads/2024/01/Spread-of-the-new-coral-disease-SCTLD-into-the-Caribbean-implications-for-Puerto-Rico.pdf

},

year  = {2019},

date = {2019-12-01},

urldate = {2019-12-01},

journal = {Reef Encounter},

volume = {34},

number = {1},

pages = {38-43},

abstract = {The ongoing deterioration and significant decline in live coral cover and diversity in coral reef communities

worldwide is strongly associated with increasing water temperatures linked to Global Climate Change, aided by

anthropogenic activities (Harvell et al. 2004, 2007, 2009; Weil and Rogers 2011; Maynard et al. 2016; Woodley et al.

2016). In the Wider Caribbean, major community structure and function decline was marked by two region-wide,

concurrent, highly virulent disease epizootics in the early 1980’s. These events almost wiped out two foundational

scleractinian species (Acropora palmata and A. cervicornis), and the keystone sea urchin Diadema antillarum. White

band disease (WBD) affected the acroporids and was caused by a complex of vibrio bacteria (Gil-Agudelo et al. 2006).

The Diadema mass mortality had all the trademark characteristics of a virulent, transmissible, bacterial or viral

infection, but the putative pathogen (pathogens) was never identified (Lessios 2016). Populations of both acroporids

and sea urchins suffered over 95% mortalities throughout the wider Caribbean (Gladfelter 1982; Lessios et al. 1984a,b;

Aronson and Precht 2001; Lessios 2016), followed by a cascade of ecological consequences (significant loss of live

coral cover, primary productivity, spatial complexity, biodiversity and fecundity; loss of ecological functions, increase

in algal cover and biomass, etc.), ending in a shift from coral- to algal-dominated communities and the loss of

ecological services to other tropical marine communities and to human beings (Aronson and Precht 2001; Weil and

Rogers 2011). Several other disease-induced mass mortalities of other cnidarians, as well as of massive, plate and

nodular reef-building genera, have in the last 30 years resulted in additional loss of biomass, diversity and live coral

cover on many Caribbean reefs (Miller et al. 2009; Weil et al. 2009a; Weil and Rogers 2011; Bastidas et al. 2011; Weil

et al. 2017). },

keywords = {biodiversity, biomass, Caribbean, communities, Coral, coral diseases, coral reefs, diversity, Puerto Rico, reef, reefs},

pubstate = {published},

tppubtype = {article}

}

@article{toonDynamics2019,

title = {Caribbean Near-Shore Coral Reef Benthic Community Response to Changes on Sedimentation Dynamics and Environmental Conditions},

author = {Abimarie Otaño-Cruz and Alfredo A. Montañez-Acuña and Noelia M. García-Rodríguez and Dakeishla M. Díaz-Morales and Elizabeth Benson and Elvira Cuevas and Jorge Ortiz-Zayas and Edwin A. Hernández-Delgado},

editor = {Edward Jeremy Hind-Ozan and Xiaoshou Liu and Douglas Fenner},

url = {https://www.frontiersin.org/articles/10.3389/fmars.2019.00551/full

https://sampr.org/wp-content/uploads/2024/01/Caribbean-Near-Shore-Coral-Reef-Benthic-Community-Response-to-Changes-on-Sedimentation-Dynamics-and-Environmental-Conditions.pdf

},

doi = {https://doi.org/10.3389/fmars.2019.00551},

year  = {2019},

date = {2019-09-06},

urldate = {2019-09-06},

journal = {Frontiers in Marine Science},

volume = {6},

issue = {551},

pages = {551},

abstract = {Coral reefs are facing unprecedented global, regional and local threats that continue to degrade near-shore habitats. Water quality degradation, due to unsustainable development practices at coastal watersheds, is one of the greatest stressors across multiple spatial scales. The goal of this study was to assess near-shore coral reef benthic community spatio-temporal response to sedimentation patterns, weather, and oceanographic dynamics at Bahía Tamarindo and Punta Soldado in Culebra Island, Puerto Rico. Benthic data were collected across a distance gradient from the shore through high-resolution images at marked belt transects. Environmental data were assessed and contrasted with benthic assemblages using multivariate correlations and multiple linear regression. Coral colony abundance and coral recruit assemblages showed significant variation among seasons, sites and distance zones (PERMANOVA, p < 0.01). Species diversity (H’n) increased at both study sites with distance from shore, and the most conspicuous coral recruit species were stress-tolerant Porites astreoides, P. porites, and Siderastrea radians. Difference in coral abundance and coral recruits per site had a strong significant negative relationship with sediment characteristics and depth (p < 0.05). Near-shore coral reef benthic community structure was significantly different between sites and distance zones from shore, with depth having an important role in shaping reef zonation. Changes in benthic community structure were associated with local sediment distribution patterns emerging from human alteration of coastal watersheds and natural events that cause terrigenous sediment deposition and sand resuspension across the reef. Coral cover was significantly lower at zones more exposed to recurrent sedimentation stress (p < 0.01). It was also correlated with sediment texture (p = 0.006) and terrigenous sediment deposition (p = 0.016). Scleractinian coral cover had an inverse relationship with gorgonian and macroalgae cover. In a short-term period, a pattern of increased dominance of encrusting calcareous algae Ramicrusta textilis and invasive sponge Dictyonella funicularis were documented. Changing land use and increased frequency of extreme weather events, as a consequence of global patterns of climate change, may play an important role shaping near-shore coral reefs benthic communities and could threaten the resilience of coastal regions. Therefore, collaborative and trans-disciplinary ecosystem-based management efforts are urgently needed to effectively reduce land-based stressors and foster near-shore coral reef recovery.},

keywords = {benthic cover, coral abundance, coral diversity, coral recruit, coral reef community structure, coral reefs, environmental stressors, near-shore coral reefs, Puerto Rico, sedimentation dynamics},

pubstate = {published},

tppubtype = {article}

}

@article{P.Ruiz-Diaz2019,

title = {A mathematical model of the interactions between \textit{Acropora cervicornis} and its environment},

author = {Aniel Nieves-González and Claudia P. Ruiz-Diaz and Carlos Toledo-Hernández and Juan S. Ramírez-Lugo},

url = {https://www.sciencedirect.com/science/article/abs/pii/S0304380019301413?via%3Dihub

},

doi = {https://doi.org/10.1016/j.ecolmodel.2019.04.004},

year  = {2019},

date = {2019-08-24},

urldate = {2019-08-24},

journal = {Ecological Modelling},

volume = {406},

pages = {7-22},

abstract = {Environmental factors associated with climate change such as increasing sea surface temperature (SST) and solar radiation (SR) have negatively impacted corals throughout their geographic ranges. One such coral, which has been seriously impacted by these stressors, is the staghorn coral Acropora cervicornis. To reduce the effects of such stressors, this coral utilizes fluorescent proteins (FPs) and melanin (M). These constitutive immune components quench reactive oxygen species (ROS) produced during thermal stress and absorb or reflect potentially damaging light. The synthesis of these components are, nonetheless, energetically costly. Hence, production of these protective compounds may be traded-off against other vital functions such as growth. In this study we develop a mathematical model, viz., a system of ordinary differential equations that simulates the growth of A. cervicornis branches under different regimes and combinations of SST and SR. The model assumes that polyps are the functional unit of the coral and that the concentration of FPs and M are inversely proportional to SST and SR intensity. To develop the model we use empirical (birth and mortality rate of polyps and the maximum number of polyps per unit area) and theoretical parameters (concentration of FPs, M produced, and trade-offs with growth). The model simulates how changes in FPs and M due to environmental changes affect the growth capacity of A. cervicornis. The model as well as its stability analysis show that polyp growth is affected by SR and SST. Hence, the model will help in understanding how corals will respond to future changes in climate.},

keywords = {Acropora cervicornis, Caribbean Coral Reefs, coral reefs, dynamical system, Lyapunov stability},

pubstate = {published},

tppubtype = {article}

}

@article{Precht2020,

title = {Non-Random Timing of Ecological Shifts on Caribbean Coral Reefs Suggests Regional Causes of Change},

author = {William F. Precht and Richard B. Aronson and Toby A. Gardner and Jennifer A. Gill and Julie P. Hawkins and Edwin A. Hernández-Delgado and Walter C. Jaap and Tim R. Mcclanahan and Melanie D. Mcfield and Thaddeus J.T. Murdoch and Maggy M. Nugues and Callum M. Roberts and Christiane K. Schelten and Andrew R. Watkinson and Isabelle M. Côté},

editor = {Marine and Coastal Programs},

url = {https://www.biorxiv.org/content/10.1101/672121v1.full

https://www.researchgate.net/publication/333988887_NON-RANDOM_TIMING_OF_ECOLOGICAL_SHIFTS_ON_CARIBBEAN_CORAL_REEFS_SUGGESTS_REGIONAL_CAUSES_OF_CHANGE

https://sampr.org/wp-content/uploads/2024/01/Non-random-Timing-of-Ecological-Shifts-on-Caribbean-Coral-Reefs-Suggests-Regional-Causes-of-Change.pdf},

doi = {https://doi.org/10.1101/672121},

year  = {2019},

date = {2019-06-24},

urldate = {2019-06-24},

journal = {Advance in Marine Biology},

volume = {87},

pages = {1-24},

abstract = {Caribbean reefs have experienced unprecedented changes in the past four decades. Of great concern is the perceived widespread shift from coral to macroalgal dominance and the question of whether it represents a new, stable equilibrium for coral-reef communities. The primary causes of the shift -- grazing pressure (top-down), nutrient loading (bottom-up) or direct coral mortality (side-in) -- still remain somewhat controversial in the coral reef literature. We have attempted to tease out the relative importance of each of these causes. Four insights emerge from our analysis of an early regional dataset of information on the benthic composition of Caribbean reefs spanning the years 1977–2001. First, although three-quarters of reef sites have experienced coral declines concomitant with macroalgal increases, fewer than 10% of the more than 200 sites studied were dominated by macroalgae in 2001, by even the most conservative definition of dominance. Using relative dominance as the threshold, a total of 49 coral-to-macroalgae shifts were detected. This total represents ∼35% of all sites that were dominated by coral at the start of their monitoring periods. Four shifts (8.2%) occurred because of coral loss with no change in macroalgal cover, 15 (30.6%) occurred because of macroalgal gain without coral loss, and 30 (61.2%) occurred owing to concomitant coral decline and macroalgal increase. Second, the timing of shifts at the regional scale is most consistent with the side-in model of reef degradation, which invokes coral mortality as a precursor to macroalgal takeover, because more shifts occurred after regional coral-mortality events than expected by chance. Third, instantaneous observations taken at the start and end of the time-series for individual sites showed these reefs existed along a continuum of coral and macroalgal cover. The continuous, broadly negative relationship between coral and macroalgal cover suggests that in some cases coral-to-macroalgae phase shifts may be reversed by removing sources of perturbation or restoring critical components such as the herbivorous sea urchin Diadema antillarum to the system. The five instances in which macroalgal dominance was reversed corroborate the conclusion that macroalgal dominance is not a stable, alternative community state as has been commonly assumed. Fourth, the fact that the loss in regional coral cover and concomitant changes to the benthic community are related to punctuated, discrete events with known causes (i.e. coral disease and bleaching), lends credence to the hypothesis that coral reefs of the Caribbean have been under assault from climate-change-related maladies since the 1970s.},

keywords = {Caribbean Coral Reefs, Coral, coral loss, macroalgal cover, macroalgal dominance, Marine biology},

pubstate = {published},

tppubtype = {article}

}

@article{Norat-Ramíreza2019,

title = {A septic waste index model to measure the impact of septic tanks on coastal water quality and coral reef communities in Rincon, Puerto Rico},

author = {J. Norat-Ramírez and P. Méndez-Lázaro and E.A. Hernández-Delgado and H. Mattei-Torres and L. Cordero-Rivera},

url = {https://www.sciencedirect.com/science/article/abs/pii/S0964569118305519

https://sampr.org/wp-content/uploads/2024/01/a-septic-waste-index-model-to-measure-the-impact-of-septic-tanks-coastal-water-quality-and-coral-reef-rincon-pr.pdf},

doi = {https://doi.org/10.1016/j.ocecoaman.2018.12.016},

year  = {2019},

date = {2019-03-01},

urldate = {2019-03-01},

journal = {Ocean & Coastal Management},

volume = {169},

pages = {201-213},

abstract = {The impact of fecal contamination of coastal waters and coral reefs is a major cause of concern in marine reserves in Puerto Rico. The measurement of the association between septic tank frequency in watersheds of creeks draining into these reserves and coastal water quality and coral reef condition is of importance in configuring pollution control policy. Fecal coliforms and enterococci assays were used to measure the density of fecal contaminants across the Tres Palmas Marine Reserve (TPMR) in Rincon, Puerto Rico. Inshore waters are intermittent creeks, receiving fecal pollution only from faulty septic tanks. Fecal indicators measurements showed higher densities near the southernmost creek mouth emptying into TPMR, a finding consistent with a larger amount of dwellings with septic tanks within this watershed (Vista Azul creek). A Septic Weight Index was constructed to analyze sewage impact from all watersheds draining into the marine reserve. Linear Regression analyses showed a significant association between these non-point source fecal pollution sources and both coastal water quality and impact on some parameters measuring the condition of Acropora palmata coral reef colonies.},

keywords = {coral reefs, Non-point source coastal fecal pollution, Septic tank pollution, Watershed analysis},

pubstate = {published},

tppubtype = {article}

}

@article{Toledo-Hernández2018,

title = {Devastation of 15-year old Community-based Coral Farming and Reef-restoration Sites in Puerto Rico by Major Hurricanes Irma and María},

author = {Carlos Toledo-Hernández and Claudia P. Ruiz-Diaz and Edwin A. Hernández-Delgado and Samuel E. Suleimán-Ramos},

editor = {James D. Ackerman and Alfonso Aguilar-Perera and Wayne J. Arendt and Rüdiger Bieler},

url = {https://www.eaglehill.us/CANAonline/CANA-access-pages/CANA-regular/CANA-053-Toledo-Hernandez.shtml

https://sampr.org/wp-content/uploads/2024/01/Devastation-of-15-year-old-Community-based-Coral-Farming-and-Reef-restoration-Sites-in-Puerto-Rico-by-Major-Hurricanes-Irma-and-Maria2018.pdf},

isbn = {2326-7119},

year  = {2018},

date = {2018-12-12},

urldate = {2018-12-12},

journal = {Caribbean Naturalist},

number = {53},

pages = {1-6},

abstract = {Category-5 hurricanes Irma and María impacted the northeastern Caribbean in September 2017 with waves in excess of 10 m. Herein we provide the frst assessment of hurricane damage to community-based coral farming and reef restoration at several locations from Culebra Island, Puerto Rico. Hurricanes destroyed 75 coral farms, killing 11,074 Acropora cervicornis (Staghorn Coral) fragments. Likewise, over 9000 recently out-planted colonies as well as most of the coral species adjacent to the outplants perished when they were buried by sand and rubble or were dislodged as a result of hurricane-generated waves. Liagora spp. (marine red algae) and other red algae rapidly colonized coral rubble and openreef substrates, threatening surviving corals of multiple species at least for several weeks after hurricane impacts.},

keywords = {Acropora cervicornis, community-based ecological rehabilitation, Coral Reef Decline, Coral Reef Ecology, coral reefs, coral reefs restauration, Coral survival, Corals},

pubstate = {published},

tppubtype = {article}

}

@article{Mercado-Molina2018,

title = {Growth facilitation by the octocoral \textit{Gorgonia ventalina} explains spatial difference in the population size structure of the common demosponge \textit{Ircinia felix}},

author = {Alex E. Mercado-Molina and Fabiola Rivera-Irizarry and Jaime Fonseca-Miranda and Yesenia Bruno-Laureano},

editor = {Paco Cárdenas},

url = {https://www.tandfonline.com/doi/full/10.1080/17451000.2017.1367098},

doi = {https://doi.org/10.1080/17451000.2017.1367098},

year  = {2018},

date = {2018-11-07},

urldate = {2018-11-07},

journal = {Marine Biology Research},

volume = {14},

issue = {1},

pages = {41 - 51},

abstract = {In this study, the demography of the common demosponge Ircinia felix was examined at Tamarindo, a coral reef located in the island municipality of Culebra, Puerto Rico. A preliminary study comparing the size structure of two subpopulations within the reef, Tamarindo Norte (TN) and Tamarindo Sur (TS), indicated that sponges at TN are significantly larger than sponges at TS. This result served as a baseline for the present comparative study in which we aimed to determine whether the spatial differences in population size structure can be explained either by a difference in rates of survival, growth, or recruitment, or a combination of these. To accomplish our goal, we followed the growth, survival and recruitment of I. felix at the two localities for one year. Growth was the only demographic parameter that differed significantly between localities. Because the most obvious distinction between the study sites was the absence of the octocoral Gorgonia ventalina at TS, we hypothesized that the faster overall growth rate of sponges at TN was related to the presence of the octocoral. To test this hypothesis, we compared growth rates between sponges associated with the octocoral and those individuals not associated. We found that sponges growing near G. ventalina grew significantly faster than non-associated sponges. This result suggests that the octocoral facilitates the growth of I. felix and therefore may account, at least in part, for the spatial differences in population size structure.},

keywords = {Acropora cervicornis, Caribbean, Climate change, Coral Reef Decline, coral reefs, Corals, Land-Based Source Pollution, Marine Protected Areas, Puerto Rico, Reef Restoration},

pubstate = {published},

tppubtype = {article}

}

@article{Mercado-Molina2018b,

title = {Tissue loss rather than colony size determines the demographic fate of the branching coral \textit{Acropora cervicornis}.},

author = {Alex E. Mercado-Molina and Claudia Patricia Ruiz-Diaz and Alberto M. Sabat},

url = {https://www.int-res.com/articles/meps_oa/m597p147.pdf

https://sampr.org/wp-content/uploads/2024/01/Tissue-loss-rather-than-colony-size-determines-the-demographic-fate-of-the-branching-coral-Acropora-cervicornis.pdf},

doi = {https://doi.org/10.3354/meps12578},

issn = {0171-8630},

year  = {2018},

date = {2018-06-11},

urldate = {2018-06-11},

journal = {Marine Ecology Progress Series},

volume = {597},

pages = {147-159},

publisher = {Inter-Research},

abstract = {Partial mortality is a common process affecting coral colonies. Yet, the impact of tissue loss on the demography of the threatened reef-building coral Acropora cervicornis has been poorly investigated. This limits our understanding of how this species will fare under unfavorable environmental conditions. In this study, we examined the growth and survival of colonies with varying degrees of partial mortality, indicated by tissue loss, for 2 yr at 2 reefs in Puerto Rico. We found that irrespective of colony size, rates of coral growth and survival declined significantly once the proportion of dead tissue exceeded 20% of the total colony size. Projections of state-matrix population models indicated that partial mortality could also have a negative impact at the population level. For instance, a 25% increase in the number of colonies with >20% tissue loss would reduce the time in which 75% of the population is lost by 3 to 4 yr. Our results provide a new perspective on the effect of partial mortality on the demography and population dynamics of A. cervicornis. First, 20% of tissue loss can be considered a threshold value in which colony fate and population growth are compromised. Second, colony size is not the most important determinant of a colony’s demographic performance; instead, the surface area lost to partial mortality is a better predictor of colony growth and survivorship. Taking into consideration the relationship between partial mortality and the demographic fate of A. cervicornis can aid in the development of stronger conservation and restoration programs.},

keywords = {Acroporids, Coral demography, Coral growth, Coral population dynamics, coral reefs, Coral survival, Partial mortality, SAMPR},

pubstate = {published},

tppubtype = {article}

}

@article{Pérez-Pagán2018,

title = {Evaluation of the effectiveness of 3D-printed corals to attract coral reef fish at Tamarindo Reef, Culebra, Puerto Rico.},

author = {Birla Sofía Pérez-Pagán and Alex E. Mercado-Molina},

url = {https://www.conservationevidence.com/individual-study/6858

},

issn = {1758-2067},

year  = {2018},

date = {2018-06-11},

urldate = {2018-06-11},

journal = {Conservation Evidence},

volume = {15},

pages = {43-47},

abstract = {The development of artificial corals using 3D-printing technology has been proposed as an alternative to aid the recovery of fish populations in degraded reefs. However, no study has empirically evaluated the potential of such artificial corals to attract fish to reef patches. We conducted an experiment to determine whether the number of fish associated with natural and 3D-printed corals differs significantly. The 3D-printed artificial corals mimicked the morphology of staghorn coral Acropora cervicornis, whose branches serve as habitat for many fish species. There is evidence indicating that fish abundance increases with habitat complexity, but no specific evidence relating to A. cervicornis. Therefore, we also investigated whether the structural complexity of both natural and artificial corals affected their effectiveness to attract fish. We found that the number of fish associated with artificial and natural corals was not significantly different. However, irrespective of coral type, fish were more abundant in corals with the highest levels of complexity. Our findings suggest that 3D-printed corals can serve as a complementary tool to improve the ecosystem function of degraded coral reefs.},

keywords = {3D-printed corals, Acropora cervicornis, Caribbean, Caribbean Coral Reefs, Caribbean Sea, Coastal Resilience, Conservation Biology, Coral, Coral Reef Ecology, Coral Reef Ecosystems, coral reefs},

pubstate = {published},

tppubtype = {article}

}

@article{Mercado-Molina2017,

title = {Growth facilitation by the octocoral \textit{Gorgonia ventalina} explains spatial difference in the population size structure of the common demosponge \textit{Ircinia felix}},

author = {Alex E. Mercado-Molina and Fabiola Rivera-Irizarry and Jaime Fonseca-Miranda and Yesenia Bruno-Laureano },

editor = {Paco Cárdenas},

url = {https://www.tandfonline.com/doi/full/10.1080/17451000.2017.1367098},

doi = {https://dx.doi.org/10.1080/17451000.2017.1367098},

year  = {2017},

date = {2017-11-07},

urldate = {2017-11-07},

journal = {Marine Biology Research},

volume = {14},

issue = {1},

pages = {41-50},

abstract = {In this study, the demography of the common demosponge Ircinia felix was examined at Tamarindo, a coral reef located in the island municipality of Culebra, Puerto Rico. A preliminary study comparing the size structure of two subpopulations within the reef, Tamarindo Norte (TN) and Tamarindo Sur (TS), indicated that sponges at TN are significantly larger than sponges at TS. This result served as a baseline for the present comparative study in which we aimed to determine whether the spatial differences in population size structure can be explained either by a difference in rates of survival, growth, or recruitment, or a combination of these. To accomplish our goal, we followed the growth, survival and recruitment of I. felix at the two localities for one year. Growth was the only demographic parameter that differed significantly between localities. Because the most obvious distinction between the study sites was the absence of the octocoral Gorgonia ventalina at TS, we hypothesized that the faster overall growth rate of sponges at TN was related to the presence of the octocoral. To test this hypothesis, we compared growth rates between sponges associated with the octocoral and those individuals not associated. We found that sponges growing near G. ventalina grew significantly faster than non-associated sponges. This result suggests that the octocoral facilitates the growth of I. felix and therefore may account, at least in part, for the spatial differences in population size structure.},

keywords = {coral reefs, demography, gorgonians, population size structure, positive interactions, sponges},

pubstate = {published},

tppubtype = {article}

}

@article{Soto-Santiago2017,

title = {Comparative demography of two common scleractinian corals: \textit{Orbicella annularis} and \textit{Porites astreoides}},

author = {Francisco J. Soto-Santiago​ and Alex Mercado-Molina and Koralis Reyes-Maldonado and Yaileen Vélez and Claudia P. Ruiz-Díaz and Alberto Sabat},

editor = {James Reimer},

url = {https://peerj.com/articles/3906/#

https://peerj.com/articles/3906/https://sampr.org/wp-content/uploads/2024/01/comparative-demography-of.pdf},

doi = {10.7717/peerj.3906},

year  = {2017},

date = {2017-10-27},

urldate = {2017-10-27},

journal = {PeerJ},

volume = {5},

pages = {1-18},

abstract = {Background: Studies directed at understanding the demography and population dynamics of corals are relatively scarce. This limits our understanding of both the dynamics of coral populations and our capacity to develop management and conservation initiatives directed at conserving such ecosystems.



Methods: From 2012 to 2014, we collected data on the growth, survival, and recruitment rates of two common Caribbean coral species, the stress-tolerant Orbicella annularis and the weedy Porites astreoides. A set of size-based population matrix model was developed for two localities in Northeastern Puerto Rico and used to estimate population growth rates ( >) and determine the life cycle transition(s) that contribute the most to spatiotemporal differences in >s. The model was parameterized by following the fate of 100 colonies of each species at the two sites for two years.



Results: Our data indicate that spatial variability in vital rates of both species was higher than temporal variability. During the first year, populations of O. annularis exhibited  s below equilibrium at Carlos Rosario (0.817) and Palomino (0.694), followed by a considerable decline at both sites during the second year (0.700 and 0.667). Populations of P. astreoides showed higher  > s than O. annularis during the first census period at Carlos Rosario (0.898) and Palomino (0.894) with a decline at one of the sites (0.681 and 0.893) during the second census period. Colony fate in both species exhibited a significant interaction with respect to location but not to time (G2 = 20.96; df = 3 for O. annularis and G2 = 9.55; df = 3 for P. astreoides). Discussion: The similar variability of  s as well as the similar survival rates for both species during the two-year census period (2012–2014) show similar variability on demographic patterns in space and time. Our results suggest that location rather than time is important for the resiliency in coral colonies. Also, P. astreoides will show higher resistance to disturbance in the future than O. annularis.},

keywords = {Akaike information criteria, Caribbean, coral reefs, demography, Lambda, Life table response analysis, Orbicella annularis, Population ecology, Porites astreoides, Resilience, Scleractinians},

pubstate = {published},

tppubtype = {article}

}

@article{Godoy-Vitorino2017,

title = {The microbial biosphere of the coral \textit{Acropora cervicornis} in Northeastern Puerto Rico},

author = {Filipa Godoy-Vitorino​ and Claudia P. Ruiz-Diaz and Abigail Rivera-Seda and Juan S. Ramírez-Lugo and Carlos Toledo-Hernández},

editor = {Robert Toonen},

url = {https://peerj.com/articles/3717/

https://sampr.org/wp-content/uploads/2024/01/The-microbial-biosphere-of-the-coral-Acropora-cervicornis-in-Northeastern-Puerto-Rico.pdf},

doi = {https://doi.org/10.7717/peerj.3717},

year  = {2017},

date = {2017-08-29},

urldate = {2017-08-29},

journal = {PeerJ},

volume = {10},

number = {3717},

pages = {15},

abstract = {Coral reefs are the most biodiverse ecosystems in the marine realm, and they not only contribute a plethora of ecosystem services to other marine organisms, but they also are beneficial to humankind via, for instance, their role as nurseries for commercially important fish species. Corals are considered holobionts (host + symbionts) since they are composed not only of coral polyps, but also algae, other microbial eukaryotes and prokaryotes. In recent years, Caribbean reef corals, including the once-common scleractinian coral Acropora cervicornis, have suffered unprecedented mortality due to climate change-related stressors. Unfortunately, our basic knowledge of the molecular ecophysiology of reef corals, particularly with respect to their complex bacterial microbiota, is currently too poor to project how climate change will affect this species. For instance, we do not know how light influences microbial communities of A. cervicornis, arguably the most endangered of all Caribbean coral species. To this end, we characterized the microbiota of A. cervicornis inhabiting water depths with different light regimes.},

keywords = {16S rDNA, Caribbean, Coral, coral reefs, Depth-related, Microbiota},

pubstate = {published},

tppubtype = {article}

}