Abstract Background Coral reefs are among the most biodiverse ecosystems on Earth yet face an increasing risk of collapse under climate change and intensifying anthropogenic pressures. Although there is strong evidence that stressors such as overfishing, sedimentation, and wastewater runoff can drive shifts in coral community structure, few studies have investigated the molecular mechanisms underlying these shifts. Integrating data across multiple layers of biological organization, from the genome to the proteome and metabolome, offers a powerful approach to understanding how coral physiology and resilience are impacted by human activities. Findings Here, we present high-coverage whole genome sequencing ( Montipora only) together with untargeted metabolomic and proteomic datasets from three coral genera ( Acropora , Pocillopora , and Montipora ) that inhabit Ulithi Atoll, Yap State, FSM. Ulithi Atoll is an ideal system for investigating how anthropogenic pressures influence coral molecular ecology and adaptation, with extensive historical ecological data available through the long-term research program of the One People One Reef collaborative to connect multi-omics data with macroecological trends. Following data cleaning and quality control, all datasets exhibited minimal technical variation among samples, providing a comprehensive baseline for future research on coral resilience across a mosaic of natural and anthropogenic stressors. Conclusions These data provide a resource for examining how anthropogenic pressures influence coral physiology and resilience across environmental gradients. They also allow the identification of biomarkers of chronic stress that may inform the development of point-of-care diagnostic tools for coral health and contribute to evidence-based reef conservation and management strategies.

Herbivorous coral reef fishes are often assigned to different functional groups based on feeding mode and presumed ecosystem processes, such as algal removal (i.e., functional herbivory). However, these functional assignments do not necessarily identify assimilated resources nor predict nutritional pathways supporting fish biomass. We used stable carbon and nitrogen isotopes of amino acids to refine our understanding of herbivory among three nominally herbivorous fishes: Chlorurus spilurus, Ctenochaetus striatus, and Naso lituratus. Amino acid carbon isotope fingerprinting indicated much higher and more variable algal carbon contribution for N. lituratus (52.0

Coral reef degradation is accelerating globally, yet monitoring efforts remain uneven in scale, accessibility, and resolution. Visual surveys of percent live coral cover offer low-cost but coarse assessments of reef health, while more advanced tools (e.g., autonomous underwater vehicles, airborne LiDAR) often remain inaccessible for many low-income, tropical nations. In this study, we used low-cost, high-resolution Structure-from-Motion (SfM) photogrammetry across 21 sites in Ulithi Atoll, Federated States of Micronesia, spanning a gradient of oceanic and lagoonal exposure, fishing pressure, and human population density, as a community-centered approach to assess reef habitat complexity and its relationships to benthic and fish communities. Habitat complexity was not strongly correlated with live coral cover or coral morphotype composition, two common indicators of reef health, but instead, was most closely associated with overall benthic community composition, including the relative abundance of sponges, macroalgae, and turf algae. Contrary to expectations, habitat complexity did not significantly correlate with total fish abundance but was a stronger predictor of fish and benthic assemblage structure across all reef types and exposure zones. Notably, several sites under active community-led management exhibited higher-than-average structural complexity despite their proximity to human settlements, suggesting that local management practices may help preserve reef architecture. SfM photogrammetry provides a scalable, community-accessible monitoring approach to inform adaptive management, particularly in remote or data-limited reef systems facing compounding climate and human pressures.

Local and global ecological stressors are leading to increased documentation of phase shifts in coral reefs from healthy stony corals to macrophytes. In more rare cases, phase shifts result in sponge, zoantharian or other dominant species. In Ulithi Atoll, Federated States of Micronesia, we have documented an unusual phase shift from reefs with a diverse stony coral assemblage to reefs dominated by a single species of stony coral: Montipora sp.—a coral-to-coral phase shift. This monospecific type of reef lowers fish diversity and biomass, impacting both ecological integrity, and livelihoods of reef-dependent human communities. In this study, we used a genomic approach to characterize such a reef. We assembled a de-novo reference genome and used RAD seq data with thousands of SNPs to determine if different reefs result from sexual or asexual reproduction, if weedy Montipora fragments are transported between islands by human activities, and if there is evidence of natural selection on specific genotypes, thus favoring spreading success. We found that sexual reproduction is predominant in the focal species, that there is no evidence of human-mediated spread, and that some genomic regions might be under selection. While such results eliminate a number of spreading hypotheses, more precise dispersal maps will be important to determine the tempo and mode of ‘invasion’ of Montipora in Ulithi Atoll. This study shows that selection and adaptation may be contributing to the success of a stony coral (e.g., Phase shift). While a stony coral may be successful in a disturbed environment, it does not necessarily provide the type of habitat that is conducive to high fish biomass and coral diversity. These results serve as a cautionary tale for restoration efforts that focus on single species coral resilience rather than ecosystem function.

As countries consider new area-based conservation targets under the Convention on Biological Diversity, protected areas (PAs) and their impacts on people and nature are coming under increasing scrutiny. We review the evidence base on PA impacts, combining the findings from existing rigorous impact evaluations with local case studies developed for this study. We identify characteristics of PA establishment and management that improve the sustainability of biodiversity conservation and justice for local communities. We find that recognizing and respecting local values and knowledge about natural resource stewardship, colearning, and comanagement are key to achieving positive impacts for nature and people. Transforming PA governance toward more inclusive conservation depends upon the ability of PAs to be designed and implemented around the values and needs of local people.

Globally, marine protected area (MPA) objectives have increasingly shifted from a primary focus on maintaining ecosystems through prohibiting extractive activities, to more equitable approaches that address the needs of both people and nature. This has led to MPAs with a diverse array of fisheries restrictions and recent debate on the type of restrictions that contribute to achieving biodiversity goals. Here we use a global dataset of 172 MPAs (representing 31 nations) alongside nine detailed case study MPAs (from Australia, Belize, Cambodia, Federated States of Micronesia, Fiji, Indonesia, Madagascar, Solomon Islands, and United States of America), including partially protected areas that allow regulated fishing, to illustrate the many diverse pathways that some MPAs have adopted to protect biodiversity and safeguard the rights and well-being of resource-dependent coastal communities. We group MPAs based on their restrictions and explore four key insights emerging from these groupings using our nine case studies: (i) MPAs use highly diverse approaches to regulate fisheries; (ii) partially protected areas can address gaps in regional fisheries management; (iii) devolving resource management rights to communities influences the chosen fisheries restrictions; and (iv) state-governed MPAs can use highly tailored fisheries restrictions to increase equity in access. We find that partially protected MPAs can offer effective and equitable pathways for biodiversity conservation if tailored to local context. Rather than focusing primarily on fully protected areas for achieving new global MPA targets, we recommend countries use a blend of locally-appropriate protection levels – from fully protected areas to partially protected MPAs to achieve positive biodiversity outcomes.

Scientists and managers rely on indicator taxa such as coral and macroalgal cover to evaluate the effects of human disturbance on coral reefs, often assuming a universally positive relationship between local human disturbance and macroalgae. Despite evidence that macroalgae respond to local stressors in diverse ways, there have been few efforts to evaluate relationships between specific macroalgae taxa and local human‐driven disturbance. Using genus‐level monitoring data from 1205 sites in the Indian and Pacific Oceans, we assess whether macroalgae percent cover correlates with local human disturbance while accounting for factors that could obscure or confound relationships. Assessing macroalgae at genus level revealed that no genera were positively correlated with all human disturbance metrics. Instead, we found relationships between the division or genera of algae and specific human disturbances that were not detectable when pooling taxa into a single functional category, which is common to many analyses. The convention to use percent cover of macroalgae as an indication of local human disturbance therefore likely obscures signatures of local anthropogenic threats to reefs. Our limited understanding of relationships between human disturbance, macroalgae taxa, and their responses to human disturbances impedes the ability to diagnose and respond appropriately to these threats.

Abstract The current ease of obtaining thousands of molecular markers challenges the notion that full phylogenetic concordance, as proposed by phylogenetic species concepts, is a requirement for defining species delimitations. Indeed, the presence of genomic islands of divergence, which may be the cause, or in some cases the consequence, of speciation, precludes concordance. Here, we explore this issue using thousands of RAD markers on two sister species of surgeonfishes (Teleostei: Acanthuridae), Zebrasoma flavescens and Z. scopas, and several populations within each species. Species are readily distinguished based on their colors (solid yellow and solid brown, respectively), yet populations and species are neither distinguishable using mitochondrial markers (cytochrome c oxidase 1), nor using 5193 SNPs (pairwise Φst = 0.034). In contrast, when using outlier loci, some of them presumably under selection, species delimitations, and strong population structure follow recognized taxonomic positions (pairwise Φst = 0.326). Species and population delimitation differences based on neutral and selected markers are likely due to local adaptation, thus being consistent with the idea that these genomic islands of divergence arose as a consequence of isolation. These findings, which are not unique, raise the question of a potentially important pathway of divergence based on local adaptation that is only evident when looking at thousands of loci.

The dynamic relationship between reefs and the people who utilize them at a subsistence level is poorly understood. This paper characterizes atoll-scale patterns in shallow coral reef habitat and fish community structure, and correlates these with environmental characteristics and anthropogenic factors, critical to conservation efforts for the reefs and the people who depend on them. Hierarchical clustering analyses by site for benthic composition and fish community resulted in the same 3 major clusters: cluster 1-oceanic (close proximity to deep water) and uninhabited (low human impact); cluster 2-oceanic and inhabited (high human impact); and cluster 3-lagoonal (facing the inside of the lagoon) and inhabited (highest human impact). Distance from village, reef exposure to deep water and human population size had the greatest effect in predicting the fish and benthic community structure. Our study demonstrates a strong association between benthic and fish community structure and human use across the Ulithi Atoll (Yap State, Federated States of Micronesia) and confirms a pattern observed by local people that an 'opportunistic' scleractinian coral (Montipora sp.) is associated with more highly impacted reefs. Our findings suggest that small human populations (subsistence fishing) can nevertheless have considerable ecological impacts on reefs due, in part, to changes in fishing practices rather than overfishing per se, as well as larger global trends. Findings from this work can assist in building local capacity to manage reef resources across an atoll-wide scale, and illustrates the importance of anthropogenic impact even in small communities.

Here we report the presence of two unusual reef types at Ulithi Atoll, Yap State, Federated States of Micronesia: 1. a corallimorph-dominated reef off the island of Mogmog is found within an otherwise coral-dominated area, and 2. a general spread of Montipora reefs that were found to dominate the reef landscapes near inhabited islands. The Montipora reefs primarily occur near villages and in disturbed areas such as near boat-launch ramps. Indigenous people in the area say these reefs are fairly recent (ca. late 1960s) and that Montipora has been spreading rapidly.