Coral Reefs Keep Two Different Scoreboards, and Protection Only Fixes One

Deep beneath the surface of Raja Ampat, the Indonesian archipelago often called the global epicenter of marine biodiversity, scientists have discovered that coral reefs keep two very different scoreboards of biological health, and that marine protection only fixes one of them. A new study published in the journal Coral Reefs shows that the sheer number of fish species on a reef and the variety of ecological roles those fish perform respond to habitat degradation and human pressure in fundamentally different ways. The finding, based on years of underwater surveys across a multi-use marine protected area, carries a stark warning for conservationists: counting species alone can mask the quiet erosion of the ecological machinery that keeps reefs alive.

The research team, led by Philippe Fernandez-Fournier of Simon Fraser University together with collaborators from Indonesian conservation organizations, Universitas Papua, The SEA People, and the National University of Singapore, set out to untangle a question that has long frustrated reef ecologists. Coral reefs are battered by a barrage of human activities, from fishing to coastal development, and these stressors interact with habitat features such as coral diversity, structural complexity, and wave exposure in ways that are notoriously difficult to disentangle. Which factors matter most for reef fish diversity, and through what pathways, has remained unclear despite decades of study.

To crack the problem, the researchers turned to a statistical technique called structural equation modeling, a framework that allows scientists to test networks of hypothesized cause-and-effect relationships rather than isolated correlations. Instead of asking simply whether fishing pressure predicts fish diversity, the approach can trace how fishing alters the reef habitat itself, and how those habitat changes then cascade upward to shape the fish communities. The team surveyed reefs across a multi-use marine protected area in Raja Ampat, measuring coral species richness, structural complexity estimated from the three-dimensional architecture of the reef, dead coral cover, fishing pressure inferred from accessibility and nearby population density, direct proximity to human settlements, marine protection status, and wave exposure.

The results reveal a striking asymmetry. Fish species richness, the raw count of different species living on a reef, was strongly predicted by two habitat features: the number of coral species present and the structural complexity of the reef. Reefs with more coral species and more intricate three-dimensional architecture supported more fish species, confirming a relationship that ecologists have documented across tropical seas. But the second measure of diversity, called functional dispersion, told a completely different story. Functional dispersion quantifies how varied the ecological traits of a fish community are, capturing differences in body size, diet, home range, and behavior. A reef can host many species that all perform similar roles, yielding high species richness but low functional dispersion, or fewer species that each occupy distinct ecological niches, yielding the opposite pattern.

Remarkably, functional dispersion showed no significant relationship with coral species richness or structural complexity at all. Instead, it was elevated on reefs with higher relative dead coral cover, a counterintuitive result that suggests degraded reefs are not simply impoverished versions of healthy ones. As coral dies and structural complexity erodes, the fish community may shift toward a different assemblage of species with different traits, some of which thrive in the altered conditions. This decoupling means that the two scoreboards of reef health are tracking separate ecological processes, and that a reef can appear species-rich while its functional portfolio quietly narrows, or vice versa.

Fishing pressure emerged as the dominant human force in the system. The researchers estimated fishing pressure not from direct catch records but from accessibility and population density, a proxy approach widely used in data-poor tropical fisheries. Reefs facing higher fishing pressure had lower functional dispersion among their fish, lower structural complexity, and higher dead coral cover. The modeling also traced an indirect pathway: fishing degrades the habitat, and the degraded habitat in turn supports fewer fish species. In other words, fishing does not just remove fish from the water; it dismantles the very architecture that fish depend on, creating a feedback loop that compounds over time.

Direct proximity to human settlements, by contrast, showed comparatively weak and largely non-significant associations with both habitat variables and fish diversity. This distinction matters because it separates two different dimensions of human impact. Living near a reef does not necessarily mean degrading it; what matters is the intensity of extraction and the physical damage it inflicts. The finding suggests that conservation strategies should focus on the specific mechanisms of harm, particularly fishing, rather than on human presence as a blanket proxy.

Marine protection, the study found, mitigated the impact of fishing pressure on fish species richness and supported more structurally complex reefs. In Raja Ampat, where a network of marine protected areas spans the Bird’s Head Seascape and zoning balances fisheries with conservation objectives, protection appears to work through habitat: by reducing fishing intensity, it preserves the three-dimensional architecture that fish need, which in turn sustains species richness. The researchers emphasize that protection did not simply add fish; it defended the habitat infrastructure that fish depend on, a mechanism that may explain why some protected areas outperform others across the globe.

The counterintuitive link between dead coral cover and elevated functional dispersion deserves particular attention. Rather than viewing dead coral as a simple indicator of decline, the results suggest that reef degradation reshuffles the functional composition of fish communities in complex ways. Some species with traits suited to rubble and exposed substrates may flourish as coral dies, temporarily increasing trait variety even as the community shifts away from its coral-dependent baseline. This dynamic complicates simple narratives of reef collapse and highlights the need to understand the interactions between environmental stressors and habitat features when designing conservation strategies for complex and biodiverse coral reef ecosystems.

As human activities continue to impact coral reefs worldwide, the study’s central message is that species richness and functional diversity are not interchangeable measures of reef health. A reef can appear species-rich while its ecological roles narrow, or host fewer species that each perform distinct and critical functions. Conservation strategies that monitor only one dimension risk missing the other, and the pathways by which fishing, protection, and habitat interact mean that effective management must defend the structural architecture of reefs as much as the fish that swim among it. In Raja Ampat, where local communities, traditional management practices, and marine protected areas converge, the research offers a technical roadmap for safeguarding one of the ocean’s last great strongholds of biodiversity, and a reminder that the health of a reef is written in more than one language.

Subject of Research: Reef fish taxonomic and functional diversity respond differently to habitat degradation and protection

Article Title: Reef fish taxonomic and functional diversity respond differently to habitat degradation and protection

Article References: Fernandez-Fournier, P., Ahmad, A., Boli, P., Manangkalangi, E., Brival, A. J. T., Patty, C. J., Huang, D., & Mooers, A. Ø. (2026). Reef fish taxonomic and functional diversity respond differently to habitat degradation and protection. Coral Reefs. https://doi.org/10.1007/s00338-026-02974-0

Image Credits: AI Generated

DOI: 10.1007/s00338-026-02974-0

Keywords: Reef, fish, taxonomic, functional, diversity, respond, differently, habitat, degradation, protection, scientific research