URI researchers uncover molecular mechanisms behind speciation in corals

(Press-News.org) Matías Gómez-Corrales, a recent biological sciences Ph.D. graduate from the University of Rhode Island, and his advisor, Associate Professor Carlos Prada, have published a paper in Nature Communications, revealing key mechanisms in speciation in corals and proposing a new hypothesis on the origin of species in the ocean. 

Their new study examines how coral species form and contributes to long-standing questions in evolutionary biology about how marine biodiversity originates. The work builds on decades of ecological, reproductive, and evolutionary studies led by national academy member Nancy Knowlton and pioneering researchers and co-authors Don Levitan and Mónica Medina — a legacy that Gómez-Corrales and Prada are continuing to develop.

A closer look at corals

One of the most iconic examples of mutualism is the relationship between reef-building corals and micro (dinoflagellate) algae. These symbionts harvest light and provide corals with more than 90% of their energy through photosynthesis. As a result, both corals and algae adjust their physiology and morphology to enhance performance across different light environments, such as those found along depth gradients.

While corals and their close relatives lack eyes, they are able to perceive light and do so using the same light-sensitive protein receptors (rhodopsin) on cones or rods in human eyes. 

Prada says their recent research revealed a new twist, uncovering the molecular mechanisms behind speciation in the ocean: “We discovered that opsin genes, the same genes responsible for vision in human eyes, play a key role in driving this process.”

The role of rhodopsin is well-established in fish adapted to different wavelengths across multiple species and geographic locales. For instance, a single amino acid substitution in an opsin gene in the Baltic herring has evolved more than 20 times independently in other species adapted to red-shifted light environments.

Traditionally, marine speciation has been attributed to rapid evolution of sperm-egg interaction proteins. This study presents a complementary view, showing that species can diverge through habitat-specific adaptation to light cues that regulate spawning, with rhodopsins mediating these cues and driving reproductive isolation in corals. This was the first time rhodopsin’s role in coral divergence was found.

Such a pattern of parallel divergence could occur independently in corals as they colonize waters with different optical properties, favoring rhodopsin divergence that fuels speciation.

This mechanism would allow corals to evolve reproductive isolation via genes involved in phototransduction signals that cue reproduction.

Speciation study

The Nature Communications study builds on earlier work by Prada, who proposed that speciation in corals occurs as a result of adaptation to live at different depths with different light environments (ecological speciation), a mechanism that has gained traction in the last two decades with examples ranging from plants to vertebrates. Unveiling the mechanisms behind reproduction isolation is central to understanding this process.

Gómez-Corrales and Prada investigated a recent divergence within a common Caribbean reef builder (Orbicella faveolata), where lineages diverged approximately 212,000 years ago across a narrow depth range in the water, less than 20 meters. The team showed that depth-related distributions are common among sister lineages of corals within the upper, sunlight-filled zone of the ocean. They focused on the Orbicella species, looking at the drivers of adaptive divergence and how corals display environmental sensing, studying coral colonies from Puerto Rico, Panama, Mexico, and Florida. Their analysis indicates divergence across depths through adaptation across different environments, highlighting avenues to increase biodiversity in the sea.

Coral’s reproductive processes are triggered by the interaction of differential light wavelengths, such as moonlight, neuropeptides (including dopamine), and temperature variation, which excite light receptors on the coral. By comparing genomes of deep and shallow lineages, Gómez-Corrales’ team demonstrated that the genes associated with environmental sensing in corals evolve under strong natural selection.

Genome differentiation between shallow and deep lineages occurs primarily in proteins responding to environmental sensing, affecting signaling pathways linked to coral reproductive cycles. This pattern is echoed at macroevolutionary scales across other aquatic species, such as jellyfish and sea anemones, in which neuropeptides, light, and temperature variations regulate reproductive physiology.

Notably, they found that corals use the same environmental cues tied to natural cycles to time reproduction. Coral species alter their reproductive timing under light and temperature manipulation experiments, hinting at a common mechanism for fine-tuning reproductive activity via environmental sensing.

Given the significant body of evidence supporting light as the primary sensory cue for coral spawning, Gómez-Corrales and Prada propose that differential timing of spawning driven by different light perceptions across depths is fine-tuned by expression changes in rhodopsin-like genes, causing corals exposed to different light environments to perceive spawning cues differently due to light. This process occurs across the coral tree of life and in all ocean basins across the world.

Understanding this research fills a key gap in understanding how reef species form, showing how speciation, light interactions, and ecology shape ocean biodiversity and inform predictions of marine ecosystems under climate change.

Prada says studies such as this highlight why it’s so important to better understand coral responses to ocean warming and ways that coral can adapt and acclimate to their environments, to highlight challenges and opportunities for conservation and restoration effort in the future.

“My passion for studying speciation stems from the gap between the vast biodiversity on coral reefs and our poor understanding of the mechanisms that generate and maintain this diversity,” adds Gómez-Corrales. “Uncovering the evolutionary processes shaping their diversification gives us important tools to help preserve them in the future.”

In addition to support from URI and the College of the Environment and Life Sciences, this project was supported by the International Coral Reef Society, the American Museum of Natural History, the National Science Foundation, the National Oceanic and Atmospheric Administration, and the Global Marine Initiative Student Research Award Program (The Nature Conservancy and URI).

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