The recent review by Veron et al. (2025) posits that quantitative genomic evidence used to understand coral evolution should be secondary to species hypotheses derived from expert opinion based on field experience. The authors argue that morphological “biological entities” should take precedence over molecular evidence when conflicts arise. This perspective required the rejection of extensive, independent molecular datasets that have progressively converged on a robust evolutionary framework for reef corals. Here, we reaffirm how prioritising subjective visual assessments over quantitative genetic and genomic data is methodologically unsound and scientifically regressive. We reject the framing of this perspective as “morphology versus molecules”. Rather, it is a fundamental divergence between two opposing philosophies: a static system anchored in non-reproducible expert judgement, and an integrative framework where genetic data provide the necessary independent test of morphological hypotheses. We show how a reliance on “field entities” obscures true morphological patterns by failing to distinguish between phenotypic plasticity, convergence, and evolutionary divergence. Effective taxonomy requires species hypotheses to be testable, and to stand or fall on the strength of reproducible evidence. Such a framework does not replace morphology; it validates it by providing an explicit, testable basis for evaluating morphological hypotheses. The integration of testable, reproducible molecular analysis with other lines of evidence including morphology is the benchmark of modern taxonomy across all Kingdoms of Life. We address the logical inconsistencies in the general arguments put forward by Veron et al. (2025) and refute their specific rejection of recent Acropora species-level revision with reproducible data.

The ability of consumers to adjust their diet in response to resource shifts is a key mechanism allowing the persistence of populations and underlying species' adaptive capacity. Yet on coral reefs, one of the marine habitats most vulnerable to global change, the extent to which species alter their diet and the consequences of dietary shifts for consumer performance and ecosystem functioning remain poorly understood. Here, we tested how dietary versatility can mediate the effects of habitat degradation on two invertivorous reef fishes— Chaetodon capistratus , a browser, and Hypoplectrus puella , an active predator—and whether diet shifts relate to variation in body condition and growth. We integrated DNA‐based gut content analyses (metabarcoding), otolith analysis, body condition and field surveys to link diet profiles to growth and relative body condition across reefs differing in coral cover. Metabarcoding revealed significant dietary variation in both species across reefs with different levels of coral cover. However, the response was more pronounced in the browser, whose diet was anthozoan‐dominated on healthier reefs, whereas it was annelid‐dominated on degraded reefs. We found significantly more variable body condition on degraded reefs in the browser, while the body condition of the active predator decreased in larger individuals on degraded reefs. Our results suggest that while dietary versatility serves as a mechanism to cope with degraded environments, the degree to which dietary shifts can buffer against the effects of habitat degradation varies between species. Overall, the variation in trophic niche across sites suggests that food webs and energy flow differ at relatively small scales between healthy and degraded reefs.

Ecological speciation through adaptation to different habitats can readily occur without strong geographic isolation when the same traits underlie both ecological divergence and reproductive isolation. In light-dependent corals with environment-mediated spawning, adaptation to varying light regimes across depths provides opportunities for such speciation. We show that depth-related distributions are common among sister lineages of corals within the photic zone. We then investigated molecular drivers of depth-associated adaptive divergence by analyzing sequence variation in proteins related to environmental sensing in depth-segregated and light-dependent lineages in the Orbicella species complex. Specifically, we analyzed 1) two genetically divergent ecotypes of Orbicella faveolata across a depth gradient, and 2) two depth-segregated sister species, O. annularis and O. franksi, with different spawning times following sunset. Genome-wide analyses indicate divergence across depths occurred through adaptation via positive selection on G-protein-coupled receptors (GPCRs). These molecules mediate chemo/photo/thermo-reception, enhancing physiological adaptation across environments, and are also involved in reproductive isolation via differences in spawning time. Our study proposes a molecular mechanism for the origin of depth-segregated coral species, common across anthozoans, in which ecological divergence operates at spatial scales smaller than their larval dispersal potential, and highlights avenues contributing to generating biodiversity in the sea.

For over 50 years I have studied corals, coral reefs, and reef-associated animals. Although much of my work was underpinned by genetics and I have dabbled in theory, I am a natural historian at heart. The many topics I pursued reflect in part what sparked my fancy but were also greatly shaped by a series of chance events, unexpected data, and unplanned opportunities. Many of the findings and ideas for which I am now known were initially met with skepticism and rejection—success required stubborn faith in my intuitions and convictions and the support of many assistants, collaborators, mentors, and leaders. Watching the sudden loss of the reefs that dazzled me as a graduate student and the subsequent steady decline of ocean life around the world has driven my interests in conservation and communication, and in the end, perhaps surprisingly, made me focus on the positive.

Both human populations and marine biodiversity are concentrated along coastlines, with growing conservation interest in how these ecosystems can survive intense anthropogenic impacts. Tropical urban centres provide valuable research opportunities because these megacities are often adjacent to mega-diverse coral reef systems. The Pearl River Delta is a prime exemplar, as it encompasses one of the most densely populated and impacted regions in the world and is located just northwest of the Coral Triangle. However, the spatial and taxonomic complexity of this biodiversity, most of which is small, cryptic in habitat and poorly known, make comparative analyses challenging. We deployed standardized settlement structures at seven sites differing in the intensity of human impacts and used COI metabarcoding to characterize benthic biodiversity, with a focus on metazoans. We found a total of 7184 OTUs, with an average of 665 OTUs per sampling unit; these numbers exceed those observed in many previous studies using comparable methods, despite the location of our study in an urbanized environment. Beta diversity was also high, with 52% of the OTUs found at just one site. As expected, we found that the sites close to point sources of pollution had substantially lower diversity (44% less) relative to sites bathed in less polluted oceanic waters. However, the polluted sites contributed substantially to the total animal diversity of the region, with 25% of all OTUs occurring only within polluted sites. Further analysis of Arthropoda, Annelida and Mollusca showed that phylogenetic clustering within a site was common, suggesting that environmental filtering reduced biodiversity to a subset of lineages present within the region, a pattern that was most pronounced in polluted sites and for the Arthropoda. The water quality gradients surrounding the PRD highlight the unique role of in situ studies for understanding the impacts of complex urbanization pressures on biodiversity.

Microbes play vital roles across coral reefs both in the environment and inside and upon macrobes (holobionts), where they support critical functions such as nutrition and immune system modulation. These roles highlight the potential ecosystem-level importance of microbes, yet most knowledge of microbial functions on reefs is derived from a small set of holobionts such as corals and sponges. Declining seawater pH — an important global coral reef stressor — can cause ecosystem-level change on coral reefs, providing an opportunity to study the role of microbes at this scale. We use an in situ experimental approach to test the hypothesis that under such ocean acidification (OA), known shifts among macrobe trophic and functional groups may drive a general ecosystem-level response extending across macrobes and microbes, leading to reduced distinctness between the benthic holobiont community microbiome and the environmental microbiome. We test this hypothesis using genetic and chemical data from benthic coral reef community holobionts sampled across a pH gradient from CO2 seeps in Papua New Guinea. We find support for our hypothesis; under OA, the microbiome and metabolome of the benthic holobiont community become less compositionally distinct from the sediment microbiome and metabolome, suggesting that benthic macrobe communities are colonised by environmental microbes to a higher degree under OA conditions. We also find a simplification and homogenisation of the benthic photosynthetic community, and an increased abundance of fleshy macroalgae, consistent with previously observed reef microbialisation. We demonstrate a novel structural shift in coral reefs involving macrobes and microbes: that the microbiome of the benthic holobiont community becomes less distinct from the sediment microbiome under OA. Our findings suggest that microbialisation and the disruption of macrobe trophic networks are interwoven general responses to environmental stress, pointing towards a universal, undesirable, and measurable form of ecosystem changed.

We use molecular analyses, color patterns, and records of distribution of mating pairs to reconstruct the global phylogeography of Alpheus lottini, a complex of cryptic coral-associated snapping shrimp species. Molecular data support the delineation of ancestral clades A, B, and C, and suggest five additional subdivisions within clades A and B. Clades A, B1, B2, and C exhibit color pattern differences and/or evidence of assortative mating, and thus merit species-level recognition. There is no evidence for assortative mating within clades A and B1, with likely reproductive compatibility (i.e., fertile clutches) in areas of sympatry. The clade diversity peaks in the Mariana Islands and the early branching clade C is restricted to the northern periphery of the Central and Western Pacific suggesting a Pacific origin of this group outside of the Coral Triangle. These findings underscore the prevalence of allopatric processes with possible ecological or microallopatric speciation in areas where clades overlap.

Aim As anthropogenic stressors on the biosphere intensify, understanding how communities respond to disturbances is critical. Biodiversity is often thought to promote the stability of communities over time and enhance ecosystem functioning. However, results have been inconsistent, and the multifaceted linkages among diversity, stability and functioning under acute disturbances remain poorly understood. We experimentally tested the responses of marine fish communities to disturbance (i.e., acute habitat loss) across a diversity gradient spanning 35 degrees of latitude in the western Atlantic Ocean to assess the diversity-stability relationship and the interplay between diversity, stability, and fish biomass recovery (as a proxy for function) in marine fish communities. Location Western Atlantic Ocean [Maine, Massachusetts, North Carolina, Florida (USA), Belize and Panama]. Time period 2016-2017. Major taxa studied Small, bottom-dwelling ('cryptobenthic') fishes. Methods We experimentally tested the response of marine fish communities to disturbance across a diversity gradient on human-made dock pilings. We holistically sampled cryptobenthic fish communities, then we imposed a severe disturbance by removing all benthic epifauna. We then compared the community stability, defined as the constancy in community composition, on disturbed and undisturbed pilings after one year. Results Diversity showed a negative effect on community stability at both the regional (across docks) and local (within docks) scales. Similarly, local diversity was negatively correlated with ecosystem function. These effects are exacerbated by the habitat loss imposed via our experimental treatment. Main conclusions Our results suggest that habitat loss may re-shuffle diverse, tropical communities more intensively than species-poor, temperate communities, which impacts biomass recovery, our proxy of functioning. Contrary to ecological theory, in small-bodied, benthos-associated vertebrate communities, biodiversity may neither promote stability nor functioning, suggesting that human disturbances may be particularly impactful in tropical, high-diversity ecosystems.

Metazoans host complex communities of microorganisms that include dinoflagellates, fungi, bacteria, archaea and viruses. Interactions among members of these complex assemblages allow hosts to adjust their physiology and metabolism to cope with environmental variation and occupy different habitats. Here, using reciprocal transplantation across depths, we studied adaptive divergence in the corals Orbicella annularis and O. franksi, two young species with contrasting vertical distribution in the Caribbean. When transplanted from deep to shallow, O. franksi experienced fast photoacclimation and low mortality, and maintained a consistent bacterial community. By contrast, O. annularis experienced high mortality and limited photoacclimation when transplanted from shallow to deep. The photophysiological collapse of O. annularis in the deep environment was associated with an increased microbiome variability and reduction of some bacterial taxa. Differences in the symbiotic algal community were more pronounced between coral species than between depths. Our study suggests that these sibling species are adapted to distinctive light environments partially driven by the algae photoacclimation capacity and the microbiome robustness, highlighting the importance of niche specialization in symbiotic corals for the maintenance of species diversity. Our findings have implications for the management of these threatened Caribbean corals and the effectiveness of coral reef restoration efforts.

Values of Fv/Fm, ΔF/Fm’, and Qm of coral transplants at the shallow and deep sites

AbstractAnalysis of environmental DNA is increasingly used to characterize ecological communities, but the effectiveness of this approach depends on the accuracy of taxonomic reference databases. The MIDORI databases, first released in 2017, were built to improve accuracy for mitochondrial metazoan (animal) sequences. MIDORI has now been significantly improved and renamed MIDORI2 (available at http://www.reference‐midori.info). Like MIDORI, MIDORI2 is built from GenBank and contains curated sequences of thirteen protein‐coding and two ribosomal RNA mitochondrial genes. Coverage has been substantially expanded to cover all eukaryotes, including fungi, green algae and land plants, other multicellular algal groups, and diverse protist lineages. MIDORI2 also now includes not only species with full binomials, but also taxa referred to by genus with species left unspecified (“sp.”). Another new feature is the updating of the databases approximately every two months with version numbers corresponding to each new GenBank release. Additional potentially erroneously annotated sequences have also been removed. Finally, the ability to export data files to BLAST+ has been added to the original ability to export preformatted data to five taxonomic assignment programs, and databases of amino acid sequences are also made available for protein‐coding genes. As a technical validation, we conducted a preliminary comparison of the performance of MIDORI2 with five taxonomic assignment programs. Results suggest that BLAST+ top hits performed better for assigning CO1 sequences than alignment‐free methods based on compositional features. Comparing MIDORI2 with two other commonly used curated databases of mitochondrial sequences, CO‐ARBitrator and BOLD, we show that MIDORI2 includes sequences from a broader range of metazoan and non‐metazoan taxa. Overall, in many contexts, MIDORI2 offers clear advantages: a higher diversity of taxa than other databases, a variety of user‐friendly features, and regular updates. MIDORI2 is particularly well‐suited for environmental DNA studies that target mitochondrial genes with broad primers.

The ocean is facing multiple pressures from human activities, including the effects of climate change. Science has a prominent role in identifying problems and communicating these to society. However, scientists are also increasingly taking an active role in developing solutions, including strategies for adapting to and mitigating climate change, increasing food security, and reducing pollution. Transmitting these solutions to society changes our narrative about the ocean and motivates actions. The United Nations triple initiatives for this decade-the Sustainable Development Goals, the Decade on Ocean Science for Sustainable Development, and the Decade of Ecosystem Restoration-provide the momentum for this change in narrative and focus. Here, we reflect on the search for solutions and the need for better ways of communicating science in a positive way. We synthesize insights from a summer school held during the COVID-19 pandemic and present some examples of successes and failures and the lessons learned from these.

CORRECTION article Front. Mar. Sci., 08 September 2022Sec. Marine Ecosystem Ecology Volume 9 - 2022 | https://doi.org/10.3389/fmars.2022.1027767

Background The formation of the Isthmus of Panama and final closure of the Central American Seaway (CAS) provides an independent calibration point for examining the rate of DNA substitutions. This vicariant event has been widely used to estimate the substitution rate across mitochondrial genomes and to date evolutionary events in other taxonomic groups. Nuclear sequence data is increasingly being used to complement mitochondrial datasets for phylogenetic and evolutionary investigations; these studies would benefit from information regarding the rate and pattern of DNA substitutions derived from the nuclear genome. Results To estimate the genome-wide neutral mutation rate (µ), genotype-by-sequencing (GBS) datasets were generated for three transisthmian species pairs in Alpheus snapping shrimp. A range of bioinformatic filtering parameters were evaluated in order to minimize potential bias in mutation rate estimates that may result from SNP filtering. Using a Bayesian coalescent approach (G-PhoCS) applied to 44,960 GBS loci, we estimated µ to be 2.64E−9 substitutions/site/year, when calibrated with the closure of the CAS at 3 Ma. Post-divergence gene flow was detected in one species pair. Failure to account for this post-split migration inflates our substitution rate estimates, emphasizing the importance of demographic methods that can accommodate gene flow. Conclusions Results from our study, both parameter estimates and bioinformatic explorations, have broad-ranging implications for phylogeographic studies in other non-model taxa using reduced representation datasets. Our best estimate of µ that accounts for coalescent and demographic processes is remarkably similar to experimentally derived mutation rates in model arthropod systems. These results contradicted recent suggestions that the closure of the Isthmus was completed much earlier (around 10 Ma), as mutation rates based on an early calibration resulted in uncharacteristically low genomic mutation rates. Also, stricter filtering parameters resulted in biased datasets that generated lower mutation rate estimates and influenced demographic parameters, serving as a cautionary tale for the adherence to conservative bioinformatic strategies when generating reduced-representation datasets at the species level. To our knowledge this is the first use of transisthmian species pairs to calibrate the rate of molecular evolution from GBS data.

This document is the work of a team assembled by the International Coral Reef Society (ICRS). The mission of ICRS is to promote the acquisition and dissemination of scientific knowledge to secure the future of coral reefs, including via relevant policy frameworks and decision-making processes. This document seeks to highlight the urgency of taking action to conserve and restore reefs through protection and management measures, to provide a summary of the most relevant and recent natural and social science that provides guidance on these tasks, and to highlight implications of these findings for the numerous discussions and negotiations taking place at the global level.

Department of Geological Sciences, Jackson School of Geosciences, The University of Texas at Austin, Austin, TX, United States, Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, LA, United States, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States, Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, FL, United States, 5 Kimbell School of Geosciences, Midwestern State University, Wichita Falls, TX, United States, Departmentof BioSciences, Rice University, Houston, TX, United States

Small cryptic invertebrates (the cryptofauna) are extremely abundant, ecologically important, and species rich on coral reefs. Ongoing ocean acidification is likely to have both direct effects on the biology of these organisms, as well as indirect effects through cascading impacts on their habitats and trophic relationships. Naturally acidified habitats have been important model systems for studying these complex interactions because entire communities that are adapted to these environmental conditions can be analyzed. However, few studies have examined the cryptofauna because they are difficult to census quantitatively in topographically complex habitats and are challenging to identify. We addressed these challenges by using Autonomous Reef Monitoring Structures (ARMS) for sampling reef-dwelling invertebrates >2 mm in size and by using DNA barcoding for taxonomic identifications. The study took place in Papua New Guinea at two reef localities, each with three sites at varying distances from carbon dioxide seeps, thereby sampling across a natural gradient in acidification. We observed sharp overall declines in both the abundance (34-56%) and diversity (42-45%) of organisms in ARMS under the lowest pH conditions sampled (7.64-7.75). However, the overall abundance of gastropods increased slightly in lower pH conditions, and crustacean and gastropod families exhibited varying patterns. There was also variability in response between the two localities, despite their close proximity, as one control pH site displayed unusually low diversity and abundances for all invertebrate groups. The data illustrate the complexity of responses of the reef fauna to pH conditions, and the role of additional factors that influence the diversity and abundance of cryptic reef invertebrates.

Impacts of marine heatwaves are worse when seaweeds and sea urchins are abundant