Shallow-water Coral Research Articles

Coral recruitment assessment as a pre-requisite experiment to restore shallow water coral communities of Palk Bay, southeast coast of India

Coral recruitment assessment as a pre-requisite experiment to restore shallow water coral communities of Palk Bay, southeast coast of India

Reef refugia in the aftermath of past episodes of global warming

In the face of rising global temperatures, coral reefs experience coral mass bleaching and mortality. Subtropical and mesophotic environments may represent refugia for reef corals under climate change, where they can survive and eventually recolonize degraded areas. Using a comprehensive database of fossil reefs, we empirically assess the efficacy of subtropical, deeper, and turbid mesophotic environments to restore coral reefs after past global warming events. We focus on tropical coral reefs over the last 275 million years and four rapid climate warming events, which coincided with global reef crises in the geological record. In the aftermath of such hyperthermal events, we observed an increase in the proportions of reefs occurring in deeper (blue) mesophotic environments. Additionally, we found a trend of reef distributions and coral shifting towards higher latitudes. The number of coral occurrences in turbid (brown mesophotic) environments also increased after hyperthermal events. Our results suggest that subtropical, blue, and brown mesophotic environments may have served as immediate refugia for shallow-water coral species escaping warming seawater. While the patterns of reef range shifts and the establishment of blue and brown mesophotic refugia following ancient hyperthermal events provide some hope for coral reefs under current climate change, re-establishement of background reef conditions took most times millions of years.Ante el incremento de temperatura global, los arrecifes coralinos están experimentando eventos masivos de blanqueamiento y mortalidad. Los ambientes subtropicales y mesofóticos pueden representar refugios para los corales arrecifales, en los cuales pueden escapar de los efectos del cambio climático, sobrevivir y desde allí recolonizar áreas previamente degradadas. Mediante el uso de una exhaustiva base de datos en arrecifes coralinos, en este estudio se evaluó empíricamente la eficacia de los ambientes subtropicales y mesofóticos, tanto de aguas turbias someras (marrones) como de aguas claras profundas (azules), en la recuperación de arrecifes coralinos después de eventos hipertermales en el pasado. Nuestro enfoque estuvo en los arrecifes coralinos tropicales durante los últimos 275 millones de años y cuatro eventos de calentamiento climático rápido, los cuales coinciden con crisis globales en la ocurrencia de arrecifes en el registro fósil. Como consecuencia de dichos eventos hipertermales, observamos un aumento del número de arrecifes en ambientes mesofóticos de aguas profundas (azules). Además, encontramos una tendencia en la distribución de arrecifes y corales que se desplazan hacia latitudes más altas. También se observó un aumento en el número de corales que estuvieron presentes en ambientes de aguas turbias (marrones) después de dichos eventos hipertermales. Nuestros resultados sugieren que, en el pasado, los ambientes subtropicales, mesofóticos azules y mesofóticos marrones pudieron haber servido como refugios inmediatos para las especies de coral de aguas someras, en los cuales encuentran condiciones atenuantes ante el calentamiento oceánico. Si bien los patrones de desplazamiento de los arrecifes en el rango latitudinal y el establecimiento de refugios mesofóticos de aguas marrones y azules posteriores a eventos hipertermales brindan una luz de esperanza para el futuro de los arrecifes coralinos de cara al cambio climático actual, nuestros resultados evidencian que el restablecimiento de los arrecifes puede tomar millones de años.

A decrease in pH, increase in temperature, and pollution exposure elicit distinct stress responses in a scleractinian coral (Desmophyllum pertusum)

Scleractinian corals create habitat that persists on geological timescales and supports some of the most diverse ecosystems on Earth. Throughout their depth range, these ecosystems are threatened by anthropogenic disturbances, including global ocean change and hydrocarbon extraction. While numerous studies have focused on how shallow-water corals respond to stressors, there is a paucity of research on deep-sea corals. Here, we analyze the gene expression patterns from a reef-forming deep-sea coral, Desmophyllum pertusum (previously Lophelia pertusa), exposed to oil and dispersant mixtures under current and projected future temperature and pH conditions. The overall gene expression patterns varied among coral colonies (genets), but dispersant exposure induced the strongest response. A Weighted-Gene Correlation Network Analysis (WGCNA) identified networks of co-expressed genes in response to different stressors. Gene ontology (GO) enrichment analysis revealed that D. pertusum exhibited the coral cellular stress response (CSR) during exposure to oil, dispersant, and a decrease in pH. Dispersant exposure elicited a response that included up-regulation of apoptosis, immune system, wound healing, and stress-related pathways. Coral nubbins exposed to oil exhibited signs of resource reallocation and a reduction in growth to maintain cellular homeostasis. The decrease in seawater pH resulted in a less severe stress response than dispersant exposure. These results support the idea that there is an underlying environmental stress response (ESR) shared by scleractinians, but that this response varies depending on the type and intensity of the stress with which they are challenged.

Severe cold-water bleaching of a deep-water reef underscores future challenges for Mesophotic Coral Ecosystems

Elevated sea surface temperatures are causing an increase in coral bleaching events worldwide, and represent an existential threat to coral reefs. Early studies of Mesophotic Coral Ecosystems (MCEs) highlighted their potential as thermal refuges for shallow-water coral species in the face of predicted 21st century warming. However, recent genetic evidence implies that limited ecological connectivity between shallow- and deep-water coral communities inhibits their effectiveness as refugia; instead MCEs host distinct endemic communities that are ecologically significant in and of themselves. In either scenario, understanding the response of MCEs to climate change is critical given their ecological significance and widespread global distribution. Such an understanding has so far eluded the community, however, because of the challenges associated with long-term field monitoring, the stochastic nature of climatic events that drive bleaching, and the paucity of deep-water observations. Here we document the first observed cold-water bleaching of a mesophotic coral reef at Clipperton Atoll, a remote Eastern Tropical Pacific (ETP) atoll with high coral cover and a well-developed MCE. The severe bleaching (>70 % partially or fully bleached coral cover at 32 m depth) was driven by an anomalously shallow thermocline, and highlights a significant and previously unreported challenge for MCEs. Prompted by these observations, we compiled published cold-water bleaching events for the ETP, and demonstrate that the timing of past cold-water bleaching events in the ETP coincides with decadal oscillations in mean zonal wind strength and thermocline depth. The latter observation suggests any future intensification of easterly winds in the Pacific could be a significant concern for its MCEs. Our observations, in combination with recent reports of warm-water bleaching of Red Sea and Indian Ocean MCEs, highlight that 21st century MCEs in the Eastern Pacific face a two-pronged challenge: warm-water bleaching from above, and cold-water bleaching from below.

Diverse and ecologically unique mesophotic coral ecosystems in the central Indian Ocean

Research on Mesophotic Coral Ecosystems (MCEs; 30–150 m) has grown exponentially in the last few decades, highlighting their rich diversity and extensive distribution. However, they are still largely underexplored compared to shallow-water coral reefs and frequently remain under-protected and under-represented in marine spatial planning. One reason for the imbalance between the high ecological value of MCEs and the limited levels of protection may be that baseline data on MCEs are largely missing to date, yet are crucial to provide evidence-based information for management actions. Here, we present data on the alpha and beta diversity of the benthic communities within MCEs in the Chagos Archipelago, Indian Ocean. Using imagery collected from Remotely Operated Vehicle surveys, benthic invertebrate megafauna were surveyed along the entire depth gradient from shallow to lower mesophotic depths (15–160 m). The diversity of the benthic communities decreased with increasing depth, from shallow water to the lower mesophotic zone. Nevertheless, the deepest parts of MCEs in the Archipelago displayed higher species richness values than several other shallow subtropical regions. In addition, the benthic communities showed high dissimilarity along the depth gradient, indicating that the key driver of community composition change with depth is species turnover (species replacement), revealing the uniqueness of MCEs. This study presents novel findings on MCEs in the central Indian Ocean, demonstrating that they host a high and unique benthic diversity, and highlighting the need to protect these ecosystems to preserve the overall biodiversity of coral reefs.

Local conditions modulated the effects of marine heatwaves on coral bleaching in subtropical Hong Kong waters

A mass coral bleaching event occurred in the summer of 2022 in subtropical Hong Kong, driven by two marine heatwaves (MHWs) with high intensities of 1.56 and 0.86 °C above a mean climate condition, both MHWs 7 days with a short gap of 4 days during the strong La Niña year. A transect survey was conducted at nine study sites in three regions, which revealed widespread coral bleaching with bleached coral cover ranging from 2.4 to 70.3%. In situ environmental data revealed the presence of a thermocline and halocline. Local conditions, including depth and wave exposure, significantly influenced the bleaching response. Shallow-water (2–4 m) corals were primarily affected, particularly in sheltered and moderately sheltered sites that exhibited higher levels of bleached coral cover (42.97 ± 15.4% and 44.93 ± 29.4%, respectively) compared to the exposed sites (31.8 ± 5.2%). Bleaching in deep waters (4–6 m) was minimal, with only a few colonies of Goniopora at two of the three sheltered sites exhibiting bleaching (1.7 ± 1.5%). Heat stress resistance differed between coral genera. Recovery rate for four common coral genera is low for Acropora tumida. Additionally, a minor hypoxia event was found to cause mortality of non-coral benthos at a sheltered site (Sharp Island). These findings highlight the alarming impact of extreme heatwaves on subtropical coral communities and underscore the importance of monitoring coral bleaching.

Variations in benthic coverage and diversity of shallow water coral reefs in Eastern coast of Sri Lanka: A combined analysis from Allen Coral Atlas and ground surveys

AbstractMonitoring changes in coral reef ecosystems for their conservation and management is important as they are frequently subject to various natural and anthropogenic threats. However, in Sri Lanka, the attention in this regard is to be further concerned for their well‐being. Therefore, this study focused on the selected shallow water (<5 m) coral reefs as Pigeon Island (PIR), Adukkuparu (AR), Salli Beach (SBR), Kayankerni (KR), and Passikuda (PR) on the Eastern coast of Sri Lanka to estimate their changes over 2020, 2021, and 2022. The remote sensing demarcations with the composition of reef ecosystems were done through the analysis of the Allen Coral Atlas data followed by field surveys. Higher accuracy levels for corals were obtained for each site due to field verifying all individual polygons and omitting unmatched polygons of the initial maps from the Allen Coral Atlas. Then, the in‐situ reef surveys were conducted over randomly selected permanent transects at each site. From 2020 to 2022, the live coral percentages have increased in PIR, AR, and SBR while reduced in KR and PR. Dead corals have facilitated the overgrowth of macroalgae. The combined area of live coral on all five reefs has slightly gone up. This increase is primarily due to the rise in live coral cover in AR and SBR. Also, prominent increments of coral diversity have resulted from those sites. Therefore, it is suggested that AR and SBR be designated as Marine Protected Areas to safeguard the newly emerging live corals.

Systematic planning shows more than half of the most species-rich ocean region is needed to include all species in representative protected areas

The Convention on Biological Diversity Target 3 aims for at least 30 % of each marine habitat to be protected by 2030. How much biodiversity will be protected depends on where this 30 % is located. The West Pacific region, having the richest marine biodiversity on Earth, is especially important for nature conservation. Here, using multiple data-driven measures of the breadth biodiversity, from species to ecosystems from the sea surface to seabed, at a spatial resolution of 0.5° (∼55 km latitude), we mapped the optimal “Representative Biodiversity Areas” (RBA) for West Pacific countries using decision support software. The measures included surface and near seabed Ecosystems, which were mapped by physical, biochemical and nutrient variables relevant to ecological functioning. Species richness, seagrass, kelp, mangrove, and shallow water coral reef biomes (biological habitats at a local scale) and seabed topographic variation (as rugosity) were also included as complementary measures to maximise representivity of biodiversity overall. The 30 % RBA generally covered 30 % of the Ecosystems, over 77 % of the Biomes of seagrass, kelp, mangrove, and shallow water corals, and 60 % of physical habitat heterogeneity (topography) and the most species rich areas. Because protecting only these four biomes was not sufficient to include all species, physical habitat heterogeneity and ecosystems should be included in conservation prioritisation because they extend offshore and to all depths. To cover the distributions of 80 % species in the region, at least 53 % of the total area should be under protection. Only 25 % of the RBA were in MPAs, and < 1 % in no-take MPAs. Three countries, Indonesia, Australia and New Zealand, occupied almost half (47 %) of the RBA, and 11 countries had more than 30 % of their Exclusive Economic Zones in the RBA. Opportunities exist to expand and merge existing MPA, increase levels of protection, and having MPA in areas of disputed or shared governance, including 5 % of RBA being in the study area’s High Seas. Consideration of the geographically uneven distribution of biodiversity is thus necessary in achieving the 30 % by 2030 target. Systematic conservation planning, as shown here, can lead to at least twice as much biodiversity being protected per area. That at least half of the West Pacific Ocean in MPA may be necessary to protect all marine biodiversity, indicates how critical it is to use resources outside MPA in an ecologically sustainable way.

Consistent Symbiodiniaceae community assemblage in a mesophotic-specialist coral along the Saudi Arabian Red Sea

IntroductionThe Red Sea is a narrow rift basin characterized by latitudinal environmental gradients which shape the diversity and distribution of reef-dwelling organisms. Studies on Symbiodiniaceae associated with select hard coral taxa present species- specific assemblages and concordant variation patterns from the North to southeast Red Sea coast at depths shallower than 30 m. At mesophotic depths, however, algal diversity studies are rare. Here, we characterize for the first-time host-associated algal communities of a mesophotic specialist coral species, Leptoseris cf. striatus, along the Saudi Arabian Red Sea coast.MethodsWe sampled 56 coral colonies spanning the eastern Red Sea coastline from the Northern Red Sea to the Farasan Banks in the South, and across two sampling periods, Fall 2020 and Spring 2022. We used Next Generation Sequencing of the ITS2 marker region in conjunction with SymPortal to denote algal assemblages.Results and discussionOur results show a relatively stable coral species-specific interaction with algae from the genus Cladocopium along the examined latitudinal gradient, with the appearance, in a smaller proportion, of presumed thermally tolerant algal taxa in the genera Symbiodinium and Durusdinium during the warmer season (Fall 2020). Contrary to shallow water corals, our results do not show a change in Symbiodiniaceae community composition from North to South in this mesophotic specialist species. However, our study highlights for the first time that symbiont communities are subject to change over time at mesophotic depth, which could represent an important phenomenon to address in future studies.

Evaluation of the ecological status of shallow-water coral reefs in China using a novel method and identification of environmental factors for coral decline

Coral reefs worldwide have faced extensive damage due to natural catastrophes and anthropogenic disturbances.The decline can cause their widespread collapse and an inability to recover from natural disturbances, highlighting the urgent need for their protection. This study conducted an extensive ecological condition assessment of seven coral reef regions in China's offshore. Our findings revealed the presence of 204 species of scleractinian corals belonging to 16 families. Massive corals were the predominant reef-building corals in all regions. The degradation of coral reef ecosystems was apparent in the present compared to historical reef conditions. The ecosystem suffered varying degrees of damage in surveyed regions according to a novel assessment approach, impling more effective measures should be taken to mitigate the local pressures. Our research establishes a baseline for understanding the status of coral reefs that can be used in future and provides a crucial foundation to designate protective zones for their conservation.

Meta-analysis reveals weak associations between reef fishes and corals.

Habitat associations underpin species ecologies in high-diversity systems. Within tropical, shallow water coral reefs, the relationship between fishes and corals is arguably the most iconic and highly scrutinized. A strong relationship between fishes and reef-building hard corals is often assumed, a belief supported by studies that document the decline of reef fishes following coral loss. However, the extent of this relationship is often unclear, as evidenced by conflicting reports. Here we assess the strength of this ecological association by relying on literature that has surveyed both fishes and corals synchronously. We quantitatively synthesize 723 bivariate correlation coefficients (from 66 papers), published over 38 years, that relate fish metrics (abundance, biomass and species richness) with the percentage of hard coral cover. Remarkably, despite extensive variation, the pattern of association on a global scale reveals a predominantly positive, albeit weak (|r| < 0.4), correlation. Even for commonly hypothesized drivers of fish-coral associations, fish family and trophic group, associations were consistently weak. These findings question our assumptions regarding the strength and ubiquity of fish-coral associations, and caution against assuming a direct and omnipresent relationship between these two iconic animal groups.

Calcification and trophic responses of mesophotic reefs to carbonate chemistry variability

Mesophotic coral ecosystems (MCEs) are extensions of adjacent shallow water coral reefs. Accessibility to these ecosystems is challenging due to their depth limits (~ 30 – 150 m) and as a result, scientific knowledge of these reef systems is limited. It has been posited that the depth limits of MCEs diminish anthropogenic effects experienced by shallow reef systems. A lack of empirical measurements to date has made this hypothesis impossible to determine for mesophotic reef metabolism. The alkalinity anomaly technique was utilized to determine rates of net ecosystem calcification (NEC) and net ecosystem production (NEP) from 30, 40 and 60 m mesophotic reefs during a 15-month period. Seawater chemistry was determined to be chemically conducive for calcification (average aragonite saturation Ωaragonite of 3.58, average calcite saturation Ωcalcite of 5.44) with estimates of NEC indicating these reef systems were net accretive and within global average values for shallow coral reefs (&amp;lt; 30 m). The strongest periods of calcification occurred in late summer and were coupled with strong autotrophic signals. These episodes were followed by suppressed calcification and autotrophy and in the case of the 60 m reefs, a switch to heterotrophy. Whilst there was variability between the three reefs depths, the overall status of the mesophotic system was net autotrophic. This determination was the opposite of trophic status estimates previously described for adjacent shallow reefs. Whilst there were periods of net dissolution, the mesophotic reef system was net accretive (i.e., gross calcification &amp;gt; gross CaCO3 dissolution). The measured inorganic carbon chemistry and estimates of NEC and NEP represent the first such biogeochemical measurements for MCEs. The values established by this study demonstrate just how close these understudied ecosystems are in terms of the known boundary thresholds for low saturation state reefs. Making predictions on how these ecosystems will respond to future climatic conditions, will require greater sampling effort over long times scales to decouple the environmental controls exerted on such ecosystems.

Advancing sun glint correction in high-resolution marine UAV RGB imagery for coral reef monitoring

Sun glint presents a significant challenge in marine ecological remote sensing by obscuring valuable features of benthic communities, thus hindering accurate monitoring of these communities. More specifically, sun glint leads to inaccurate coral reef identification when it comes to utilize the high-resolution marine Unmanned Aerial Vehicle (UAV) imagery. Despite the availability of many physical models that address this problem using ocean remote sensing satellite images, there is still a lack of effective sun glint correction solutions for high-resolution RGB imagery obtained by consumer-grade UAVs in marine ecological monitoring, particularly at the centimeter level. In this study, an innovative sun glint correction pipeline combining a Foreground Attention-based Semantic Segmentation Network (FANet) with optical flow-based pixel propagation has been proposed, aiming to achieve accurate sun glint detection and restoration of real texture of coral reefs. To further understand the inner mode of sun glint segmentation FANet model, we conduct explainable analysis to ensure that it learns the informative sun glint features and makes reliable decisions. According to the comprehensive experimental evaluation using three datasets, our FANet model exhibits accurate and effective sun glint detection, achieving an IoU range of 70.86%–83.96%. Moreover, the sun-glint free images processed by our sun glint correction method have been employed for large-scale image stitching and shallow-water coral reef habitat semantic mapping. The results demonstrate that our sun glint correction approach successfully restores the texture of coral reefs and prepares a reliable foundation for subsequent downstream applications. We believe that our method as an open-source sun glint correction solution in high-resolution marine UAV RGB images is able to enhance the accuracy and efficiency of various marine ecological remote sensing tasks at a low-cost. The relevant code can be found in https://github.com/jyqinnn/Sun-glint-correction.

Incorporating drone photography to investigate microhabitat use of territorial algal farmers in shallow water coral reef

Incorporating drone photography to investigate microhabitat use of territorial algal farmers in shallow water coral reef

Marine heatwaves in the Great Barrier Reef and Coral Sea: their mechanisms and impacts on shallow and mesophotic coral ecosystems

The Great Barrier Reef (GBR) World Heritage Area and adjacent Coral Sea Marine Park are under serious threat from global climate change. This study used Daily Optimally Interpolated Sea Surface Temperature (DOISST) data to identify major marine heatwaves (MHWs) that have occurred in this region over the last three decades (1992–2022). We then used Himawari-8 (H-8) SST data to map significant MHW events that occurred between 2015 and 2022. We investigated the mechanisms underlying the MHWs, assessed thier impact on shallow and mesophotic coral reef ecosystems and identified potential coral refugia. MHWs in this region have increased in frequency, intensity and spatial extent. El Niño, especially when it is in phase with positive Indian Ocean Dipole, was the key remote driver leading to intense MHWs. However, the more recent strong MHWs (e.g., 2017 and 2022) occurred in the abscence of these climatic events, signifying the impacts of long-term climate change and local drivers. We also found that reduced wind speed and shoaling mixed layer depth, often together with reduced cloudiness, were the main local drivers pre-conditioning these MHWs. Anomalous air-sea heat flux into the ocean, mainly controlled by shortwave solar radiation (cloudiness) and latent heat flux (wind), was the most constant contributor to the 2015–16 and 2019–20 MHW events. However, local oceanographic dynamics, especially horizontal advection and turbulent mixing, played important roles in MHW heat budgets. This study confirmed that shallow-water coral bleaching severity was positively related to the cumulative MHW intensity in the 2015–16 and 2019–20 MHW events. We identified shallow reefs along the path of the North Queensland Current as potential coral refugia from bleaching because of the cooler waters upwelled from the ocean current. We also found that, except during weather events such as tropical cyclones, mesophotic reefs in the Coral Sea Marine Park may be less susceptible to severe bleaching as the MHWs were more confined within the shallow mixed layer.

Morphological and genetic mechanisms underlying the plasticity of the coral Porites astreoides across depths in Bermuda

The widespread decline of shallow-water coral reefs has fueled interest in assessing whether mesophotic reefs can act as refugia replenishing deteriorated shallower reefs through larval exchange. Here we explore the morphological and molecular basis facilitating survival of planulae and adults of the coral Porites astreoides (Lamarck, 1816; Hexacorallia: Poritidae) along the vertical depth gradient in Bermuda. We found differences in micro-skeletal features such as bigger calyxes and coarser surface of the skeletal spines in shallow corals. Yet, tomographic reconstructions reveal an analogous mineral distribution between shallow and mesophotic adults, pointing to similar skeleton growth dynamics. Our study reveals patterns of host genetic connectivity and minimal symbiont depth-zonation across a broader depth range than previously known for this species in Bermuda. Transcriptional variations across life stages showed different regulation of metabolism and stress response functions, unraveling molecular responses to environmental conditions at different depths. Overall, these findings increase our understanding of coral acclimatory capability across broad vertical gradients, ultimately allowing better evaluation of the refugia potential of mesophotic reefs.

Characterization of macroalgal-associated microbial communities from shallow to mesophotic depths at Manawai, Papahānaumokuākea Marine National Monument, Hawai'i.

The Papahānaumokuākea Marine National Monument, Hawai'i, is one of the most isolated and protected archipelagos in the world, making it a natural laboratory to examine macroalgal-microbial diversity because of limited direct anthropogenic impacts. We collected the most abundant macroalgae from nine sites ranging from shallow subtidal (1.5 m) to mesophotic (75 m) depths around Manawai (Pearl and Hermes Atoll). We characterized the macroalgal bacterial communities via high-throughput amplicon sequencing and compared the influence of host phylum, species, site, and depth on these relationships at a single atoll. Ochrophyta species had the lowest bacterial diversity compared to Chlorophyta and Rhodophyta. Site and/or depth may influence the microbial community structure associated with Microdictyon setchellianum, indicating a possible disconnect of these microbial communities among habitats. Chondria tumulosa, a cryptogenic species with invasive traits, differed in associated microbiota compared to the native Laurencia galtsoffii, an alga from the same family collected at the same site and depth. While there was overlap of bacterial communities across sites for some algal species, the majority had minimal macroalgal-microbial community connectivity across Manawai. This mesophotic system, therefore, did not appear to be refugia for shallow water coral reefs at microscopic scales. Additional studies are required to identify other significant influences on microbial community variation.

Reef structure of the Florida Reef Tract for the period 2005–2020

Shallow-water coral reefs of the Florida Reef Tract compose the third largest reef in the world, but during the last several decades, scleractinian (stony) corals have suffered unprecedented declines from global and local stressors. A program to evaluate the effects of high-temperature bleaching events was initiated by The Nature Conservancy’s Florida Reef Resilience Program in 2005 and surveys have been completed across at least some portion of the entire region every year since. The program adopted a demographic (colony-based) assessment approach, which records colony species, size (height and maximum diameter), and estimated partial mortality (percent barren skeleton). Because reef structure is critical to ecosystem functioning and services, data from 2005 to 2020 were analyzed to describe the abundance, size, and morphological complexity of stony coral colonies forming the biogenic reef. Colony height, footprint, surface area, and volume summed for 6016 transects were used to describe reef structure and averages were used to characterize the components that contributed to the structure. Nearly 150,000 colonies representing 49 species were reported during this period and results demonstrated both spatial and temporal changes for the region and for geographic subregions. Some subregions showed increasing colony density, especially for three small, hemispheric species, and declining average colony size.

Genomic survey sequencing and complete mitochondrial genome of the elkhorn coral crab Domecia acanthophora (Desbonne in Desbonne &amp; Schramm, 1867) (Decapoda: Brachyura: Domeciidae)

Abstract The elkhorn coral crab Domecia acanthophora inhabits shallow-water coral reefs in the Western Atlantic. The species has a wide distribution and, although primarily associated with endangered Acropora corals, has been recorded from a myriad of hosts. Here we conducted the first genomic survey and complete mitochondrial assemblage and characterisation of any species of Domeciidae, as well as the first species within Trapezioidea. The estimated size of the nuclear genome ranged from 0.64 Gbp to 1.76 Gbp, revealing a small genome. Repetitive elements of the genome were estimated here at 66.4% and 74%, respectively, with the majority of the repetitive elements consisting of LINE, LTR, and satellite DNA. The assembled A-T rich mitochondrial genome consisted of 15,568 bp in length, with 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes and two ribosomal RNA (rRNA) genes. A 619 bp long non-coding region was identified as the supposed D-loop/control region, containing eight microsatellites. The 22 tRNA genes, ranging from 65 to 71 bp in length, displayed a typical “cloverleaf” secondary structure, with the exception of tRNA-Ser1 which lacked part of the DHU arm and tRNA-Asp displayed a deletion of the TΨC loop but not the arm. Two transposition events of two tRNA genes were also found when comparing the gene order of D. acanthophora to that of the brachyuran basic gene order, which had not been reported before. Despite belonging to a widely distributed, well-known superfamily of coral-associated crabs, the Trapezioidea, very little was known about this species from a genetics perspective, which is remedied here by providing a new genomic resource for D. acanthophora.

The use of three-dimensional uCT imaging technique in the description of a new species ofStenopusLatreille, 1819 (Decapoda: Stenopodidea: Stenopodidae), with a revised key to the species ofStenopus

AbstractMembers of the shrimp genus StenopusLatreille, 1819 generally inhabit shallow-water coral reefs. Individuals are colorful, with many of them highly sought in the aquarium trade. A recent biodiversity cruise to the Saya de Malha Banks in the western Indian Ocean collected a new species of Stenopus from rather deep waters, at 192–216 m depth. This species is unusual in having a long rostrum overreaching the scaphocerite and a red and white color pattern, unique for Stenopus. A badly damaged specimen from French Polynesia likely belongs to the new species. The characteristics of the new species are illustrated by X-ray microcomputed tomography images (uCT imaging), line drawings, and color photographs. A key is also provided for the 12 known species of Stenopus.