Coral Reef Species Research Articles

Dongsha Atoll is an important stepping-stone that promotes regional genetic connectivity in the South China Sea.

BackgroundUnderstanding region-wide patterns of larval connectivity and gene flow is crucial for managing and conserving marine biodiversity. Dongsha Atoll National Park (DANP), located in the northern South China Sea (SCS), was established in 2007 to study and conserve this diverse and remote coral atoll. However, the role of Dongsha Atoll in connectivity throughout the SCS is seldom studied. In this study, we aim to evaluate the role of DANP in conserving regional marine biodiversity.MethodsIn total, 206 samples across nine marine species were collected and sequenced from Dongsha Atoll, and these data were combined with available sequence data from each of these nine species archived in the Genomic Observatories Metadatabase (GEOME). Together, these data provide the most extensive population genetic analysis of a single marine protected area. We evaluate metapopulation structure for each species by using a coalescent sampler, selecting among panmixia, stepping-stone, and island models of connectivity in a likelihood-based framework. We then completed a heuristic graph theoretical analysis based on maximum dispersal distance to get a sense of Dongsha’s centrality within the SCS.ResultsOur dataset yielded 111 unique haplotypes across all taxa at DANP, 58% of which were not sampled elsewhere. Analysis of metapopulation structure showed that five out of nine species have strong regional connectivity across the SCS such that their gene pools are effectively panmictic (mean pelagic larval duration (PLD) = 78 days, sd = 60 days); while four species have stepping-stone metapopulation structure, indicating that larvae are exchanged primarily between nearby populations (mean PLD = 37 days, sd = 15 days). For all but one species, Dongsha was ranked within the top 15 out of 115 large reefs in the South China Sea for betweenness centrality. Thus, for most species, Dongsha Atoll provides an essential link for maintaining stepping-stone gene flow across the SCS.ConclusionsThis multispecies study provides the most comprehensive examination of the role of Dongsha Atoll in marine connectivity in the South China Sea to date. Combining new and existing population genetic data for nine coral reef species in the region with a graph theoretical analysis, this study provides evidence that Dongsha Atoll is an important hub for sustaining connectivity for the majority of coral-reef species in the region.

Climate change impacts on the ecological dynamics of two coral reef species, the humphead wrasse (Cheilinus undulatus) and crown-of-thorns starfish (Ancanthaster planci)

This study investigates the hypothesis that climate change influences the distribution of the corallivore crown-of-thorns starfish Ancanthaster planci L. and one of its predators, the endangered humphead wrasse Cheilinus undulatus (Rüpell 1835). The aim is to provide a robust global distribution estimation examining the potential habitat gaps and overlays between the two species considering the predator-prey interaction. A single-parameter perturbation design with the species distribution model MaxEnt was applied to select the best performing model run for analysing the global and local trends in Indonesia based upon projected climate change under the IPCC RCP6.0 emission scenario. The paper represents the first global modelling study about the future distributions for both species by 2050. The simulations showed a slight decline of potential suitability for A. planci but gains for C. undulatus with a poleward shift for both. C. undulatus thrives under higher temperatures, whereas A. planci seems to be sensitive to increasing temperature in Indonesia. However, whilst future climate change is expected to benefit C. undulatus, the species remain highly vulnerable to (often illegal) fishing pressures and appropriate monitoring and management measures remain a priority to ensure their conservation in the long term.

Development of spectral library for coral reef benthic compositions in Gulf of Mannar

Knowledge on in situ spectral characteristics of individual end-members are essential as they provide much needed base for analysing the data obtained through remote sensing systems. This study intends to develop a comprehensive spectral library for different coral reef species and its associated benthic compositions present in Gulf of Mannar, India. In this regard, a field programme was designed to acquire different radiometric quantities that belong to different coral reef benthic compositions. Radiometric quantities for each end-member is recorded based on two different conditions (i) in situ and (ii) exposed. These two modes of measurements helped in understanding the confounding effect of water column in spectral characteristics of coral reef environments. Once the radiometric quantities were acquired from field, further steps such as deriving reflectance parameters, removal of non-illuminated wavebands, smoothing of signatures, checking for consistency, and compilation of spectral signatures to formulate a spectral library were performed. Further, compilation of spectral signatures to develop a comprehensive spectral library was carried out using spectral library building module of ENVI-5.1.

Quantifying the diet diversity of herbivorous coral reef fishes using systematic review and DNA metabarcoding

AbstractHerbivorous reef fishes are an important component of coral reef ecosystems and a focal point in reef management. Herbivore diets have been examined using a myriad of methods, making it difficult to compare between analyses and to examine consistency or variability in diet across large spatial scales or heterogeneous environments. Here, we present a method to quantify and validate the diet diversity of these important coral reef species. We compile a database of information on Pacific herbivorous reef fishes through a systematic review of published diet data, and for those studies in which appropriate information is reported, we calculate a single Simpson's Diversity Index value to represent the diet diversity of each. We then validate this approach by examining the diet diversity of five species using DNA metabarcoding to sequence the algae present in their stomach contents. The two approaches provided comparable estimates of diet diversity, and we find evidence for considerable diet variability both within functional groups and between closely related species. Although there is a wide range of diet specialization within each functional and taxonomic group, parrotfishes and detritivorous surgeonfishes appear to have more limited diets than other nominal herbivorous fishes in our survey. This may make them more vulnerable to habitat degradation, which is important considering that both groups face considerable fishing pressure in Hawaiʻi and elsewhere in the Pacific. Finally, we demonstrate how this approach to quantifying diet can be incorporated into trait matrices that offer valuable insight into the dissimilarity between species, regardless of their taxonomic and functional classification. This analysis offers a simplified quantitative index of diet diversity that can contribute to better management of herbivores and increased understanding of their functional effects on changing, degraded reefs.

Novel species interactions and environmental conditions reduce foraging competency at the temperate range edge of a range-extending coral reef fish

Poleward range extensions of coral reef species can reshuffle temperate communities by generating competitive interactions that did not exist previously. However, novel environmental conditions and locally adapted native temperate species may slow tropical invasions by reducing the ability of invaders to access local resources (e.g. food and shelter). We test this hypothesis on wild marine fish in a climate warming hotspot using a field experiment encompassing artificial prey release. We evaluated seven behaviours associated with foraging and aggressive interactions in a common range-extending coral reef fish (Abudefduf vaigiensis) and a co-shoaling temperate fish (Microcanthus strigatus) along a latitudinal temperature gradient (730 km) in SE Australia. We found that the coral reef fish had reduced foraging performance (i.e. slower prey perception, slower prey inspection, decreased prey intake, increased distance to prey) in their novel temperate range than in their subtropical range. Furthermore, higher abundance of temperate fishes was associated with increased retreat behaviour by coral reef fish (i.e. withdrawal from foraging on released prey), independent of latitude. Where their ranges overlapped, temperate fish showed higher foraging and aggression than coral reef fish. Our findings suggest that lower foraging performance of tropical fish at their leading range edge is driven by the combined effect of environmental factors (e.g. lower seawater temperature and/or unfamiliarity with novel conditions in their extended temperate ranges) and biological factors (e.g. increased abundance and larger body sizes of local temperate fishes). Whilst a future increase in ocean warming is expected to alleviate current foraging limitations in coral reef fishes at leading range edges, under current warming native temperate fishes at their trailing edges appear able to slow the range extension of coral reef fishes into temperate ecosystems by limiting their access to resources.

In vitro Symbiosis of Reef-Building Coral Cells With Photosynthetic Dinoflagellates

Coral reefs are the biodiversity hot spots of the oceans, but they have suffered from increasing environmental stresses caused principally by anthropogenic global warming. The keystone species of coral reefs are scleractinian corals, which maintain obligatory symbiotic relationships with photosynthetic dinoflagellates. Understanding cellular and molecular mechanisms of symbiosis is therefore essential for future preservation of coral reefs. To date, however, almost no in vitro experimental systems have been devised to illuminate such mechanisms. To this end, our previous study established stable in vitro cell culture lines, including IVB5, originating from planula larvae of the scleractinian coral, Acropora tenuis. Here, we show that soon after mixture with the dinoflagellate, Breviolum minutum, flattened amorphous coral cells with endodermal properties exhibited elevated locomotor activity using filopodia and lamellipodia and interacted with dinoflagellates. Several minutes thereafter, coral cells began to incorporate B. minutum, and in vitro symbiosis appeared to have been accomplished within 30 min. Nearly a half of the coral cells had incorporated algal cells within 24 h in a reproducible manner. Coral cells that harbored algal cells gradually became round and less mobile, and the algal cells sometimes settled in vacuole-like structures in coral cell cytoplasm. This symbiosis state was maintained for at least a month. The IVB5 line of A. tenuis therefore provides an experimental system to explore cellular and molecular mechanisms involved in coral-dinoflagellate symbiosis at the single-cell level, results of which may be useful for future preservation of coral reefs.

Distinct Phenotypes Associated with Mangrove and Lagoon Habitats in Two Widespread Caribbean Corals, Porites astreoides and Porites divaricata

AbstractAs coral reefs experience dramatic declines in coral cover throughout the tropics, there is an urgent need to understand the role that non-reef habitats, such as mangroves, play in the ecological niche of corals. Mangrove habitats present a challenge to reef-dwelling corals because they can differ dramatically from adjacent reef habitats with respect to key environmental parameters, such as light. Because variation in light within reef habitats is known to drive intraspecific differences in coral phenotype, we hypothesized that coral species that can exploit both reef and mangrove habitats will exhibit predictable differences in phenotypes between habitats. To investigate how intraspecific variation, driven by either local adaptation or phenotypic plasticity, might enable particular coral species to exploit these two qualitatively different habitat types, we compared the phenotypes of two widespread Caribbean corals, Porites divaricata and Porites astreoides, in mangrove versus lagoon habitats on Turneffe Atoll, Belize. We document significant differences in colony size, color, structural complexity, and corallite morphology between habitats. In every instance, the phenotypic differences between mangrove prop root and lagoon corals exhibited consistent trends in both P. divaricata and P. astreoides. We believe this study is the first to document intraspecific phenotypic diversity in corals occupying mangrove prop root versus lagoonal patch reef habitats. A difference in the capacity to adopt an alternative phenotype that is well suited to the mangrove habitat may explain why some reef coral species can exploit mangroves, while others cannot.

Morphological traits of reef corals predict extinction risk but not conservation status

AbstractAimThe current assessment of extinction risk in reef corals by the International Union for Conservation of Nature (IUCN) has been criticized, because coral life‐history traits associated with resilience are not reflected in the conservation status. We aimed to carry out a quantitative assessment of the link between reef coral traits and species extinction risk informed by extinctions of reef corals observed in the fossil record.LocationGlobal.Time periodPlio‐Pleistocene and present day.Major taxa studiedScleractinian reef corals.MethodsWe used morphological traits, phylogenetic information and evidence of extinction during the Plio‐Pleistocene to predict the extinction risk of contemporary reef corals. Our model was trained using 138 Caribbean fossil coral species and an automatic machine learning algorithm. We then used this model to predict the extinction risk of 674 modern coral species.ResultsModel validation confirmed 77% accuracy in predicting extinction risk of fossil corals. Extinction risk predicted by our model showed a near‐random (57%) match with the IUCN conservation status. Our model also suggested that corals in the Least Concern or Near Threatened categories might be at higher risk of extinction than currently believed.Main conclusionsMorphological traits of fossil corals linked to their extinction risk in the Plio‐Pleistocene Caribbean Sea are known to reflect the vulnerability of extant corals. However, the results from our fossil‐calibrated model do not match the IUCN assessment of reef corals, with increased overall extinction risk. This does not necessarily indicate near‐future extinction risk, because fossil extinctions are spread over thousands of years. However, we show the applicability of using fossil data to inform the extinction risk of modern corals and recommend that future assessments of extinction risk of reef corals should consider incorporating the relationship between morphological traits and resilience, calibrated by fossil data, to maximize the utility of the extinction risk assessment.

The Microbiome of the Reef Macroalga Sargassum ilicifolium in Singapore

The large canopy-forming macroalga, Sargassum ilicifolium, provides shelter and food for numerous coral reef species, but it can also be detrimental at high abundances where it outcompetes other benthic organisms for light and space. Here, we investigate the microbial communities associated with S. ilicifolium in Singapore, where it is an abundant and important member of coral reef communities. We collected eight complete S. ilicifolium thalli from eight island locations along an approximate 14 km east-to-west transect. Each thallus was dissected into three separate parts: holdfast, vesicles, and leaves. We then characterized the bacterial communities associated with each part via polymerase chain reaction (PCR) amplification of the 16S rRNA gene V4 region. We then inferred predicted metagenome functions using METAGENassist. Despite the comparatively short distances between sample sites, we show significant differences in microbial community composition, with communities further differentiated by part sampled. Holdfast, vesicles and leaves all harbor distinct microbial communities. Functional predictions reveal some separation between holdfast and leaf communities, with higher representation of sulphur cycling taxa in the holdfast and higher representation of nitrogen cycling taxa in the leaves. This study provides valuable baseline data that can be used to monitor microbial change, and helps lay the foundation upon which we can begin to understand the complexities of reef-associated microbial communities and the roles they play in the functioning and diversity of marine ecosystems.

Physiological Responses of Coral Reef Species to Emerging Threats of Anthropogenic Climate Change

Anthropogenic climate change is a threat to countless species and ecosystems around the world, including the coral reefs. Coral Reefs provide habitat to hundreds of thousands of species and play a big role in maintaining biological diversity. Unfortunately, around 50-70% of all coral reefs are under direct threat from human activities such as deforestation and overfishing. Major threats to the survival of coral reefs include increasing sea surface temperatures and ocean acidification, as they lead to bleaching and reduction in coral calcification. Due to the rapidly changing climate, conservation efforts should be aimed at protecting species that can tolerate a wide range of temperatures and buffer pH changes. This paper discusses recent research on tolerance and persistence of various species that make up the coral reefs and how this information can be integrated into current conservation practices to better protect the coral reefs.

Gill morphology and formulae of crayfishes (Decapoda: Astacidea: Parastacidae) from New Guinea and New Zealand and a comparison with other selected species of crayfishes

AbstractThe Infraorder Astacidea comprises four superfamilies of decapod crustaceans: the freshwater Astacoidea and Parastacoidea and the marine Enoplometopoidea and Nephropoidea. The gill morphology of four species of crayfishes belonging to Astacoidea and Parastacoidea, two coral reef species of Enoplometopoidea, and 2 deep-water species of Nephropoidea are described and illustrated for comparisons and to determine characters characteristic to members of the family Parastacidae (Parastacoidea) from New Guinea. Morphology of the arthrobranchs and pleurobranchs were similar among all species, having a single stem with filament, but podobranchs of the parastacoideans differed from those of Astacoidea, being corrugated and tubular and having filaments. The astacoidean P. virginalis had a plate-like lamella with filament. The two nephropoid and two enoplometopoid species were similar to each other; their podobranch had a flat blade-like lamella without a filament and a shaft with a filament. The gill formulae of the New Guinea species of Cherax were the same as those of the Australian congeners, but the formula of the New Zealand Paranephrops planifronsWhite, 1842 was the same as those of the South American parastacids.

Seasonal dynamics of fatty acid biomarkers in the soft coral Sinularia flexibilis, a common species of Indo-Pacific coral reefs

Year-round fluctuation in environmental conditions have a considerable influence on the level of biomarkers, that are usually applied for monitoring marine invertebrates. To date, no data on annual cycles of fatty acid (FA) biomarkers in tropical soft corals are available. The FA composition of the alcyonarian Sinularia flexibilis containing symbiotic microalgae was studied during a year. Two major FAs, 20:4n-6 and 16:0, determined the level of polyunsaturated and saturated FAs (PUFAs and SFAs). The insignificant variations in PUFA content indicated a relatively stable level of phospholipids that formed the structural base of coral cell biomembranes. No clear relationship between the PUFA markers of photosynthetic symbionts and the solar radiation was found. The three-fold increase in the SFA level in the summer correlated with the water temperature and indicated a rise in the level of neutral lipids that made up the energy reserve of corals. The seasonal changes in FA biosynthesis, membrane fluidity, and coral nutrition are discussed.

Targeted predator defenses of sponges shape community organization and tropical marine ecosystem function

AbstractDefenses that target particular consumers often influence community organization, ecosystem function, and diversity maintenance. In coral reef, mangrove, and seagrass ecosystems, sponges affect substratum stability, water clarity, diversity of associated species, and survival of habitat‐providing organisms, key roles not duplicated by other organisms. Whether and how predators control sponges are much disputed. Substantial ecosystem consequences of losing or gaining sponges motivated definitive experiments on how predators control sponge distribution and abundance. Caribbean sponges of 94 species representing 13 taxonomic orders and three linked habitats (coral reefs, mangroves, and seagrass meadows) were exposed to seven predator species representing different habitats and degrees of spongivory in 4,493 in situ trials. The resulting data force reassessment of popular interpretations of several patterns and processes. Contrary to extract pellet assays that declare most sponges deterrent, 78% of these 94 species were eaten by at least one predator. But “palatability” is consumer dependent: a sponge species eaten by one predator can be rejected by other predators, and predator species differed in what sponges they ate in 55.4% (214/392) of pairwise comparisons between predators. Because spongivore species are usually restricted to particular habitats, they impose abrupt boundaries on sponges’ habitat distributions, reflecting inverse relationships between accessibility and palatability to each predator. Thus a seagrass‐dwelling starfish eats only 9% of seagrass sponge species, but 70% of coral reef species, and 78% of mangrove species. Reef‐dwelling angelfishes completely consume only 13% of reef species, but 29% of seagrass species, and 63% of mangrove species. Defenses that target specific predators reveal that spongivore influence on community organization cannot be inferred from extract pellet/omnivore assays that assume defenses target all predators equally. In fact, pellet data wrongly predicted actual consumption of living sponges of that pellet's species in 43% of field experiments with spongivores. In contrast with herbivore–plant interactions, opportunistic spongivory is at least as important as routine spongivory for community organization and ecosystem function. Potential for loss of key functional roles of sponges, if opportunistic predators gain access to sponge species that lack defenses against them, must inform conservation plans for coral reef, mangrove, and seagrass ecosystems.

涠洲岛造礁石珊瑚群落变化特征及其环境影响因子

以涠洲岛造礁石珊瑚群落为研究对象，分析其群落物种组成、多样性、Raunkiaer频度和种间Spearman轶相关，探讨群落组成与水环境因子的相关性，并结合近10年来涠洲岛造礁石珊瑚变化情况，找出涠洲岛造礁石珊瑚群落的主导影响因素。结果表明：（1）近10年来涠洲岛造礁石珊瑚覆盖率显著降低，珊瑚形态组成趋于块状化，尽管珊瑚群落多样性较高，但群落分布较松散，群落结构较不稳定，部分优势种种间竞争较激烈。（2）悬浮物含量是影响石珊瑚群落最显著的环境因子。石珊瑚优势种群在不同水深中分布差异显著，泥沙覆盖率、营养盐对不同石珊瑚种群影响差异较大，大型海藻覆盖率在局部区域对优势珊瑚形成较强的竞争关系。（3）营养盐和泥沙沉积物的增加与涠洲岛近海养殖业及生活排污、海岸工程及海岸侵蚀密切相关。;For the Weizhou Island, which is geographically independent, the human-induced influence is more significant to the rapid degradation of its coral reef ecosystems. the identification of dominant influencing factors on different temporal scales remains a challenge for the local aquatic environment. It is, therefore, essential to explore the ecological status of the coral reefs and the potential threats in Weizhou Island. The primary aim of this study is to explore the dominant influencing factors for the degradation of the scleractinian coral community in Weizhou Island within the 10 years of 2009-2019. To this end, the species composition, diversity, Raunkiaer frequency and Spearman correlation of the community were analyzed. The correlations between the community composition and environmental variations of water were further discussed. The identification of the dominant factors was performed through analyzing the ecological changes of scleractinian coral community in Weizhou Island over 10 years. Results demonstrated that, the coverage of scleractinian coral in the study area significantly decreased, with the changes of the coral reef in morphology, e.g., block. It was noted that, the diversity of the scleractinian coral community was relatively high, but scarred distribution in space of the coral community was observed. Furthermore, the ecological structure was unstable due to the intense competition among some dominant species. It was believed that the high loads of suspended sediments were the most important factor to affect the ecological characteristics of the scleractiniane coral community in Weizhou Island. The spatial distribution of the dominant species was highly related to the water depths, whilst the sediment coverages and nutrient sources significantly affected the diversity of coral populations. Further, relatively strong competition between local large algae and the dominant species of coral reefs was observed. We also observed that the environmental factors, nutrients and sediments, were closely correlated with the aquaculture, human sewage, coastal engineering, coastal erosion, etc.

Genome survey sequencing of the Caribbean spiny lobster Panulirus argus: Genome size, nuclear rRNA operon, repetitive elements, and microsatellite discovery.

Background Panulirus argus is an ecologically relevant species in shallow water hard-bottom environments and coral reefs and target of the most lucrative fishery in the greater Caribbean region.MethodsThis study reports, for the first time, the genome size and nuclear repetitive elements, including the 45S ribosomal DNA operon, 5S unit, and microsatellites, of P. argus.ResultsUsing a k-mer approach, the average haploid genome size estimated for P. argus was 2.17 Gbp. Repetitive elements comprised 69.02% of the nuclear genome. In turn, 30.98% of the genome represented low- or single-copy sequences. A considerable proportion of repetitive sequences could not be assigned to known repeat element families. Taking into account only annotated repetitive elements, the most frequent belonged to Class I-LINE which were noticeably more abundant than Class I-LTR-Ty- 3/Gypsy, Class I-LTR-Penelope, and Class I-LTR-Ty-3/Bel-Pao elements. Satellite DNA was also abundant. The ribosomal operon in P. argus comprises, in the following order, a 5′ ETS (length = 707 bp), ssrDNA (1,875 bp), ITS1 (736 bp), 5.8S rDNA (162 bp), ITS2 (1,314 bp), lsrDNA (5,387 bp), and 3′ ETS (287 bp). A total of 1,281 SSRs were identified.

Yes, we can use it: a formal test on the accuracy of low-pass nanopore long-read sequencing for mitophylogenomics and barcoding research using the Caribbean\xa0spiny lobster Panulirus argus

BackgroundWhole mitogenomes or short fragments (i.e., 300–700 bp of the cox1 gene) are the markers of choice for revealing within- and among-species genealogies. Protocols for sequencing and assembling mitogenomes include ‘primer walking’ or ‘long PCR’ followed by Sanger sequencing or Illumina short-read low-coverage whole genome (LC-WGS) sequencing with or without prior enrichment of mitochondrial DNA. The aforementioned strategies assemble complete and accurate mitochondrial genomes but are time consuming and/or expensive. In this study, I first tested whether mitogenomes can be sequenced from long-read nanopore sequencing data exclusively. Second, I explored the accuracy of the long-read assembled genomes by comparing them to a ‘gold’ standard reference mitogenome retrieved from the same individual using Illumina sequencing. Third and lastly, I tested if the long-read assemblies are useful for mitophylogenomics and barcoding research. To accomplish these goals, I used the Caribbean spiny lobster Panulirus argus, an ecologically relevant species in shallow water coral reefs and target of the most lucrative fishery in the greater Caribbean region. ResultsLC-WGS using a MinION ONT device and various de-novo and reference-based assembly pipelines retrieved a complete and highly accurate mitogenome for the Caribbean spiny lobster Panulirus argus. Discordance between each of the long-read assemblies and the reference mitogenome was mostly due to indels at the flanks of homopolymer regions. Although not ‘perfect’, phylogenetic analyses using entire mitogenomes or a fragment of the cox1 gene demonstrated that mitogenomes assembled using long reads reliably identify the sequenced specimen as belonging to P. argus and distinguish it from other related species in the same genus, family, and superorder.ConclusionsThis study serves as a proof-of-concept for the future implementation of in-situ surveillance protocols using the MinION to detect mislabeling in P. argus across its supply chain. Mislabeling detection will improve fishery management in this overexploited lobster. This study will additionally aid in decreasing costs for exploring meta-population connectivity in the Caribbean spiny lobster and will aid with the transfer of genomics technology to low-income countries.

Growth and maturation of three commercially important coral reef species from American Samoa

This study presents age-based life history information on three small-bodied species targeted in the American Samoan fishery: Chlorurus japanensis palecheek parrotfish/fuga-alosama, Lethrinus rubrioperculatus spotcheek emperor/fiola pa`o`omumu, and Naso lituratus orangespine unicornfish/ili`ilia. Age and reproductive information were derived from sagittal otoliths and gonads. Maximum observed ages were 7 years for C. japanensis, 10 years for L. rubrioperculatus, and 25 years for N. lituratus. Due to a limited numbers of immature samples, a proxy for size at 50% maturity (L50) was derived from the relationship between asymptotic fork length (L∞) and L50 based on data published for species from similar geographic regions and respective families. L50 was estimated at 20.9 cm for C. japanensis, 20.4 cm for L. rubrioperculatus, and 17.5 cm for N. lituratus. Derived estimates were within 1 % of the L50 calculated for C. japanensis and N. lituratus from the limited number of immature samples collected in this study, indicating that for regions where sampling ability is limited, derived relationships between L∞ and L50 can be used to calculate an appropriate proxy. Naso lituratus demonstrated a biphasic mortality schedule with a higher than expected total mortality rate in the first 7 years of life. The age-based demographic information presented here can be used for future stock assessments and ecosystem models, which should facilitate improved management.

Modelling the optical properties of coral reefs and its implication for optical remote sensing

Effective monitoring of coral reefs remains a major goal in marine ecology and conservation as these communities representing the most productive ecosystems and hosting approximately one third of all known marine species have been seriously threatened by various anthropogenic activities and climate change events. Space-borne reflectance data are commonly used to monitor coral reefs and improve their management practices, yet an effective use of such data remains a challenge due to a high level of spatial heterogeneity of coral reef communities and surrounding water environments. Thus, it is crucial to understand the optical properties coral reef environments and their influence on the spectral remote sensing reflectance. This study presents an optical model based on field and laboratory data that relates the inherent optical properties (IOPs, such as absorption and backscattering) of the water constituents (phytoplankton, suspended sediments, colored dissolved organic matter, water itself) and coral components (symbiotic + coralline algae) to remote sensing reflectance via the bidirectional quantity (f/Q) of the upwelling light field. The absorption and backscattering coefficients are parameterized as a function of the individual contributions of coral component (symbiotic and coralline algae) and water constituents and the bidirectionality factor f/Q is derived as a function of solar-sensor zenith angles and IOPs. The wider applicability of these parameterizations is tested in diverse water types (with chlorophyll-a concentration 0.07–1239 mg m−3, suspended sediment concentration 0.1–104 g m−3, absorption coefficient of colored dissolved organic matter 0.02 to 8.8 m−1 at 412 nm). Modelled reflectance spectra were compared with in-situ data and Hydrolight radiative transfer simulations. For various coral reef species and water types, the modelled spectral reflectance and associated features across a spectral range of 400–750 nm showed good agreement with measured and simulated data within the error of 17%. The effect of strong attenuation of light by water which potentially affects and alters the spectral shapes and magnitudes of reflectance is further examined and discussed. This work will have significant implications for optical remote sensing of the coral reef ecosystems in diverse oceanic environments.

Habitat mapping using deep neural networks

Habitat mapping is an important and challenging task that helps in monitoring, managing, and preserving ecosystems. It becomes more challenging when marine habitats are mapped, as it is difficult to get quality images in an underwater environment. Moreover, achieving good location accuracy in underwater environments is an additional issue. Sonar imagery has good quality but is hard to be analyzed. Therefore, camera imagery is used for research purposes. Our research targets marine habitats - more specifically, coral reef marine habitats. Recognition of coral reef in underwater images poses a significant difficulty due to the nature of the data. Many species of coral reef have similar characteristics, i.e. higher inter-class similarity and lower intra-class similarity. Spatial borders between coral reef classes are hard to separate, as they tend to appear together in groups. For these reasons, the classification of coral reef species requires aid from marine biologists. This research work presents a technique for accurate coral reef classification using deep convolutional neural networks. The proposed approach has been validated on Moorea Labeled Corals (MLC), an imbalanced dataset, which is a subset of Moorea Coral Reef Long Term Ecological Research (MCR LTER) packaged for computer vision research. A custom valid patch dataset is extracted using the annotation files provided with the dataset. Two image enhancement algorithms and data-driven feature extraction techniques are employed using several pre-trained deep convolutional neural networks as feature extractors. Local-SPP technique is combined with feature extractors and followed by 2-layers multi-layer perceptron (MLP) classifier to achieve high classification rates.

Angels in disguise: sympatric hybridization in the marine angelfishes is widespread and occurs between deeply divergent lineages.

Hybridization events are not uncommon in marine environments where physical barriers are attenuated. Studies of coral reef taxa have suggested that hybridization predominantly occurs between parapatric species distributed along biogeographic suture zones. By contrast, little is known about the extent of sympatric hybridization on coral reefs, despite the large amount of biogeographic overlap shared by many coral reef species. Here, we investigate if the propensity for hybridization along suture zones represents a general phenomenon among coral reef fishes, by focusing on the marine angelfishes (family Pomacanthidae). Although hybridization has been reported for this family, it has not been thoroughly surveyed, with more recent hybridization studies focusing instead on closely related species from a population genetics perspective. We provide a comprehensive survey of hybridization among the Pomacanthidae, characterize the upper limits of genetic divergences between hybridizing species and investigate the occurrence of sympatric hybridization within this group. We report the occurrence of hybridization involving 42 species (48% of the family) from all but one genus of the Pomacanthidae. Our results indicate that the marine angelfishes are among the groups of coral reef fishes with the highest incidences of hybridization, not only between sympatric species, but also between deeply divergent lineages.