ELEVATED RATES OF MORPHOLOGICAL AND FUNCTIONAL DIVERSIFICATION IN REEF‐DWELLING HAEMULID FISHES

The relationship between habitat complexity and species richness is well established but comparatively little is known about the evolution of morphological diversity in complex habitats. Reefs are structurally complex, highly productive shallow‐water marine ecosystems found in tropical (coral reefs) and temperate zones (rocky reefs) that harbor exceptional levels of biodiversity. We investigated whether reef habitats promote the evolution of morphological diversity in the feeding and locomotion systems of grunts (Haemulidae), a group of predominantly nocturnal fishes that live on both temperate and tropical reefs. Using phylogenetic comparative methods and statistical analyses that take into account uncertainty in phylogeny and the evolutionary history of reef living, we demonstrate that rates of morphological evolution are faster in reef‐dwelling haemulids. The magnitude of this effect depends on the type of trait; on average, traits involved in the functional systems for prey capture and processing evolve twice as fast on reefs as locomotor traits. This result, along with the observation that haemulids do not exploit unique feeding niches on reefs, suggests that fine‐scale trophic niche partitioning and character displacement may be driving higher rates of morphological evolution. Whatever the cause, there is growing evidence that reef habitats stimulate morphological and functional diversification in teleost fishes.     

A novel algorithm with differential evolution and coral reef optimization for extreme learning machine training

Extreme learning machine (ELM) is a novel and fast learning method to train single layer feed-forward networks. However due to the demand for larger number of hidden neurons, the prediction speed of ELM is not fast enough. An evolutionary based ELM with differential evolution (DE) has been proposed to reduce the prediction time of original ELM. But it may still get stuck at local optima. In this paper, a novel algorithm hybridizing DE and metaheuristic coral reef optimization (CRO), which is called differential evolution coral reef optimization (DECRO), is proposed to balance the explorative power and exploitive power to reach better performance. The thought and the implement of DECRO algorithm are discussed in this article with detail. DE, CRO and DECRO are applied to ELM training respectively. Experimental results show that DECRO-ELM can reduce the prediction time of original ELM, and obtain better performance for training ELM than both DE and CRO.     

Thermal acclimation in clownfish: An integrated biomarker response and multi-tissue experimental approach

The effects of increased temperature were tested in Amphiprion ocellaris, using a cellular diagnostics approach (in several tissues) combined with an organismal approach (body condition). Clownfish were exposed to a one month experiment following two temperature treatments: control (26 °C) and elevated temperature (30 °C). Fish were sampled at 0, 7, 14, 21 and 28 days for (1) assessment of stress biomarkers (catalase, lipid peroxidation, glutathione-S-transferase, superoxide dismutase, acetylcholinesterase, heat shock protein 70 kDa and ubiquitin – in brain, gills, liver, intestine and muscle), (2) estimation of integrated biomarker response index based on the biomarkers tested and (3) assessment of Fulton’s K index. Results show all biomarkers except acetylcholinesterase responded consistently and significantly to elevated temperature across tissue types suggesting they are suitable indicators of thermal stress in A. ocellaris. Biomarker levels were tissue-specific, and in addition, the most reactive tissues to temperature were muscle, gills and liver which suggest that highly oxygenated tissues seem to be the most responsive under thermal stress. The most responsive sampling times to increased temperature were T7 and T28: thermal stress was observed after 7 days of exposure (biomarker levels increased), then a pattern of decrease in biomarker levels towards the end of the experiment was observed, which may suggest fish were able to acclimate to exposure conditions. This indicates that A. ocellaris probably lives far from its upper thermal limit and is capable of adjusting the protein quality control system and enzymes’ activities to protect cell functions under elevated temperatures. The temperature treatment did not significantly influence body condition of the animals but biomarkers were negatively correlated to wet body weight. This suggests that thermal acclimation incurs at some energetic cost. In conclusion, these results suggest that this coral reef fish species presents a significant acclimation potential under ocean warming scenarios of +4 °C.     

Finding Nemo’s Genes: A chromosome‐scale reference assembly of the genome of the orange clownfish Amphiprion percula

The iconic orange clownfish, Amphiprion percula, is a model organism for studying the ecology and evolution of reef fishes, including patterns of population connectivity, sex change, social organization, habitat selection and adaptation to climate change. Notably, the orange clownfish is the only reef fish for which a complete larval dispersal kernel has been established and was the first fish species for which it was demonstrated that antipredator responses of reef fishes could be impaired by ocean acidification. Despite its importance, molecular resources for this species remain scarce and until now it lacked a reference genome assembly. Here, we present a de novo chromosome‐scale assembly of the genome of the orange clownfish Amphiprion percula. We utilized single‐molecule real‐time sequencing technology from Pacific Biosciences to produce an initial polished assembly comprised of 1,414 contigs, with a contig N50 length of 1.86 Mb. Using Hi‐C‐based chromatin contact maps, 98% of the genome assembly were placed into 24 chromosomes, resulting in a final assembly of 908.8 Mb in length with contig and scaffold N50s of 3.12 and 38.4 Mb, respectively. This makes it one of the most contiguous and complete fish genome assemblies currently available. The genome was annotated with 26,597 protein‐coding genes and contains 96% of the core set of conserved actinopterygian orthologs. The availability of this reference genome assembly as a community resource will further strengthen the role of the orange clownfish as a model species for research on the ecology and evolution of reef fishes.     

Pelagic Subsidies Underpin Fish Productivity on a Degraded Coral Reef

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Optimizing return‐on‐effort for coral nursery and outplanting practices to aid restoration of the Great Barrier Reef

Coral nursery and outplanting practices have grown in popularity worldwide for targeted restoration of degraded “high value” reef sites, and recovery of threatened taxa. Success of these practices is commonly gauged from coral propagule growth and survival, which fundamentally determines the return‐on‐effort (RRE) critical to the cost‐effectiveness and viability of restoration programs. In many cases, RRE has been optimized from past successes and failures, which therefore presents a major challenge for locations such as the Great Barrier Reef (GBR) where no local history of restoration exists to guide best practice. In establishing the first multi‐taxa coral nursery on the GBR (Opal Reef, February 2018), we constructed a novel scoring criterion from concurrent measurements of growth and survivorship to guide our relative RRE, including nursery propagule numbers (stock density). We initially retrieved RRE scores from a database of global restoration efforts to date (n = 246; 52 studies) to evaluate whether and how success commonly varied among coral taxa. We then retrieved RRE scores for Opal Reef using initial growth and survivorship data for six key coral taxa, to demonstrate that RRE scores were high for all taxa predominantly via high survivorship over winter. Repeated RRE scoring in summer is therefore needed to capture the full dynamic range of success where seasonal factors regulating growth versus survivorship differ. We discuss how RRE scoring can be easily adopted across restoration practices globally to standardize and benchmark success, but also as a tool to aid decision‐making in optimizing future propagation (and outplanting) efforts.     

Rapid development of a restored oyster reef facilitates habitat provision for estuarine fauna

Oyster reef restoration has become a principal strategy for ameliorating the loss of natural Crassostrea virginica populations and increasing habitat provision. In 2014, a large‐scale, high‐relief, 23‐ha subtidal C. virginica reef was restored at the historically productive Half Moon Reef in Matagorda Bay, TX, using concrete and limestone substrates. Encrusting and motile fauna were sampled seasonally until 17 months postrestoration at the restored reef and at adjacent unrestored sites. Restored oysters developed rapidly and were most abundant 3 months postrestoration, with subsequent declines possibly due to interacting effects of larval settlement success on new substrate versus post‐settlement mortality due to competitors and predators. Oyster densities were 2× higher than in a restored oyster population in Chesapeake Bay that was reported to be the largest reestablished metapopulation of native oysters in the world. Resident fauna on the restored reef were 62% more diverse, had 433% greater biomass, and comprised a distinct faunal community compared to unrestored sites. The presence of three‐dimensional habitat was the most important factor determining resident faunal community composition, indicating that substrate limitation is a major hindrance for oyster reef community success in Texas and other parts of the Gulf of Mexico. There were only minor differences in density, biomass, and diversity of associated fauna located adjacent (13 m) versus distant (150 m) to the restored reef. The two substrate types compared had little influence on oyster recruitment or faunal habitat provision. Results support the use of reef restoration as a productive means to rebuild habitat and facilitate faunal enhancement.