Are mesophotic coral ecosystems distinct communities and can they serve as refugia for shallow reefs?

We analyzed an extensive dataset of over 9000 benthic and suprabenthic species found throughout the Gulf of Mexico (GoMx) to assess whether mesophotic coral ecosystems represent distinct assemblages and evaluate their potential to serve as refugia for shallow reef communities. We assessed community structure of the overall benthic community from 0 to 300 m via non-metric multidimensional scaling (NMDS) of species presence across depth bands. We used the Jaccard index of similarity to calculate the proportion of shared species between adjacent depth bands, measure species turnover with depth, and assess taxonomic overlap between shallow reefs versus progressively deeper depth bands. NMDS ordinations showed that the traditionally defined mesophotic range (30–150 m) as a whole is not a distinct community. In contrast, taxonomically distinct communities, determined by hierarchical clustering, were found at 0–70, 60–120, 110–200, and 190–300 m. Clustering highlighted an important separation in the benthic community at ~60 m, which was especially important for actinopterygian fishes. Species turnover between adjacent depths decreased with depth for all taxa combined and individual taxa, with peaks at ~60, 90–120, and 190–200 m. Fishes showed lower turnover from shallow to upper mesophotic depths (0–50 m) than all taxa combined, a substantial peak at 60 m, followed by a precipitous and continued decline in turnover thereafter. Taxonomic overlap between shallow (0–20 m) and progressively deeper zones declined steadily with depth in all taxa and individual taxa, suggesting that mid- and lower mesophotic habitats have less (but not inconsequential) potential to serve as refugia (60–150 m, 15–25% overlap with shallow habitats) than upper mesophotic zones (30–60 m, 30–45% overlap with shallow habitats) for all taxa combined. We conclude that the traditional mesophotic zone is home to three ecological communities in the GoMx, one that is confluent with shallow reefs, a distinct mesophotic assemblage spanning 60–120 m, and a third that extends onto the outer continental shelf.     

How much can physics do for protein design?

Physics and physical chemistry are an important thread in computational protein design, complementary to knowledge-based tools. They provide molecular mechanics scoring functions that need little or no ad hoc parameter readjustment, methods to thoroughly sample equilibrium ensembles, and different levels of approximation for conformational flexibility. They led recently to the successful redesign of a small protein using a physics-based folded state energy. Adaptive Monte Carlo or molecular dynamics schemes were discovered where protein variants are populated as per their ligand-binding free energy or catalytic efficiency. Molecular dynamics have been used for backbone flexibility. Implicit solvent models have been refined, polarizable force fields applied, and many physical insights obtained.     

How accessible are coral reefs to people? A global assessment based on travel time

The depletion of natural resources has become a major issue in many parts of the world, with the most accessible resources being most at risk. In the terrestrial realm, resource depletion has classically been related to accessibility through road networks. In contrast, in the marine realm, the impact on living resources is often framed into the Malthusian theory of human density around ecosystems. Here, we develop a new framework to estimate the accessibility of global coral reefs using potential travel time from the nearest human settlement or market. We show that 58% of coral reefs are located < 30 min from the nearest human settlement. We use a case study from New Caledonia to demonstrate that travel time from the market is a strong predictor of fish biomass on coral reefs. We also highlight a relative deficit of protection on coral reef areas near people, with disproportional protection on reefs far from people. This suggests that conservation efforts are targeting low‐conflict reefs or places that may already be receiving de facto protection due to their isolation. Our global assessment of accessibility in the marine realm is a critical step to better understand the interplay between humans and resources.     

How well do mean field theories of spiking quadratic-integrate-and-fire networks work in realistic parameter regimes?

We use mean field techniques to compute the distribution of excitatory and inhibitory firing rates in large networks of randomly connected spiking quadratic integrate and fire neurons. These techniques are based on the assumption that activity is asynchronous and Poisson. For most parameter settings these assumptions are strongly violated; nevertheless, so long as the networks are not too synchronous, we find good agreement between mean field prediction and network simulations. Thus, much of the intuition developed for randomly connected networks in the asynchronous regime applies to mildly synchronous networks.     

How much can we know about the causes of evolutionary trends?

One of the first questions that paleontologists ask when they identify a large-scale trend in the fossil record (e.g., size increase, complexity increase) is whether it is passive or driven. In this article, I explore two questions about driven trends: (1) what is the underlying cause or source of the directional bias? and (2) has the strength of the directional bias changed over time? I identify two underdetermination problems that prevent scientists from giving complete answers to these two questions.     

How can storage time and temperature affect enzymic activities in urines?

We measured a tubular brush-border enzyme (alanine aminopeptidase, AAP) and a lysosomal hydrolase (N-acetyl-beta-D-glucosaminidase, NAG) in morning urines from 15 healthy normal subjects to check if different storage times and temperatures could modify enzyme concentrations. Short-term (24 h) storage time at room temperature or 4 degrees C does not affect AAP and NAG activities. Both enzymes are well preserved at -70 degrees C. AAP dramatically falls after 1 month at -20 degrees C, lowering to about 8% of the initial value after only 4 days of storage. On the contrary, NAG is well preserved at these storage conditions. Centrifugation has revealed not critical for measurement of these two enzymes.     

Do elevated nutrients and organic carbon on Philippine reefs increase the prevalence of coral disease?

Characterizations of Philippine coral diseases are very limited. The two most common, ulcerative white spot disease (UWS) and massive Porites growth anomalies (MPGA), target the genus Porites, a dominant reef-building genus. This is the first investigation in the Philippines to detect positive correlations between coral disease, nutrient levels, and organic carbon. A total of 5,843 Porites colonies were examined. Water and sediment samples were collected for analyses of nutrients (total nitrogen and phosphorus) and total organic carbon at 15 sites along a 40.5 km disease gradient, which was previously shown to positively correlate with human population levels. Results suggest that outbreaks of UWS and MPGAs are driven by elevated nutrient and organic carbon levels. Although the variables analyzed could be proxies for other causative agents (e.g., high sediment levels), the results provide quantitative evidence linking relatively higher coral disease prevalence to an anthropogenically impacted environment.     

Biotic resistance on coral reefs? Direct and indirect effects of native predators and competitors on invasive lionfish

Coral Reefs - Biotic resistance is the ability of an ecological community to prevent or limit the establishment or success of non-indigenous species. Native species can confer resistance by...     

New taxonomy and niche partitioning on coral reefs: jack of all trades or master of some?

Recent taxonomic advances are challenging widely held theories of the ecology and evolution of coral reef Invertebrates and communities. Large numbers of sibling species have been discovered across a variety of higher taxa. Differences in distribution, behavior and life history characteristics among sibling species demonstrate that niche diversification is more finely tuned, and interactions among organisms more specific, than most reef ecologists believed previously. Ecological and evolutionary understanding depends on good taxonomy.     

Harvesting before a fire: How much energy and organics can Greece gain?

Mediterranean-type climate regions like Greece have to face many problems, such as fuel, wood, paper and animal food deficiencies. In addition, great amounts of money are spent every year on fire fighting. The suggested harvesting of mediterranean-type ecosystems every 10 years will contribute to a combined solution of all these problems.     

How much can the orientation of G's eigenvectors tell us about genetic constraints?

A key goal in evolutionary quantitative genetics is to understand how evolutionary trajectories are constrained by pleiotropic coupling among multiple traits. Because studying pleiotropic constraints directly at the molecular genetic level remains very difficult, several analytical approaches attempt to draw conclusions about constraints by relating the orientation of the eigenvectors of the traits' (co)variance matrix to vectors of multivariate selection. On the basis of explicit models of genetic architecture, I here argue that the value of such approaches is greatly overestimated. The reason is that eigenvector orientation can be highly unstable and lack a biologically meaningful relationship with the underlying traits' genetic architecture. Genetic constraints are more profitably explored through experimental approaches avoiding the mathematical abstraction inherent in eigenanalysis.     

How much can history constrain adaptive evolution? A real‐time evolutionary approach of inversion polymorphisms in Drosophila subobscura

Chromosomal inversions are present in a wide range of animals and plants, having an important role in adaptation and speciation. Although empirical evidence of their adaptive value is abundant, the role of different processes underlying evolution of chromosomal polymorphisms is not fully understood. History and selection are likely to shape inversion polymorphism variation to an extent yet largely unknown. Here, we perform a real‐time evolution study addressing the role of historical constraints and selection in the evolution of these polymorphisms. We founded laboratory populations of Drosophila subobscura derived from three locations along the European cline and followed the evolutionary dynamics of inversion polymorphisms throughout the first 40 generations. At the beginning, populations were highly differentiated and remained so throughout generations. We report evidence of positive selection for some inversions, variable between foundations. Signs of negative selection were more frequent, in particular for most cold‐climate standard inversions across the three foundations. We found that previously observed convergence at the phenotypic level in these populations was not associated with convergence in inversion frequencies. In conclusion, our study shows that selection has shaped the evolutionary dynamics of inversion frequencies, but doing so within the constraints imposed by previous history. Both history and selection are therefore fundamental to predict the evolutionary potential of different populations to respond to global environmental changes.     

How can “Super Corals” facilitate global coral reef survival under rapid environmental and climatic change?

Coral reefs are in a state of rapid global decline via environmental and climate change, and efforts have intensified to identify or engineer coral populations with increased resilience. Concurrent with these efforts has been increasing use of the popularized term “Super Coral” in both popular media and scientific literature without a unifying definition. However, how this subjective term is currently applied has the potential to mislead inference over factors contributing to coral survivorship, and the future trajectory of coral reef form and functioning. Here, we discuss that the information required to support a single definition does not exist, and in fact may never be appropriate, i.e. “How Super is Super”? Instead, we advocate caution of this term, and suggest a workflow that enables contextualization and clarification of superiority to ensure that inferred or asserted survivorship is appropriate into future reef projections. This is crucial to robustly unlock how “Super Corals” can be integrated into the suite of management options required to facilitate coral survival under rapid environmental and climate change.     

“Choice” and destiny: the substrate composition and mechanical stability of settlement structures can mediate coral recruit fate in post-bleached reefs

Increasingly frequent and intense ocean warming events seriously test the buffer and recovery capacities of tropical coral reefs. Post-disturbance, available settlement structures on a reef (often dead coral skeletons) vary considerably in their mechanical stability and substrate composition, critically influencing coral recruit settlement choice and fate. In the wake of a coral mass mortality in the Lakshadweep archipelago, we examine (1) the relative availability of recruit settlement structures (from stable to unstable: reef platform, dead massive coral, consolidated rubble, dead corymbose coral, dead tabular coral, and unconsolidated rubble) in 12 recovering reefs across three atolls in the archipelago, (2) the substrate composition [crustose coralline algae (CCA), mixed turf, macroalgae] of these structural forms, and (3) whether the choice and fate of young coral are mediated by the substrate and stability of different structural forms. For this, we measured the abundance and distribution of recruit (<1 cm), juvenile (1–5 cm), and young adult (5–10) corals of 24 common coral genera. Four years after the mass mortality, reefs differed considerably in composition of settlement structures. The structures themselves varied significantly in substrate cover with dead tables largely covered in CCA [60 ± 6.05 % (SE)] and dead corymbose coral dominated by mixed turf (61.83 ± 3.8 %). The youngest visible recruits (<1 cm) clearly preferred CCA-rich structures such as dead massives and tables. However, older size classes were rarely found on unstable structures (strongly “avoiding” tables, Ivlev’s electivity index, E = ?0.5). Our results indicate that while substrate cover might mediate coral choice, the mechanical stability of settlement structures is critical in determining post-settlement coral survival. The composition and availability of settlement structures on a reef may serve as a characteristic signature of its recovery potential, aiding in assessments of reef resilience.     

Multiple disturbances and the global degradation of coral reefs: are reef fishes at risk or resilient?

Increased frequency of disturbances and anthropogenic activities are predicted to have a devastating impact on coral reefs that will ultimately change the composition of reef associated fish communities. We reviewed and analysed studies that document the effects of disturbance‐mediated coral loss on coral reef fishes. Meta‐analysis of 17 independent studies revealed that 62% of fish species declined in abundance within 3 years of disturbances that resulted in >10% decline in coral cover. Abundances of species reliant on live coral for food and shelter consistently declined during this time frame, while abundance of some species that feed on invertebrates, algae and/or detritus increased. The response of species, particularly those expected to benefit from the immediate loss of coral, is, however, variable and is attributed to erratic replenishment of stocks, ecological versatility of species and sublethal responses, such as changes in growth, body condition and feeding rates. The diversity of fish communities was found to be negatively and linearly correlated to disturbance‐mediated coral loss. Coral loss >20% typically resulted in a decline in species richness of fish communities, although diversity may initially increase following small declines in coral cover from high coverage. Disturbances that result in an immediate loss of habitat complexity (e.g. severe tropical storms), have a greater impact on fishes from all trophic levels, compared with disturbances that kill corals, but leave the reef framework intact (e.g. coral bleaching and outbreaks of Acanthaster planci). This is most evident among small bodied species and suggests the long‐term consequences of coral loss through coral bleaching and crown‐of‐thorn starfish outbreaks may be much more substantial than the short‐term effects currently documented.     

Abundance and reproductive patterns of the excavating sponge Cliona vermifera: a threat to Pacific coral reefs?

Cliona vermifera is a common excavating sponge in coral reefs from the East Pacific. Abundance and reproductive patterns of the sponge in a Mexican Pacific coral reef over a 4-year period are herein described. Sponge abundance was estimated along three transects 50 m long which were randomly placed on the reef, and along each one, a piece of coral rubble and a branch of a live coral from the Pocillopora spp. coral colony closest to the transect were collected at random, approximately every 2 m, yielding 25 pieces of each category per transect (and 75 pieces total of each category). A 2-way ANOVA revealed that invasion was significantly higher in living coral colonies (34.8 %) than in rubble (13.7 %). It also indicated that the abundance in both coralline substrates showed a temporal variation without a clear pattern of increase over the years. It was estimated that 60–85 % of sponges in the population reproduced sexually every year. The sponge proved gonochoristic, with a sex ratio strongly departing from parity (1 male: 3 females). Over the 4-year study period, at least two cohorts of oocytes with densities of up to 3.5 oocytes per mm² tissue were observed. Spermatogenesis lasted about a month, but often producing more than a pulse from July to November, coupled with peaks of oocyte maturation. Fertilization occurred internally to produce encapsulated zygotes that were released in one or more spawning events from July to November. In the following months (December to February), which were the periods of lowest temperature (~18.5–20 °C), no gametic activity occurred in the sponges. Because anomalous temperature rises that are detrimental to corals do not appear to negatively affect the reproduction and abundance of C. vermifera, it is likely that the excavating activity of this sponge may be compromising the health of those coral reefs that are recurrently affected by episodes of thermal stress.     

High-resolution habitat and bathymetry maps for 65,000 sq. km of Earth’s remotest coral reefs

Coral Reefs - With compelling evidence that half the world’s coral reefs have been lost over the last four decades, there is urgent motivation to understand where reefs are located and their...