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AIM: The geological and palaeo‐climatic forces that produced the unique biodiversity in the Red Sea are a subject of vigorous debate. Here, we review evidence for and against the hypotheses that: (1) Red Sea fauna was extirpated during glacial cycles of the Pleistocene and (2) coral reef fauna found refuge within or just outside the Red Sea during low sea level stands when conditions were inhospitable. LOCATION: Red Sea and Western Indian Ocean. METHODS: We review the literature on palaeontological, geological, biological and genetic evidence that allow us to explore competing hypotheses on the origins and maintenance of shallow‐water reef fauna in the Red Sea. RESULTS: Palaeontological (microfossil) evidence indicates that some areas of the central Red Sea were devoid of most plankton during low sea level stands due to hypersaline conditions caused by almost complete isolation from the Indian Ocean. However, two areas may have retained conditions adequate for survival: the Gulf of Aqaba and the southern Red Sea. In addition to isolation within the Red Sea, which separated the northern and southern faunas, a strong barrier may also operate in the region: the cold, nutrient‐rich water upwelling at the boundary of the Gulf of Aden and the Arabian Sea. Biological data are either inconclusive or support these putative barriers and refugia, but no data set, that we know of rejects them. Genetic evidence suggests that many endemic lineages diverged from their Indian Ocean counterparts long before the most recent glaciations and/or are restricted to narrow areas, especially in the northern Red Sea. MAIN CONCLUSIONS: High endemism observed in the Red Sea and Gulf of Aden appears to have multiple origins. A cold, nutrient‐rich water barrier separates the Gulf of Aden from the rest of the Arabian Sea, whereas a narrow strait separates the Red Sea from the Gulf of Aden, each providing potential isolating barriers. Additional barriers may arise from environmental gradients, circulation patterns and the constriction at the mouth of the Gulf of Aqaba. Endemics that evolved within the Red Sea basin had to survive glacial cycles in relatively low salinity refugia. It therefore appears that the unique conditions in the Red Sea, in addition to those characteristics of the Arabian Peninsula region as a whole, drive the divergence of populations via a combination of isolation and selection.

Aim Herbivorous reef fishes are considered to have difficulty digesting plant material at extratropical temperatures and are thus largely restricted to tropical waters where they are thought to have evolved. However, the herbivorous Kyphosidae, with both temperate and tropical species, provides an ideal opportunity to test this view. Previous studies have resolved the taxonomy and distribution patterns of all species. Here, we use a calibrated phylogeny to analyse the age, geographical origin and pattern of diversification of kyphosids to determine their origins in space and time, and thus refine hypotheses on the evolutionary origins of herbivory in reef fishes. Location Pacific Ocean, Atlantic Ocean, Indian Ocean, Western Australia. Methods The age and geographic origin of Kyphosidae were determined by incorporating fossil calibrations and species distributions onto a phylogeny of all extant species based on fragments from mitochondrial markers and three nuclear markers, and using Bayesian modelling to reconstruct ancestral distributions. Evolution of both diet and tooth shape was also examined using ancestral reconstruction. Results Ancestral reconstruction suggested a subtropical, Southern Hemisphere Indo‐Pacific origin for the family. The chronogram indicates that Kyphosus originated in the early Miocene and that tropical diversity reflects very recent diversification. Main conclusions Contrary to the general perception that herbivorous reef fishes invaded high latitudes from the tropics, herbivorous kyphosids evolved at intermediate latitudes in the Southern Hemisphere and subsequently diversified into low latitudes where several species dispersed recently to achieve circumglobal distributions. The southern temperate/subtropical reef environment appears to have generated episodes of diversification in several, well‐established, widespread reef fish taxa. Some of these reef fish taxa have remained restricted to southern temperate reef environments despite a long tenure in the Cenozoic (e.g. odacines and aplodactylids), and some such as the kyphosids which diversified very recently in both hemispheres resulting in both regional endemics and species with worldwide distributions.

In ectotherms, growth rate, body size and maturation rate covary with temperature, with the direction and magnitude of variation predicted by the Temperature‐Size Rule (TSR). Nutritional quality or availability of food, however, may vary over latitudinal gradients, resulting in ambiguous effects on body size and maturation rate. The Temperature‐Constraint Hypothesis (TCH) predicts that marine herbivorous ectotherms are nutritionally compromised at latitudes exceeding 30°. This provides an opportunity to resolve the contrasting demographic responses of ectotherms to variation in temperature and nutritional status over latitudinal gradients. This study uses analysis of demographic rates to evaluate the predictions of the TSR in a marine herbivorous ectotherm sampled over a significant latitudinal gradient. The direction and magnitude of demographic variation was established in the marine herbivorous fish, Odax pullus (the butterfish), and compared with that of a phylogenetically related but trophically distinct species, the carnivorous Notolabrus fucicola (the banded wrasse). Both species were sampled at three locations across the length of New Zealand covering latitudes between 35°S and 49°S. Growth rate, mean size‐at‐age, age‐ and size‐at‐maturity, life span and abundance were estimated for each species at each location. Demographic traits of both taxa varied with latitude. Both species showed slower initial growth rates, and matured later at a larger body size at higher latitudes than populations sampled at lower latitudes. In addition, abundances increased significantly at higher latitudes in both species. These results were consistent with the TSR but not with the TCH, confirming that nutritional ecology (herbivore vs. carnivory) did not determine demographic patterns over a biologically significant latitudinal gradient. Results from this study suggest that the absence of herbivorous reef fishes from the higher latitudes of the Northern Hemisphere may not reflect a general physiological mechanism as suggested by the TCH and highlights the need to clarify the evolutionary histories of the marine biota of each hemisphere.

The Great Barrier Reef (GBR) provides a globally significant demonstration of the effectiveness of large-scale networks of marine reserves in contributing to integrated, adaptive management. Comprehensive review of available evidence shows major, rapid benefits of no-take areas for targeted fish and sharks, in both reef and nonreef habitats, with potential benefits for fisheries as well as biodiversity conservation. Large, mobile species like sharks benefit less than smaller, site-attached fish. Critically, reserves also appear to benefit overall ecosystem health and resilience: outbreaks of coral-eating, crown-of-thorns starfish appear less frequent on no-take reefs, which consequently have higher abundance of coral, the very foundation of reef ecosystems. Effective marine reserves require regular review of compliance: fish abundances in no-entry zones suggest that even no-take zones may be significantly depleted due to poaching. Spatial analyses comparing zoning with seabed biodiversity or dugong distributions illustrate significant benefits from application of best-practice conservation principles in data-poor situations. Increases in the marine reserve network in 2004 affected fishers, but preliminary economic analysis suggests considerable net benefits, in terms of protecting environmental and tourism values. Relative to the revenue generated by reef tourism, current expenditure on protection is minor. Recent implementation of an Outlook Report provides regular, formal review of environmental condition and management and links to policy responses, key aspects of adaptive management. Given the major threat posed by climate change, the expanded network of marine reserves provides a critical and cost-effective contribution to enhancing the resilience of the Great Barrier Reef.

1. Marine herbivorous fishes are considered to be of critical importance in determining the biological structure of shallow reef environments, and by implication have key roles in carbon flux in reef ecosystems. Despite this, the nutritional processes that underpin these critical ecological roles have received comparatively little attention. 2. Here we give an overview of recent progress in the nutritional ecology of marine herbivorous fishes, and then examine two recent paradigms that we consider important in the development of the field: (i) the role of temperature in latitudinal gradients of diversity and abundance, and (ii) the impact of these fishes on coral reefs. Our aim is to illustrate how an integrative nutritional ecology approach can enrich insights gained from studies of fish herbivory, and to emphasize the distinctive differences between herbivory in marine and terrestrial systems. 3. We argue that much of the work on trophic biology in marine herbivorous fishes has focused on the ecological impacts of fishes on reefs, the deterrent properties of marine algae, and the morphological and mechanical aspects of ingestion. This has come at the expense of two of the elements necessary for an integrative understanding of feeding ecology, that is, food composition and the physiological processes involved in nutrient extraction and utilization. Together, these factors have hindered the development of the nutritional framework for analysing food resources, feeding patterns and evolutionary trends that has proved successful for terrestrial vertebrate herbivores. 4. The reef grazing and algal secondary metabolite paradigms, while both extremely productive, have failed to develop the clear predictive framework for diet choice required in broader contexts such as reef management and understanding the evolution of herbivory. The lack of a focus on nutritional factors has led to premature conclusions on the influence of temperature on algal digestion, both at the level of digestive processes and the biogeography of marine faunas. 5. Some marine herbivorous fishes appear to be bending the 'rules' of hindgut fermentation, especially with respect to temperature and fermentation substrates, and so the study of nutritional ecology in these animals has potential to generate novel insights for the field of vertebrate nutrition in general.

AIM: The Red Sea is characterised by a unique fauna and historical periods of desiccation, hypersalinity and intermittent isolation. The origin and contemporary composition of reef‐associated taxa in this region can illuminate biogeographical principles about vicariance and the establishment (or local extirpation) of existing species. Here we aim to: (1) outline the distribution of shallow water fauna between the Red Sea and adjacent regions, (2) explore mechanisms for maintaining these distributions and (3) propose hypotheses to test these mechanisms. LOCATION: Red Sea, Gulf of Aden, Arabian Sea, Arabian Gulf and Indian Ocean. METHODS: Updated checklists for scleractinian corals, fishes and non‐coral invertebrates were used to determine species richness in the Red Sea and the rest of the Arabian Peninsula and assess levels of endemism. Fine‐scale diversity and abundance of reef fishes within the Red Sea were explored using ecological survey data. RESULTS: Within the Red Sea, we recorded 346 zooxanthellate and azooxanthellate scleractinian coral species of which 19 are endemic (5.5%). Currently 635 species of polychaetes, 211 echinoderms and 79 ascidians have been documented, with endemism rates of 12.6%, 8.1% and 16.5% respectively. A preliminary compilation of 231 species of crustaceans and 137 species of molluscs include 10.0% and 6.6% endemism respectively. We documented 1071 shallow fish species, with 12.9% endemic in the entire Red Sea and 14.1% endemic in the Red Sea and Gulf of Aden. Based on ecological survey data of endemic fishes, there were no major changes in species richness or abundance across 1100 km of Saudi Arabian coastline. MAIN CONCLUSIONS: The Red Sea biota appears resilient to major environmental fluctuations and is characterized by high rates of endemism with variable degrees of incursion into the Gulf of Aden. The nearby Omani and Arabian Gulfs also have variable environments and high levels of endemism, but these are not consistently distinct across taxa. The presence of physical barriers does not appear to explain species distributions, which are more likely determined by ecological plasticity and genetic diversity.

Parrotfishes are considered to have a major influence on coral reef ecosystems through grazing the benthic biota and are also primary fishery targets in the Indo-Pacific. Consequently, the impact of human exploitation on parrotfish communities is of prime interest. As anthropogenic and environmental factors interact across spatial scales, sampling programs designed to disentangle these are required by both ecologists and resource managers. We present a multi-scale examination of patterns in parrotfish assemblage structure, size distribution and diversity across eight oceanic islands of Micronesia. Results indicate that correlates of assemblage structure are scale-dependent; biogeographic distributions of species and island geomorphology hierarchically influenced community patterns across islands whereas biophysical features and anthropogenic pressure influenced community assemblage structure at the within-island scale. Species richness and phylogenetic diversity increased with greater broad-scale habitat diversity associated with different island geomorphologies. However, within-island patterns of abundance and biomass varied in response to biophysical factors and levels of human influence unique to particular islands. While the effect of fishing activities on community composition and phylogenetic diversity was obscured across island types, fishing pressure was the primary correlate of mean parrotfish length at all spatial scales. Despite widespread fishery-induced pressure on Pacific coral reefs, the structuring of parrotfish communities at broad spatial scales remains a story largely dependent on habitat. Thus, we propose better incorporation of scale-dependent habitat effects in future assessments of overexploitation on reef fish assemblages. However, strong community-level responses within islands necessitate an improved understanding of the phylogenetic and functional consequences of altering community structure.

Epulopiscium sp. type B (Lachnospiraceae) is an exceptionally large, highly polyploid, intestinal symbiont of the coral reef dwelling surgeonfish Naso tonganus . These obligate anaerobes do not form mature endospores and reproduce solely through the production of multiple intracellular offspring. This likely makes them dependent on immediate transfer to a receptive host for dispersal. During reproduction, only a small proportion of Epulopiscium mother-cell DNA is inherited. To explore the impact of this unusual viviparous lifestyle on symbiont population dynamics, we investigated Epulopiscium sp. type B and their fish hosts collected over the course of two decades, at island and reef habitats near Lizard Island, Australia. Using multi-locus sequence analysis, we found that recombination plays an important role in maintaining diversity of these symbionts and yet populations exhibit linkage disequilibrium (LD). Symbiont populations showed spatial but not temporal partitioning. Surgeonfish are long-lived and capable of traveling long distances, yet the population structures of Epulopiscium suggest that adult fish tend to not roam beyond a limited locale. Codiversification analyses and traits of this partnership suggest that while symbionts are obligately dependent on their host, the host has a facultative association with Epulopiscium . We suggest that congression of unlinked markers contributes to LD estimates in this and other recombinant populations of bacteria. The findings here inform our understanding of evolutionary processes within intestinal Lachnospiraceae populations.

The bumphead parrotfish (Bolbometopon muricatum) is an iconic coral reef species of commercial, subsistence, and cultural value that has faced severe declines across the Indo-Pacific. In this study, we summarized the age-based biological characteristics of B. muricatum based on comprehensive surveys of a small-scale but high-yield fishery in Solomon Islands. We examined the full breadth of the life history, including pelagic larval duration, growth patterns throughout the ontogeny (post-settlement, juvenile, and adult), life span, mortality, age at maturity, and reproductive timing, as well as the size-dependent relative contribution of females to overall reproductive effort. The age-based demographic information supports a sexual pattern of functional gonochorism, whereby sex ratios were consistent throughout the lifespan. After a 25-day pelagic larval duration, the species growth pattern is comparatively slow and differs by sex, where males generally reach larger sizes at a given age than females. This growth pattern is associated with a long life span (at least 30 yrs) and low mortality rates (< 0.2 yr−1). Annual and lunar tracking of ovary weights confirmed cyclical spawning activity synchronized just prior to new moon throughout the year. Surprisingly, ovary weights declined in the largest and oldest females, implying lower reproductive output. Instead, lower ovary weights may reflect alternative mating strategies among the largest females whereby spawning frequency and strategy differs among females of different body sizes. These results highlight several novel and previously unknown aspects of this species’ biology, and our analyses generate information that can strengthen population models, facilitate stock assessments, support regional management, and provide a baseline for comparative work.

Cells rely on diffusion to move metabolites and biomolecules. Diffusion is highly efficient but only over short distances. Although eukaryotic cells have broken free of diffusion-dictated constraints on cell size, most bacteria and archaea are forced to remain small. Exceptions to this rule are found among the bacterial symbionts of surgeonfish; Epulopiscium spp. are cigar-shaped cells that reach lengths in excess of 600 μm. A large Epulopiscium contains thousands of times more DNA than a bacterium such as Escherichia coli, but the composition of this DNA is not well understood. Here, we present evidence that Epulopiscium contains tens of thousands of copies of its genome. Using quantitative, single-cell PCR assays targeting single-copy genes, we have determined that copy number is positively correlated with Epulopiscium cell size. Although other bacteria are known to possess multiple genomes, polyploidy of the magnitude observed in Epulopiscium is unprecedented. The arrangement of genomes around the cell periphery may permit regional responses to local stimuli, thus allowing Epulopiscium to maintain its unusually large size. Surveys of the sequences of single-copy genes (dnaA, recA, and ftsZ) revealed genetic homogeneity within a cell consistent with only a small amount ([almost equal to]1%) of the parental DNA being transferred to the next generation. The results also suggest that the abundance of genome copies in Epulopiscium may allow for an unstable genetic feature, a long mononucleotide tract, in an essential gene. With the evolution of extreme polyploidy and large cell size, Epulopiscium has acquired some of the advantages of eukaryotic cells.