Complex migration and the development of genetic structure in subdivided populations: an example from Caribbean coral reef ecosystems

A matrix‐based projection model is used in conjunction with the results of a coupled bio‐physical dispersal model to examine the spread of alleles through subdivided populations over time, and the associated development of genetic structural patterns. Applying this approach, it becomes possible to quantitatively evaluate the contribution of spatially explicit migration towards patterns of genetic structure observed in the field. To provide a concrete example, the model was used to examine genetic dispersal between coral reef patches of the Caribbean. Using generic life‐history parameters, the model shows the formation of a strong genetic break between eastern and western patches, as well as the development of a gradient along the length of the Bahamian archipelago, corresponding with evidence previously collected for coral and fish species. The data also suggest that Jamaica and the Cayman Islands are important stepping stones between the reefs of the northern Caribbean (Hispaniola and the Bahamas) and the Mesoamerican Barrier Reef. The model provides an effective means of evaluating regional‐scale genetic connectivity through time and identifying natural clusters of genetic exchange.     

Patchiness of local species richness and its implication for large-scale diversity patterns: an example from the middle Miocene of the Paratethys

The best hope for understanding global diversity patterns is to compare local assemblages, which are mostly preserved in taphonomically-complex shell beds. The present study investigates the variability in faunal composition and diversity at the scale of a single outcrop. A total of 152 species (3315 shells) occurred in 25 samples from 5 tempestitic shell beds. Although sampling intensity was high, total species richness was not captured by far at the hierarchical levels present (outcrop, shell beds, samples) because the majority of species is rare. In contrast, sampling intensity was sufficient to cover the most abundant species, as indicated by stable evenness values. Four taxa dominate the assemblage, but their rank order differs strongly between individual shell beds and individual samples; significant differences between some shell beds are evident for faunal composition, and one shell bed differs from all others with respect to species accumulation curves. Within shell beds, rarefaction curves are generally characterized by strongly overlapping confidence intervals, but outliers occur in three of five shell beds. Patchiness is additionally indicated by a wide scatter of diversity indices in some shell beds and by a wide scatter of samples of one shell bed in an ordination on faunal composition. Most of the outcrop-scale variability in faunal composition and diversity can be related to differences between shell beds. This suggests that sampling a single shell bed of the outcrop is insufficient to characterize the local fauna and its diversity, even when sampling intensity (i.e. the number of samples and shells) within the shell bed was high. Similarly, a single sample from such a shell bed may not be sufficient to characterize its diversity, even when the number of counted shells was high. It is therefore confirmed that sampling strategy and sampling intensity are crucial to confidently characterize the shelly assemblages at such a small spatial scale and that dispersed sampling effort with many small replicate samples will characterize a local assemblage and its diversity better than a few large samples. Diversity comparisons of individual samples between localities must account for the high variability present at the smaller spatial scale, as observed in our study.     

Hyperspectral discrimination of coral reef benthic communities in the western Caribbean

Determining a subset of wavelengths that best discriminates reef benthic habitats and their associated communities is essential for the development of remote sensing techniques to monitor them. This study measured spectral reflectance from 17 species of western Caribbean reef biota including coral, algae, seagrasses, and sediments, as well as healthy and diseased coral. It sought to extend the spectral library of reef-associated species found in the literature and to test the spectral discrimination of a hierarchy of habitats, community groups, and species. We compared results from hyperspectral reflectance and derivative datasets to those simulated for the three visible multispectral wavebands of the IKONOS sensor. The best discriminating subset of wavelengths was identified by multivariate stepwise selection procedure (discriminant function analysis). Best discrimination at all levels was obtained using the derivative dataset based on 6–15 non-contiguous wavebands depending on the level of the classification, followed by the hyperspectral reflectance dataset which was based on as few as 2–4 non-contiguous wavebands. IKONOS wavebands performed worst. The best discriminating subset of wavelengths in the three classification resolutions, and particularly those of the medium resolution, was in agreement with those identified by Hochberg and Atkinson (2003) and Hochberg et al. (2003) for reef communities worldwide. At all levels of classification, reflectance wavebands selected by the analysis were similar to those reported in recent studies carried out elsewhere, confirming their applicability in different biogeographical regions. However the greater accuracies achieved using the derivative datasets suggests that hyperspectral data is required for the most accurate classification of reef biotic systems.     

Facilitation in Caribbean coral reefs: high densities of staghorn coral foster greater coral condition and reef fish composition

Recovery of the threatened staghorn coral (Acropora cervicornis) is posited to play a key role in Caribbean reef resilience. At four Caribbean locations (including one restored and three extant populations), we quantified characteristics of contemporary staghorn coral across increasing conspecific densities, and investigated a hypothesis of facilitation between staghorn coral and reef fishes. High staghorn densities in the Dry Tortugas exhibited significantly less partial mortality, higher branch growth, and supported greater fish abundances compared to lower densities within the same population. In contrast, partial mortality, branch growth, and fish community composition did not vary with staghorn density at the three other study locations where staghorn densities were lower overall. This suggests that density-dependent effects between the coral and fish community may only manifest at high staghorn densities. We then evaluated one facilitative mechanism for such density-dependence, whereby abundant fishes sheltering in dense staghorn aggregations deliver nutrients back to the coral, fueling faster coral growth, thereby creating more fish habitat. Indeed, dense staghorn aggregations within the Dry Tortugas exhibited significantly higher growth rates, tissue nitrogen, and zooxanthellae densities than sparse aggregations. Similarly, higher tissue nitrogen was induced in a macroalgae bioassay outplanted into the same dense and sparse aggregations, confirming greater bioavailability of nutrients at high staghorn densities. Our findings inform staghorn restoration efforts, suggesting that the most effective targets may be higher coral densities than previously thought. These coral-dense aggregations may reap the benefits of positive facilitation between the staghorn and fish community, favoring the growth and survivorship of this threatened species.     

Diazotrophic diversity in the Caribbean coral, Montastraea cavernosa

Previous research on the Caribbean coral Montastraea cavernosa reported the presence of cyanobacterial endosymbionts and nitrogen fixation in orange, but not brown, colonies. We compared the diversity of nifH gene sequences between these two color morphs at three locations in the Caribbean and found that the nifH sequences recovered from M. cavernosa were consistent with previous studies on corals where members of both the α-proteobacteria and cyanobacteria were recovered. A number of nifH operational taxonomic units (OTUs) were significantly more abundant in the orange compared to the brown morphs, and one specific OTU (OTU 17), a cyanobacterial nifH sequence similar to others from corals and sponges and related to the cyanobacterial genus Cyanothece, was found in all orange morphs of M. cavernosa at all locations. The nifH diversity reported here, from a community perspective, was not significantly different between orange and brown morphs of M. cavernosa.     

Bipartite life cycle of coral reef fishes promotes increasing shape disparity of the head skeleton during ontogeny: an example from damselfishes (Pomacentridae)

Background  

Quantitative studies of the variation of disparity during ontogeny exhibited by the radiation of coral reef fishes are lacking. Such studies dealing with the variation of disparity, i.e. the diversity of organic form, over ontogeny could be a first step in detecting evolutionary mechanisms in these fishes. The damselfishes (Pomacentridae) have a bipartite life-cycle, as do the majority of demersal coral reef fishes. During their pelagic dispersion phase, all larvae feed on planktonic prey. On the other hand, juveniles and adults associated with the coral reef environment show a higher diversity of diets. Using geometric morphometrics, we study the ontogenetic dynamic of shape disparity of different head skeletal units (neurocranium, suspensorium and opercle, mandible and premaxilla) in this fish family. We expected that larvae of different species might be relatively similar in shapes. Alternatively, specialization may become notable even in the juvenile and adult phase.     

Corals from an Early Jurassic coral reef in British Columbia: refuge on an oceanic island reef

An Early Jurassic (Sinemurian) reef in the Telkawa Range, British Columbia Canada, yields coral species previously known from Morocco, Great Britain, Italy, Peru, and Chile. The principal constructional coral, Phacelostylophyllum rugosum (Laube), known from the Upper Triassic Dolomite Alps in northern Italy, is a holdover species. This coral survived the mass extinctions of the end-Triassic without leaving any other Jurassic records outside Canada. Other corals from the Telkwa reef include Stylophyllopsis victoriae (Duncan) and Actinastraea minima Beauvais known from Jurassic rocks of the Tethys. Closely related corals, Phacelostylophyllum chocolatensis (Wells) and Actinastraea plana (Duncan), are from southern Peru. The paleogeographic Occurrence of the Canadian reef in the volcanic terrane of Stikinia supports the contention that volcanic islands in distant outposts of the ancient Pacific served as refugia. In the aftermath of the end-Triassic reef decimation affecting the Tethys, corals and reef-building activities continued on ancient islands of the ancestral Pacific. The Hispanic Corridor, connecting the western Tethys with the western Pacific, may have played an important role during Sinemurian time. ***Reef; corals, Triassic, Jurassic, extinctions, paleobiogeography.     

Genotypic diversity and spatial-temporal distribution of Symbiodinium clones in an abundant reef coral

Genetic data are rapidly advancing our understanding of various biological systems including the ecology and evolution of coral-algal symbioses. The fine-scale interactions between individual genotypes of host and symbiont remain largely unstudied and constitute a major gap in knowledge. By applying microsatellite markers developed for both host and symbiont, we investigated the intracolony diversity, prevalence and stability of Symbiodinium glynni (type D1) multilocus genotypes in association with dense populations of Pocillopora at two sites in the Gulf of California. The genetic diversity and allelic frequencies in reef populations of S. glynni remained stable over 3 years. Common clone genotypes persisted over this period, and no temporal population subdivision (Φ(PT) = 0.021 and -0.003) was detected. Collections from circular plots showed no statistical correlation between related Pocillopora individuals and their associations with particular S. glynni genotypes, with no spatial structuring or clonal aggregation across a reef for the symbiont. From permanent linear transects, samples were analysed from multiple locations within a colony and some were resampled approximately 1 year later. Many of these multisampled colonies (approximately 53%) were dominated by a single S. glynni genotype and tended to associate with the same symbiont genotype(s) over time, while colony ramets often possessed unrelated symbiont genotypes. In contrast to the species level, associations between genotypes of Pocillopora and S. glynni are apparently more flexible over space and time. The abundance of sexually recombinant genotypes of S. glynni combined with greater flexibility might provide adaptive mechanisms for these symbioses to evolve rapidly to changes in environmental conditions and allow particular symbiont genotypes to spread through a host population.     

Complex interactions in the control of coral zonation on a Caribbean reef flat

Summary This study uses short-term assays and long-term transplant experiments to document the potential importance of fish predation and herbivory to the distribution and abundance of reef-building corals in a Caribbean back-reef system. Experimental manipulations of fish access reveal that the zonal patterns of the two reef-building corals Porites astreoides and P. porites f. furcata, dominant on shallow back-reef habitats, are strongly associated with the feeding intensity of parrotfishes. Differential palatability of the two corals to parrotfishes, the proximity of protective cover for large grazers and the availability of small refugia to harbor a cryptic grazer fauna are suggested as major features contributing to the observed patterns. A model predicting the interactions of various algivore/corallivore guilds on the relative dominance of Porites and algal populations is presented.     

Temperature influences selective mortality during the early life stages of a coral reef fish

For organisms with complex life cycles, processes occurring at the interface between life stages can disproportionately impact survival and population dynamics. Temperature is an important factor influencing growth in poikilotherms, and growth-related processes are frequently correlated with survival. We examined the influence of water temperature on growth-related early life history traits (ELHTs) and differential mortality during the transition from larval to early juvenile stage in sixteen monthly cohorts of bicolor damselfish Stegastes partitus, sampled on reefs of the upper Florida Keys, USA over 6 years. Otolith analysis of settlers and juveniles coupled with environmental data revealed that mean near-reef water temperature explained a significant proportion of variation in pelagic larval duration (PLD), early larval growth, size-at-settlement, and growth during early juvenile life. Among all cohorts, surviving juveniles were consistently larger at settlement, but grew more slowly during the first 6 d post-settlement. For the other ELHTs, selective mortality varied seasonally: during winter and spring months, survivors exhibited faster larval growth and shorter PLDs, whereas during warmer summer months, selection on PLD reversed and selection on larval growth became non-linear. Our results demonstrate that temperature not only shapes growth-related traits, but can also influence the direction and intensity of selective mortality.     

Deep-water coral banks: an example from the “Calcare di Mendicino” (Upper Miocene, Northern Calabria, Italy)

Summary The “Calcare di Mendicino” is a mixed carbonatesiliciclastic informal unit of Miocene (Late Tortonian-Early Messinian age), that crops out extensively in the northwestern part of the Calabria. In the Scannelle quarry near Belsito (Cosenza), four stratigraphic sections were studied to define the sedimentological and paleoecological setting. The carbonate body records the development of a deep-water coral bank characterized by a low-diverse community of azooxanthellate scleractinian (Oculina andDendrophyllia) and stylasterine hydrozoans colonies. Two main stages of bioconstruction development can be distinguished: a thicket and a bank stage. Among the biostromal dwellers the more common are bryozoans, echinoids, benthic foraminifers, gastropods, and bivalves. A higher content of planktonic foraminifers occur in the thicket stage. The coral bank flourished within the aphotic zone, with deep currents loaded with nutrients and siliciclastic sediments. The upper part of the “Calcare di Mendicino” carbonate body has been affected by a pervasive dolomitization destroying almost completely the sedimentary structures and the biofacies. The lower part, the main object of this paper, preserves the microfacies but it experienced a widespread recrystallization obliterating the primary geochemical characteristics. The diagenetic history, partly hidden, reveals three main stages: primary marine with isopachous fibrous cements, deep burial with cavities infilled by sparry calcite, and meteoric-phreatic with dog-tooth cements.     

Lower Devonian reef structures in Russia: an example from the Urals

The Lower Devonian reefs of the Urals were formed in two different environmental settings: (1) the Novaya Zemlya-West-Uralian reefs were rigid organic structures that grew at a passive platform at the eastern margin of Baltica; (2) reefal limestones from the Eastern Urals developed in an island arc during a phase of volcanism. The reef belts can be traced for more than 2,500 km. The largest barrier reefs (up to 1,500 m thick) formed during the Pragian-Lower Emsian (West-Urals zone) and Emsian (East-Urals zone). They are characterized by rather uniform faunal and sedimentary features from the Arctic Ocean as south as near the Aral Lake. The Uralian reef facies was constructed mainly with algal and microbial communities (calcimicrobes and cyanobacteria) in association with low-diverse metazoan assemblages. In the Lower Devonian reefs of both regions, there are similar groups of organisms comprising some of the major taxa of reef-builders and reef-dwellers. The distinctive feature of the Lower Devonian reefs of both regions is the stromatolite-like framework structure. A clear palaeobiogeographic link is obvious between West-Uralian and East-Uralian environment settings during the Early Devonian.     

Mangrove and coral reef sponge faunas: untold stories about shallow water Porifera in the Caribbean

Sponge faunas from coral reefs and mangrove ecosystems in the Caribbean have mostly been studied from an ecological perspective, with researchers considering the effects of physical and biological factors on their species distribution. To discern evolutionary patterns, this study analyzed the systematic composition, taxonomic diversity, and ecological properties (reproductive strategies, size, shape, endosymbiosis) of mangrove and reef sponge assemblages from seven distant Caribbean localities. Species composition was compared by use of cluster analysis (Sørensen’s), and taxonomic diversity by use of the biodiversity index average taxonomic distinctness (AvTD). Mangrove and reef-associated sponge faunas were found to be statistically dissimilar, with the AvTD values suggesting stronger taxonomic bias toward specific groups in mangroves, irrespective of geographic distance. Most Demospongiae orders have 30–50% more species in coral reefs than in mangroves. The richest reef genera (Agelas, Aplysina, Callyspongia, Petrosia, and Xestospongia) rarely colonize contiguous mangrove formations. The distribution and diversity of suprageneric taxa suggest that coral reef sponge assemblages might represent an older fauna. This historical interpretation would place mangrove subtidal habitats as the youngest marine ecosystem, rather than a below-optimum ecosystem. Life history traits support a biological split discussed here from the perspective of distinct evolutionary histories and different environmental conditions.     

Species-specific habitat distribution of coral reef fish assemblages in relation to habitat characteristics in an Okinawan coral reef

We determined the species-specific habitat associations of coral reef fishes and environmental characteristics in an Okinawan coral reef in Japan. We focused on three families (Pomacentridae, Gobiidae and Labridae) and attempted to determine differences in habitat utilization. We selected six sites along the coast of Amitori Bay, from the entrance to the innermost part, in order to cover a wide range of habitat characteristics (exposed habitat, semi-exposed habitat and sheltered habitat). The species diversity of coral assemblages was greater at the exposed and semi-exposed habitats, whereas branching coral mostly covered the sheltered habitat. The environmental factors that determine the species-specific spatial association in fishes differed among families. Both biological characteristics (coral morphology and coral species diversity) and physical characteristics (water depth and wave exposure) affected the spatial association of pomacentrids and gobiids. In contrast, physical characteristics such as substrate complexity and water depth affected the species-specific spatial association of labrid species. Further study is needed to determine the ecological factors that regulate the species-specific habitat preference in Okinawan coral reefs.     

Late Miocene ostracod assemblages from eastern Mediterranean coral reef complexes (central Crete,Greece)

Ostracods from ten Late Miocene coral reef complexes built by Siderastrea, Tarbellastrea and Porites, cropping out in the Messara Plain (southern Iraklion basin, central Crete), have been investigated and five assemblages have been recognised, which point to different marine environments: (1) assemblage from the basal sandy silts, dominated by very shallow inner-infralittoral species, such as Cyamocytheridea meniscus, Cyamocytheridea obstipa, Cyamocytheridea dertonensis, Cytheretta semiornata and Nonurocythereis seminulum; (2) assemblage from the coral reef complexes within which Grinioneis haidingeri, Aurila cicatricosa, Cimbaurila diecii, Tenedocythere cruciata, Pokornyella italica and Callistocythere quadrangula are dominant and point to a stable inner-infralittoral environment characterised by warm, quiet and well-oxygenated waters; (3) assemblage from the silts intercalated among the coral reef complexes, mainly characterised by Neomonoceratina laskarevi, Cytheridea acuminata, Phlyctenophora farkasi and Aurila albicans together with Callistocythere spp., Xestoleberis communis and Xestoleberis dispar, which points to a very shallow marine environment rich in aquatic vegetation; (4) assemblage from the upper silts, which records the absolute dominance of Xestoleberis species, reflecting a very shallow and highly-vegetated environment and (5) assemblage from the uppermost silty clays, dominated by Hemicytherura defiorei, Xestoleberis spp. and Palmoconcha dertobrevis, accompanied by Acanthocythereis hystrix, Cytherella scutulum, Bairdoppilata conformis, Semicytherura spp., Krithe sp., Cytheropteron alatum, Bythocypris sp. and Pseudocythere caudata, which suggest deeper marine environments probably located in the outer infralittoral/inner-circalittoral zones. The studied section has been dated by means of calcareous nannoplankton to be not younger than Zone MNN9 (Early Tortonian), which is the biostratigraphical datum recorded in the fine-grained deposits that overlie the coral reef complexes. An age not older than Tortonian can be inferred by the stratigraphical distribution of the recognized ostracods. Thus, the coral reef complexes have been tentatively referred to the Early Tortonian.     

Bacterial diversity associated with the Brazilian endemic reef coral Mussismilia braziliensis

Aims:  We performed the first characterization of the microbiota associated with the reef coral Mussismilia braziliensis by means of a culture-independent approach.
Methods and Results:  The main groups were Proteobacteria , Cyanobacteria and unclassified bacteria according to the 16S rDNA libraries. Most of the sequences of the mucus of healthy and diseased M. braziliensis did not find close matches in GenBank (i.e. >97% 16S rDNA similarity). Most of the sequences of seawater and mucus of healthy coral fell into tight clusters (17 and 15 clusters respectively). In contrast, most of the sequences of mucus of diseased coral did not form clusters. The rarefaction curves indicate saturation in the recovery of higher taxa (approximately 40 phyla). However, the number of species in the coral mucus ( n  = 130–170) and seawater ( n  = 170) did not reach a plateau.
Conclusions:  The coral microbiota encompasses several potentially novel species and higher taxa. The microbiota of M. braziliensis appears to be species-specific. Diseased coral may have provided a suitable place for colonization by opportunistic bacteria, resulting in a greater bacterial diversity.
Significance and Impact of the Study:  The first study on the diversity of the microbiota of the endemic and endangered of extinction coral M. braziliensis .     

Genetic diversity loss associated to high mortality and environmental stress during the recruitment stage of a coral reef fish

We investigated the short-term impact of environmental-induced stress on survival and neutral genetic diversity of recently settled juveniles of a damselfish, Dascyllus aruanus, using spatiotemporal caging experiments in various natural environmental conditions in Moorea (French Polynesia). Juveniles’ mortality was followed at five study sites and overall four experiments, mortality rates ranged from 0 to 45%. Mortality rate and average daily water temperature were positively correlated (P = 0.018). Juveniles’ mortality rate and allelic richness estimated from ten microsatellite loci were negatively correlated (P = 0.046). Together, an overdominance of heterozygotes was observed within hostile environments. These results suggest that an allelic richness loss may be expected as a direct consequence of unfavorable environmental conditions. Thus, a worrisome scenario on demographic and genetic consequences may be expected from habitat degradation in the context of global change and human pressure increases.