A functional approach to the structural complexity of coral assemblages based on colony morphological features

Colony morphological features is among the best predictor of the scleractinian coral's function in reef ecosystems. However, morphological traits are categorical and to convert this information into a quantitative value as well as estimate their influence on ecosystem process remain a challenge. Here, we propose a trait-based approach to quantify morphological diversity and assess the structural complexity of the habitat provided by corals. We used a previously published dataset that is related to a bleaching event that affected the coral reef off Tikus Island in Indonesia in 1983. We found clear signs of recovery of the coral assemblage's complexity toward pre El Niño conditions five years after the event. Independent of the change observed in species richness, this return in structural complexity was accompanied by a global decrease in species number associated with each particular morphological entity (Functional Redundancy) and an increase in the number of single-species entities (Functional Vulnerability). Together with species loss, we show an overall functional erosion of the coral assemblage and suggest that the role of the coral reef habitat could be strongly imperiled under repeated or synergistic disturbances. This approach offers an opportunity for a better understanding of coral responses to natural and anthropogenic disturbances

Reproductive isolation among Acropora Species (Scleractinia: Acroporidae) in a marginal coral assemblage

Hybridization was proposed as being an important source of evolutionary novelty in broadcast-spawning reef-building corals. In addition, hybridization was hypothesized to be more frequent at the periphery of species' ranges and in marginal habitats. We tested the potential for hybridization in 2 ways: observations of the time of spawning and non-choice interspecific fertilization experiments of 4 sympatric Acropora species in a non-reefal coral assemblage at Chinwan Inner Bay (CIB), Penghu Is., Taiwan. We found that colonies of more than 1 species rarely released gametes at the same time, thus limiting the opportunities for cross-fertilization in the wild. On the few occasions when different species released gametes in synchrony, interspecific fertilization in experimental crosses was uniformly low (the proportion of eggs fertilized ranged 0%-4.58% with a mode of 0%), and interspecific-crossed embryos ceased development and died within 12 h after initially being fertilized. Ecological and experimental analyses indicated that reproductive isolation exists in these 4 Acropora species even though they have the opportunities to spawn synchronously, suggesting that hybridization is not very frequent in this marginal coral habitat at CIB

Temporal and Spatial Variations in spatial variations in symbiont communities of catch bowl coral Isopora palifera (Scleractinia: Acroporidae) on reefs in Kenting National Park, Taiwan

Acclimatization through Symbiodinium shuffling is one of potential mechanisms in reef-building corals to survive environmental stress. In our previous study, the catch bowl coral Isopora palifera in Tantzei Bay (TZB), Nanwan, Kenting National Park (KNP), southern Taiwan was demonstrated to shuffle thermal-tolerant Symbiodinium D1a and thermal-sensitive Symbiodinium C3 in response to seasonal variations in sea surface temperatures (SSTs) in 2000 and 2001. In this study, we reexamined the temporal dynamics of the Symbiodinium community of I. palifera in TZB in 2006-2009. In addition, spatial variations in Symbiodinium communities in I. palifera were also examined at 6 other sites of Nanwan, KNP in 2009, including a site located at a nuclear power plant outlet (NPP-OL) in southern Taiwan with a yearly mean SST 0.6-1.5 degrees C higher compared to the other sites. Phylotyping and DNA sequence analyses of Symbiodinium ribosomal 28S and ITS2 markers showed that I. palifera colonies at TZB continued to show seasonal shuffling, but shifted to thermal-sensitive type C3 dominant in 2006-2009. This differed from the symbiont community originally dominated by the thermal-tolerant Symbiodinium D1a in 2000 and 2001 after the 1998 mass-bleaching event. Significant differences in spatial variations of the symbiont community in Nanwan were detected with I. palifera colonies at the NPP-OL dominated by Symbiodinium D1a. Our study results suggest that I. palifera can acclimatize to SST anomalies by shuffling to thermal-tolerant Symbiodinium D1a and can revert to thermal-sensitive C3 when the stress disappears, but will maintain the thermally tolerant Symbiodinium D1a as the dominant symbiont if the heat stress continues

Analyses of corallimorpharian transcriptomes provide new perspectives on the evolution of calcification in the Scleractinia (corals)

Corallimorpharians (coral-like anemones) have a close phylogenetic relationship with scleractinians (hard corals) and can potentially provide novel perspectives on the evolution of biomineralization within the anthozoan subclass Hexacorallia. A survey of the transcriptomes of three representative corallimorpharians led to the identification of homologs of some skeletal organic matrix proteins (SOMPs) previously considered to be restricted to corals. Carbonic anhydrases (CAs), which are ubiquitous proteins involved in CO2 trafficking, are involved in both coral calcification and photosynthesis by endosymbiotic Symbiodinium (zooxanthellae). These multiple roles are assumed to place increased demands on the CA repertoire and have presumably driven the elaboration of the complex CA repertoires typical of corals (note that "corals" are defined here as reef-building Scleractinia). Comparison of the CA inventories of corallimorpharians with those of corals reveals that corals have specifically expanded the secreted and membrane-associated type CAs, whereas similar complexity is observed in the two groups with respect to other CA types. Comparison of the CA complement of the nonsymbiotic corallimorph Corynactis australis with that of Ricordea yuma, a corallimorph which normally hosts Symbiodinium, reveals similar numbers and distribution of CA types and suggests that an expansion of the CA repertoire has been necessary to enable calcification but may not be a requirement to enable symbiosis. Consistent with this idea, preliminary analysis suggests that the CA complexity of zooxanthellate and nonzooxanthellate sea anemones is similar. The comparisons above suggest that although there are relatively few new genes in the skeletal organic matrix of corals (which controls the skeleton deposition process), the evolution of calcification required an expanded repertoire of secreted and membrane- associated CAs

Mitochondrial genome rearrangements in the Scleractinia/Corallimorpharia complex: implications for coral phylogeny

Corallimorpharia is a small Order of skeleton-less animals that is closely related to the reef-building corals (Scleractinia) and of fundamental interest in the context of understanding the potential impacts of climate change in the future on coral reefs. The relationship between the nominal Orders Corallimorpharia and Scleractinia is controversial-the former is either the closest outgroup to the Scleractinia or alternatively is derived from corals via skeleton loss. This latter scenario, the "naked coral" hypothesis, is strongly supported by analyses based on mitochondrial (mt) protein sequences, whereas the former is equally strongly supported by analyses of mt nucleotide sequences. The "naked coral" hypothesis seeks to link skeleton loss in the putative ancestor of corallimorpharians with a period of elevated oceanic CO2 during the Cretaceous, leading to the idea that these skeleton-less animals may be harbingers for the fate of coral reefs under global climate change. In an attempt to better understand their evolutionary relationships, we examined mt genome organization in a representative range (12 species, representing 3 of the 4 extant families) of corallimorpharians and compared these patterns with other Hexacorallia. The most surprising finding was that mt genome organization in Corallimorphus profundus, a deep-water species that is the most scleractinian-like of all corallimorpharians on the basis of morphology, was much more similar to the common scleractinian pattern than to those of other corallimorpharians. This finding is consistent with the idea that C. profundus represents a key position in the coral corallimorpharian transition

Fine intervals are required when using point intercept transects to assess coral reef status

The Point Intercept Transect (PIT) method has commonly been used in recent decades for estimating the status of coral reef benthic communities. It is a simple method that is efficiently performed underwater, as benthic components are recorded only as presence or absence at specific interval points along transects. Therefore, PIT is also popular in citizen science activities such as Reef Check programs. Longer intervals are commonly associated with longer transects, yet sampling interval length can significantly influence benthic coverage calculations. Despite this, the relative accuracy of longer or shorter intervals related to transect length has not been tested for PIT. In this study, we tested the optimum intervals of PIT for several commonly used transect lengths using the bootstrap method on empirical data collected on tropical coral reefs and non-reefal coral communities. Our results recommend fine intervals of 10 cm or shorter, depending on the length of the transect, to increase the accuracy of estimating benthic community status on coral reefs. Permanent transects should also be considered in long-term monitoring programs to improve data quality

Symbiodinium spp. associated with scleractinian corals from Dongsha Atoll (Pratas), Taiwan, in the South China Seal

Dongsha Atoll (also known as Pratas) in Taiwan is the northernmost atoll in the South China Sea and a designated marine national park since 2007. The marine park's scope of protection covers the bio-resources of its waters in addition to uplands, so it is important to have data logging information and analyses of marine flora and fauna, including their physiology, ecology, and genetics. As part of this effort, we investigated Symbiodinium associations in scleractinian corals from Dongsha Atoll through surveys carried out at two depth ranges (shallow, 1-5 m; and deep, 10-15 m) in 2009 and during a bleaching event in 2010. Symbiodinium composition was assessed using restriction fragment length polymorphism (RFLP) of 28S nuclear large subunit ribosomal DNA (nlsrDNA). Our results showed that the 796 coral samples from seven families and 20 genera collected in 2009 and 132 coral samples from seven families and 12 genera collected in 2010 were associated with Symbiodinium C, D and C+D. Occurrence of clade D in shallow water (24.5%) was higher compared to deep (14.9%). Due to a bleaching event in 2010, up to 80010 of coral species associated with Symbiodinium C underwent moderate to severe bleaching. Using the fine resolution technique of denaturing gradient gel electrophoresis (DGGE) of internal transcribed spacer 2 (ITS2) in 175 randomly selected coral samples, from 2009 and 2010, eight Symbiodinium C types and two Symbiodinium D types were detected. This study is the first baseline survey on Symbiodinium associations in the corals of Dongsha Atoll in the South China Sea, and it shows the dominance of Symbiodinium Glade C in the population

Mitochondrial and nuclear genes suggest that stony corals are monophyletic but most families of stony corals are not (Order Scleractinia, Class Anthozoa, Phylum Cnidaria)

Modern hard corals (Class Hexacorallia; Order Scleractinia) are widely studied because of their fundamental role in reef building and their superb fossil record extending back to the Triassic. Nevertheless, interpretations of their evolutionary relationships have been in flux for over a decade. Recent analyses undermine the legitimacy of traditional suborders, families and genera, and suggest that a non-skeletal sister clade (Order Corallimorpharia) might be imbedded within the stony corals. However, these studies either sampled a relatively limited array of taxa or assembled trees from heterogeneous data sets. Here we provide a more comprehensive analysis of Scleractinia (127 species, 75 genera, 17 families) and various outgroups, based on two mitochondrial genes (cytochrome oxidase I, cytochrome b), with analyses of nuclear genes (ßtubulin, ribosomal DNA) of a subset of taxa to test unexpected relationships. Eleven of 16 families were found to be polyphyletic. Strikingly, over one third of all families as conventionally defined contain representatives from the highly divergent "robust" and "complex" clades. However, the recent suggestion that corallimorpharians are true corals that have lost their skeletons was not upheld. Relationships were supported not only by mitochondrial and nuclear genes, but also often by morphological characters which had been ignored or never noted previously. The concordance of molecular characters and more carefully examined morphological characters suggests a future of greater taxonomic stability, as well as the potential to trace the evolutionary history of this ecologically important group using fossils

Recurrent disturbances and the degradation of hard coral communities in Taiwan

Recurrent disturbances can have a critical effect on the structure and function of coral reef communities. In this study, long-term changes were examined in the hard coral community at Wanlitung, in southern Taiwan, between 1985 and 2010. In this 26 year interval, the reef has experienced repeated disturbances that include six typhoons and two coral-bleaching events. The frequency of disturbance has meant that species susceptible to disturbance, such as those in the genus Acropora and Montipora have almost disappeared from the reef. Indeed, almost all hard coral species have declined in abundance, with the result that total hard coral cover in 2010 (17.7%) was less than half what it was in 1985 (47.5%). In addition, macro-algal cover has increased from 11.3% in 2003 to 28.5% in 2010. The frequency of disturbance combined with possible chronic influence of a growing human population mean that a diverse reef assemblage is unlikely to persist on this reef into the future

BioTIME: A database of biodiversity time series for the Anthropocene.

MotivationThe BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene.Main types of variables includedThe database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record.Spatial location and grainBioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km2 (158 cm2) to 100 km2 (1,000,000,000,000 cm2).Time period and grainBioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year.Major taxa and level of measurementBioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates.Software format.csv and .SQL