scholarly journals Transects, quadrats, or points? What is the best combination to get a precise estimation of a coral community?

2019 ◽  
Author(s):  
Luis M. Montilla ◽  
Emy Miyazawa ◽  
Alfredo Ascanio ◽  
María López-Hernández ◽  
Gloria Mariño-Briceño ◽  
...  
Keyword(s):  
Community Structure ◽  
Coral Reef ◽  
Effect Size ◽  
Standard Error ◽  
Scleractinian Coral ◽  
Statistical Power ◽  
Coral Community ◽  
Sampling Effort ◽  
Precise Estimation

ABSTRACTThe characteristics of coral reef sampling and monitoring are highly variable, with numbers of units and sampling effort varying from one study to another. Numerous works have been carried out to determine an appropriate effect size through statistical power, however, always from a univariate perspective. In this work, we used the pseudo multivariate dissimilarity-based standard error (MultSE) approach to assess the precision of sampling scleractinian coral assemblages in reefs of Venezuela between 2017 and 2018 when using different combinations of number of transects, quadrats and points. For this, the MultSE of 36 sites previously sampled was estimated, using four 30m-transects with 15 photo-quadrats each and 25 random points per quadrat. We obtained that the MultSE was highly variable between sites and is not correlated with the univariate standard error nor with the richness of species. Then, a subset of sites was re-annotated using 100 uniformly distributed points, which allowed the simulation of different numbers of transects per site, quadrats per transect and points per quadrat using resampling techniques. The magnitude of the MultSE stabilized by adding more transects, however, adding more quadrats or points does not improve the estimate. For this case study, the error was reduced by half when using 10 transects, 10 quadrats per transect and 25 points per quadrat. We recommend the use of MultSE in reef monitoring programs, in particular when conducting pilot surveys to optimize the estimation of the community structure.

scholarly journals The use of pseudo-multivariate standard error to improve the sampling design of coral monitoring programs

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8429
Author(s):  
Luis M. Montilla ◽  
Emy Miyazawa ◽  
Alfredo Ascanio ◽  
María López-Hernández ◽  
Gloria Mariño-Briceño ◽  
...  
Keyword(s):  
Community Structure ◽  
Coral Reef ◽  
Standard Error ◽  
Scleractinian Coral ◽  
Statistical Power ◽  
Sampling Design ◽  
Sampling Effort ◽  
Monitoring Programs ◽  
Coral Monitoring

The characteristics of coral reef sampling and monitoring are highly variable, with numbers of units and sampling effort varying from one study to another. Numerous works have been carried out to determine an appropriate effect size through statistical power; however, these were always from a univariate perspective. In this work, we used the pseudo multivariate dissimilarity-based standard error (MultSE) approach to assess the precision of sampling scleractinian coral assemblages in reefs of Venezuela between 2017 and 2018 when using different combinations of number of transects, quadrats and points. For this, the MultSE of 36 sites previously sampled was estimated, using four 30m-transects with 15 photo-quadrats each and 25 random points per quadrat. We obtained that the MultSE was highly variable between sites and is not correlated with the univariate standard error nor with the richness of species. Then, a subset of sites was re-annotated using 100 uniformly distributed points, which allowed the simulation of different numbers of transects per site, quadrats per transect and points per quadrat using resampling techniques. The magnitude of the MultSE stabilized by adding more transects, however, adding more quadrats or points does not improve the estimate. For this case study, the error was reduced by half when using 10 transects, 10 quadrats per transect and 25 points per quadrat. We recommend the use of MultSE in reef monitoring programs, in particular when conducting pilot surveys to optimize the estimation of the community structure.

scholarly journals Metamorphosis of a Scleractinian Coral in Response to Microbial Biofilms

2004 ◽  
Vol 70 (2) ◽  
pp. 1213-1221 ◽  
Author(s):  
Nicole S. Webster ◽  
Luke D. Smith ◽  
Andrew J. Heyward ◽  
Joy E. M. Watts ◽  
Richard I. Webb ◽  
...  
Keyword(s):  
Community Structure ◽  
Coral Reef ◽  
Scleractinian Coral ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Marine Invertebrate ◽  
Principal Component ◽  
Coralline Algae ◽  
Larval Metamorphosis ◽  
Microbial Biofilms ◽  
Wide Range

ABSTRACT Microorganisms have been reported to induce settlement and metamorphosis in a wide range of marine invertebrate species. However, the primary cue reported for metamorphosis of coral larvae is calcareous coralline algae (CCA). Herein we report the community structure of developing coral reef biofilms and the potential role they play in triggering the metamorphosis of a scleractinian coral. Two-week-old biofilms induced metamorphosis in less than 10% of larvae, whereas metamorphosis increased significantly on older biofilms, with a maximum of 41% occurring on 8-week-old microbial films. There was a significant influence of depth in 4- and 8-week biofilms, with greater levels of metamorphosis occurring in response to shallow-water communities. Importantly, larvae were found to settle and metamorphose in response to microbial biofilms lacking CCA from both shallow and deep treatments, indicating that microorganisms not associated with CCA may play a significant role in coral metamorphosis. A polyphasic approach consisting of scanning electron microscopy, fluorescence in situ hybridization (FISH), and denaturing gradient gel electrophoresis (DGGE) revealed that coral reef biofilms were comprised of complex bacterial and microalgal communities which were distinct at each depth and time. Principal-component analysis of FISH data showed that the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Cytophaga-Flavobacterium of Bacteroidetes had the largest influence on overall community composition. A low abundance of Archaea was detected in almost all biofilms, providing the first report of Archaea associated with coral reef biofilms. No differences in the relative densities of each subdivision of Proteobacteria were observed between slides that induced larval metamorphosis and those that did not. Comparative cluster analysis of bacterial DGGE patterns also revealed that there were clear age and depth distinctions in biofilm community structure; however, no difference was detected in banding profiles between biofilms which induced larval metamorphosis and those where no metamorphosis occurred. This investigation demonstrates that complex microbial communities can induce coral metamorphosis in the absence of CCA.

scholarly journals Impacts of Stony Coral Tissue Loss Disease (SCTLD) on Coral Community Structure at an Inshore Patch Reef of the Upper Florida Keys Using Photomosaics

2021 ◽  
Vol 8 ◽  
Author(s):  
Graham Kolodziej ◽  
Michael S. Studivan ◽  
Arthur C. R. Gleason ◽  
Chris Langdon ◽  
Ian C. Enochs ◽  
...  
Keyword(s):  
Community Structure ◽  
Coral Reef ◽  
Coral Cover ◽  
Florida Keys ◽  
Coral Community ◽  
Tissue Loss ◽  
Coral Tissue ◽  
Coral Mortality ◽  
Stony Coral ◽  
Reef Tract

Since the appearance of stony coral tissue loss disease (SCTLD) on reefs off Miami in 2014, this unprecedented outbreak has spread across the entirety of Florida’s coral reef tract, as well as to many territories throughout the Caribbean. The endemic zone reached the upper Florida Keys by 2016, resulting in partial or complete mortality of coral colonies across numerous species. Disease was first observed at Cheeca Rocks (Islamorada, Florida) in the beginning of 2018, with reports of coral mortality peaking mid-year. The disease was still present at Cheeca Rocks as of March 2020, however, to a lesser degree compared to the initial outbreak. Annual monitoring efforts have been ongoing at Cheeca Rocks since 2012, including repeated benthic photomosaics of a 330 m2 survey zone, spanning six replicate sites. As such, a repository of coral community composition data exists for before and after the disease outbreak that was analyzed to assess the impacts of SCTLD on reef communities at an upper Florida Keys inshore reef. Cheeca Rocks is hypothesized to be a resilient reef due to its persistent high coral cover despite its inshore location, which subjects corals to fluctuating water quality and marginal environmental conditions. Coral populations here have been shown to recover from bleaching events and heat stress with minimal coral mortality. Though colonies of coral species characterized as highly and moderately susceptible to SCTLD (e.g., Colpophyllia natans, Diploria labyrinthiformis, Pseudodiploria strigosa, Orbicella annularis, and O. faveolata) suffered mortality as a result of the outbreak with an average loss of 16.42% relative cover by species, the overall impacts on coral cover and community structure were relatively low, contributing to a loss of total coral cover of only 1.65%. Comparison of photomosaic data to other studies indicate Cheeca Rocks may not have been affected as severely as other sites on Florida’s coral reef tract, underlying this site’s potential role in coral resilience to stressors including bleaching events, land-based pollution, and disease epizootics.

scholarly journals Scleractinian coral community structure and distribution in the coastal waters surrounding Hainan Island

2017 ◽  
Vol 25 (10) ◽  
pp. 1123-1130 ◽  
Author(s):  
Hongying Zhou ◽  
Xuemei Yao ◽  
Li Li ◽  
Taonian Geng ◽  
Ying Zhang
Keyword(s):  
Community Structure ◽  
Coastal Waters ◽  
Scleractinian Coral ◽  
Hainan Island ◽  
Coral Community

scholarly journals Abundance and Characteristics of Microplastics in Seawater and Corals From Reef Region of Sanya Bay, China

2021 ◽  
Vol 8 ◽  
Author(s):  
Xinming Lei ◽  
Hao Cheng ◽  
Yong Luo ◽  
Yuyang Zhang ◽  
Lei Jiang ◽  
...  
Keyword(s):  
Community Structure ◽  
Coral Reef ◽  
Hainan Island ◽  
Coral Community ◽  
Coral Tissue ◽  
Knowledge Gaps ◽  
Polyp Size ◽  
Coral Reef Ecosystems ◽  
Seawater Environment ◽  
Sanya Bay

Microplastics (MPs) contamination is widespread in the coral reef ecosystems leading to the exposure of both corals and other biotas. Knowledge gaps still exist concerning patterns in MPs abundance spatially. This work quantified the MPs abundance and characteristics in the seawater and corals in the Sanya Bay, Hainan Island. MPs abundance was detected in the seawater and coral samples ranging from 15.50 to 22.14 items L–1, and 0.01 to 3.60 items polyp–1, respectively. We found the predominant size and type of MPs in seawater and corals were smaller than 2 mm and fiber. Further analysis revealed that the characteristics of MPs in the corals were significantly different from those in the seawater environment, indicating that the MPs are selectively enriched in corals. Furthermore, the MPs particles ingested and retained in coral tissue may be related to the polyp size. This study shows that MPs are present in the whole coral reef region and the coral community structure would be potentially harmed by these contaminants.

scholarly journals Shifting communities after­­ typhoon damage on an upper mesophotic reef in Okinawa, Japan

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3573 ◽  
Author(s):  
Kristine N. White ◽  
David K. Weinstein ◽  
Taku Ohara ◽  
Vianney Denis ◽  
Javier Montenegro ◽  
...  
Keyword(s):  
Community Structure ◽  
Coral Reefs ◽  
Scleractinian Coral ◽  
Community Dynamics ◽  
Coral Community ◽  
Long Term Effects ◽  
High Coverage ◽  
Stable Community ◽  
Mesophotic Reef

Very few studies have been conducted on the long-term effects of typhoon damage on mesophotic coral reefs. This study investigates the long-term community dynamics of damage from Typhoon 17 (Jelawat) in 2012 on the coral community of the upper mesophotic Ryugu Reef in Okinawa, Japan. A shift from foliose to bushy coral morphologies between December 2012 and August 2015 was documented, especially on the area of the reef that was previously recorded to be poor in scleractinian genera diversity and dominated by foliose corals. Comparatively, an area with higher diversity of scleractinian coral genera was observed to be less affected by typhoon damage with more stable community structure due to less change in dominant coral morphologies. Despite some changes in the composition of dominant genera, the generally high coverage of the mesophotic coral community is facilitating the recovery of Ryugu Reef after typhoon damage.

scholarly journals Defining variation in pre-human ecosystems can guide conservation: An example from a Caribbean coral reef

2019 ◽  
Author(s):  
Aaron O’Dea ◽  
Mauro Lepore ◽  
Andrew H. Altieri ◽  
Melisa Chan ◽  
Jorge Manuel Morales-Saldaña ◽  
...  
Keyword(s):  
Community Structure ◽  
Coral Reef ◽  
Human Impact ◽  
Historical Context ◽  
Stable State ◽  
Coral Community ◽  
Conservation Priorities ◽  
Novel Ecosystem ◽  
Caribbean Coral ◽  
Time Substitution

AbstractThere is a consensus that Caribbean coral reefs are a pale shadow of what they once were, yet a reef’s pre-human state is typically assumed or estimated using space-for-time substitution approaches. These approaches may fail to account for past variation before human impact which could mislead conservation priorities and actions. In this study we use a suite of fossilised mid-Holocene (7.2-5.6 ka) fringing reefs in Caribbean Panama to define the Historical Range of Variation (HRV) in coral community structure before human-impact to provide context for the states of modern reefs in the same area. Using the abundances of coral taxa to quantify communities, we found that most of the modern coral communities exist in novel ecosystem states with no fossil precedence. We do however identify one modern reef that is indistinguishable in coral community structure from the mid-Holocene reefs. Reef-matrix cores show that the community on this reef has remained in a stable state for over 760 years, suggesting long-term resistance to the region-wide shift to novel states. Without historical context this robust and stable reef would be overlooked since it does not fulfil expectations of what a “pristine” coral reef should look like. This example illustrates how defining past variation using the fossil record can place modern degradation in historical context and improve conservation recommendations.

scholarly journals When and how to calculate the Bayes factor with an interval null hypothesis

2019 ◽  
Author(s):  
Bence Palfi ◽  
Zoltan Dienes
Keyword(s):  
Big Data ◽  
Effect Size ◽  
Standard Error ◽  
Null Hypothesis ◽  
Bayes Factor ◽  
Null Model ◽  
Negligible Effect ◽  
Effect Sizes ◽  
Point Null Hypothesis

Existing calculators of the Bayes factor typically represent the prediction of the null-hypothesis with a point null model (e.g., Dienes & Mclatchie, 2018; Morey & Rouder, 2015; Wagenmakers et al., 2018). The point null model remains a good approximation of the null hypothesis as long as the standard error of the estimate of interest is large relative to the range of theoretically negligible effect sizes. However, this assumption may be violated, for instance, when there is big data and the standard error becomes comparable to or smaller than the range of effect sizes that is meaningless according to the theory. In this case, the conclusion that was based on the point null model may not be scientifically valid. Here, we introduce a case study to demonstrate why is it critical to calculate the Bayes factor with an interval null hypothesis rather than a point null hypothesis when the smallest meaningful effect size is not approximately zero relative to the standard error.

scholarly journals Eastern Pacific Coral Reef Provinces, Coral Community Structure and Composition: An Overview

2016 ◽  
pp. 107-176 ◽  
Author(s):  
Peter W. Glynn ◽  
Juan J. Alvarado ◽  
Stuart Banks ◽  
Jorge Cortés ◽  
Joshua S. Feingold ◽  
...  
Keyword(s):  
Community Structure ◽  
Coral Reef ◽  
Coral Community ◽  
Eastern Pacific

How to Detect Publication Bias in Psychological Research

2019 ◽  
Vol 227 (4) ◽  
pp. 261-279 ◽  
Author(s):  
Frank Renkewitz ◽  
Melanie Keiner
Keyword(s):  
Publication Bias ◽  
Effect Size ◽  
Statistical Power ◽  
Type I Error ◽  
Psychological Research ◽  
Type I ◽  
True Effect Size ◽  
Questionable Research Practices ◽  
True Effect ◽  
Meta Analyses

Abstract. Publication biases and questionable research practices are assumed to be two of the main causes of low replication rates. Both of these problems lead to severely inflated effect size estimates in meta-analyses. Methodologists have proposed a number of statistical tools to detect such bias in meta-analytic results. We present an evaluation of the performance of six of these tools. To assess the Type I error rate and the statistical power of these methods, we simulated a large variety of literatures that differed with regard to true effect size, heterogeneity, number of available primary studies, and sample sizes of these primary studies; furthermore, simulated studies were subjected to different degrees of publication bias. Our results show that across all simulated conditions, no method consistently outperformed the others. Additionally, all methods performed poorly when true effect sizes were heterogeneous or primary studies had a small chance of being published, irrespective of their results. This suggests that in many actual meta-analyses in psychology, bias will remain undiscovered no matter which detection method is used.

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