Halimeda biomass,growth rates and sediment generation on reefs in the central great barrier reef province

The average biomass ofHalimeda per m² of solid substratum increased progressively on a series of reefs situated at increasing distances from the shore in the central Great Barrier Reef. There was none on a reef close inshore, increasing to nearly 500 g m^?2 total biomass (?90% calcium carbonate) on an oceanic atoll system in the Coral Sea. The biomass measured contained 13 species ofHalimeda but was dominated by only two species,H. copiosa andH. opuntia, except on the atoll whereH. minima was dominant. Three sand-dwelling species were also present but did not occur anywhere in substantial quantities. Growth rates of the dominant species were measured bv tagging individual branch tips. A mean value of 0.16 segments d^?1 was recorded but 41% of the branch tips did not grow any new segments whilst only 1% grew more than one per day. The number of branch tips per unit biomass was very constant and has been used in conjunction with growth rates and biomass to calculate productivity rates, and thence sedimentation, in the lagoon of one of the reefs. Biomass doubling time of 15 d and production of 6.9 g dry wt m^?2 d^?1 are considerably higher than previously reported values forHalimeda vegetation and there was little seasonal change detected over a whole year. Those values indicate annual accretion of 184.9 g m^?2 year^?1 ofHalimeda segment debris over the entire lagoon floor (5.9 km²) of Davies Reef, equivalent to 0.13 mm year^?1 due toHalimeda alone, or 1 m every 1,892 years when other contributions to that sediment are taken into account.     

Corals and starfish devastation of the great barrier reef: Aggregation methods

Aggregation methods allow one to replace a large scale dynamical system (micro-system) by a reduced dynamical system (macro-system) governing a small number of global variables. This aggregation of variables can be performed when two time scales exist, a fast time scale and a slow time scale. Perturbation theory allows to obtain an approximated aggregated dynamical system which describes the behaviour of a few number of slow time varying variables which are constants of motion of the fast part of the micro-system. Aggregation methods are applied to the case of the devastation of the great barrier reef by the starfishes. We recall the Antonelli/Kazarinoff model which implies a stable limit cycle for the corals and starfish populations. This prey-predator model describes the interactions between two species of corals and the starfish. Then, we generalize the Antonelli/Kazarinoff model to the case of two spatial patches with a fast part describing the starfish migration on the patches and the human manipulation of the communities by divers and, a slow part describing the growth and the interactions between the populations. We obtain an aggregated model governing the total coral densities on the patches and the total starfish population. This model can exhibit stable limit cycle oscillations and a Hopf bifurcation. The critical value of the bifurcation parameter is expressed in terms of the proportions of coral species and starfish on the two patches. This implies for example that rather than random killing of starfish by the Australian military, it may be better to send teams of divers to outbreaking reefs when they first occur who will then manipulate the community structure to increase protection.     

Population growth rates: issues and an application

Current issues in population dynamics are discussed in the context of The Royal Society Discussion Meeting 'Population growth rate: determining factors and role in population regulation'. In particular, different views on the centrality of population growth rates to the study of population dynamics and the role of experiments and theory are explored. Major themes emerging include the role of modern statistical techniques in bringing together experimental and theoretical studies, the importance of long-term experimentation and the need for ecology to have model systems, and the value of population growth rate as a means of understanding and predicting population change. The last point is illustrated by the application of a recently introduced technique, integral projection modelling, to study the population growth rate of a monocarpic perennial plant, its elasticities to different life-history components and the evolution of an evolutionarily stable strategy size at flowering.     

Notes on the influence of particulate organic matter (POM) on light conditions at a coral reef of the Australian great barrier reef

On the outer slope of a coral reef in the Great Barrier Reef, at a depth of 11-12 in without artificial light, bright red and rose colours were observed to occur on coelenterates, because masses of floating luminescent bacteria in the environment.     

Reassessing the trophic role of reef sharks as apex predators on coral reefs

Apex predators often have strong top-down effects on ecosystem components and are therefore a priority for conservation and management. Due to their large size and conspicuous predatory behaviour, reef sharks are typically assumed to be apex predators, but their functional role is yet to be confirmed. In this study, we used stomach contents and stable isotopes to estimate diet, trophic position and carbon sources for three common species of reef shark (Triaenodon obesus, Carcharhinus melanopterus and C. amblyrhynchos) from the Great Barrier Reef (Australia) and evaluated their assumed functional role as apex predators by qualitative and quantitative comparisons with other sharks and large predatory fishes. We found that reef sharks do not occupy the apex of coral reef food chains, but instead have functional roles similar to those of large predatory fishes such as snappers, emperors and groupers, which are typically regarded as high-level mesopredators. We hypothesise that a degree of functional redundancy exists within this guild of predators, potentially explaining why shark-induced trophic cascades are rare or subtle in coral reef ecosystems. We also found that reef sharks participate in multiple food webs (pelagic and benthic) and are sustained by multiple sources of primary production. We conclude that large conspicuous predators, be they elasmobranchs or any other taxon, should not axiomatically be regarded as apex predators without thorough analysis of their diet. In the case of reef sharks, our dietary analyses suggest they should be reassigned to an alternative trophic group such as high-level mesopredators. This change will facilitate improved understanding of how reef communities function and how removal of predators (e.g., via fishing) might affect ecosystem properties.     

Population divergence with or without admixture: selecting models using an ABC approach

Genetic data have been widely used to reconstruct the demographic history of populations, including the estimation of migration rates, divergence times and relative admixture contribution from different populations. Recently, increasing interest has been given to the ability of genetic data to distinguish alternative models. One of the issues that has plagued this kind of inference is that ancestral shared polymorphism is often difficult to separate from admixture or gene flow. Here, we applied an approximate Bayesian computation (ABC) approach to select the model that best fits microsatellite data among alternative splitting and admixture models. We performed a simulation study and showed that with reasonably large data sets (20 loci) it is possible to identify with a high level of accuracy the model that generated the data. This suggests that it is possible to distinguish genetic patterns due to past admixture events from those due to shared polymorphism (population split without admixture). We then apply this approach to microsatellite data from an endangered and endemic Iberian freshwater fish species, in which a clustering analysis suggested that one of the populations could be admixed. In contrast, our results suggest that the observed genetic patterns are better explained by a population split model without admixture.     

Bathymetric adaptations of reef-building corals at davies reef,great barrier reef,Australia. I. Long-term growth responses of Acropora formosa (Dana 1846)

In situ rates of linear growth (branch extension) were measured for Acropora formosa (Dana) at depths of 5, 10, and 15 m. Estimates of radial branch growth and internal accretion were made at the shallowest and deepest sites. In addition, reciprocal transplant experiments between these two sites were conducted using branches of different lengths. The in situ results showed that individual branches at the deep site extended twice as fast, and deposited more calcium carbonate than branches at the shallow site. Branch initiation, however, was more rapid at the shallow site. Thus, if the extension of new lateral branches were included to obtain a measure of overall growth, rates were highest at the shallow site. The initial length of the transplanted branches significantly affected growth rates. Longer branches showed greater overall growth within all treatments. Branch extension rates, however, increased with initial branch length at the deep site, while tending to remain constant at the shallow site. This result is interpreted as evidence that the extension of each branch tip at the deep site was supported by translocated metabolites derived from a greater volume of zooxanthellae-bearing tissue than at the shallow site. A. formosa exhibits different growth patterns at different depths. At the deep site, extension is favoured over branch initiation. Consequently, translocation from a greater volume of tissue is presumably available to sustain the higher extension rate at each tip. At the shallow site, where extension is less rapid but branch initiation is more rapid, each tip probably receives translocate from a smaller volume of tissue. These mechanisms result in different growth forms at the two sites and are apparently adaptations to different environmental conditions. Light or water motion, or a combination of the two are proposed as probable controlling factors.     

Distribution,burrowing, and growth rates of the clam Tridacna crocea on interior reef flats

Summary Larvae of the burrowing clam Tridacna crocea (Tridacnidae) settle preferentially on top of detached coral heads lying on the surface of the interior reef flat in the Great Barrier Reef province. This species burrows as it grows, eroding the central top surfaces of coral boulders, producing structures that superficially resemble micro-atolls. Storm surges roll these coral heads onto the now flattened surface, killing the live population of clams, and exposing the fresh underside for unimpeded larval settlement. As these clams grow and burrow into the substratum, the coral head becomes progressively flattened and finally breaks apart. Field observations and growthring data documented growth rate; growth rates plus burrow volumes were converted to annual sediment production. At average population densities approximately 140 gm/m²/yr of coral are eroded. Concomitant with erosion is a calcium carbonate increase in the shell of these clams amounting to 60gm/m²/yr. Assuming a stable population structure, with annual mortality equal to annual estimated growth, total sediment production is 200 gm/m²/yr. Clams are usually aggregated at higher densities, however, with numbers regularly exceeding 100 clams/m². Consequently maximum sediment production rate locally is often 4,500 gm/m²/yr.     

Accurate estimation of substitution rates with neighbor-dependent models in a phylogenetic context

Most models and algorithms developed to perform statistical inference from DNA data make the assumption that substitution processes affecting distinct nucleotide sites are stochastically independent. This assumption ensures both mathematical and computational tractability but is in disagreement with observed data in many situations--one well-known example being CpG dinucleotide hypermutability in mammalian genomes. In this paper, we consider the class of RN95 + YpR substitution models, which allows neighbor-dependent effects--including CpG hypermutability--to be taken into account, through transitions between pyrimidine-purine dinucleotides. We show that it is possible to adapt inference methods originally developed under the assumption of independence between sites to RN95 + YpR models, using a mathematically rigorous framework provided by specific structural properties of this class of models. We assess how efficient this approach is at inferring the CpG hypermutability rate from aligned DNA sequences. The method is tested on simulated data and compared against several alternatives; the results suggest that it delivers a high degree of accuracy at a low computational cost. We then apply our method to an alignment of 10 DNA sequences from primate species. Model comparisons within the RN95 + YpR class show the importance of taking into account neighbor-dependent effects. An application of the method to the detection of hypomethylated islands is discussed.     

Bathymetric adaptations of reef-building corals at davies reef,great barrier reef,Australia. II. Light saturation curves for photosynthesis and respiration

Light saturation (P-I) curves for oxygen production and consumption were constructed in the laboratory for corals collected from depths of 1 to 45 m on the southeastern (seaward) side of Davies Reef, Great Barrier Reef, Australia. This depth range represents a gradient of from 82.6 to 2.9% of surface light, which was measured as photosynthetic photon flux density (PPFD) between 400 and 700 nm. Adaptative changes in photokinetic parameters were observed over the entire range of light intensities. The compensation intensity (I_c), I_k, the intensity at which photosynthesis was 95% light saturated (I_0.95), and the respiration rate (?R), all decreased with decreasing light intensity. The maximal rate of photosynthesis when normalized on the basis of coral chlorophyll-a content (P_ma^g) tended to decrease with decreasing irradiance but the change was not statistically significant. The $\text{P}\text{R}$ ratio ($\text{P}{}_{\mathrm{m}}{}^{\mathrm{g}}\text{?R}$), the initial slope of a light saturation curve (α), and the maximum rate of photosynthesis when normalized by coral protein content (P_mp^g), all increased with decreasing light intensity. The logarithms of the values for each variable parameter were proportional to the logarithms of the fraction of the surface PPFD (T) transmitted to the depth at which the corals grew. This enabled changes in these parameters to be accurately estimated for corals growing at any depth on the reef. Comparison of experimental data with published values for “saturating” irradiance and P_ma^g, suggests that the endosymbiotic algae within reef-building corals are photosynthetically intermediate between classical “sun” and “shade” plants.     

Maximum likelihood estimation of population growth rates based on the coalescent.

We describe a method for co-estimating 4Nemu (four times the product of effective population size and neutral mutation rate) and population growth rate from sequence samples using Metropolis-Hastings sampling. Population growth (or decline) is assumed to be exponential. The estimates of growth rate are biased upwards, especially when 4Nemu is low; there is also a slight upwards bias in the estimate of 4Nemu itself due to correlation between the parameters. This bias cannot be attributed solely to Metropolis-Hastings sampling but appears to be an inherent property of the estimator and is expected to appear in any approach which estimates growth rate from genealogy structure. Sampling additional unlinked loci is much more effective in reducing the bias than increasing the number or length of sequences from the same locus.     

Recruitment dynamics and first year growth of the coral reef surgeonfish Ctenochaetus striatus,with implications for acanthurid growth models

Newly recruited Ctenochaetus striatus were monitored over a 16-month period in American Samoa, 2002–2003. During this period, a mass recruitment of age-0 C. striatus occurred in March 2002 with numbers reaching 22.9 recruits m^?2. This program provided an invaluable opportunity to (1) analyze the dynamics of a mass recruitment episode and to assess its significance with respect to more typical patterns of recruitment and (2) establish the pattern of recruit growth during their first year of life. Age-based analysis indicated that the mass recruitment generated about 90 % of annual recruitment, but recruit mortality was high; thus, most recruitment was provided by continuous settlement throughout the year. The mass event appeared to be a short-lived pulse with recruits residing on the reef an average of 14.1 d compared with 161.1 d for other recruits. Recruits grew rapidly, achieving 90 % of their adult size during their first year, and they formed their first otolith annulus after 1 yr, thereby providing a firm basis for otolith interpretation of fish ages during the early life history phase of this species. The extensive age-based documentation of their first year growth in this study validates the distinctive “square” growth pattern exhibited by acanthurids as described in the literature (i.e., long life span with rapid initial growth that quickly reaches an asymptotic size), and it demonstrates the impact that the presence of age-0 fish has when generating growth parameters for populations exhibiting square growth. We found that the parameters from the re-parameterized von Bertalanffy growth function have preferred characteristics when modeling square growth in fish and that fixing age-at-length zero to pelagic larval duration is a preferable method to constrain growth models when lacking age-0 fish.     

Size-spectra as indicators of the effects of fishing on coral reef fish assemblages

The data requirements and resources needed to develop multispecies indicators of fishing impacts are often lacking and this is particularly true for coral reef fisheries. Size-spectra, relationships between abundance and body-size class, regardless of taxonomy, can be calculated from simple sizeabundance data. Both the slope and the mid-point height of the relationship can be compared at different fishing intensities. Here, we develop size-spectra for reef fish assemblages using body size- abundance data collected by underwater visual census in each of ten fishing grounds across a known gradient of fishing intensity in the Kadavu Island group, Fiji. Slopes of the size-spectra became steeper (F_9,69=3.20, p<0.01) and the height declined (F_9,69=15.78, p<0.001) with increasing fishing intensity. Regressions of numbers of individuals per size class across grounds were negative for all size classes, although the slope was almost zero for the smallest size class. Response to exploitation of each size class category was greatest for larger fish. Steepening of the slope with increasing fishing intensity largely resulted from reductions in the relative abundance of large fish and not from the ecological release of small fish following depletion of their predators. The slope and height of the size-spectrum appear to be good indicators of fishing effects on reef fish assemblages.     

Behavioural models of population growth rates: implications for conservation and prediction

Conservation biologists often wish to predict how vertebrate populations will respond to local or global changes in conditions such as those resulting from sea-level rise, deforestation, exploitation, genetically modified crops, global warming, human disturbance or from conservation activities. Predicting the consequences of such changes almost always requires understanding the population growth rate and the density dependence. Traditional means of directly measuring density dependence are often extremely difficult and have the problem that if the environment changes then it is necessary to remeasure the density dependence. We describe an alternative approach that does not require such long datasets and can be used to predict the density dependence under novel conditions. Game theory can be used to describe behavioural decisions that individuals make in response to interference, prey depletion, territorial behaviour or social dominance, and the resultant fitness consequences. It is then possible to predict how survival or reproductive output changes with population size. From this we can then make predictions about the responses of populations to environmental changes. We will illustrate how this can be applied to a range of species and a range of applied problems.     

Effects of sample size on estimates of population growth rates calculated with matrix models

Background

Matrix models are widely used to study the dynamics and demography of populations. An important but overlooked issue is how the number of individuals sampled influences estimates of the population growth rate (λ) calculated with matrix models. Even unbiased estimates of vital rates do not ensure unbiased estimates of λ–Jensen''s Inequality implies that even when the estimates of the vital rates are accurate, small sample sizes lead to biased estimates of λ due to increased sampling variance. We investigated if sampling variability and the distribution of sampling effort among size classes lead to biases in estimates of λ.

Methodology/Principal Findings

Using data from a long-term field study of plant demography, we simulated the effects of sampling variance by drawing vital rates and calculating λ for increasingly larger populations drawn from a total population of 3842 plants. We then compared these estimates of λ with those based on the entire population and calculated the resulting bias. Finally, we conducted a review of the literature to determine the sample sizes typically used when parameterizing matrix models used to study plant demography.

Conclusions/Significance

We found significant bias at small sample sizes when survival was low (survival = 0.5), and that sampling with a more-realistic inverse J-shaped population structure exacerbated this bias. However our simulations also demonstrate that these biases rapidly become negligible with increasing sample sizes or as survival increases. For many of the sample sizes used in demographic studies, matrix models are probably robust to the biases resulting from sampling variance of vital rates. However, this conclusion may depend on the structure of populations or the distribution of sampling effort in ways that are unexplored. We suggest more intensive sampling of populations when individual survival is low and greater sampling of stages with high elasticities.     

Kinetic models for growth and product formation on multiple substrates

Hydrolyzates from lignocellulosic biomass contain a mixture of simple sugars; the predominant ones being glucose, cellobiose and xylose. The fermentation of such mixtures to ethanol or other chemicals requires an understanding of how each of these substrates is utilized.Candida lusitaniae can efficiently produce ethanol from both glucose and cellobiose and is an attractive organism for ethanol production. Experiments were performed to obtain kinetic data for ethanol production from glucose, cellobiose and xylose. Various combinations were tested in order to determine kinetic behavior with multiple carbon sources. Glucose was shown to repress the utilization of cellobiose and xylose. However, cellobiose and xylose were simultaneously utilized after glucose depletion. Maximum volumetric ethanol production rates were 0.56, 0.33, and 0.003 g/L-h from glucose, cellobiose and xylose, respectively. A kinetic model based on cAMP mediated catabolite repression was developed. This model adequately described the growth and ethanol production from a mixture of sugars in a batch culture.     

On stochastic logistic population growth models with immigration and multiple births

This paper develops a stochastic logistic population growth model with immigration and multiple births. The differential equations for the low-order cumulant functions (i.e., mean, variance, and skewness) of the single birth model are reviewed, and the corresponding equations for the multiple birth model are derived. Accurate approximate solutions for the cumulant functions are obtained using moment closure methods for two families of model parameterizations, one for badger and the other for fox population growth. For both model families, the equilibrium size distribution may be approximated well using the Normal approximation, and even more accurately using the saddlepoint approximation. It is shown that in comparison with the corresponding single birth model, the multiple birth mechanism increases the skewness and the variance of the equilibrium distribution, but slightly reduces its mean. Moreover, the type of density-dependent population control is shown to influence the sign of the skewness and the size of the variance.     

Detecting and cleaning outliers for robust estimation of variogram models in insect count data

Outlier detection and cleaning procedures were evaluated to estimate mathematical restricted variogram models with discrete insect population count data. Because variogram modeling is significantly affected by outliers, methods to detect and clean outliers from data sets are critical for proper variogram modeling. In this study, we examined spatial data in the form of discrete measurements of insect counts on a rectangular grid. Two well-known insect pest population data were analyzed; one data set was the western flower thrips, Frankliniella occidentalis (Pergande) on greenhouse cucumbers and the other was the greenhouse whitefly, Trialeurodes vaporariorum (Westwood) on greenhouse cherry tomatoes. A spatial additive outlier model was constructed to detect outliers in both the isolated and patchy spatial distributions of outliers, and the outliers were cleaned with the neighboring median cleaner. To analyze the effect of outliers, we compared the relative nugget effects of data cleaned of outliers and data still containing outliers after transformation. In addition, the correlation coefficients between the actual and predicted values were compared using the leave-one-out cross-validation method with data cleaned of outliers and non-cleaned data after unbiased back transformation. The outlier detection and cleaning procedure improved geostatistical analysis, particularly by reducing the nugget effect, which greatly impacts the prediction variance of kriging. Consequently, the outlier detection and cleaning procedures used here improved the results of geostatistical analysis with highly skewed and extremely fluctuating data, such as insect counts.