Hydrolithon spp. (Rhodophyta, Corallinales) overgrow live corals (Cnidaria, Scleractinia) in Yemen

In Yemen, off the northwestern coast in the Gulf of Aden, the coralline algae Hydrolithon rupestre (Foslie) Penrose 1996 and H. murakoshii Iryu and Matsuda 1996 have been observed to overgrow and kill living Porites lutea Milne-Edwards and Haime, 1860. Similarly, Hydrolithon onkodes (Heydrich) Penrose and Woelkerling 1992 and H. rupestre were observed overgrowing Stylophora pistillata (Esper, 1797). Competitive interactions between P. lutea and H. murakoshii were monitored from 2006 to 2009 at two sites and showed an average linear growth of 8.3 (±1.9 SD) mm?year^?1 over the coral. The small polyps of S. pistillata and P. lutea combined with putative chemical compounds produced by Hydrolithon spp. are likely to allow the coralline overgrowth. Although corallines can locally kill coral tissues, the CCA/coral interactions do not seem to affect the overall live coral cover at the study sites.     

Model selection criteria for overdispersed data and their application to the characterization of a host-parasite relationship

In the statistical modeling of a biological or ecological phenomenon, selecting an optimal model among a collection of candidates is a critical issue. To identify an optimal candidate model, a number of model selection criteria have been developed and investigated based on estimating Kullback’s (Information theory and statistics. Dover, Mineola, 1968) directed or symmetric divergence. Criteria that target the directed divergence include the Akaike (2nd international symposium on information theory. Akadémia Kiadó, Budapest, Hungary, pp 267–281, 1973, IEEE Trans Autom Control AC 19:716–723, 1974) information criterion, AIC, and the “corrected” Akaike information criterion (Hurvich and Tsai in Biometrika 76:297–307, 1989), AICc; criteria that target the symmetric divergence include the Kullback information criterion, KIC, and the “corrected” Kullback information criterion, KICc (Cavanaugh in Stat Probab Lett 42:333–343, 1999; Aust N Z J Stat 46:257–274, 2004). For overdispersed count data, simple modifications of AIC and AICc have been increasingly utilized: specifically, the quasi Akaike information criterion, QAIC, and its corrected version, QAICc (Lebreton et al. in Ecol Monogr 62(1):67–118 1992). In this paper, we propose analogues of QAIC and QAICc based on estimating the symmetric as opposed to the directed divergence: QKIC and QKICc. We evaluate the selection performance of AIC, AICc, QAIC, QAICc, KIC, KICc, QKIC, and QKICc in a simulation study, and illustrate their practical utility in an ecological application. In our application, we use the criteria to formulate statistical models of the tick (Dermacentor variabilis) load on a white-footed mouse (Peromyscus leucopus) in northern Missouri.     

n-Octyl esters of long-chain fatty acids are not anthropogenic pollution markers

n-Octyl esters of higher fatty acids have been reported as markers of urban wastewater in sediments, polychaeta, fish, crabs and oysters (Chaler et al. in J Chromatogr A 1046:203–210, 2004)). However, up to date, there were no subsequent studies to confirm this claim. Likewise, Chaler and co-workers did not consider that the mentioned compounds might occur naturally in the environment. Here we found seven n-octyl straight-chain alkanoates, from C-20 to C-26, in the wild-growing plant Heracleum sphondylium L., Apiaceae, from 14 locations. Those plant metabolites were unambiguously identified by gas chromatographic co-injection of the synthesized esters with the inflorescence washings. All identified octyl esters represent new natural compounds, except for octyl docosanoate. Since we have demonstrated that n-octyl esters occur naturally, and in abundance, they cannot be recognized any longer as wastewater markers. Additionally, here we provide evidences that the compounds identified by Chaler et al. (2004) are in fact 2-ethylhexyl esters, mistakenly identified as n-octyl esters.     

Miniaturisierung des Wachstumshemmtestes mit der Grünalge Desmodesmus subspicatus nach DIN 38412 Teil 33

Background, aim, and scope Biological test systems have been successfully used to analyse and assess the ecotoxicological potentials of sediments and dredged materials. In compliance with the German directive for dredged-material management (HABAB-WSV, BfG 2000) standardised bioassays with organisms of different trophic levels are applied to limnic sediments. The growth-inhibition test with the green alga Desmodesmus subspicatus according to DIN 38412 part 33 is one of three mandatory bioassays (Guidance paper “Ökotoxikologische Baggergutuntersuchungen”, BfG 2007). The laboratories of the German Federal Institute of Hydrology (BfG) conduct this algal test in agreement with the DIN standard in test tubes of 10?ml volume. In the following, this method is called the “conventional method” or “DIN-method”. The research described below was conducted in the BfG in a diploma-thesis aiming to develop a miniaturized algae test procedure that uses microtiter plates, but yields comparable results. Automation and miniaturization should increase the throughput capacity and reduce the time and labour requirements. Materials and methods The growth-inhibition test with the green alga Desmodesmus subspicatus according to DIN standard 38412 part 33 was taken as the starting point for the miniaturization. The testing method in microtiter plates was optimised by systematic examination of the cultivation conditions, coverages of the wells, and settings of the measuring instruments. To verify the results of the miniaturized test procedure, 25 environmental samples (20 pore waters and five single substances) were tested with the conventional and the miniaturized procedure. The results of both test procedures were compared using statistical analyses. Results The comparison of the growth inhibition test results from the microtiter plates with those from the conventional procedure indicated an average deviation of about 20?%-points. In approximately 30?% of the cases, a statistical verification with the Mann-Whitney-U-Test showed agreement of the inhibition values obtained with both methods. A method to express the ecotoxicological potential of a sample is the pT-value (Krebs 1988). The pT-values were determined based on the toxicities obtained using serial dilution. (Krebs 1988). When comparing both methods 10 out of 20 environmental samples had the same pT-value (50?%). In 40?% of the samples, the deviation was one pT-value, in 10?% it was more than one pT-value. Discussion During the optimization of the method, different parameters of the algal growth inhibition test were examined and adapted to the miniaturized system, so that all criteria required after DIN 38412 part 33 should be met. However, the miniaturized test did not reliably achieve these validity criteria, namely the increase in the biomass by a factor of 30 in the controls. This criterion was only fulfilled in two out of 31 test runs. The validation of the miniaturized growth inhibition test on the basis of a statistical comparison with the conventional method showed partially highly significant differences. Overall, significantly different inhibition values were found in about 60?% of the cases. Conclusions Without further adjustments and optimization it is not possible to substitute the conventional method by the miniaturized system. Recommendations and perspectives Further research is required to miniaturize the test procedure and to perform the algae test on microtiter plates. The validity criteria of the DIN standard, such as the increase of biomass production in the controls, should be reliably met. Basically, the aim of miniaturizing the algae test procedure is the increase in throughput capacity and, at the same time, reduced work efforts by automation. However, the test results of the miniaturized method should be comparable to those of the conventional method.     

Using surface drifter observations to measure tidal vortices and relative diffusion at Aransas Pass,Texas

Tidal vortices play an important role in the flushing of coastal regions. At the mouth of a tidal inlet, the input of circulation by the ebb tide may force the formation of a starting-jet dipole vortex. The continuous ebb jet current also creates a periodic sequence of secondary vortices shed from the inlet mouth. In each case, these tidal vortices have a shallow aspect ratio, with a lateral extent much greater than the water depth. These shallow vortices affect the transport of passive tracers, such as nutrients and sediment from the estuary to the ocean and vice versa. Field observation of tidal vortices primarily relies on ensemble averaging over several vortex events that are repeatable in space and can be sampled by a fixed Eulerian measurement grid. This paper presents an adaptive approach for locating and measuring within tidal vortices that propagate offshore near inlets and advect along variable trajectories set by the wind-driven currents. A field experiment was conducted at Aransas Pass, Texas to measure these large-scale vortices. Locations of the vortices produced during ebb tide were determined using near real-time updates from surface drifters deployed near or within the inlet during ebb tide, and the paths of towed acoustic Doppler current profiler (ADCP) transects were selected by analysis of the drifter observations. This method allowed ADCP transects to be collected within ebb generated tidal vortices, and the paths of the drifters indicated the presence of both the starting-jet dipole and the secondary vortices of the unstable ebb tidal jet. Drifter trajectories were also used to estimate the size of each observed vortex as well as the statistics of relative diffusion offshore of Aransas Pass. The field data confirmed the starting-jet spin-up time (time until the vortex dipole begins to propagate offshore) measured in the laboratory by Bryant et al. [6] and that the Strouhal condition of \(St=0.2\) predicts the shedding of secondary vortices from the inlet mouth. The size of the rotational core of the vortex is also shown to be approximated physically by the inlet width or by \(0.02UT\) , where U is the maximum velocity through the inlet channel and T is the tidal period, and confirms results found in laboratory experiments by Nicolau del Roure et al. [23]. Additionally, the scale of diffusion was approximately 1–15 km and the apparent diffusivity was between 2–130  \(m^2/s\) following Richardsons law.     

Functional ANOVA starting from discrete data: an application to air quality data

A nonparametric functional approach is proposed to compare the mean functions of $k$ k samples of curves. In practice, curves data are usually collected in a discrete form and hence they must be pre-processed to use purely functional techniques. However, in the context of $k$ k -sample tests, the pre-processing step can have effects in terms of power reduction. Hall and Van Keilegom (Stat Sin 17:1511–1531, 2007) proposed a methodology to minimizing these effects in the context of tests for the equality of two distribution functions. Their procedure is here extended to the case of $k$ k -sample hypothesis tests. The asymptotic validity of the procedure is established and its finite sample performance is analyzed through Monte Carlo experiments. As an illustration, the method is applied to air quality data collected from several monitoring stations placed at different geographical locations at the center of Spain.     

The wave-induced solute flux from submerged sediment

The issue of the transport of dissolved nutrients and contaminants between the sediment in the bottom of a lake or reservoir and the body of water above it is an important one for many reasons. In particular the biological and chemical condition of the body of water is intricately linked to these mass transport processes. As the review by Boudreau (Rev Geophys 38(3):389–416, 2000) clearly demonstrates those transport processes are very complex involving mechanisms as diverse as the wave-induced flux between the sediment and the overlying water and the effect of burrowing animals on the transport within the sediment as well as basic diffusion mechanisms. The present paper focuses on one facet of these transport processes; we re-examine the balance of diffusion and wave-induced advection and demonstrate that the wave-induced flux of a solute from submerged sediment is not necessarily purely diffusive as suggested by Harrison et al. (J Geophys Res 88:7617–7622, 1983) but can be dominated by a mean or time-averaged flux induced by the advective fluid motion into and out of the sediment caused by the fluctuating pressure waves associated with wave motion. Indeed along the subtidal shoreline where the fluctuating bottom pressures are greatest, wave-induced advection will dominate the mean, time-averaged transport of solute into or out of the sediment as suggested in the work of Riedl et al. (Mar Biol 13:210–221, 1972). However, the present calculations also indicate that this advective flux decreases rapidly with increasing depth so that further away from the shoreline the advective flux becomes negligible relative to the diffusive flux and therefore the latter dominates in deeper water.     

Bootstrap confidence intervals for adaptive cluster sampling design based on Horvitz–Thompson type estimators

Perez and Pontius (J Stat Comput Simul 76:755–764, 2006) introduced several bootstrap methods under adaptive cluster sampling using a Horvitz–Thompson type estimator. Using a simulation study, they showed that their proposed methods provide confidence intervals with highly understated coverage rates. In this article, we first show that their bootstrap methods provide biased bootstrap estimates. We then define two bootstrap methods, based on the method of Gross (Proceeding of the survey research methods section. American Statistical Association, Alexandria, VA, pp 181–184, 1980) and Bootstrap With Replacement, that provide unbiased bootstrap estimates of the population mean with bootstrap variances matching the corresponding unbiased variance estimator. Using a simulation study, we show that the bootstrap confidence intervals based on our proposed methods have better performance than those based on available bootstrap methods, in the sense of having coverage proportion closer to the nominal coverage level. We also compare the proposed intervals to empirical likelihood based intervals in small samples.     

Statistical modeling to assess drinking water crisis

We modify the beta distribution by adding a parameter ρ ≥ 0 to capture the urgency level with which nations address drinking water crises. In essence, the urgency parameter relates to region’s environmental or development levels. The modified version is named an urgency biased beta distribution (UBBD). Its statistical properties are considered and illustrated by analysis of the drinking water data in the World Health Organization (2011) report. The methodology of this article is applicable to similar data sets arising in ecological, engineering, medical, business, marketing, and communication, etc. studies.     

Analysis of periodic patterns of daily precipitation through simultaneous modeling of its serially observed occurrence and amount

Precipitation is of great importance to agriculture, environment and ecosystem as a regular precipitation pattern is usually vital to healthy plants; excessive or insufficient rainfall can be harmful. Periodic patterns of precipitation can be studied based on regularly observed data over time. Since regularly observed precipitation data are generally skewed with many zeros, two common analysis approaches have been proposed recently. One approach investigates precipitation using a two-part model where the occurrence and positive amount of precipitation are analyzed separately (Piantadosi et al. in Environ Model Assess 14:431–438, 2009), whereas the other approach handles occurrence and amount simultaneously using a Tweedie’s compound Poisson model for independent observations (Hasan and Dunn in Int J Climatol 32:1006–1017, 2012). The former approach fails to maintain the regular temporal structure of serially observed precipitation, whereas the latter approach ignores serial dependence. As there is generally substantial serial correlation in the observed sequence of precipitation data over time, we introduce a compound Poisson state-space model with serially correlated random effects for daily precipitation data. This approach characterizes both occurrence and amount of precipitation simultaneously while accounting for the corresponding serial correlation. Our main results depend only on the first- and second-moment assumptions of unobserved random effects. We illustrate our method with the analysis of the daily precipitation data recorded at Mount Washington, NH, USA.     

Waves and turbulence in katabatic winds

The measurements taken during the Vertical Transport and Mixing Experiment (VTMX, October, 2000) on a northeastern slope of Salt Lake Valley, Utah, were used to calculate the statistics of velocity fluctuations in a katabatic gravity current in the absence of synoptic forcing. The data from ultrasonic anemometer-thermometers placed at elevations 4.5 and 13.9 m were used. The contributions of small-scale turbulence and waves were isolated by applying a high-pass digital (Elliptical) filter, whereupon the filtered quantities were identified as small-scale turbulence and the rest as internal gravity waves. Internal waves were found to play a role not only at canonical large gradient Richardson numbers $(\overline{\hbox {Ri}_\mathrm{g} } >1)$ , but sometimes at smaller values $(0.1 < \overline{\hbox {Ri}_\mathrm{g}}<1)$ , in contrast to typical observations in flat-terrain stable boundary layers. This may be attributed, at least partly, to (critical) internal waves on the slope, identified by Princevac et al. [1], which degenerate into turbulence and help maintain an active internal wave field. The applicability of both Monin-Obukhov (MO) similarity theory and local scaling to filtered and unfiltered data was tested by analyzing rms velocity fluctuations as a function of the stability parameter z/L, where L is the Obukhov length and z the height above the ground. For weaker stabilities, $\hbox {z/L}<1$ , the MO similarity and local scaling were valid for both filtered and unfiltered data. Conversely, when $\hbox {z/L}>1$ , the use of both scaling types is questionable, although filtered data showed a tendency to follow local scaling. A relationship between z/L and $\overline{\hbox {Ri}_\mathrm{g} }$ was identified. Eddy diffusivities of momentum $\hbox {K}_\mathrm{M}$ and heat $\hbox {K}_\mathrm{H}$ were dependent on wave activities, notably when $\overline{\hbox {Ri}_\mathrm{g} } > 1$ . The ratio $\hbox {K}_{\mathrm{H}}/\hbox {K}_{\mathrm{M}}$ dropped well below unity at high $\overline{\hbox {Ri}_\mathrm{g} }$ , in consonance with previous laboratory stratified shear layer measurements as well as other field observations.     

A general solution of Benjamin-type gravity current in a channel of non-rectangular cross-section

We consider the steady-state propagation of a high-Reynolds-number gravity current in a horizontal channel along the horizontal coordinate x. The bottom and top of the channel are at z =?0, H, and the cross-section is given by the quite general form ?f ₁(z) ≤?y ≤?f ₂(z) for 0 ≤?z ≤?H, where f _1,2 are piecewise continuous functions and f ₁ +?f ₂ >?0 for ${z \in(0,H)}$ . The interface of the current is horizontal, the (maximum) thickness is h, its density is ρ _c . The reduced gravity g′ =?|ρ _c /ρ _a ? 1|g (where ${- g\hat{z}}$ is the gravity acceleration and ρ _a the density of the ambient) drives the current with speed U into the stationary ambient fluid. We show that the dimensionless Fr =?U/(g′ h)^1/2, the rate of energy dissipation (scaled with the rate of pressure work), and the dimensionless head-loss Δ/h, can be expressed by compact formulas which involve three integrals over the cross-section areas of the current and ambient. By some standard manipulations these integrals are simplified into quite simple line-integrals of the shape-function of the channel, f(z) =?f ₁(z) +?f ₂(z), and of z f(z). This theory applies to Boussinesq and non-Boussinesq currents of “heavy” (bottom) and “light” (top) type. The classical results of Benjamin (J Fluid Mech 31:209–248, 1968) for a rectangular channel are fully recovered. We also recover the Fr results of Marino and Thomas (J Fluid Eng 131(5):051201, 2009) for channels of shape y =?±b z ^α (where b, α are positive constants); in addition, we consider the energy dissipation of these flows. The results provide insights into the effect of the cross-section shape on the behavior of the steady-state current, in quite general cases, for both heavy-into-light and light-into-heavy fluid systems, Boussinesq and non-Boussinesq. In particular, we show that a very deep current displays ${Fr = \sqrt{2}}$ , and is dissipative; the value of Fr and rate of dissipation (absolute value) decrease when the thickness of the current increases. However, in general, energy considerations restrict the thickness of the current by a clear-cut condition of the form h/H ≤?a _max ?< 1.     

Atypical plant–herbivore association of algal food and a kleptoplastic sea slug (Elysia clarki) revealed by DNA barcoding and field surveys

The identity of food sources and feeding preferences of specialist herbivores have been commonly inferred from spatial associations between consumer and food items. However, such basic information for well-known marine herbivores, sacoglossans (sea slugs), and their algal diets remains disappointingly lacking, especially from field studies. The sacoglossan, Elysia clarki (Pierce et al. in Molluscan Res 26:23–38, 2006), is kleptoplastic and sequesters chloroplasts from algal food to photosynthesize, so DNA identification of sequestered chloroplasts was employed to verify the algal species fed upon by the slug across its geographic range. The molecular information on the algae consumed by E. clarki was combined with field surveys of slugs and algae in slug habitats in the Florida Keys in July and August of 2008 in order to evaluate whether the diet of this herbivore could be predicted based on its spatial association with algae in the field. A considerable mismatch between food availability and kleptoplast identity was recorded. E. clarki commonly occupied areas devoid of potential food and often contained symbiotic plastids from algal species different from those most frequently found in the surveyed habitats. In three of the four study sites, algal species present were poor predictors of slug diet. These findings suggest that the photosynthetic capability of E. clarki may release the slug from the constraint of requiring proximity to its food sources and may allow for the potential lack of spatial coupling between this herbivore and its algal food. This combination of field surveys and DNA barcoding provided critical and previously unavailable information on herbivore feeding in this marine system.     

Comment on “Use of local tidal records to identify relative sea level change: accuracy and error for decision makers” by Powell VA, McGlashan DJ, Duck RW (2012) J Coast Conserv

In this Comment we refer to our strong reservations concerning the paper by Powell et al. J Coast Conserv, (2012) recently published on the Online First web site of the Journal of Coastal Conservation. The paper makes a number of comments on data obtained from the Permanent Service for Mean Sea Level (PSMSL) and British Oceanographic Data Centre (BODC) which are incorrect or misleading. In addition, some of their comments on sea-level science in general need to be challenged and corrected.     

A robust weighted EM algorithm for use-availability data

Wildlife sampling for habitat selection often combines a random background sample with a random sample of used sites, because the background sample could contain too few used sites to be informative for rare species. This approach is referred to as use-availability sampling. Two variants are considered where there is: (1) a random background sample including used and unused sites augmented with a sample of used sites, and (2) a sample of used sites augmented with a contaminated background sample, i.e. use is not recorded. A weighted estimator first proposed by Manski and Lerman (Econometrica 45(8):1977?C1988, 1977) forms the basis for our suggested approach. The weighted estimator has been shown to perform better than the usual unweighted approach with uncontaminated data and mis-specified logit models (Xie and Manski in Sociol Methods Res 17(3):283?C302, 1989). A weighted EM algorithm is developed for use with contaminated background data. We show that the weighted estimator continues to perform well with contaminated data and maintains its robustness to model mis-specification. The weighted estimator has not been previously used for use-availability sampling due to reliance on the assumption that only the intercept is biased, which is valid for a correct logit model. We show that adjusting the intercept may not eliminate the bias with an incorrect logit model. In this case, the weighted estimator is a relatively simple and effective alternative.     

A note on a non-stationary point source spatial model

A point source, non-stationary covariance structure model is proposed, having only one additional parameter over a standard, stationary covariance structure, spatial model. Additionally, the proposed model is demonstrated to fit better than the three extra parameter, point source, non-stationary spatial model proposed by Ecker and De Oliveira (Commun Stat Theory Methods 37:2066–2078, 2008). The proposed model is fit from a Bayesian perspective and illustrated using a house sales dataset from Cedar Falls, Iowa.     

Finite area smoothing with generalized distance splines

Most conventional spatial smoothers smooth with respect to the Euclidean distance between observations, even though this distance may not be a meaningful measure of spatial proximity, especially when boundary features are present. When domains have complicated boundaries leakage (the inappropriate linking of parts of the domain which are separated by physical barriers) can occur. To overcome this problem, we develop a method of smoothing with respect to generalized distances, such as within domain distances. We obtain the generalized distances between our points and then use multidimensional scaling to find a configuration of our observations in a Euclidean space of 2 or more dimensions, such that the Euclidian distances between points in that space closely approximate the generalized distances between the points. Smoothing is performed over this new point configuration, using a conventional smoother. To mitigate the problems associated with smoothing in high dimensions we use a generalization of thin plate spline smoothers proposed by Duchon (Constructive theory of functions of several variables, pp 85–100, 1977). This general method for smoothing with respect to generalized distances improves on the performance of previous within-domain distance spatial smoothers, and often provides a more natural model than the soap film approach of Wood et al. (J R Stat Soc Ser B Stat Methodol 70(5):931–955, 2008). The smoothers are of the linear basis with quadratic penalty type easily incorporated into a range of statistical models.     

Horizontal transport,mixing and retention in a large,shallow estuary: Río de la Plata

We use field data and a high-resolution three-dimensional (3D) hydrodynamic numerical model to investigate the horizontal transport and dispersion characteristics in the upper reaches of the shallow Río de la Plata estuary, located between the Argentinean and Uruguayan coasts, with the objective of relating the mixing characteristics to the likelihood of algal bloom formation. The 3D hydrodynamic model was validated with an extensive field experiment including both, synoptic profiling and in situ data, and then used to quantify the geographic variability of the local residence time and rate of dispersion. We show that during a high inflow regime, the aquatic environment near the Uruguayan coast, stretching almost to the middle of the estuary, had short residence time and horizontal dispersion coefficient of around 77 \(\mathrm {m}^{2}\,\mathrm {s}^{-1}\) , compared to the conditions along the Argentinean coastal regime where the residence time was much longer and the dispersion coefficient (40 \(\mathrm {m}^{2}\,\mathrm {s}^{-1}\) ) much smaller, making the Argentinian coastal margin more susceptible for algae blooms.     

Extension of the skin shear stress Li’s relationship to the flat bed

A proper estimation of the skin shear stress τ _s is necessary for a proper evaluation of sediment flux at the sediment–fluid interface. Several empirical formulas of the skin shear stress have been proposed in the literature for rippled bed as function of the factor form η/λ (η and λ are respectively the height and wavelength of the bedform). These formulas express that in the presence of bedform, τ _s is a partition of the total shear stress τ _b . In contrast, when the bottom is flat, τ _s is exactly equal to τ _b . Based on in situ measurements, Li (J Geophys Res 99:791–799, 1994) has proposed a new formula of τ _s depending on u _*/η (u _* is the friction velocity, ${u_{*}=\sqrt{\tau_{b}/\rho}}$ ), but not as a function of η/λ. This formulation appears physically more realistic, but does not cover the flat bottom range. The purpose of this short note is therefore the extension of the Li’s expression to this type of bottom.