Virginia Institute of Marine Science

AbstractIt is well known that statistical power calculations can be valuable in planning an experiment. There is also a large literature advocating that power calculations be made whenever one performs a statistical test of a hypothesis and one obtains a statistically nonsignificant result. Advocates of such post-experiment power calculations claim the calculations should be used to aid in the interpretation of the experimental results. This approach, which appears in various forms, is fundamentally flawed. We document that the problem is extensive and present arguments to demonstrate the flaw in the logic.KEY WORDS: Bioequivalence testingBurden of proofObserved powerRetrospective power analysisStatistical powerType II error

No other environmental variable of such ecological importance to estuarine and coastal marine ecosystems around the world has changed so drastically, in such a short period of time, as dissolved oxygen. While hypoxic and anoxic environments have existed through geological time, their occurrence in shallow coastal and estuarine areas appears to be increasing, most likely accelerated by human activities. Several large systems, with historical data, that never reported hypoxia at the turn of the 19th century (e.g., Kattegat, the sea between Sweden and Denmark) now experience severe seasonal hypoxia. Synthesis of literature pertaining to benthic hypoxia and anoxia revealed that the oxygen budgets of many major coastal ecosystems have been adversely affected mainly through the process of eutrophication (the production of excess organic matter). It appears that many ecosystems that are now severely stressed by hypoxia may be near or at a threshold of change or collapse (loss of fisheries, loss of biodiversity, alteration of food webs).

Polybrominated diphenyl ethers (PBDEs) have been widely used to flame-retard products common in homes and the workplace, and subsequently, they have become widely dispersed in the environment. Detailed compositional knowledge of these complex PBDE mixtures is crucial to a fuller understanding of their toxicological potencies and environmental fate due to selective congener biomagnification, degradation, and transport. Utilizing recenttechnical enhancements and newly available commercial standards, we developed a method capable of analyzing a larger suite of mono- through deca-BDEs. We then characterized the congener composition of six common technical flame-retardant mixtures: two penta-BDE products (DE-71 and Bromkal 70-5DE) two octa-BDE products (DE-79 and Bromkal 79-8DE) and two deca-BDE products (Saytex 102E and Bromkal 82-0DE). PBDEs were analyzed by gas chromatography/mass spectrometry (GC/MS). Structural conformations based on fragmentation patterns and molecular ions were established by electron-capture negative ionization (ECNI) and electron ionization (El). Sixty-four commercially available PBDE standards were chromato-graphed on two GC columns (DB-1HT and DB-5HT) and relative retention indexes (RRI) calculated. Thirty-nine PBDEs were identified in these products, 29 at concentrations >0.02% by weight. Of these, 12 previously unreported congeners have been confirmed as commercial mixture components. Four of these congeners were detected >0.02% w/w (BDE-144, -171, -180, and -201) and three (BDE-75, -184, and -194) at <0.02%. Five other congeners (four <0.02% by weight) were tentatively identified based on their molecular ion and ECNI fragmentation in the absence of corresponding analytical standards.

In 5 recent years (2000–2004), the Changjiang (Yangtze) River has discharged past Datong (600 km from the river mouth) an average of ∼250 million tons (mt) of sediment per year, a decrease of more than 40% since the 1950s and 1960s, whereas water discharge at Datong has increased slightly. Water and sediment discharge data from the upper, middle, and lower reaches of the river suggest that the reduction of the Changjiang sediment load has occurred in two phases between 1950 and 2002: following the closure of the Danjiangkou Reservoir on the Hanjiang tributary in 1968 and following the installation of numerous dams and water‐soil conservation works in the Jialingjijang catchment after 1985. As the Three Gorges Dam (TGD) started operating in 2003, the Changjiang entered a third phase of sediment reduction with annual sediment loads at Datong less than 200 mt/yr. Upon completion of the Three Gorges Dam (TGD) in 2009, the sediment load at Datong will decrease to ∼210 mt/yr for the first 20 years, then will recover to ∼230 mt/yr during 2030–2060, and will reach ∼310 mt/yr during 2060–2110. From the sediment budget and sediment erosion data for the Changjiang subaqueous delta, it can be assumed that the delta will be eroded extensively during the first five decades after TGD operation and then will approach a balance during the next five decades as sediment discharging from TGD again increases.

Biodiversity at multiple levels - genotypes within species, species within functional groups, habitats within a landscape - enhances productivity, resource use, and stability of seagrass ecosystems. Several themes emerge from a review of the mostly indirect evidence and the few experiments that explicitly manipulated diversity in seagrass systems. First, because many seagrass communities are dominated by 1 or a few plant species, genetic and phenotypic diversity within such foundation species has important influences on ecosystem productivity and stability. Second, in seagrass beds and many other aquatic systems, consumer control is strong, extinction is biased toward large body size and high trophic levels, and thus human impacts are often mediated by interactions of changing 'vertical diversity' (food chain length) with changing 'horizontal diversity' (heterogeneity within trophic levels). Third, the openness of marine systems means that ecosystem structure and processes often depend on interactions among habitats within a landscape (landscape diversity). There is clear evidence from seagrass systems that advection of resources and active movement of consumers among adjacent habitats influence nutrient fluxes, trophic transfer, fishery production, and species diversity. Future investigations of biodiversity effects on processes within seagrass and other aquatic ecosystems would benefit from broadening the concept of biodiversity to encompass the hierarchy of genetic through landscape diversity, focusing on links between diversity and trophic interactions, and on links between regional diversity, local diversity, and ecosystem processes. Maintaining biodiversity and biocomplexity of seagrass and other coastal ecosystems has important conservation and management implications.

Abstract Many methods have been developed in the last 70 years to predict the natural mortality rate, M, of a stock based on empirical evidence from comparative life history studies. These indirect or empirical methods are used in most stock assessments to (i) obtain estimates of M in the absence of direct information, (ii) check on the reasonableness of a direct estimate of M, (iii) examine the range of plausible M estimates for the stock under consideration, and (iv) define prior distributions for Bayesian analyses. The two most cited empirical methods have appeared in the literature over 2500 times to date. Despite the importance of these methods, there is no consensus in the literature on how well these methods work in terms of prediction error or how their performance may be ranked. We evaluate estimators based on various combinations of maximum age (tmax), growth parameters, and water temperature by seeing how well they reproduce &amp;gt;200 independent, direct estimates of M. We use tenfold cross-validation to estimate the prediction error of the estimators and to rank their performance. With updated and carefully reviewed data, we conclude that a tmax-based estimator performs the best among all estimators evaluated. The tmax-based estimators in turn perform better than the Alverson–Carney method based on tmax and the von Bertalanffy K coefficient, Pauly’s method based on growth parameters and water temperature and methods based just on K. It is possible to combine two independent methods by computing a weighted mean but the improvement over the tmax-based methods is slight. Based on cross-validation prediction error, model residual patterns, model parsimony, and biological considerations, we recommend the use of a tmax-based estimator (M=4.899tmax−0.916, prediction error = 0.32) when possible and a growth-based method (M=4.118K0.73L∞−0.33 , prediction error = 0.6, length in cm) otherwise.

Author Posting. © The Oceanography Society, 2013. This article is posted here by permission of The Oceanography Society for personal use, not for redistribution. The definitive version was published in Oceanography 26, no. 3 (2013): 124–131, doi:10.5670/oceanog.2013.54.

Summary In a population with Allee effects a positive relationship exists between fitness and population size or density. Allee effects may result in extinction thresholds and are therefore crucial in conservation and management. It has been shown theoretically that Allee effects can be driven by predation; however, there are few empirical data. Previous empirical work on Allee effects has emphasized that taxa with life‐history characteristics such as co‐operative breeding may be prone to such effects. Because predation is a general ecological mechanism, Allee effects may be more widespread than previously thought. We used a series of simple heuristic models to develop a theoretical framework for understanding predation‐driven Allee effects as a function of predator functional and aggregative responses. Predators can create an Allee effect if they have a type I (linear) or type II (saturating) functional response without a type III (sigmoid) aggregative response, or vice versa. In addition, predation must be the main driver of prey dynamics, and prey must have little spatial or temporal refuge from predation. We highlighted several, mainly unrecognized, examples of predation‐driven Allee effects from the literature, the majority of which came from systems that had been perturbed by exploitation or introduced predators. Synthesis and applications . Allee effects can arise from a general ecological process under a variety of different combinations of functional and aggregative responses. Allee effects may thus be present in a broad spectrum of different taxa with different types of life history, not only those taxa, such as broadcast spawners and co‐operative breeders, on which empirical work has focused thus far. Conservation biologists and managers working with heavily exploited or threatened populations, or attempting reintroductions, should be aware of the possibility of a threshold population size or density below which extinction is likely. These thresholds can occur regardless of species life history, if predation is a major source of mortality and spatial and temporal predation refuges are limited.

At a restored reef site and a control site in the Choptank River, Maryland, USA, we partially quantified the effect of oyster reef restoration on the removal of nutrients from the water column by determining seasonal fluxes of oxygen (O 2 ), ammonium (NH 4 + ), combined nitrate and nitrite (NO 2+ 3 ), di-nitrogen (N 2 ) and soluble reactive phosphorus (SRP) and by assessing the assimilation of nutrients by macrofauna. Fluxes of O 2 , NH 4 + , NO 2+ 3 and SRP at the restored site were enhanced by at least one order of magnitude during all seasons. Seasonal denitrification rates at the restored site, measured as flux of N 2 -N, ranged from 0.3 to 1.6 mmol N 2 -N m -2 h -1 , with August rates among the highest ever recorded for an aquatic system. In addition to oysters (131 oysters m -2 ; average shell height = 114 mm; age = 2 to 7 yr), the restored reef provided habitat for 24 585 other macrobenthic organisms per square meter compared to 2265 organisms m -2 at the control site. Restoration enhanced the average standing stock of assimilated nutrients by 95 g N m -2 and 15 g P m -2 . Nitrogen and phosphorus in shells of live oysters and mussels accounted for 47 and 48% of total nitrogen and phosphorus standing stocks, respectively. Our results demonstrate that oyster reef restoration can significantly increase denitrification rates and enhance nutrient sequestration via assimilation into bivalve shells.

virtualspecies is a freely available package for R designed to generate virtual species distributions, a procedure increasingly used in ecology to improve species distribution models. This package combines the existing methodological approaches with the objective of generating virtual species distributions with increased ecological realism. The package includes 1) generating the probability of occurrence of a virtual species from a spatial set of environmental conditions (i.e. environmental suitability), with two different approaches; 2) converting the environmental suitability into presence–absence with a probabilistic approach; 3) introducing dispersal limitations in the realised virtual species distributions and 4) sampling occurrences with different biases in the sampling procedure. The package was designed to be extremely flexible, to allow users to simulate their own defined species–environment relationships, as well as to provide a fine control over every simulation parameter. The package also includes a function to generate random virtual species distributions. We provide a simple example in this paper showing how increasing ecological realism of the virtual species impacts the predictive performance of species distribution models. We expect that this new package will be valuable to researchers willing to test techniques and protocols of species distribution models as well as various biogeographical hypotheses.

Oceanic or coastal spawning grounds of fish are often distant from nursery areas. Fish larvae require appropriate currents and sufficient and suitable food during transit to reach the nursery area at the proper time, size, and condition. Meteorologic and oceanographic factors influence food availability and transport direction and time. Annual variation in these controlling factors could affect recruitment success. Certain generalizations can be made that apply to marine and estuarine systems. Reproduction occurs in a selected portion of the speciesˈ total range. Spawning often takes place close to gyral, upwelling, or other directional circulations that frequently are associated with major current systems. The coupling of spawning to natural oceanographic transport systems for eggs and larvae is advantageous to a species as long as those systems operate normally. The details of such coupling, and the consequences for eggs and larvae of deviations from usual transport mechanisms, remain poorly understood. Investigation of year-class success requires a clearer understanding of the natural variability and periodicity inherent in these physical processes. Further research is needed to resolve these details, including environmental cues to reproductive behavior and relative importance of passive and behaviorally mediated transport; to statistically analyze atmospheric and oceanographic cycles; and to quantify transport mechanisms for spawner-recruit models and predictions of year-class success.

Southern Ocean primary productivity plays a key role in global ocean biogeochemistry and climate. At the Southern Ocean sea ice edge in coastal McMurdo Sound, we observed simultaneous cobalamin and iron limitation of surface water phytoplankton communities in late Austral summer. Cobalamin is produced only by bacteria and archaea, suggesting phytoplankton-bacterial interactions must play a role in this limitation. To characterize these interactions and investigate the molecular basis of multiple nutrient limitation, we examined transitions in global gene expression over short time scales, induced by shifts in micronutrient availability. Diatoms, the dominant primary producers, exhibited transcriptional patterns indicative of co-occurring iron and cobalamin deprivation. The major contributor to cobalamin biosynthesis gene expression was a gammaproteobacterial population, Oceanospirillaceae ASP10-02a. This group also contributed significantly to metagenomic cobalamin biosynthesis gene abundance throughout Southern Ocean surface waters. Oceanospirillaceae ASP10-02a displayed elevated expression of organic matter acquisition and cell surface attachment-related genes, consistent with a mutualistic relationship in which they are dependent on phytoplankton growth to fuel cobalamin production. Separate bacterial groups, including Methylophaga, appeared to rely on phytoplankton for carbon and energy sources, but displayed gene expression patterns consistent with iron and cobalamin deprivation. This suggests they also compete with phytoplankton and are important cobalamin consumers. Expression patterns of siderophore- related genes offer evidence for bacterial influences on iron availability as well. The nature and degree of this episodic colimitation appear to be mediated by a series of phytoplankton-bacterial interactions in both positive and negative feedback loops.

We present a new modeling system for wave‐current interaction based on unstructured grids and thus suitable for very large‐scale high‐resolution multiscale studies. The coupling between the 3D current model (SELFE) and the 3rd generation spectral wave model (WWM‐II) is done at the source code level and the two models share same sub‐domains in the parallel MPI implementation in order to ensure parallel efficiency and avoid interpolation. We demonstrate the accuracy, efficiency, stability and robustness of the coupled SELFE‐WWM‐II model with a suite of progressively challenging benchmarks with analytical solution, laboratory data, and field data. The coupled model is shown to be able to capture important physics of the wave‐current interaction under very different scales and environmental conditions with excellent convergence properties even in complicated test cases. The challenges in simulating the 3D wave‐induced effects are highlighted as well, where more research is warranted.

Nutrient pollution and reduced grazing each can stimulate algal blooms as shown by numerous experiments. But because experiments rarely incorporate natural variation in environmental factors and biodiversity, conditions determining the relative strength of bottom-up and top-down forcing remain unresolved. We factorially added nutrients and reduced grazing at 15 sites across the range of the marine foundation species eelgrass (Zostera marina) to quantify how top-down and bottom-up control interact with natural gradients in biodiversity and environmental forcing. Experiments confirmed modest top-down control of algae, whereas fertilisation had no general effect. Unexpectedly, grazer and algal biomass were better predicted by cross-site variation in grazer and eelgrass diversity than by global environmental gradients. Moreover, these large-scale patterns corresponded strikingly with prior small-scale experiments. Our results link global and local evidence that biodiversity and top-down control strongly influence functioning of threatened seagrass ecosystems, and suggest that biodiversity is comparably important to global change stressors.

The continental shelf of the Ross Sea exhibits substantial variations in physical forcing, ice cover, and biological processes on a variety of time and space scales. Its circulation is characterized by advective inputs from the east and exchanges with off-shelf regions via the troughs along the northern portions. Phytoplankton biomass is greater there than anywhere else in the Antarctic, although nitrate is rarely reduced to levels below 10 μmol L −1 . Overall growth is regulated by irradiance (via ice at the surface and by the depths of the mixed layers) and iron concentrations. Apex predators reach exceptional abundances, and the world's largest colonies of Adélie and emperor penguins are found there. Krill are represented by two species ( Euphausia superba near the shelf break and Euphausia crystallorophias throughout the continental shelf region). Equally important and poorly known is the Antarctic silverfish ( Pleuragramma antarcticum ), which is also consumed by most upper-trophic-level predators. Future changes in the Ross Sea environment will have profound and unpredictable effects on the food web.

Vetter (1988) noted that her review of the estimation of the instantaneous natural mortality rate (M) was initiated by a discussion among colleagues that identified M as thesingle most impor ta nt but least well-estimated parameter in fishery models. A lthough much has been accomplished in the inter vening years, M remains one of the most difficult parameters to estimate in fishery stock assessments. A number of novel approaches using tagging and telemetry data provide promise for making reliable direct estimates of M for a given stock (Hearn et al., 1998 ; Frusher and Hoenig, 2001; Hightower et al., 2001; Latour et al., 2003; Pollock et al., 2004). However, such methods are often impracticableand fishery scientists must approximate M by using estimates made for other stocks of the same or similarspecies or by predicting M from features of the species’ life history (Beverton and Holt, 1959; Beverton, 1963; Alverson and Carney, 1975; Pauly, 1980; Hoenig, 1983; Peterson and Wroblewski, 1984; Roff, 1984; Gunderson and Dygert, 1988; Chen and Watanabe, 1989; Charnov, 1993;Jensen, 1996; Lorenzen, 1996).

[1] Tide effects on the structure of the near-field Changjiang River plume and on the extension of the far-field plume have often been neglected in analysis and numerical simulations, which is the focus of this study. Numerical experiments highlighted the crucial role of the tidal forcing in modulating the Changjiang River plume. Without the tidal forcing, the plume results in an unrealistic upstream extension along the Jiangsu coast. With the tidal forcing, the vertical mixing increases, resulting in a strong horizontal salinity gradient at the northern side of the Changjiang River mouth along the Jiangsu coast, which acts as a dynamic barrier and restricts the northward migration of the plume. Furthermore, the tidal forcing produces a bidirectional plume structure in the near field, and the plume separation is located at the head of the submarine canyon. A significant bulge occurs around the head of the submarine canyon and rotates anticyclonically, which carries a large portion of the diluted water toward the northeast and merges into the far-field plume. A portion of the diluted water moves toward the southeast, which is mainly caused by tidal rectification. This bidirectional plume structure is more evident under certain wind conditions. During the neap tide with the reduced tidal energy, the near-field plume extends farther offshore, and the bulge becomes less evident. These dynamic behaviors are maintained and are fundamentally important in the region around the river mouth even under the summer monsoon and the shelf currents, although in the far field the wind forcing and shelf currents eventually dominate the plume extension.

article Curriculum recommendations for the undergraduate program in computer science: a working report of the ACM committee on curriculum in computer sciences Share on Authors: Richard H. Austing University of Maryland University of MarylandView Profile , Bruce H. Barnes National Science Foundation National Science FoundationView Profile , Delle. T. Bonnette University of Southwestern Louisiana University of Southwestern LouisianaView Profile , Gerald L. Engel Virginia Institute of Marine Science Virginia Institute of Marine ScienceView Profile , Gordon Stokes Brigham Young University Brigham Young UniversityView Profile Authors Info & Claims ACM SIGCSE BulletinVolume 9Issue 2June 1977 pp 1–16https://doi.org/10.1145/988948.988950Online:01 June 1977Publication History 68citation233DownloadsMetricsTotal Citations68Total Downloads233Last 12 Months3Last 6 weeks2 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access

Boon, J.D., 2012. Evidence of sea level acceleration at U.S. and Canadian tide stations, Atlantic Coast, North America.Evidence of statistically significant acceleration in sea level rise relative to land is found in a recent analysis of monthly mean sea level (mmsl) at tide stations on the Atlantic coast of North America. Serial trend analysis was used at 11 U.S. Atlantic coast stations and 1 Canadian station (Halifax, Nova Scotia) with record lengths exceeding 75 years to examine change in the linear trend rate of rise over time. Deriving trend estimates that apply in the median year of fixed-length mmsl series, reversals in rate direction (increasing or decreasing) were observed around 1939–40 and again in the mid-1960s except at the northeasternmost stations in the latter period. What has not been observed until recently is a sharp reversal (in 1987) followed by a uniform, near-linear change in rise rate that infers constant acceleration at eight mid- to NE Atlantic tide stations, change not seen at SE U.S. Atlantic stations. Quadratic regression and analysis of variance applied to mmsl series over the last 43 years (1969–2011) confirms that addition of a quadratic term representing acceleration is statistically significant at 16 tide stations from Virginia to Nova Scotia. Previous quadratic model studies have focused on sea level series of longer spanning periods with variable serial trends undermining quadratic expression of either accelerating or decelerating sea level. Although the present 43-year analysis offers no proof that acceleration will be long lived, the rapidity of the nascent serial trend increase within the region of interest is unusual. Assuming constant acceleration exists and continues, the regression model projects mmsl by 2050 varying between 0.2 and 0.9 m above mean sea level (MSL) in the NE region and between −0.3 and 0.4 m above MSL in the SE region.

Seagrasses have received considerable attention over the past 2 decades because of the multiple ecological roles they play in estuarine and coastal ecosystems and concerns over worldwide losses of seagrass habitat due to direct and indirect human impacts. Restoration and conservation efforts are underway in some areas of the world, but progress may be limited by the paucity of information on the role of seeds in bed dynamics. Although flowering occurs in most of the 58 seagrass species, seed germination data exist for only 19 of the 42 species that have some period of dormancy, with only 93 published references to field and/or laboratory studies. This review addresses critical issues in conservation and restoration of seagrasses involving seed dormancy (e.g. environmental vs physiological), existence and type of seed bank (transient or persistent), and factors influencing seed germination (e.g. salinity, temperature, light). Results of many earlier published studies relating seed germination to various environmental factors may need re-examination given more recent published data which show a confounding influence of oxygen level on the germination process. We highlight the importance of conducting ecologically meaningful germination studies, including germination experiments conducted in sediments. We also identify questions for future research that may figure prominently in landscape level questions regarding protected marine or estuarine reserves, habitat fragmentation, and restoration.