Statistical Estimation and Model Selection of Species-Accumulation Functions

Abstract:  Soberón and Llorente (1993) proposed pure-birth stochastic processes as theoretical models for species-accumulation curves, and these processes have frequently been used to describe the progress of biological inventories. We describe, in algorithmic form, an alternative statistical analysis based on a likelihood approach ( Díaz-Francés & Gorostiza 2002 ) that provides mathematical rigor to the ideas in Soberón and Llorente (1993) and improves the estimation of the models by incorporating the facts that the variance of the error is not constant and that the observations are correlated. Additionally, we used the likelihood ratios between candidate models as an objective procedure for model selection, allowing comparison between the goodness of fit of various models. The software for these statistical methods can now be downloaded off the Internet. We used two examples of butterfly data sets to illustrate the use of the methods and the software.     

Effects of salinity and temperature on Corophium volutator and C. arenarium (Crustacea: Amphipoda), with particular reference to distribution

The responses of the post-embryonic stages of Corophium volutator (Pallas) and C. arenarium Crawford to the combined effects of salinity and temperature show that gravid females have a wider tolerance than nongravid adult females which in turn are more tolerant than adult males. C. volutator is more tolerant of low salinity (2 to 10) than C. arenarium, but the latter is more tolerant of salinities above 45. The embryos of C. volutator develop normally and hatch at lower salinities and temperatures than those of C. arenarium, in which successful development was recorded at higher temperatures. Females undergoing a pre-copulatory moult failed to lay eggs below salinities of 3 (C. volutator) and 10 (C. arenarium), but in both species the lowest salinity at which all females moulted and laid eggs was 20. The results are discussed in relation to the distribution of both species.     

环境因素对六氯苯厌氧降解活性的影响

在厌氧污泥具备了较好的六氯苯（HCB）降解能力的基础上,采用标准血清瓶实验方法考察了反应温度、初始pH、摇床转速和营养元素等环境因素对厌氧污泥降解HCB活性的影响。实验设计的反应温度为25、30、35和40℃;初始pH为5.0、6.0、7.0和8.0;摇床转速为0和150r·min-1;营养元素有葡萄糖和维生素b12。用HCB浓度随时间的减少来表征微生物对其的降解活性。结果表明,反应温度对HCB的降解速率有很大影响,适宜温度为35℃左右。初始pH对HCB降解活性没有显著影响,但显示出有随初始pH增大而HCB降解活性增加的趋势。与静置条件相比,一定的混合作用有利于提高HCB的降解活性。有葡萄糖存在条件下,维生素b12对HCB的降解活性有明显的促进作用。温度及外加碳源（葡萄糖）是影响HCB厌氧降解活性的重要因素,并推测葡萄糖在HCB降解过程中提供电子供体方面发挥了重要作用。     

Dissecting the spatial scales of mercury accumulation in Ontario lake sediment

Total mercury concentration was analyzed in 171 lakes from pre-industrial (>30 cm depth; Hg_{pre-industrial}) and present-day sediments (0.5–1 cm; Hg_present-day). Numerous hot or cold spots of sediment mercury enrichment (Hg EF; Hg_{pre-industrial}/Hg_present-day) were evident as determined by local tests of autocorrelation, although in most cases, the maximum correlation among sites was not the nearest neighbor, indicating a strong influence of watershed characteristics. Hg EF was correlated with the area of open water (ha) (r = 0.91, p = 0.035), mine tailings (r = 0.94, p = 0.019), and organic deposits in surficial geology of the watershed (r = −0.91, p = 0.034). Through use of local rather than global regression coefficients, R² increased from 0.20 (p = 0.005) to 0.60 (p = 0.013). A broad spatial pattern (>500 km) observed only in Hg_{pre-industrial} was best explained by mean annual precipitation (shared variance = 3.5%), while finer spatial patterns only observed in Hg_present-day and Hg EF were best explained by pH (average shared variance = 10.8%).     

A summary of the 209 PCB congener nomenclature

Primary publications of congener numbering shorthand systems for PCB congener identification were reviewed, including the original Ballschmiter-Zell (BZ) system; recommended changes by Schulte and Malisch, and Guitart et al.; and listings by the Chemical Abstracts Service. Comparisons of the various congener numbering shorthands and chlorine substitution numberings in the structural name listings are presented. Several changes, to adhere more closely to IUPAC rules, have been incorporated into the BZ structural nomenclature, and these resulted in renumbering congeners. These corrected listings have been erroneously identified as "IUPAC" numbers, a misnomer, because IUPAC has not published a shorthand system. Guitart pointed out additional inconsistencies with IUPAC rules for nine congeners which would result in further order changes, but did not recommend renumbering, to avoid further confusion. We noted an additional error in the structural name for congener 97, named 2,2',3',4,5 using Ballschmiter and Zell nomenclature and 2,2',3,4',5' using strict IUPAC nomenclature. This renaming would cause the renumbering of the IUPAC number system reported by Guitart for isomers 91 through 98. No further changes are recommended, however. Tables summarizing each publication, and the discrepancies between them are provided in hopes of clarifying the current state of the nomenclature.     

Predicting community sensitivity to ozone, using Ellenberg Indicator values

This paper develops a regression-based model for predicting changes in biomass of individual species exposed to ozone (RS(p)), based on their Ellenberg Indicator values. The equation (RS(p)=1.805-0.118Light-0.135 square root Salinity) underpredicts observed sensitivity but has the advantage of widespread applicability to almost 3000 European species. The model was applied to grassland communities to develop two further predictive tools. The first tool, percentage change in biomass (ORI%) was tested on data from a field-based ozone exposure experiment and predicted a 27% decrease in biomass over 5 years compared with an observed decrease of 23%. The second tool, an index of community sensitivity to ozone (CORI), was applied to 48 grassland communities and suggests that community sensitivity to ozone is primarily species-driven. A repeat-sampling routine showed that nine species were the minimum requirement to estimate CORI within 5%.     

Biomonitoring with Gammarus pulex at the Meuse (NL), Aller (GER) and Rhine (F) rivers with the online Multispecies Freshwater Biomonitor

Biological early warning systems represent a set of tools that may be able to respond to certain chemical monitoring requirements of recent European legislation, the Water Framework Directive (WFD2000/60/EC), that aims to improve and protect water quality across Europe. In situ biomonitoring was performed along the rivers Meuse (NL), Aller (GER) and Rhine (F) within the frame of the European Union-funded Project SWIFT-WFD. Gammarus pulex was used as a test organism during the evaluation of the Multispecies Freshwater Biomonitor(R) (MFB), an online biomonitor to quantitatively record different behaviour patterns of animals. At the river Meuse G. pulex reacted to pulse exposure of either a mixture of trace metals or of several organic xenobiotics, by showing up to 20% decreased locomotory activity (already at the 1st pulse) and increased mortality (at 2nd or 3rd pulse only). G. pulex deployed within the MFB system were observed to survive well at the monitoring station on the Aller (100%) and monitoring did not result in the measurement of chemical irregularities. In contrast, deployment at the monitoring station on the Rhine river demonstrated that the test organism was able to detect chemical irregularities by up to 20% decreased locomotory activity in the animals. The MFB proved to be an alert system for water quality monitoring at sensitive sites and sites with accidental pollution.     

Poplar for the phytomanagement of boron contaminated sites

Boron (B) is a widespread environmental contaminant that is mobile relative to other trace elements. We investigated the potential of hybrid poplar (Populus sp.) for B phytomanagement using a lysimeter experiment and a field trial on B-contaminated wood-waste. In both studies, poplars enhanced evapotranspiration from the wood-waste, reduced B leaching, and accumulated B in the aerial portions of the tree. When grown in a substrate containing 30 mg/kg B, poplar leaves had an average B concentration of 845 mg/kg, while the stems contained 21 mg/kg B. Leaf B concentrations increased linearly with leaf age. A decomposition experiment revealed that abscised leaves released 14% of their B during the winter months. Fertiliser application enhanced tree growth without decreasing the leaf B concentrations. Harvesting alternate rows of trees on a contaminated site would reduce leaching from the site while removing B. Harvested plant material may provide bioenergy, stock fodder, or an amendment for B-deficient soils.     

Chemcatcher and DGT passive sampling devices for regulatory monitoring of trace metals in surface water

This work aimed to evaluate whether the performance of passive sampling devices in measuring time-weighted average (TWA) concentrations supports their application in regulatory monitoring of trace metals in surface waters, such as for the European Union's Water Framework Directive (WFD). The ability of the Chemcatcher and the diffusive gradient in thin film (DGT) device sampler to provide comparable TWA concentrations of Cd, Cu, Ni, Pb and Zn was tested through consecutive and overlapping deployments (7-28 days) in the River Meuse (The Netherlands). In order to evaluate the consistency of these TWA labile metal concentrations, these were assessed against total and filtered concentrations measured at relatively high frequencies by two teams using standard monitoring procedures, and metal species predicted by equilibrium speciation modeling using Visual MINTEQ. For Cd and Zn, the concentrations obtained with filtered water samples and the passive sampling devices were generally similar. The samplers consistently underestimated filtered concentrations of Cu and Ni, in agreement with their respective predicted speciation. For Pb, a small labile fraction was mainly responsible for low sampler accumulation and hence high measurement uncertainty. While only the high frequency of spot sampling procedures enabled the observation of higher Cd concentrations during the first 14 days, consecutive DGT deployments were able to detect it and provide a reasonable estimate of ambient concentrations. The range of concentrations measured by spot and passive sampling, for exposures up to 28 days, demonstrated that both modes of monitoring were equally reliable. Passive sampling provides information that cannot be obtained by a realistic spot sampling frequency and this may impact on the ability to detect trends and assess monitoring data against environmental quality standards when concentrations fluctuate.     

Environmental release of dioxins from reservoir sources during beach nourishment programs

In late 1990s, USEPA/FDA made an important connection regarding the presence of elevated levels of dioxins (e.g., 1500 ng kg⁻¹ TEQ) in ball clays mined in Mississippi (USA) from a geological deposit dated to ∼40 million years (Mississippi Embayment) that stretches over several states (northern part of Mississippi to Kentucky) and levels of dioxins in selected animal food sources. Following a recent beach nourishment program along the mid-Atlantic coast of the US, a number of dark gray, blue tinted nuggets of varying sizes were found on beach strands and near the shoreline. Using the presence of these balls of clay (shape, color, and knowledge regarding their use in pottery) on the beach, together with our direct experience analyzing ball clays for dioxins, we made a possible association between these clays and elevated dioxins. Concerns regarding the potential of nourishment programs to cause severe damage to our beaches drove us to test the dioxin content of nourishment exposed clays. A number of the nuggets, along with freshly dredged and deposited sand (collected the morning after nourishment) with the same coloration, and others (sun-bleached), collected approximately 2 weeks after the completion of the nourishment efforts, were analyzed for the presence of PCDD/Fs, PCBs, and selected semi-volatile chlorinated organics. The clay PCDD/F WHO2005-TEQs (dry weight; ND = DL; EMPC = EMPC) ranged from 0.41 to 5.78 ng kg⁻¹ with an average of 2.64 ng kg⁻¹, whereas the sand sample’s TEQs ranged from 0.18 to 0.31 ng kg⁻¹ PCDD/F WHO-2005, with an average of 0.22 ng kg⁻¹. The average total tetra- through octachlorinated dibenzo-p-dioxin concentration was 2700 ng kg⁻¹ (with a maximum of 5800 ng kg⁻¹) for the clays and 8.5 ng kg⁻¹ (with a maximum of 16.8 ng kg⁻¹) for the sand samples. The congener 2,3,7,8-TCDD (TEF = 1) was detected in half of the clay samples (0.11-0.77 ng kg⁻¹). All of the clay and sand samples displayed an unambiguous and dominating 1,4,6,9-chlorination pattern across homolog groups. No other chlorinated aromatics were detected above background levels. The observations, along with the absence or an extremely low level of polychlorinated dibenzofurans, together with the mineralogical analysis, supports the conclusion that off-shore dredging activities are reaching reservoir sources containing dioxin-tainted, smectic/kaolinite clay minerals. Subsequent beach erosion provides additional environmental releases over time, as buried balls of clay from previous nourishment efforts become exposed.