Estimating species richness and accumulation by modeling species occurrence and detectability

A statistical model is developed for estimating species richness and accumulation by formulating these community-level attributes as functions of model-based estimators of species occurrence while accounting for imperfect detection of individual species. The model requires a sampling protocol wherein repeated observations are made at a collection of sample locations selected to be representative of the community. This temporal replication provides the data needed to resolve the ambiguity between species absence and nondetection when species are unobserved at sample locations. Estimates of species richness and accumulation are computed for two communities, an avian community and a butterfly community. Our model-based estimates suggest that detection failures in many bird species were attributed to low rates of occurrence, as opposed to simply low rates of detection. We estimate that the avian community contains a substantial number of uncommon species and that species richness greatly exceeds the number of species actually observed in the sample. In fact, predictions of species accumulation suggest that even doubling the number of sample locations would not have revealed all of the species in the community. In contrast, our analysis of the butterfly community suggests that many species are relatively common and that the estimated richness of species in the community is nearly equal to the number of species actually detected in the sample. Our predictions of species accumulation suggest that the number of sample locations actually used in the butterfly survey could have been cut in half and the asymptotic richness of species still would have been attained. Our approach of developing occurrence-based summaries of communities while allowing for imperfect detection of species is broadly applicable and should prove useful in the design and analysis of surveys of biodiversity.     

Crown ratio influences allometric scaling in trees

Allometric theories suggest that the size and shape of organisms follow universal rules, with a tendency toward quarter-power scaling. In woody plants, however, structure is influenced by branch death and shedding, which leads to decreasing crown ratios, accumulation of heartwood, and stem and branch tapering. This paper examines the impacts on allometric scaling of these aspects, which so far have been largely ignored in the scaling theory. Tree structure is described in terms of active and disused pipes arranged as an infinite branching network in the crown, and as a tapering bundle of pipes below the crown. Importantly, crown ratio is allowed to vary independently of crown size, the size of the trunk relative to the crown deriving from empirical results that relate crown base diameter to breast height diameter through crown ratio. The model implies a scaling relationship in the crown which reduces to quarter-power scaling under restrictive assumptions but would generally yield a scaling exponent somewhat less than three-quarters. For the whole tree, the model predicts that scaling between woody mass and foliage depends on crown ratio. Measurements on three boreal tree species are consistent with the model predictions.     

Food remains in Confuciusornis sanctus suggest a fish diet

Despite hundreds of excellent fossils of Confuciusornis, the most abundant group of birds in the Early Cretaceous, ‘Jehol Biota’ in China, there is yet no indication of the food choice of these birds. Here, we describe fish remains preserved in the alimentary system of a specimen of Confuciusornis sanctus from the Jiufotang Formation. This find is about five million years younger than all previously published confuciusornithid birds from the Yixian Formation. Although it is unknown how common fish was in the diet of Confuciusornis, the find does not support previous hypotheses that it fed on plants or grain.     

A carbon budget of a small humic lake: an example of the importance of lakes for organic matter cycling in boreal catchments

Lakes play an important role in the cycling of organic matter in the boreal landscape, due to the frequently high extent of bacterial respiration and the efficient burial of organic carbon in sediments. Based on a mass balance approach, we calculated a carbon budget for a small humic Swedish lake in the vicinity of a potential final repository for radioactive waste in Sweden, in order to assess its potential impact on the environmental fate of radionuclides associated with organic matter. We found that the lake is a net heterotrophic ecosystem, subsidized by organic carbon inputs from the catchment and from emergent macrophyte production. The largest sink of organic carbon is respiration by aquatic bacteria and subsequent emission of carbon.dioxide to the atmosphere. Although the annual burial of organic carbon in the sediment is a comparatively small sink, it results in the build-up of the largest carbon pool in the lake. Hence, lakes may simultaneously disperse and accumulate organic-associated radionuclides leaking from a final repository.     

The use of a sequential leaching procedure for assessing the heavy metal leachability in lime waste from the lime kiln at a caustizicing process of a pulp mill

A five-stage sequential leaching procedure was used to fractionate 13 heavy metals (Cd, Cu, Pb, Cr, Zn, Fe, Mn, Al, Ni, Co, As, V, Ba) and sulphur (S) in lime waste from the lime kiln at the causticizing plant of Stora Enso Oyj Veitsiluoto Pulp Mills at Kemi, Northern Finland, into the following fractions: (1) water-soluble fraction (H₂O), (2) exchangeable fraction (CH₃COOH), (3) easily reduced fraction (HONH₃Cl), (4) oxidizable fraction (H₂O₂ + CH₃COONH₄), and (5) residual fraction (HF + HNO₃ + HCl). Although metals were leachable in all fractions, the highest concentrations for most of the metals were observed in the residual fraction (stage 5). It was also notable that the total heavy metal concentrations in lime waste did not exceed the maximal allowable heavy metal concentrations for soil conditioner agents set by the ministry of the Agricultural and Forestry in Finland. The heavy metals concentrations in lime waste were also lower than the maximal allowable heavy metals concentrations of the European Union Directive 86/278/EEC on the protection of environment, and in particular of the soil, when sewage sludge is used in agriculture. The Ca concentration (420 g kg⁻¹; d.w.) was about 262 times higher than the typical value of 1.6 g kg⁻¹ (d.w.) in arable land in Central Finland. However, the concentration Mg (0.2 g kg⁻¹; d.w.) in lime waste was equal to the Mg concentration in arable land in the Central Finland. The lime waste has strongly alkaline pH (12.8) and a neutralizing value (i.e. liming effect) of 47.9% expressed as Ca equivalents (d.w.). This indicates lime waste to be a potential soil conditioner and improvement as well as a pH buffer.     

Measuring bioavailability of polychlorinated biphenyls in soil to earthworms using selective supercritical fluid extraction

If the release mechanisms during selective chemical extraction of persistent organic pollutants (POP) mimic release mechanisms in natural systems during biological uptake, then a selective non-exhaustive extraction could give a quantitative measure of the bioavailable POP fraction. Supercritical fluid extraction (SFE) is suggested as a possible technique to estimate the amount of bioavailable polychlorinated biphenyls (PCBs) at contaminated sites and hence serve as a new tool in risk assessment. The uptake of PCBs by earthworm (Eisenia foetida) was investigated. PCB contaminated soil was pre-extracted with selective non-exhaustive SFE (50 degrees C, 350 bar, 1h), which removed on average 70% of the individual PCBs. Earthworms were placed in this pre-extracted soil, as well as in untreated soil. After 10 days, the PCB uptake by earthworms in the two systems was compared. The bioaccumulation factor (BAF) was 83% lower in the pre-extracted system than in the untreated system, demonstrating that SFE extracts primarily bioavailable contaminants. From the data, the bioavailable fraction could also be calculated to be 75%, which is very close to the 70% removed by SFE under the applied conditions. This suggests that the chemical methodology is capable of measuring the bioavailable fraction very accurately in this system.     

Characterization of organic compounds in aerosol particles from a coniferous forest by GC-MS

Atmospheric aerosol particles were collected in a Finnish Scots pine forest as part of a European Union project. Sampling was done in March-April 2003 with a high-volume sampler. Dynamic ultrasonic-assisted solvent extraction and gas chromatography-mass spectrometry (GC-MS) were applied to the analysis of aerosol samples for analytes such as n-alkanes, polycyclic aromatic hydrocarbons (PAH), oxidized polycyclic aromatic hydrocarbons (oxy-PAHs), sesquiterpenes (SQT) and oxidized sesquiterpenes (oxy-SQT). The highest concentrations were found for the n-alkanes, which were present in a wide range (C11-C32) indicating both biogenic and anthropogenic sources. PAH compounds were found in every sample while oxy-PAH compounds were present in low concentrations in a few samples. A few oxidized monoterpenes, most notably (-)-verbenone and pinonaldehyde, were found in several samples in concentrations clearly exceeding the PAH concentrations. The effect of temperature could be seen in most samples, where the concentrations of n-alkanes declined with decreasing temperatures. Particle formation events were accompanied by higher concentrations of heavy n-alkanes, verbenone and pinonaldehyde.