Analysis of two-way layout of count data with negative binomial variation

A number of methods has been proposed for dealing with single-factor or factorial experiments when the requirements for performing the normal theory analysis of variance procedure are not satisfied. This paper suggests the use of the likelihood ratio statistic for testing the main effects and the interaction between the factors in two-way layout of count data following negative binomial distributions with a common dispersion parameter. The likelihood ratio statistic for testing the equality of the dispersion parameters of several groups of count data is also derived. The methods is illustrated by an example concerning the study of spatial and temporal variation of bacterial counts.     

Soil fauna and soil microflora as possible indicators of soil pollution

Research on biological indicators of soil pollution is hampered by soil variability and temporal and spatial fluctuations of numbers of soil animals. These characters on the other hand promote a high biological diversity in the soil. A high diversity combined with persistent soil pollutants increases the chance to select good indicators. However research on these topics is still limited. Examples of specific indicators are the changed arthropod species patterns due to pesticide influence and the changed soil enzyme activity under the influence of specific heavy metals. Another approach is to look for organisms that give a general indication of soil pollution. In this respect the earthworm species Allolobophora caliginosa proved to be sensitive for different types of manure especially pig manure with copper, for sewage sludge, for municipal waste compost and for fly ash. A third way of indication is by organisms accumulating pollutants. For some heavy metals (Cd, Zn), earthworms are very efficient accumulators. More research is needed especially on the specific relation between biological responses and abiotic soil characteristics.     

Dose-time-response functions for toxic chemicals

In many situations, the effect of a toxic chemical on a biological system depends on both the intensity and the duration of exposure. The dependence on the time dimension can be the expression of a range of processes including the physical accumulation of toxic chemicals or their metabolites and the functional accumulation of damage. Measures and functions that have been used to describe this dependence are reviewed.Some of these functions are compared through a case study of the neurotoxicity of methylmercury. Use is made of data that indicates a dependency between the blood concentration at which monkeys were exposed and the length of time before damage was detected. Several exposure functions are fitted to these data and their appropriateness is compared. Using the most appropriate function, an exposure-response relationship is developed using probit analysis. An alternative data analysis procedure is also investigated. The apparent threshold after a 100 day exposure is estimated to be greater by a factor of 3–5 compared to the threshold for chronic exposure. Applying this factor to man, the blood concentration threshold for chronic exposure is estimated to be 40–170 ppb, a finding consistent with recent reports of neurological damage in humans exposed below the generally accepted threshold.     

Determination of biomass burning emission factors: Methods and results

Biomass burning, in a broad sense, encompasses different burning practices, including open and confined burnings, and different types of vegetation. Emission factors of gaseous or particulate trace compounds are directly dependent both on the fuel type and the combustion process. Emission factors are generally calculated by stoichiometric considerations using the carbon mass balance method, applied either to combustion chamber experiments or to field experiments based on ground-level measurements or aircraft sampling in smoke plumes. There have been a number of experimental studies in the last 10 years to investigate wildfires in tropical, temperate, or boreal regions. This article presents an overview of measurement methods and experimental data on emission factors of reactive or radiatively active trace compounds, including trace gases and particles. It focuses on fires in tropical regions, that is, forest and savanna fires, agricultural burns, charcoal production, use of fuelwood, and charcoal combustion.     

Factor analysis of trace-element data from tree-bark samples in The Netherlands

Monte Carlo-assisted factor analysis has been applied to a data set of 20 trace-element concentrations in tree-bark samples obtained from 123 locations in The Netherlands, with the aim to investigate the suitability of bark as a biomonitor for air pollution. A Monte Carlo approach was used to give more insight to the uncertainties and significance levels of the factor analysis results. Notwith-standing a rather strong influence of soil material on the concentration levels, factor analysis enabled the identification of five significant pollution source types, all of which corresponded with source types found in an earlier biomonitoring study in The Netherlands using epiphytic lichens. A more detailed comparison with the lichen results showed a remarkable difference in lead concentrations between bark and lichen. It was concluded that bark can be successfully employed as a biomonitor for air pollution. The power of factor analysis to adequately determine the soil contribution may render extensive sample washing procedures superfluous.     

Multimedia environmental monitoring: 50 years at Hanford

Environmental monitoring has been an ongoing activity on the U.S. Department of Energy's Hanford Site in southeastern Washington for almost 50 years. Objectives are to detect and assess potential impacts of Site operations on air, surface and ground waters, foodstuffs, fish, wildlife, soil and vegetation. Data from monitoring effects are used to calculate the overall radiological dose to humans working onsite or residing in nearby communities. In 1989, measured Hanford Site perimeter concentrations of airborne radionuclides were below applicable guidelines. Concentrations of radionuclides and nonradiological water quality in the Columbia River were in compliance with applicable standards. Foodstuffs irrigated with river water taken downstream of the Site showed radionuclide levels that were similar to those found in foodstuffs from control areas. Low levels of ¹³⁷Cs and ⁹⁰Sr in most onsite wildlife samples and concentrations of radionuclides in soils and vegetation from on- and offsite locations were typical of those attributable to worldwide fallout. The calculated dose potentially received by a maximally exposed individual (i.e., based on hypothetical, worst-case assumptions for all routes of exposure) in 1989 (0.05 mrem/yr) was similar to those calculated for 1985 through 1988.In addition to monitoring radioactivity in fish and wildlife, population numbers of key species are determined. Chinook salmon (Oncorhynchus tshawytscha) spawning in the Columbia River at Hanford has increased in recent years with a concomitant increase in winter roosting activity of bald eagles (Haliaeetus leucocephalus). An elk (Cervus elaphus) herd, established by immigration in 1972, is also increasing. The Hanford Site currently serves as a refuge for Canada goose (Branta canadensis), great blue heron (Ardea herodias), and various plants and other animals, e.g., mule deer (Odocoileus hemionus), and coyotes (Canis latrans).     

Characterization of microbial communities from coastal waters using microarrays

Molecular methods, including DNA probes, were used to identify and enumerate pathogenic Vibrio species in the Chesapeake Bay; our data indicated that Vibrio vulnificus exhibits seasonal fluctuations in number. Our work included a characterization of total microbial communities from the Bay; development of microarrays that identify and quantify the diversity of those communities; and observation of temporal changes in those communities. To identify members of the microbial community, we amplified the 16S rDNA gene from community DNA isolated from a biofilm sample collected from the Chesapeake Bay in February, 2000. The resultant 75 sequences were 95% or more similar to 7 species including two recently described Shewanella species, baltica and frigidimarina, that have not been previously isolated from the Chesapeake. When the genera of bacteria from biofilm after culturing are compared to those detected by subcloning amplified 16S fragments from community DNA, the cultured sample exhibited a strong bias. In oysters collected in February, the most common bacteria were previously unknown. Based on our 16S findings, we are developing microarrays to detect these and other microbial species in these estuarine communities. The microarrays will detect each species using four distinct loci, with the multiple loci serving as an internal control. The accuracy of the microarray will be measured using sentinel species such as Aeromonas species, Escherichia coli, and Vibrio vulnificus. Using microarrays, it should be possible to determine the annual fluctuations of bacterial species (culturable and non-culturable, pathogenic and non-pathogenic). The data may be applied to understanding patterns of environmental change; assessing the health of the Bay; and evaluating the risk of human illness associated with exposure to and ingestion of water and shellfish.     

Life-history parameters and vertical distribution of Maurolicus muelleri in Masfjorden in summer

Population characteristics, individual life-history variables, feeding and vertical distribution of the mesopelagic fish Müller's pearlside Maurolicus muelleri collected in 1990 in Masfjorden, western Norway, are reported as well as environmental variables from the fjord. Minimum size at maturity was far smaller than reported from previous investigations in the same region. Fecundity was size-dependent and total egg numbers were higher than reported from other investigations of M. muelleri world wide, while the number of maturing eggs was far lower than observed in the same region earlier. Food concentration in the fjord was an order of magnitude lower than previous early summer observations, and several factors indicated that feeding opportunities may have been low for a long period. Daily feeding rate (g prey g^-1 fish) decreased with increasing fish size. These observations fit well with a model of maximizing fitness by means of a flexible size at maturity. Minimum age at maturity seems to be achieved at the expense of fecundity. M. muelleri was concentrated in a 20 to 30 m deep sound scattering layer (SSL). The SSL stayed close to the surface during the night and at 100 to 180 m during the daytime. The vertical position of the SSL varied instantaneously with changes in surface light intensity, remaining at 10^-3 to 10^-4 mol m^-1 s^-1 at the top of the SSL. Stomach fullness was highest during the night; feeding intensity seems to have been peaked at dusk. Cladocerans were the main prey ranked by number, copepods by biomass. Intake of large copepods increased with fish size.     

The modern theory of biological evolution: an expanded synthesis

In 1858, two naturalists, Charles Darwin and Alfred Russel Wallace, independently proposed natural selection as the basic mechanism responsible for the origin of new phenotypic variants and, ultimately, new species. A large body of evidence for this hypothesis was published in Darwins Origin of Species one year later, the appearance of which provoked other leading scientists like August Weismann to adopt and amplify Darwins perspective. Weismanns neo-Darwinian theory of evolution was further elaborated, most notably in a series of books by Theodosius Dobzhansky, Ernst Mayr, Julian Huxley and others. In this article we first summarize the history of life on Earth and provide recent evidence demonstrating that Darwins dilemma (the apparent missing Precambrian record of life) has been resolved. Next, the historical development and structure of the modern synthesis is described within the context of the following topics: paleobiology and rates of evolution, mass extinctions and species selection, macroevolution and punctuated equilibrium, sexual reproduction and recombination, sexual selection and altruism, endosymbiosis and eukaryotic cell evolution, evolutionary developmental biology, phenotypic plasticity, epigenetic inheritance and molecular evolution, experimental bacterial evolution, and computer simulations (in silico evolution of digital organisms). In addition, we discuss the expansion of the modern synthesis, embracing all branches of scientific disciplines. It is concluded that the basic tenets of the synthetic theory have survived, but in modified form. These sub-theories require continued elaboration, particularly in light of molecular biology, to answer open-ended questions concerning the mechanisms of evolution in all five kingdoms of life.Dedicated to Prof. Dr. Dr. hc mult. Ernst Mayr on the occasion of his 100th birthdayThis revised version was published online in March 2004, with corrections to the caption of Figure 6.