The contribution of small individuals to density-body size relationships: examination of energetic equivalence in reef fishes

A key relationship in ecology is that between density and body size, with the emphasis placed on energetic rules constraining the abundance of larger organisms below that of smaller organisms. Most studies have focused upon the density-body size relationship at the species level. However, energy is gathered at an individual level. We therefore examined this relationship in a coral reef fish assemblage, focusing on individuals. Using a comprehensive data set, with over 14,000 observations we found that the relationship between local density and adult body size differs from the linear relationship predicted by the energetic equivalence rule. However, excluding the smallest size classes, the relationship between body size and individual abundance for intermediate to larger fish did not depart from the predicted –0.75. Unlike plants and intermediate to large reef fishes, the smallest fishes appear to have constraints that may reflect different patterns of resource acquisition.     

Association of acid-producing thiobacilli with degradation of concrete: analysis by ‘signature’ fatty acids from the polar lipids and lipopolysaccharide

Summary The acid-producing thiobacilli contain fatty acid components in the polar lipids and lipopolysaccharide lipid A that are sufficiently unusual that they can be utilized as signature lipid biomarkers for these organisms in environmental samples. Studies in microcosms have shown correlations between activity of these organisms, measured by recovery and viable counting, and the degradation of concrete. The signature lipid analysis provides a detection assay requiring neither separation of the organisms from the substratum nor growth prior to determination. The presence of acid-producing thiobacilli was demonstrated in microcosm samples and degenerating concrete from the Hamburg (F.R.G.) sewer system.     

The Origin of Eukaryotes Is Suggested as the Symbiosis of Pyrococcus into γ-Proteobacteria by Phylogenetic Tree Based on Gene Content

Attempts were made to define the relationship among the three domains (eukaryotes, archaea, and eubacteria) using phylogenetic tree analyses of 16S rRNA sequences as well as of other protein sequences. Since the results are inconsistent, it is implied that the eukaryotic genome has a chimeric structure. In our previous studies, the origin of eukaryotes to be the symbiosis of archaea into eubacteria using the whole open reading frames (ORF) of many genomes was suggested. In these studies, the species participating in the symbiosis were not clarified, and the effect of gene duplication after speciation (in-paralog) was not addressed. To avoid the influence of the in-paralog, we developed a new method to calculate orthologous ORFs. Furthermore, we separated eukaryotic in-paralogs into three groups by sequence similarity to archaea, eubacteria (other than -proteobacteria), and -proteobacteria and treated them as individual organisms. The relationship between the three ORF groups and the functional classification was clarified by this analysis. The introduction of this new method into the phylogenetic tree analysis of 66 organisms (4 eukaryotes, 13 archaea, and 49 eubacteria) based on gene content suggests the symbiosis of pyrococcus into -proteobacteria as the origin of eukaryotes.     

Scope for growth in Gammarus pulex,a freshwater benthic detritivore

Although toxic substances affect the physiological processes of individual organisms, their ecological impacts occur at the population and community levels. However, physiological processes can often be assessed more easily and precisely than population and community ones. Here we argue that scope for growth, the difference between the energy input to an organism from its food and the output from respiratory metabolism, can give a good physiological measure of stress that, at least in principle, is straightforwardly related to population and community processes. We describe, in detail, how scope for growth can be measured in Gammarus pulex (Crustacea, Amphipoda). The results indicate that both zinc and low pH can significantly reduce the scope for growth of individuals and that the most sensitive component of the energy budget is food absorption.     

Implicit frequency dependence and kin selection in fluctuating environments

Summary I consider a general model of a fluctuating environment in which the environmental state each year is drawn at random from some given distribution. Each year organisms must choose what action to perform before the environmental state for that year is known. There is no interaction with kin. In this scenario, natural selection will tend to produce organisms which maximize their geometric mean fitness. In this paper I introduce the idea of the profile of a strategy. This function quantifies how the strategy peforms for each environmental state. I show that there is a unique profile such that a strategy is optimal if and only if it has this profile. I then give a characterization of the optimal profile which generalizes previous work by others in this area. The characterization of the optimal profile has a game theoretical interpretation. Motivated by this I introduce a game in which individuals play the field in a constant environment. This game may be interpreted as a cooperative game between kin. The key result of this paper shows that a strategy maximizes geometric mean fitness in the original fluctuating environment problem if and only if it is an evolutionarily stable strategy of the deterministic environment game. It is well known that an optimal strategy in a fluctuating environment may be mixed, involving adaptive coin-flipping. Others have previously noted that this may result in some individuals sacrificing individual reproductive success for the good of the genotype. My analysis shows that one may regain the concept of individual optimization if the quantity maximized is suitably defined. Under an optimal strategy every action taken maximizes the expected number of offspring produced, where this expectation is not calculated using the true distribution of environmental states, but a distribution modified to take account of the actions of kin.     

Genetic and cultural pools: Some suggestions for a unified theory of biocultural evolution

By introducing the concept of the natural selection of individual organisms, Darwin was able to cut through the mystification surrounding theological discussions of the origin of species. By placing the concept of an individual struggle for satisfaction in an analogous conceptual framework, a similar feat may be performed with regard to the mystification and reification surrounding much of contemporary social science. The proposed theory states that individuals are the generating force behind the origin, spread, and transformations of sociocultural complexes and that all sociocultural phenomena are explicable in terms of the differential replication of ideas by individuals as this is conditioned by selective pressures generated by particular material conditions of life. The theory is used to illuminate certain key issues in evolution, such as adaptation, group selection, and free will This is a revised version of a paper originally presented at the Seventieth Annual Meetings of the American Anthropological Association in New York, November 19, 1971.     

Evolutionary optimization and neural network models of behavior

One of the main challenges to the adaptionist program in general and the use of optimization models in behavioral and evolutionary ecology, in particular, is that organisms are so constrained' by ontogeny and phylogeny that they may not be able to attain optimal solutions, however those are defined. This paper responds to the challenge through the comparison of optimality and neural network models for the behavior of an individual polychaete worm. The evolutionary optimization model is used to compute behaviors (movement in and out of a tube) that maximize a measure of Darwinian fitness based on individual survival and reproduction. The neural network involves motor, sensory, energetic reserve and clock neuronal groups. Ontogeny of the neural network is the change of connections of a single individual in response to its experiences in the environment. Evolution of the neural network is the natural selection of initial values of connections between groups and learning rules for changing connections. Taken together, these can be viewed as design parameters. The best neural networks have fitnesses between 85% and 99% of the fitness of the evolutionary optimization model. More complicated models for polychaete worms are discussed. Formulation of a neural network model for host acceptance decisions by tephritid fruit flies leads to predictions about the neurobiology of the flies. The general conclusion is that neural networks appear to be sufficiently rich and plastic that even weak evolution of design parameters may be sufficient for organisms to achieve behaviors that give fitnesses close to the evolutionary optimal fitness, particularly if the behaviors are relatively simple.     

Effects of UV-B on motility and photoorientation in the cyanobacterium,Phormidium uncinatum

UV-B irradiation has a detrimental effect on the survival of populations of the filamentous cyanobacterium, Phormidium uncinatum, at levels slightly higher than those currently measured at the surface of the earth. The organisms are not damaged or killed by UV-B radiation at 300 nm of 200 Wm^-2 for up to 20 h; but slightly increased levels of UV-B irradiation (2 h of 200 Wm^-2 at 300 nm) drastically impair motility, phototactic orientation and photophobic responses. These photosynthetic organisms require a narrow light intensity range for growth so that any decrease in their ability to actively search for and move into areas of favorable light conditions is bound to affect the survival of a population. The fluorescence yield of both phycobilins and chlorophyll is not altered even after 20 h of UV-B irradiation (200 Wm^-2 at 270 nm) indicating that UV-B at that dose does not affect the photosynthetic apparatus. The organisms are killed either by too bright intensities which bleach the photosynthetic pigments or by the lack of energy when they are unable to avoid moving into dark areas.     

Microbial contributions to the evolution of the ‘steady state’ carbon dioxide system

Various processes for the production of carbon dioxide by microorganisms are presented. It is postulated that a microniche developed in a reducing environment; a symbiotic relationship between alga-like organisms and bacterium-like organisms in the microniche governed the production of carbon dioxide resulting in the establishment of the steady state carbon dioxide system in the sea.     

Preservation and computer-aided microscopic analysis of planktonic Protozoa and algae

Samples of microplankton and larger nanoplankton (5 to 200 m) are preserved with a combination of Lugol's solution and DaFano's fixative. Organisms are then settled on a gelatin-coated slide, dried and embedded in 40 percent glycerin. Counting and sizing is performed under a microscope using a drawing tube, which facilitates measuring the organisms with a microcomputer-interfaced caliper. An interactive computer program, written in BASIC, allows for estimating the volumes of cells in up to 40 shape/species categories. The program then saves data on a disk, retrieves them, and calculates the results either for individual species (abundance, biomass, and mean cell volume) or as a pooled size spectrum of all organisms measured.     

Genetic variation detected by use of the M13 “DNA fingerprint” probe in Malus,Prunus, and Rubus (Rosaceae)

Summary Recently, DNA fingerprints have been reported in a wide array of organisms. We used the M13 repeat probe on several genera and species in the angiosperm family Rosaceae. Four apple cultivars could be differentiated when any one of five restriction enzymes was used to analyze minisatellite DNA. Similarly, four individual trees of Prunus serotina (black cherry) exhibited different fingerprints with each of four enyzmes. A total of 14 Rubus (blackberries and raspberries) plants representing four species were investigated with two enzymes. Extensive inter-and intraspecific variation was found. However, some closely growing plants had identical fingerprints, probably due to their being derived through vegetative propagation.     

Asymmetries in population growth regulated by intraspecific competition: Empirical studies and model tests

Summary The linearity assumption in the logistic model of population growth is violated for nearly all organisms. Two simple models, the -logistic and the -Ricker, are shown to account for asymmetric patterns of population growth for 27 species of Drosophila and for a variety of other organisms, where the data were derived from the literature. These models are developed so as to aid laboratory and field ecologists to anticipate the dynamics of various experimental organisms. Potential problems of data gathering and model applications for experimental ecologists and wild life management biologists are identified. Intraspecific asymmetries offer alternative explanations to the habitat selection model, and the higher order interactions or coalitions model, for interspecific competition.     

An Ecologically-informed Ontology for Environmental Ethics

Since the inception of their subject as a distinct area of study in philosophy, environmental ethicists have quarreled over the choice of entities with which an environmental ethic should be concerned. A dichotomous ontology has arisen with the ethical atomists, e.g., Singer and Taylor, arguing for moral consideration of individual organisms and the holists, e.g., Rolston and Callicott, focussing on moral consideration of systems. This dichotomous view is ecologically misinformed and should be abandoned. In this paper, I argue that the organization of the natural world, as viewed by some ecologists and evolutionary biologists, is structured on various levels that are not reducible to one another. This hierarchical view, expressed by Salthe and Eldredge, provides the most complete and accurate ontology for environmental ethics.     

Composition and structure of aquatic organism communities in various water conditions of a paddy field

The purpose of this study was to clarify the differences of the community structure and the diversity of aquatic organisms (i) among sampling sites that the distances from inlets or outlets were different each other, and (ii) between the floodwater and the irrigation water during the crop season in a paddy field. The irrigation water was sampled from one inlet. The taxonomical groups and the number of aquatic organisms ranging in size from 30µm to 2cm in the floodwater and the irrigation water were surveyed approximately every 10days during the growth period of the rice plant. Aquatic organisms were classified mainly at the order level. Thirty-eight taxonomical groups of aquatic organisms were found in the floodwater, while 18 groups were found in the irrigation water. We were not able to find the differences of the community structure of aquatic organisms among the sites. In the floodwater, the number of taxonomical group increased and the community structure changed during the late flooding period (over 50days after the onset of flooding) at any site, while those in the irrigation water hardly changed. Although the community structure of aquatic organisms differed between the floodwater and the irrigation water throughout the flooding period, the differences became especially bigger during the late flooding period. Principal component analysis showed that three groups (Pennales, Dinoflagellida, Choreotrichida) characterized the community structure in the irrigation water. Their population densities tended to be the highest at the site near inlets and the lowest at the site far from inlets.     

The eco-field: A new paradigm for landscape ecology

In the spirit of the theory of biocomplexity and of the non-linear emergent characters of ecological systems, the eco-field is a new paradigm that integrates the vision of the landscape as a neutral matrix (like a habitat) in which organisms are living, and contemporarily as a product of the human mind. Eco-field is defined a cognitive field created by the interference between functional traits and the real world. Species-specific environmental suitability is the result of the quality of the different eco-fields and the landscape becomes a cognitive entity. The eco-field paradigm can be extended to the emergent properties of the systems. The eco-field of emergences is the geographic space in which the emergent properties appear. The eco-field of organisms and the eco-field of emergences, like results of aggregated entities, have in common the multidimensionality of landscapes, refusing the vision of landscape like a neutral geographic matrix for organisms and processes.     

Patterns of intramolecular carbon isotopic heterogeneity within amino acids of autotrophs and heterotrophs

A survey of the intramolecular C isotopic composition of a variety of organisms was conducted to investigate the potential of intramolecular isotopic measurements as a tracer of biological or geochemical processes. Based on a consideration of inorganic C sources and enzymatic fractionations, contrasting predictions were made for the relative ¹³C enrichments of the -carboxyl carbons fixed by the anapleurotic ()-carboxylation pathway during amino acid synthesis by photoautotrophs and heterotrophs. To test the model predictions, the stable C isotopic compositions of the acid hydrolyzable C fraction, the total amino acid -carboxyl C fraction and the -carboxyl C of glutamate from a variety of autotrophic and heterotrophic organisms were compared. The relative ¹³C enrichments of carboxyl carbons in the bulk amino acid fraction and in glutamate conformed qualitatively to model predictions. Macroalgal taxa possessed a significantly less enriched carboxyl C fraction than did either C3 or C4 vascular plants, indicating the presence of a different -carboxylation pathway operating in these organisms. In most multicellular heterotrophs, the isotopic composition of the amino acid carboxyl carbons closely resembled that of their food sources. Amino acids are apparently assimilated into tissue proteins directly from their diets without significant metabolic modification. However, shifts in the isotopic composition of the carboxyl C fractions in some organisms were detected that were consistent with the occurrence of significant resynthesis of amino acids from non-amino acid precursors. Comparison of plant leaves and roots provided evidence of environmentally controlled assimilate partitioning. Intramolecular isotopic measurements of biological molecules provide unique insights into the origins and transformations of bio-molecules.     

Sources of variation in consumer-diet δ<Superscript>15</Superscript>N enrichment: a meta-analysis

Measurements of ¹⁵N of consumers are usually higher than those of their diet. This general pattern is widely used to make inferences about trophic relationships in ecological studies, although the underlying mechanisms causing the pattern are poorly understood. However, there can be substantial variation in consumer-diet ¹⁵N enrichment within this general pattern. We conducted an extensive literature review, which yielded 134 estimates from controlled studies of consumer-diet ¹⁵N enrichment, to test the significance of several potential sources of variation by means of meta-analyses. We found patterns related to processes of nitrogen assimilation and excretion. There was a significant effect of the main biochemical form of nitrogenous waste: ammonotelic organisms show lower ¹⁵N enrichment than ureotelic or uricotelic organisms. There were no significant differences between animals feeding on plant food, animal food, or manufactured mixtures, but detritivores yielded significantly lower estimates of enrichment. ¹⁵N enrichment was found to increase significantly with the C:N ratio of the diet, suggesting that a nitrogen-poor diet can have an effect similar to that already documented for fasting organisms. There were also differences among taxonomic classes: molluscs and crustaceans generally yielded lower ¹⁵N enrichment. The lower ¹⁵N enrichment might be related to the fact that molluscs and crustaceans excrete mainly ammonia, or to the fact that many were detritivores. Organisms inhabiting marine environments yielded significantly lower estimates of ¹⁵N enrichment than organisms inhabiting terrestrial or freshwater environments, a pattern that was influenced by the number of marine, ammonotelic, crustaceans and molluscs. Overall, our analyses point to several important sources of variation in ¹⁵N enrichment and suggest that the most important of them are the main biochemical form of nitrogen excretion and nutritional status. The variance of estimates of ¹⁵N enrichment, as well as the fact that enrichment may be different in certain groups of organisms should be taken into account in statistical approaches for studying diet and trophic relationships.     

The palirrhotrophic origin of energy metabolism

It is proposed that the earliest cellular organisms relied upon a novel type of energy transduction termed palirrhotrophy, which generates a high-energy currency chemiosmotically by exploiting the rhythmic variations in salinity which occur in the estuarine environment. Calculations based on estimates of contemporary chemiosmotic transduction efficiency suggest that such a mechanism could produce usable energy in high yield. The minimum polypeptide requirement for palirrhotrophy compares favorably with that of a fermentative pathway. It is suggested that palirrhotrophic organisms exist today but are difficult to detect.     

Phycoerythrins of the oxyphotobacterium Prochlorococcus marinus are associated to the thylakoid membrane and are encoded by a single large gene cluster

An intrinsic divinyl-chlorophyll a/b antenna and a particular form of phycobiliprotein, phycoerythrin (PE) III, coexist in the marine oxyphotobacterium Prochlorococcus marinus CCMP 1375. The genomic region including the cpeB/A operon of P. marinus was analysed. It encompasses 10153 nucleotides that encode three structural phycobiliproteins and at least three (possibly five) different polypeptides analogous to cyanobacterial or red algal proteins involved either in the linkage of subunits or the synthesis and attachment of chromophoric groups. This gene cluster is part of the chromosome and is located within a distance of less than 110 kb from a previously characterized region containing the genes aspA-psbA-aroC. Whereas the Prochlorococcus phycobiliproteins are characterized by distinct deletions and amino acid replacements with regard to analogous proteins from other organisms, the gene arrangement resembles the organization of phycobiliprotein genes in some other cyanobacteria, in particular marine Synechococcus strains. The expression of two of the Prochlorococcus polypeptides as recombinant proteins in Escherichia coli allowed the production of individual homologous antisera to the Prochlorococcus and PE subunits. Experiments using these sera show that the Prochlorococcus PEs are specifically associated to the thylakoid membrane and that the protein level does not significantly vary as a function of light irradiance or growth phase.     

The incidence,in soils and other habitats,of micro-organisms producing 2-ketogluconic acid

Summary A most probable number method is described, using paper chromatography, for enumerating bacteria which produce 2-ketogluconic acid in soils and other habitats. Using this method it has been shown that highest numbers of this group of organisms are associated with habitats rich in organic matter. An enhancement of this group of organisms in the rhizosphere of barley plants has been demonstrated and also a marked stimulation around starch-containing pellets buried in soil.the late