Surrounding space the ontology of organism-environment relations

Summary The history of evolution is a history of development from less to more complex organisms. This growth in complexity of organisms goes hand in hand with a concurrent growth in complexity of environments and of organism-environment relations. It is a concern with this latter aspect of evolutionary development that motivates the present paper. We begin by outlining a theory of organism-environment relations. We then show that the theory can be applied to a range of different sorts of cases, both biological and non-biological, in which objects are lodged or housed within specific environments, or niches. Biological science is interested in types — for example in genotypes, phenotypes, and environment types — and in regularities that can serve as the basis for the formulation of laws or general principles. Types, however, can exist only through their corresponding tokens. Our theory of token environments is meant to plug this gap and to provide a first step towards a general theory of causally relevant spatial volumes.     

Reproductive allometry in Malaysian rain forest trees: Biomechanics versus optimal allocation

Summary Quantitative predictions of reproductive allometry in iteroparous plants may be derived from two bodies of theory: biomechanics and optimal allocation theory. Biomechanical theory predicts allometric scaling exponents between reproductive (R) and vegetative (V) biomass in the range of 0.44–1.33, while very general models of life history evolution predictR–V exponents > 1 in all cases. These predictions are examined in light of allometric patterns of flower and fruit production in 32 species of Malaysian rain forest trees. Among these species the mean estimatedR–V exponents are in the range 1.8–2.0 for staminate flower, pistillate flower and fruit production. This range of exponent values provides unambiguous support for some of the general predictions of optimal allocation models, but not for biomechanical theory. Optimal allocation models also predict a positive relationship between species size andR–V slope and a positive relationship between species size andR–V intercept parameters. The latter, but not the former prediction is supported by the data.R–V allometries in sexes of dioecious species were also found to differ in intercept, though not slope, reflecting smaller sizes at reproductive onset in staminate trees. Further critical examinations of reproductive allometry are encouraged as a relatively unexplored avenue for increasing the contact of theory and data in studies of life history evolution in long-lived organisms such as tropical trees.     

The nature and dynamics of world religions: a life-history approach

In contrast with tribal and archaic religions, world religions are characterized by a unique emphasis on extended prosociality, restricted sociosexuality, delayed gratification and the belief that these specific behaviours are sanctioned by some kind of supernatural justice. Here, we draw on recent advances in life history theory to explain this pattern of seemingly unrelated features. Life history theory examines how organisms adaptively allocate resources in the face of trade-offs between different life-goals (e.g. growth versus reproduction, exploitation versus exploration). In particular, recent studies have shown that individuals, including humans, adjust their life strategy to the environment through phenotypic plasticity: in a harsh environment, organisms tend to adopt a ‘fast'' strategy, pursuing smaller but more certain benefits, while in more affluent environments, organisms tend to develop a ‘slow'' strategy, aiming for larger but less certain benefits. Reviewing a range of recent research, we show that world religions are associated with a form of ‘slow'' strategy. This framework explains both the promotion of ‘slow'' behaviours such as altruism, self-regulation and monogamy in modern world religions, and the condemnation of ‘fast'' behaviours such as selfishness, conspicuous sexuality and materialism. This ecological approach also explains the diffusion pattern of world religions: why they emerged late in human history (500–300 BCE), why they are currently in decline in the most affluent societies and why they persist in some places despite this overall decline.     

Situatedness and Problematic Boundaries: Conceptualizing Life's Complex Ecological Context

A key challenge in conceptualizing ecological complexity is to allow simultaneously for particularity, contingency, and structure, and for such structure to be internally differentiated,dynamically tied to its context, and subject torestructuring. Because all organisms live insuch dynamic ecological circumstances, philosophy of ecology could become the leading site for addressing difficult conceptual questions concerning the situatedness or positionality of organisms –humans included – in their changing and intersecting worlds.     

Evolutionary stability of plant communities and the maintenance of multiple dispersal types

S.A. Levin, D. Cohen, and A. Hastings (1984, Theor. Popul. Biol. 19, 169–200) and D. Cohen and S.A. Levin (1991, Theor. Popul. Biol. 39, 63–99) by analytic solution of the problem of invasion of a single dispersal type by any other, have provided a theory for evolutionarily stable strategies for seed dispersal in a random environment. Here the results of Cohen and Levin are extended to describe evolutionarily stable combinations of dispersal types. Such combinations of two types are coalitions that cannot be invaded by any other, although in isolation either of the types in the combination is invasible by others. These combinations appear when there is a negative correlation between the seed production of sites in successive years, or when environments are spatially heterogeneous, or presumably under other circumstances. In this work, we examine only the case of negative correlations. For this situation the configuration of evolutionarily stable strategies (ESS) and evolutionarily stable combinations (ESC) depends upon the ratio of (precompetitive) survival rates of dispersersing and nondispersing seeds, which is denoted by α. For low values of α, the purely nondispersing type is an ESS. At a somewhat higher value of α, the purely dispersing type can invade the nondispersing type, and the two types form an ESC, i.e., a combination that cannot be invaded by any other type. For still larger values of α, the purely nondispersing type is excluded by the ESC. Finally, for the largest values of α, pure dispersal is the ESS. In cases where a single dispersal type cannot exclude all others, the stationary distribution of types has a large spread. It can be adequately approximated by equations for conditional means of the proportions of various types at a site of a given quality, but these means must be conditioned upon the prior history at each site. For some purposes we have found that the history of as many as 8–10 generations is required for a good approximation. This phenomenon appears to preclude simple analytic approximations for the ESC.     

Expansion of genome coding regions by acquisition of new genes

As it is the case for non-coding regions, the coding regions of organisms can be expanded or shrunk during evolutionary processes. However, the dynamics of coding regions are expected to be more correlated with functional complexity and diversity than are the dynamics of non-coding regions. Hence, it is interesting to investigate the increase of diversity in coding regions – the origin and evolution of new genes – because this provides a new component to the genetic variation underlying the diversity of living organisms. Here, we examine what is known about the mechanisms responsible for the increase in gene number. Every mechanism affects genomes in a distinct way and to a different extent and it appears that certain organisms favor particular mechanisms. The detail of some interesting gene acquisitions reveals the extreme dynamism of genomes. Finally, we discuss what is known about the fate of new genes and conclude that many of the acquisitions are likely to have been driven by natural selection; they increase functional complexity, diversity, and/or adaptation of species. Despite this, the correlation between complexity of life and gene number is low and closely related species (with very similar life histories) can have very different number of genes. We call this phenomenon the G-value paradox.     

Halophily and halotolerance in cyanophytes

The survival, growth and distribution of organisms in hypersaline environments is discussed using cyanophytes (cyanobacteria) as examples. The distinction between halophilic (Na⁺-requiring) and halotolerant organisms is not adequate to describe the entire spectrum of adaptations to salt. The classical division into stenohaline (narrow) and euryhaline (wide) adaptational types, with optima identified as oligo-, meso- and polyhaline, better reflects both organismal adaptations and the environmental conditions to which these are adjusted and is therefore recommended as a conceptual model.Two independent properties of organisms are growth and survival. Organisms requiring narrow ranges of salt concentration are considered specialists and are restricted to environments with relatively constant salinities at any particular concentration. Organisms which tolerate wide ranges of fluctuation in salinity are considered generalists. The existence of separate and distinct microbial assemblages in these two types of environments is demonstrated in marine intertidal zones and seasonal salt works, representative of fluctuating salinity, and in the open ocean. The hypersaline ponds of Yallahs, Jamaica, and Solar Lake, Sinai represent different but relatively constant salinities. It is concluded that cyanophytes speciate along the salinity gradient, and that separate halophilic taxa occupy environments with relatively constant salinities.Proceedings of the fourth College Park Colloquium on Chemical EvolutionLimits of Life, University of Maryland, College Park, 18–20 October 1978.     

Effects of the water discharge on periphyton abundance and diversity in a large river (River Danube,Hungary)

This paper examines the relevance of intermediate disturbance theory in the context of in a large river the algal flora attaching to artificial substrata. It was observed that the theory is in good agreement with most of the communities analysed, however, with different frequency intervals compared to phytoplankton. Floods provided the most significant disturbances. As a rough generalization, we can say that in case of floods following each other in 8–14 days, respectively, the disturbance is of medium frequency. In case of 8 days, high frequency is more typical while in case of 14 days, low frequency is more characteristic. Owing to the fact that riverine periphytic algal organisms are attached in different ways and with differing efficiencies, the changes in the total mass occurring as a result of changes in water discharge lead to changes in diversity. The analysis of individual numbers can help in investigating the intensity of the disturbing effect on the algal communities. Negative correlation was found between water discharge and numbers of individuals, that is, the numbers of algae increase with low water discharge and decrease with high water level in the river. This second observation is valid only within a certain range of discharges (in this case up to 100 m³ s^–1), which will be specific to particular rivers and individual reaches. Below the upper limit of the range, the increased water flows carry more nutrients to the organisms but with no severe wash-off effect. Beyond the upper limit (in this case in range 100–400 m³ s^–1) the numbers of individuals is roughly in inverse proportion to the wash-off effect of the current, and the community is in equilibrium. In cases when discharge surpasses 400 m³ s^–1 decrease in individual numbers is general. We suggest that in the environments similar to the study area, the periphyton of the artificial substrata (e.g., pontoons) undergo similar processes. In respect of the periphyton formed on the surface of the riverbeds in large rivers with considerable changes in water level, a more complex system can be supposed where part of the periphyton is periodically dried and flooded alternately.     

Relative Amino Acid Composition Signatures of Organisms and Environments

Background

Identifying organism-environment interactions at the molecular level is crucial to understanding how organisms adapt to and change the chemical and molecular landscape of their habitats. In this work we investigated whether relative amino acid compositions could be used as a molecular signature of an environment and whether such a signature could also be observed at the level of the cellular amino acid composition of the microorganisms that inhabit that environment.

Methodologies/Principal Findings

To address these questions we collected and analyzed environmental amino acid determinations from the literature, and estimated from complete genomic sequences the global relative amino acid abundances of organisms that are cognate to the different types of environment. Environmental relative amino acid abundances clustered into broad groups (ocean waters, host-associated environments, grass land environments, sandy soils and sediments, and forest soils), indicating the presence of amino acid signatures specific for each environment. These signatures correlate to those found in organisms. Nevertheless, relative amino acid abundance of organisms was more influenced by GC content than habitat or phylogeny.

Conclusions

Our results suggest that relative amino acid composition can be used as a signature of an environment. In addition, we observed that the relative amino acid composition of organisms is not highly determined by environment, reinforcing previous studies that find GC content to be the major factor correlating to amino acid composition in living organisms.     

From stochastic environments to life histories and back

Environmental stochasticity is known to play an important role in life-history evolution, but most general theory assumes a constant environment. In this paper, we examine life-history evolution in a variable environment, by decomposing average individual fitness (measured by the long-run stochastic growth rate) into contributions from average vital rates and their temporal variation. We examine how generation time, demographic dispersion (measured by the dispersion of reproductive events across the lifespan), demographic resilience (measured by damping time), within-year variances in vital rates, within-year correlations between vital rates and between-year correlations in vital rates combine to determine average individual fitness of stylized life histories. In a fluctuating environment, we show that there is often a range of cohort generation times at which the fitness is at a maximum. Thus, we expect ‘optimal’ phenotypes in fluctuating environments to differ from optimal phenotypes in constant environments. We show that stochastic growth rates are strongly affected by demographic dispersion, even when deterministic growth rates are not, and that demographic dispersion also determines the response of life-history-specific average fitness to within- and between-year correlations. Serial correlations can have a strong effect on fitness, and, depending on the structure of the life history, may act to increase or decrease fitness. The approach we outline takes a useful first step in developing general life-history theory for non-constant environments.     

Regulation of boreal forest understory vegetation: the roles of resources and herbivores

To understand inter-trophic linkages between components of the boreal forest understory vegetation, three hypotheses were tested: survival, growth and abundance of grasses and legumes were controlled by (i) resource availability alone, (ii) by herbivores alone, and (iii) by both resource availability and herbivores. The hypotheses were tested using three experimental treatments – fertilization, herbivore exclusion, and fertilization plus herbivore exclusion – in three areas having different densities of resident herbivores, mostly snowshoe hares and ground squirrels. The highest density of snowshoe hares is comparable to natural levels during peaks in the snowshoe hare cycle. As the density of herbivores increased so too did the level of response by the measured variables – survival, growth of transplants and leaf area index of established vegetation. In general, fertilization resulted in a decrease in survival and growth of transplants, and fences increased survival and growth; both responses were more noticeable at higher herbivore densities. Fertilizer and herbivore exclosure fences had only negligible effects on established grass and legume abundance at all hare densities. We have shown that some hypotheses of vegetation regulation are over-simplified because different species groups (i.e., grasses and legumes) are regulated by different factors, at different life history stages, and sometimes these factors act in opposing directions. We argue that during the increase phase and peak of the snowshoe hare cycle (high herbivore density), growth and survival of establishing plants is regulated by herbivores. During the decline and low phases of the snowshoe hare cycle herbivores will have little impact on early life stages, whereas the established, mature, vegetation will be resource-regulated. Because of the variability in responses to the same manipulations we may begin to understand which plant life history stages are most vulnerable to consumer and resource regulation, the magnitudes of these sources of regulation at each of these stages, and how these vary among species groups and types of environments.     

A coalescent process with simultaneous multiple mergers for approximating the gene genealogies of many marine organisms

We describe a forward-time haploid reproduction model with a constant population size that includes life history characteristics common to many marine organisms. We develop coalescent approximations for sample gene genealogies under this model and use these to predict patterns of genetic variation. Depending on the behavior of the underlying parameters of the model, the approximations are coalescent processes with simultaneous multiple mergers or Kingman’s coalescent. Using simulations, we apply our model to data from the Pacific oyster and show that our model predicts the observed data very well. We also show that a fact which holds for Kingman’s coalescent and also for general coalescent trees–that the most-frequent allele at a biallelic locus is likely to be the ancestral allele–is not true for our model. Our work suggests that the power to detect a “sweepstakes effect” in a sample of DNA sequences from marine organisms depends on the sample size.     

Environs: The Superniches of Ecosystems

Evolution proceeds by natural selection of heritable variationsof individual organisms based on direct influences of environment.However, indirect effects probably vastly outweigh direct onesin ecosystems. Therefore, why is evolution based on direct effectsonly? The ecological niche represents the point of direct contactbetween organisms and their environments. To encompass indirectinfluences, niches are extended to new structures, environs,which are units of organism-environment coevolution. The motiveforce for coevolution is closure of outputs back upon inputsof the organism members of ecosystems. Closure is achieved bybiogeochemical cycling and feedback interactions, direct andindirect, between organisms. To the extent that closure doesnot occur, there is no imperative for organism-environment coevolution.Coevolution at the system level based on indirect effects iscompatible with normal evolution at the individual organismlevel based on direct effects. The organism is the unit of thelatter, but environs are the unit of coevolution.     

Isolation and characterization of rapidly-growing,marine, nitrogen-fixing strains of blue-green algae

Five strains of heterocystous blue-green algae capable of high rates of growth and nitrogenase activity were isolated from shallow coastal environments. Growth of the organisms was characterized with respect to temperature, NaCl concentration in the medium, and nitrogen source. The temperature optima ranged from 35–42°C, and all but one of the strains displayed a requirement for added NaCl. The generation times under N₂-fixing conditions were 5.1–5.9 h, and were as low as 3.4 h for growth on NH₄Cl. Nitrogenase activity (C₂H₂ reduction) was high throughout the logarithmic growth phase of each strain. The maximum value observed for one strain was 65.5 nmoles C₂H₄ produced/mg protein x min, and the average values for the five strains ranged from 24.5–46.7 nmoles C₂H₄/mg protein x min. The organisms all belong to the genusAnabaena. The growth and nitrogenase activity of these strains are much higher than those of the heterocystous blue-green algae commonly used for investigation of nitrogen metabolism, and they thus should prove to be useful physiological tools. Their prevalence, as judged by the ease of their enrichment and isolation, in bay and estuarine environments suggests that they are important contributors of combined nitrogen.     

Dynamics of age- and size-structured populations in fluctuating environments: Applications of stochastic matrix models to natural populations

Recent developments of the theory of stochastic matrix modeling have made it possible to estimate general properties of age- and size-structured populations in fluctuating environments. However, applications of the theory to natural populations are still few. The empirical studies which have used stochastic matrix models are reviewed here to examine whether predictions made by the theory can be generally found in wild populations. The organisms studied include terrestrial grasses and herbs, a seaweed, a fish, a reptile, a deer and some marine invertebrates. In all the studies, the stochastic population growth rate (ln λ _s ) was no greater than the deterministic population growth rate determined using average vital rates, suggesting that the model based only on average vital rates may overestimate growth rates of populations in fluctuating environments. Factors affecting ln λ _s include the magnitude of variation in vital rates, probability distribution of random environments, fluctuation in different types of vital rates, covariances between vital rates, and autocorrelation between successive environments. However, comprehensive rules were hardly found through the comparisons of the empirical studies. Based on shortcomings of previous studies, I address some important subjects which should be examined in future studies.     

Heavy metals (Cu,Zn, Pb,Cd) in sediment,zooplankton and epibenthic invertebrates from the area of the continental slope of the Banc d'Arguin (Mauritania)

The concentrations of copper, zinc, lead and cadmium in the surface sediment (upper 5 mm) were generally higher in the silt fraction than in the bulk sediment. No significant geographical trend in the metal concentrations of the surface sediments was found, nor a correlation between concentrations in bulk sediment as well as in the silt fraction and the % silt could be established. In general, the metal concentrations in both bulk sediment and silt are lower, when compared to marine environments in other climatological regions.In zooplankton, the metal concentrations were relatively high: expressed in µg g^–1 on a dry weight (D.W.) basis, they ranged from 15–90 for copper, 70–580 for zinc, 12–55 for lead and 4–10 for cadmium.In epibenthic invertebrate species, both in crustaceans and bivalve molluscs, the concentrations of copper, zinc, and lead were in the same order of magnitude as compared to corresponding species from other geographical latitudes. Cadmium concentrations were relatively low, ranging from 0.13–0.42 µg g^–1 D.W. in the bivalve molluscs Pitaria tumens and from 0.04–0.27 µg g^–1 D.W. in the shrimp Processa elegantula. Also in the crab species Ilia spinosa, Inachus sp. and Pagurus sp., the cadmium concentrations were low, varying between 0.1 and 0.2 µg g^–1 D.W.No significant relation between the metal concentration in whole-body samples and sediment (either bulk or silt) was present. Also no gradient was apparent in concentrations in organisms sampled at different depths (5 to 200 m) along two off-shore transects perpendicular to the Banc d'Arguin. Data indicated lower metal concentration in epibenthic organisms from sampling stations along a northern transect (southwest of Cap Blanc) than in organisms from the southern transect, off Cap Timiris.Evidence was obtained for a considerable atmospheric input of heavy metals, in particular zinc and lead, in a certain area along the continental slope of the Banc d'Arguin.     

Influence of pH and Temperature on Enumeration of Cellulose- and Hemicellulose-Degrading Thermophilic Anaerobes in Neutral and Alkaline Icelandic Hot Springs

Cellulose- and hemicellulose-degrading thermophilic anaerobes were enumerated in biomat samples of various temperatures from two different hot springs in the Hveragerǒi area of Iceland: one spring had a pH near 7, the second had a pH near 9. The most-probable-number technique was used for enumeration of bacteria in the samples, with media at many different temperatures (37 to 90°C) and two pH values (7 and 9). There were generally more xylan-degrading then cellulose-utilizing organisms in both environments. There was no growth at 80°C in the neutral spring or at 37°C in the alkaline spring. However, there were large numbers of both types of organisms in the alkaline spring at 80°C and in the neutral spring at 37°C. No cultures grew from the most-probable-number tubes inoculated with the Hveragerǒi samples and incubated at 90°C or with media at pH 9. However, xylan-degrading cultures at 70°C were enriched at pH 9 with samples from some other Icelandic hot springs.     

An assessment of terminology for intraspecific diversity in fishes,with a focus on “ecotypes” and “life histories”

Understanding and preserving intraspecific diversity (ISD) is important for species conservation. However, ISD units do not have taxonomic standards and are not universally recognized. The terminology used to describe ISD is varied and often used ambiguously. We compared definitions of terms used to describe ISD with use in recent studies of three fish taxa: sticklebacks (Gasterosteidae), Pacific salmon and trout (Oncorhynchus spp., “PST”), and lampreys (Petromyzontiformes). Life history describes the phenotypic responses of organisms to environments and includes biological parameters that affect population growth or decline. Life‐history pathway(s) are the result of different organismal routes of development that can result in different life histories. These terms can be used to describe recognizable life‐history traits. Life history is generally used in organismal‐ and ecology‐based journals. The terms paired species/species pairs have been used to describe two different phenotypes, whereas in some species and situations a continuum of phenotypes may be expressed. Our review revealed overlapping definitions for race and subspecies, and subspecies and ecotypes. Ecotypes are genotypic adaptations to particular environments, and this term is often used in genetic‐ and evolution‐based journals. “Satellite species” is used for situations in which a parasitic lamprey yields two or more derived, nonparasitic lamprey species. Designatable Units, Evolutionary Significant Units (ESUs), and Distinct Population Segments (DPS) are used by some governments to classify ISD of vertebrate species within distinct and evolutionary significant criteria. In situations where the genetic or life‐history components of ISD are not well understood, a conservative approach would be to call them phenotypes.

The terminology used to describe intraspecific diversity is varied and often used ambiguously. “Ecotype” was originally used to describe patterns in genes and ecology, and recent studies employing this term tend to report a genetic basis in ISD. By contrast, “life history” describes biological parameters that affect demography, and this term tends to be used in organismal‐ and ecology‐based journals.     

Evolution of Integrated Causal Structures in Animats Exposed to Environments of Increasing Complexity

Natural selection favors the evolution of brains that can capture fitness-relevant features of the environment''s causal structure. We investigated the evolution of small, adaptive logic-gate networks (“animats”) in task environments where falling blocks of different sizes have to be caught or avoided in a ‘Tetris-like’ game. Solving these tasks requires the integration of sensor inputs and memory. Evolved networks were evaluated using measures of information integration, including the number of evolved concepts and the total amount of integrated conceptual information. The results show that, over the course of the animats'' adaptation, i) the number of concepts grows; ii) integrated conceptual information increases; iii) this increase depends on the complexity of the environment, especially on the requirement for sequential memory. These results suggest that the need to capture the causal structure of a rich environment, given limited sensors and internal mechanisms, is an important driving force for organisms to develop highly integrated networks (“brains”) with many concepts, leading to an increase in their internal complexity.