Evolutionary psychology and the brain

The human brain is a set of computational machines, each of which was designed by natural selection to solve adaptive problems faced by our hunter-gatherer ancestors. These machines are adaptive specializations: systems equipped with design features that are organized such that they solve an ancestral problem reliably, economically and efficiently. The search for functionally specialized computational adaptations has now begun in earnest. A host of specialized systems have recently been found, including ones designed for sexual motivation, social inference, judgment under uncertainty and conditioning, as well as content-rich systems for visual recognition and knowledge acquisition.     

Earthworms counterbalance the negative effect of microorganisms on plant diversity and enhance the tolerance of grasses to nematodes

Plant community composition is affected by a wide array of soil organisms with diverse feeding modes and functions. Former studies dealt with the high diversity and complexity of soil communities by focusing on particular functional groups in isolation, by grouping soil organisms into body size classes or by using whole communities from different origins. Our approach was to investigate both the individual and the interaction effects of highly abundant soil organisms (microorganisms, nematodes and earthworms) to evaluate their impacts on grassland plant communities. Earthworms increased total plant community biomass by stimulating root growth. Nematodes reduced the biomass of grasses, but this effect was alleviated by the presence of earthworms. Non-leguminous forb biomass increased in the presence of nematodes, probably due to an alleviation of the competitive strength of grasses by nematodes. Microorganisms reduced the diversity and evenness of the plant community, but only in the absence of earthworms. Legume biomass was not affected by soil organisms, but Lotus corniculatus flowered earlier in the presence of microorganisms and the number of flowers decreased in the presence of nematodes. The results indicate that earthworms have a profound impact on the structure of grassland plant communities by counterbalancing the negative effects of plant-feeding nematodes on grasses and by conserving the evenness of the plant community. We propose that interacting effects of functionally dissimilar soil organisms on plant community performance have to be taken into account in future studies, since individual effects of soil organism groups may cancel out each other in functionally diverse soil communities.     

Organizing Self‐Organizing Systems

Industrial symbiosis examines cooperative management of resource flows through networks of businesses known in the literature as industrial ecosystems. These industrial ecosystems have previously been portrayed as having characteristics of complex adaptive systems, but with insufficient attention to the internal and external phenomena describing their genesis. Drawing on biological, ecological, organizational, and systems theory, a discontinuous three‐stage model of industrial symbiosis is presented. The model proceeds from a random formative stage involving numerous actors engaging in material and energy exchanges, to conscious recognition and intentional pursuit of network benefits, to institutionalization of beliefs and norms enabling successful collaborative behavior. While there is much variation, with no single path to this outcome, the recognition of benefits is seen as an emergent property characteristic of these self‐organized systems that move beyond the initial stage.     

Biological evolution as an expression of body-plan potentialities.

A growing bulk of recent data from different fields as molecular biology, developmental biology, genetics, paleontology and phylogenetics shows that organisms play a more active role in their evolution than what postulated by the random variation-natural selection paradigm of the neo-Darwinian synthesis. Organisms show during development and morphogenesis autopoietic processes which are related to their body-plan potentialities. These potentialities are expressed through regulatory networks in which a plastic genome participates together with proteins and other substances in an epigenetic space. The epigenetic systems which arise from this interaction may be inherited and then assume a significant role in evolution becoming the source of new acquired characters. The acquisition of new traits through the epigenetic systems is influenced directly by environmental cues. If this process is coherent with the environmental demands it co-operates with natural selection in organism adaptation. An outstanding role in this context may be played by phenotypic plasticity if, as emerges in recent views, it may constitute a general basis for genetic assimilation processes.     

Adaptive Significance of Intra- and Interspecific Differences in the Feeding Repertoires of Cichlid Fishes

Intraspecific modulatory multiplicity in the feeding mechanismof cichlids as elucidated by electromyography has profound implicationson small-scale trophic events the sum of which is the very coreof such large-scale population and evolutionary phenomena asefficiency of trophic exploitation niche width and overlap competitionand adaptation. The greatest paradox emerging from the studyon intra and interspecific differences in feeding repertoiresof cichlid fishes is that the most specialized taxa are notonly remarkable specialists in a narrow sense but also jacks-of-all-trades.If specialists are simultaneously jacks of-all-trades how couldthey have evolved according to the widely accepted hypothesisthat broadening the range of usable resources prevents speciesfrom specializing on individual types? The organism can be considered to be composed of structuralelements and functional components that exert mutual influences.As a result, a network of interacting constraints is set up.The nature of the network determines the direction and rangeof evolutionary changes the possibilities of optimizing adaptationsand built-in variability of the trait. A change in the networkcan put a static trait into a different context to become dynamic.These changes in variability due to changes in the structureof the network cannot be explained in terms of simple adaptationto the external environment. Fitness is considered to dependon the nature of a network of interacting constraints. The possibilitiesof optimization the sensitivity of the phenotypic traits toenvironmental differences and the correlated evolutionary responsesof different traits are all related to this network of interactingconstraints between the elements and components of the organism.Thus the experimental and comparative studies of these networksof interacting constraints should become an increasingly moreimportant focus for morphologists as they attempt to refinetheir understanding of adaptation.     

An immunochemical method for detection and analysis of changes in methylome

DNA methylation is an important epigenetic modification involved in the ability of an organism to respond to stress and adaptation. It has been implicated in development, differentiation, oncogenesis, chromatin remodelling, nutrigenomics, and appears to play a pivotal role in many regulatory and adaptive functions. It is therefore important to analyze the status of DNA methylation and its changes under various developmental, carcinogenic, pharmacological, and environmental conditions. In this report we describe an immunochemical method for the detection of genome wide DNA methylation and its alterations under various conditions along with the analysis of DNA methyltransferase activity. The ability of this approach to detect and provide a map of methylomic changes in a genome facilitates assessment of various agents and conditions which can alter this important epigenetic signal. This experimental system permits rapid evaluation of potential target genes which would be modulated by DNA methylation changes and thus the gene networks that govern the processes.     

Movement of protistan trophic groups in soil–plant continuums

Protists, functionally divided into consumers, phototrophs, and parasites act as integral components and vital regulators of microbiomes in soil–plant continuums. However, the drivers of community structure, assembly mechanisms, co-occurrence patterns, and the associations with human pathogens and different protistan trophic groups remain unknown. Here, we characterized the phyllosphere and soil protistan communities associated with three vegetables under different fertilization treatments (none and organic fertilization) at five growth stages. In this study, consumers were the most diverse soil protist group, had the role of inter-kingdom connector, and were the primary biomarker for rhizosphere soils which were subjected to decreasing deterministic processes during plant growth. In contrast, phototrophs had the greatest niche breadth and formed soil protistan hubs, and were the primary biomarkers for both bulk soils and the phyllosphere. Parasites had minimal input to microbial co-occurrence networks. Organic fertilization increased the relative abundance (RA) of pathogenic protists and the number of pathogen–consumer connections in rhizosphere soils but decreased protistan richness and the number of internal protistan links. This study advances our understanding of the ecological roles and potential links between human pathogens and protistan trophic groups associated with soil–plant continuums, which is fundamental to the regulation of soil–plant microbiomes and maintenance of environmental and human health.     

Macroevolution: macrogenesis and typogenesis

One can distinguish two levels (and stages) of macroevolutionary processes: the lower (macrogenesis) and higher (typogenesis) ones. The macrogenesis represents macroevolutionary alterations of separate structures; the typogenesis is the forming of general Bauplan (type of organization) of a new macrotaxon on a base of initial macrogenesis. Discrete (or quantum) character of many macroevolutionary transformations is caused by various mechanisms, which are based on properties of integrated organismic systems and are characterized by threshold effect of their action. Initial macrogenesis can be resulted from the morphofunctional preadaptations; the pattern (or regime) transformations of morphofunctional organismic systems; emerging of dichotomy of morphogenetic programs and their following switching; the ontogenetic heterochronies (in particular, paedomorphosis); the allometric structural changes (and possibly some other mechanisms). The initial macrogenesis forms a base for qualitatively new adaptation and essentially influences on other systems in whole organism. That changes the selection vectors significantly. All these alterations trigger the typogenesis. The latter represents a complex of organismic systems transformations, integrated by selection and interconnections of various systems in whole organism. The important role in typogenesis belongs to the key alterations of some limiting organismic system that trigger and direct evolutionary changes of depended organismic systems. In course of typogenesis evolution, new macrotaxon occupies new adaptive zone.     

Mesoscopic structure conditions the emergence of cooperation on social networks

Background

We study the evolutionary Prisoner''s Dilemma on two social networks substrates obtained from actual relational data.

Methodology/Principal Findings

We find very different cooperation levels on each of them that cannot be easily understood in terms of global statistical properties of both networks. We claim that the result can be understood at the mesoscopic scale, by studying the community structure of the networks. We explain the dependence of the cooperation level on the temptation parameter in terms of the internal structure of the communities and their interconnections. We then test our results on community-structured, specifically designed artificial networks, finding a good agreement with the observations in both real substrates.

Conclusion

Our results support the conclusion that studies of evolutionary games on model networks and their interpretation in terms of global properties may not be sufficient to study specific, real social systems. Further, the study allows us to define new quantitative parameters that summarize the mesoscopic structure of any network. In addition, the community perspective may be helpful to interpret the origin and behavior of existing networks as well as to design structures that show resilient cooperative behavior.     

HOW STABLE ‘SHOULD’ EPIGENETIC MODIFICATIONS BE? INSIGHTS FROM ADAPTIVE PLASTICITY AND BET HEDGING

Although there is keen interest in the potential adaptive value of epigenetic variation, it is unclear what conditions favor the stability of these variants either within or across generations. Because epigenetic modifications can be environmentally sensitive, existing theory on adaptive phenotypic plasticity provides relevant insights. Our consideration of this theory suggests that stable maintenance of environmentally induced epigenetic states over an organism's lifetime is most likely to be favored when the organism accurately responds to a single environmental change that subsequently remains constant, or when the environmental change cues an irreversible developmental transition. Stable transmission of adaptive epigenetic states from parents to offspring may be selectively favored when environments vary across generations and the parental environment predicts the offspring environment. The adaptive value of stability beyond a single generation of parent–offspring transmission likely depends on the costs of epigenetic resetting. Epigenetic stability both within and across generations will also depend on the degree and predictability of environmental variation, dispersal patterns, and the (epi)genetic architecture underlying phenotypic responses to environment. We also discuss conditions that favor stability of random epigenetic variants within the context of bet hedging. We conclude by proposing research directions to clarify the adaptive significance of epigenetic stability.     

The consequences of mass mortality events for the structure and dynamics of biological communities

Mass mortality events (MMEs) are rapidly occurring, substantial population losses that transpire within a short time interval relative to the generation time of the affected organism. Previous work has established that MMEs appear to be increasing in frequency and magnitude; however, currently, there is little understanding of the consequences of MMEs for biological communities. Here, we use theory and empirical data from observed MMEs to understand how MMEs impact the structure and dynamics of communities. To do so, we build upon existing resource pulse and trophic cascade theory to show that MMEs both share similarities and diverge from these ecological phenomena, producing distinct short‐ and long‐term impacts by jointly altering the effects of species interactions across trophic levels and providing an influx of resources from decaying biomass. Second, we investigate how the magnitude of MMEs, trophic level of the impacted species, overall food web structure and ecosystem type may mediate the resulting ecological response. Third, we compare the understanding gained by our models to existing observational data on MMEs. Our synthesis, offers an empirical path forward for understanding MMEs through experimentation and improved observational data collection. While complex, resolving the consequences of MMEs should be a high research priority due to their role in determining how ecological systems respond to environmental change driven by rare events.     

Epigenetic Regulation in Plant Responses to the Environment

In this article, we review environmentally mediated epigenetic regulation in plants using two case histories. One of these, vernalization, mediates adaptation of plants to different environments and it exemplifies processes that are reset in each generation. The other, virus-induced silencing, involves transgenerationally inherited epigenetic modifications. Heritable epigenetic marks may result in heritable phenotypic variation, influencing fitness, and so be subject to natural selection. However, unlike genetic inheritance, the epigenetic modifications show instability and are influenced by the environment. These two case histories are then compared with other phenomena in plant biology that are likely to represent epigenetic regulation in response to the environment.     

Comparison of size-structured and species-level trophic networks reveals antagonistic effects of temperature on vertical trophic diversity at the population and species level

It is predicted that warmer conditions should lead to a loss of trophic levels, as larger bodied consumers, which occupy higher trophic levels, experience higher metabolic costs at high temperature. Yet, it is unclear whether this prediction is consistent with the effect of warming on the trophic structure of natural systems. Furthermore, effects of temperature at the species level, which arise through a change in species composition, may differ from those at the population level, which arise through a change in population structure. We investigate this by building species-level trophic networks, and size-structured trophic networks, as a proxy for population structure, for 18 648 stream fish communities, from 4 145 234 individual fish samples, across 7024 stream locations in France from 1980 to 2008. We estimated effects of temperature on total trophic diversity (total number of nodes), vertical trophic diversity (mean and maximum trophic level) and distribution of biomass across trophic level (correlation between trophic level and biomass) in these networks. We found a positive effect of temperature on total trophic diversity in both species- and size-structured trophic networks. We found that maximum trophic level and biomass distribution decreased in species-level and size-structured trophic networks, but the mean trophic level decreased only in size-structured trophic networks. These results show that warmer temperatures associate with a lower vertical trophic diversity in size-structured networks, and a higher one in species-level networks. This suggests that vertical trophic diversity is shaped by antagonistic effects of temperature on population structure and on species composition. Our results hence demonstrate that effects of temperature do not only differ across trophic levels, but also across levels of biological organisation, from population to species level, implying complex changes in network structure and functioning with warming.     

Self-organization vs Watchmaker: stochastic gene expression and cell differentiation

Cell differentiation and organism development are traditionally described in deterministic terms of program and design, echoing a conventional clockwork perception of the cell on another scale. However, the current experimental reality of stochastic gene expression and cell plasticity is poorly consistent with the ideas of design, purpose and determinism, suggesting that the habit of classico-mechanistic interpretation of life phenomena may handicap our ability to adequately comprehend and model biological systems. An alternative conceptualization of cell differentiation and development is proposed where the developing organism is viewed as a dynamic self-organizing system of adaptive interacting agents. This alternative interpretation appears to be more consistent with the probabilistic nature of gene expression and the phenomena of cell plasticity, and is coterminous with the novel emerging image of the cell as a self-organizing molecular system. I suggest that stochasticity, as a principle of differentiation and adaptation, and self-organization, as a concept of emergence, have the potential to provide an interpretational framework that unites phenomena across different scales of biological organization, from molecules to societies.Edited by R.J. Sommer     

A systems-analytical approach to macro-evolutionary phenomena.

Two sets of evolutionary phenomena find no explanation through current theory. For the static phenomena (such as homology, homonomy, systematic weight, and "Type") there is no causal base, although these principles are responsible for all phenomena of predictable order in the living world. The dynamic phenomena (such as homodynamy, coadaptation, parallel evolution, orthogenesis, Cartesian transformation, typostrophy, hetermorphosis, systemic mutation, and spontaneous atavism) have no causal explanation, although they are responsible for all directed phenomena in macroevolution. These phenomena share one unifying principle which can be explained by a system theory of evolution based on, but extending, the current synthetic theory. This system theory envisages feedback conditions between genotype and phenotype by which the chances of successful adaptation increase if the genetic units, by insertion of superimposed genes, copy the functional dependencies of those phene structures for which they code. This positive feedback of the adaptive speed (or probability) within a single adaptive direction is compensated by negative feedback in most of the alternative directions. The negative feedback operates as selection not be environmental but by systemic conditions developed by the organization of the organism. The consequences are an imitatively organized system of gene interractions, the rehabilitation of classical systematics, the reality of the "natural system," and, in general, the resolution of the contradiction between neodarwinists and their critics, between reductionists and holists, between "a priori" and "a posteriori" views, between idealism and materialism, and between the notions of freedom and of purpose in evolution.     

Phenotypic plasticity: Eco-Devo and evolution

Phenotypic plasticity refers to the ability of an organism to alter its physiology/morphology/behavior in response to changes in environmental conditions. Although encompassing various phenomena spanning multi-ple levels of organization, most plastic responses seem to take place by altering gene expression and eventually altering ontogenetic trajectory in response to environmental variation. Epigenetic modifications provide a plausi-ble link between the environment and alterations in gene expression, and the alterations in phenotype based on environmentally induced epigenetic modifications can be inherited transgenerationally. Even closely related species and populations with different genotypes may exhibit differences in the patterns and the extents of plastic responses, indicating the wide existence of plasticity genes which are independent of trait means and directly respond to environmental stimuli by triggering phenotypic changes. The ability of plasticity is not only able to affect the adaptive evolution of species significantly, but is also an outcome of evolutionary processes. Therefore, phenotypic plasticity is a potentially important molder of adaptation and evolution.     

New insights into bacterial adaptation through in vivo and in silico experimental evolution

Microbiology research has recently undergone major developments that have led to great progress towards obtaining an integrated view of microbial cell function. Microbial genetics, high-throughput technologies and systems biology have all provided an improved understanding of the structure and function of bacterial genomes and cellular networks. However, integrated evolutionary perspectives are needed to relate the dynamics of adaptive changes to the phenotypic and genotypic landscapes of living organisms. Here, we review evolution experiments, carried out both in vivo with microorganisms and in silico with artificial organisms, that have provided insights into bacterial adaptation and emphasize the potential of bacterial regulatory networks to evolve.     

Toward an understanding of microbial communities through analysis of communication networks

Bacteria receive signals from diverse members of their biotic environment. They sense their own species through the process of quorum sensing, which detects the density of bacterial cells and regulates functions such as bioluminescence, virulence, and competence. Bacteria also respond to the presence of other microorganisms and eukaryotic hosts. Most studies of microbial communication focus on signaling between the microbe and one other organism for empirical simplicity and because few experimental systems offer the opportunity to study communication among various types of organisms. But in the real biological world, microorganisms must carry on multiple molecular conversations simultaneously between diverse organisms, thereby constructing communication networks. We propose that biocontrol of plant disease, the process of suppressing disease through application of a microorganism, offers a model for the study of communication among multiple organisms. Successful biocontrol requires the sending and receiving of signals between the biocontrol agent and the pathogen, plant host, and microbial community surrounding the host. We are using Bacillus cereus, a biocontrol agent, and the organisms it must interact with, to dissect a communication network. This system offers an excellent starting point for study because its members are defined and well studied. An understanding of signaling in the B. cereus biocontrol system may provide a model for network communication among organisms that share a habitat and provide a new angle of analysis for understanding the interconnections that define communities. This revised version was published online in August 2006 with corrections to the Cover Date.