Beyond the phenotypic gambit: molecular behavioural ecology and the evolution of genetic architecture

Most studies of behaviour examine traits whose proximate causes include sensory input and neural decision-making, but conflict and collaboration in biological systems began long before brains or sensory systems evolved. Many behaviours result from non-neural mechanisms such as direct physical contact between recognition proteins or modifications of development that coincide with altered behaviour. These simple molecular mechanisms form the basis of important biological functions and can enact organismal interactions that are as subtle, strategic and interesting as any. The genetic changes that underlie divergent molecular behaviours are often targets of selection, indicating that their functional variation has important fitness consequences. These behaviours evolve by discrete units of quantifiable phenotypic effect (amino acid and regulatory mutations, often by successive mutations of the same gene), so the role of selection in shaping evolutionary change can be evaluated on the scale at which heritable phenotypic variation originates. We describe experimental strategies for finding genes that underlie biochemical and developmental alterations of behaviour, survey the existing literature highlighting cases where the simplicity of molecular behaviours has allowed insight to the evolutionary process and discuss the utility of a genetic knowledge of the sources and spectrum of phenotypic variation for a deeper understanding of how genetic and phenotypic architectures evolve.     

The bimodal role of filamin in controlling the architecture and mechanics of F-actin networks

Reconstituted actin filament networks have been used extensively to understand the mechanics of the actin cortex and decipher the role of actin cross-linking proteins in the maintenance and deformation of cell shape. However, studies of the mechanical role of the F-actin cross-linking protein filamin have led to seemingly contradictory conclusions, in part due to the use of ill-defined mechanical assays. Using quantitative rheological methods that avoid the pitfalls of previous studies, we systematically tested the complex mechanical response of reconstituted actin filament networks containing a wide range of filamin concentrations and compared the mechanical function of filamin with that of the cross-linking/bundling proteins alpha-actinin and fascin. At steady state and within a well defined linear regime of small non-destructive deformations, F-actin solutions behave as highly dynamic networks (actin polymers are still sufficiently mobile to relax the stress) below the cross-linking-to-bundling threshold filamin concentration, and they behave as covalently cross-linked gels above that threshold. Under large deformations, F-actin networks soften at low filamin concentrations and strain-harden at high filamin concentrations. Filamin cross-links F-actin into networks that are more resilient, stiffer, more solid-like, and less dynamic than alpha-actinin and fascin. These results resolve the controversy by showing that F-actin/filamin networks can adopt diametrically opposed rheological behaviors depending on the concentration in cross-linking proteins.     

Quantitative analysis of aspartate receptor signaling complex reveals that the homogeneous two-state model is inadequate: development of a heterogeneous two-state model

The two-state model of receptor activation, in which a receptor population exists in equilibrium between a single on-state and a single off-state, has long been considered a viable model for the signaling behavior of bacterial chemoreceptors. Here, we show that this simple, homogeneous two-state model is adequate for a pure receptor population with just one adaptation state, but fails to account quantitatively for the observed linear relationship between the apparent attractant affinity (K(1/2)) and kinase activity (V(obs)(apo)) as the adaptation state is varied. Further analysis reveals that the available data are instead consistent with a heterogeneous two-state model in which covalent modification of receptor adaptation sites changes the microscopic properties of the on-state or off-state. In such a system, each receptor molecule retains a single on-state and off-state, but covalent adaptation generates a heterogeneous population of receptors exhibiting a range of different on-states or off-states with different microscopic parameters and conformations. It follows that covalent adaptation transforms the receptor from a simple, two-state toggle switch into a variable switch. In order to identify the microscopic parameters most sensitive to covalent adaptation, six modified, two-state models were examined in which covalent adaptation alters a different microscopic parameter. The analysis suggests that covalent adaptation primarily alters the ligand-binding affinity of the receptor off-state (K(D1)). By contrast, models in which covalent adaptation alters the ligand-binding affinity of the receptor on-state, the maximal kinase stimulation of the on-state or off-state, cooperative interactions between receptors, or the assembly of the receptor-kinase signaling complex are inconsistent with the available evidence. Overall, the findings support a heterogeneous two-state model in which modification of the receptor adaptation sites generates a population of receptors with heterogeneous off-states differing in their attractant affinities.In the process of testing the effects of covalent adaptation on the assembly of the receptor-kinase signaling complex, a new method for estimating the stoichiometric ratio of receptor and CheA in the ternary signaling complex was devised. This method suggests that the ratio of receptor dimers to CheA dimers in the assembled complex is 6:1 or less.     

Molecular evolution: dynamic combinatorial libraries, autocatalytic networks and the quest for molecular function

The principles of Darwinian evolution have been explored in molecular systems such as autocatalytic networks and dynamic combinatorial libraries. Molecular evolution in such systems manifests itself as ligand or receptor amplification by selection. Research efforts exploring these concepts may provide a mechanism for the identification of novel catalysts, molecular receptors and bioactive molecules.     

The dynamic nature of mollusc egg surface architecture and its relation to the microtubule network

Dynamic changes in the surface architecture pattern of embryos of the slipper limpet (Crepidula fornicata, Mollusca) were found in this study to correlate with the dynamic activity and pattern of the underlying mitotic spindle microtubule network, revealed by fluorescent labelling and confocal imaging techniques. Examination of a series of optical sections indicate that this network appears to be spatially co-ordinated together as a whole throughout the embryo. The microtubule pattern also associated with abnormal multipolar spindles resulting from an applied static magnetic field, indicating that the pattern may be generated by a natural endogenous field source. The patterning characteristics of the surface and microtubule network together provide further morphological evidence for a primary morphogenetic or developmental field system which organises the primary body axis and co-ordinates the pattern of cleavage.     

Between migration load and evolutionary rescue: dispersal,adaptation and the response of spatially structured populations to environmental change

The evolutionary potential of populations is mainly determined by population size and available genetic variance. However, the adaptability of spatially structured populations may also be affected by dispersal: positively by spreading beneficial mutations across sub-populations, but negatively by moving locally adapted alleles between demes. We develop an individual-based, two-patch, allelic model to investigate the balance between these opposing effects on a population''s evolutionary response to rapid climate change. Individual fitness is controlled by two polygenic traits coding for local adaptation either to the environment or to climate. Under conditions of selection that favour the evolution of a generalist phenotype (i.e. weak divergent selection between patches) dispersal has an overall positive effect on the persistence of the population. However, when selection favours locally adapted specialists, the beneficial effects of dispersal outweigh the associated increase in maladaptation for a narrow range of parameter space only (intermediate selection strength and low linkage among loci), where the spread of beneficial climate alleles is not strongly hampered by selection against non-specialists. Given that local selection across heterogeneous and fragmented landscapes is common, the complex effect of dispersal that we describe will play an important role in determining the evolutionary dynamics of many species under rapidly changing climate.     

Molecular modeling studies and anti-TB activity of trisubstituted indolizine analogues; molecular docking and dynamic inputs

A series of trisubstituted indolizine analogues has been designed as a result of a fragment-based approach to target the inhibition of mycobacterial enoyl-acyl carrier protein reductase. Anti-tuberculosis (TB) screening of the characterized compounds by a resazurin microplate assay method revealed that ethyl group at second position of indolizine nucleus exhibited activity against susceptible and multidrug-resistant strains of Mycobacterium tuberculosis at concentration of 5.5 and 11.3 μg/mL, respectively. A molecular docking study was also conducted to evaluate the stability of the active compounds, and compound with ethyl substitution at second position of indolizine nucleus showed the highest free binding energy of ΔG ?24.11 (kcal/mol), a low clash score of 3.04, and high lipo score of ?13.33. Indolizine analog with ethyl substitution at second position demonstrated Molecular Mechanics/Generalized Born Surface Area (?23.85 kcal/mol). Two molecular dynamics studies were computed (100 ps and 50 ns) to calculate the relationship between the potential and kinetic energies of the active anti-TB compound with time and temperature. The discovery of this lead may have a positive impact on anti-TB drug discovery.     

Locomotory Responses of the Cave Cyprinid Phreatichthys Andruzzii Chemical Signals from Conspecifics and Related Species: New Findings

Previous research on chemical communication among hypogean fishes have suggested that these species are attracted, as are epigean species, by the odour of non-injured conspecifics. Considerations on the biological meaning of such responses and some doubts about the reliability of the experimental procedure previously utilised, have led us to reconsider the matter and verify the results already obtained in the cave cyprinid Phreatichthys andruzzii. Using a new methodological approach we ascertained not only the absence of positive chemotaxis to odour of known or unknown conspecifics, but also the presence of a strong negative chemotaxis towards the odour of unfamiliar conspecifics and of individuals belonging to the closely related species Barbus conchonius. The biological meaning and the adaptive value of these reactions are briefly discussed.     

Patterns of multiallelic polymorphism maintained by migration and selection

Evolution at a multiallelic locus under the joint action of migration and viability selection is investigated. Generations are discrete and nonoverlapping. The monoecious, diploid population is subdivided into finitely many panmictic colonies that exchange adult migrants independently of genotype. The forward migration matrix is arbitrary, but time independent and ergodic (i.e., irreducible and aperiodic). Several examples of globally attracting multiallelic equilibria are presented. Migration can cause global fixation even if, without migration, there is a globally attracting multiallelic equilibrium in every colony. Migration can also cause the global fixation of an allele that, without migration, is eliminated in every colony. Without dominance, generically, the number of alleles present at equilibrium cannot exceed the number of colonies. Some general properties and examples of the Levene model are studied in detail. If in each colony there is either no dominance or, without migration, a globally attracting internal equilibrium, then there exists a globally attracting equilibrium with migration. Therefore, if an internal equilibrium exists, it is the global attractor.     

Ecological networks: delving into the architecture of biodiversity

In recent years, the analysis of interaction networks has grown popular as a framework to explore ecological processes and the relationships between community structure and its functioning. The field has rapidly grown from its infancy to a vibrant youth, as reflected in the variety and quality of the discussions held at the first international symposium on Ecological Networks in Coimbra—Portugal (23–25 October 2013). The meeting gathered 170 scientists from 22 countries, who presented data from a broad geographical range, and covering all stages of network analyses, from sampling strategies to effective ways of communicating results, presenting new analytical tools, incorporation of temporal and spatial dynamics, new applications and visualization tools.¹ During the meeting it became evident that while many of the caveats diagnosed in early network studies are successfully being tackled, new challenges arise, attesting to the health of the discipline.     

Sex ratio selection and multi-factorial sex determination in the housefly: a dynamic model

Sex determining (SD) mechanisms are highly variable between different taxonomic groups and appear to change relatively quickly during evolution. Sex ratio selection could be a dominant force causing such changes. We investigate theoretically the effect of sex ratio selection on the dynamics of a multi-factorial SD system. The system considered resembles the naturally occurring three-locus system of the housefly, which allows for male heterogamety, female heterogamety and a variety of other mechanisms. Sex ratio selection is modelled by assuming cost differences in the production of sons and daughters, a scenario leading to a strong sex ratio bias in the absence of constraints imposed by the mechanism of sex determination. We show that, despite of the presumed flexibility of the SD system considered, equilibrium sex ratios never deviate strongly from 1 : 1. Even if daughters are very costly, a male-biased sex ratio can never evolve. If sons are more costly, sex ratio can be slightly female biased but even in case of large cost differences the bias is very small (<10% from 1 : 1). Sex ratio selection can lead to a shift in the SD mechanism, but cannot be the sole cause of complete switches from one SD system to another. In fact, more than one locus remains polymorphic at equilibrium. We discuss our results in the context of evolution of the variable SD mechanism found in natural housefly populations.     

Divergent selection and heterogeneous migration rates across the range of Sitka spruce (Picea sitchensis)

Gene flow and effective population size (N(e)) should depend on a population's position within its range: those near the edges are expected to have smaller N(e) and lower relative emigration rates, whereas those nearer the centre should have larger N(e) and higher relative emigration rates. In species with continuous ranges, this phenomenon may limit the ability of peripheral populations to respond to divergent selection. Here, we employ Sitka spruce as a model to test these predictions. We previously genotyped 339 single nucleotide polymorphisms (SNPs) in 410 individuals from 13 populations, and used these data to identify putative targets of divergent selection, as well as to explore the extent to which central-peripheral structure may impede adaptation. Fourteen SNPs had outlier F(ST) estimates suggestive of divergent selection, of which nine were previously associated with phenotypic variation in adaptive traits (timing of autumn budset and cold hardiness). Using coalescent simulations, we show that populations from near the centre of the range have higher effective populations sizes than those from the edges, and that central populations contribute more migrants to marginal populations than the reverse. Our results suggest that while divergent selection appears to have shaped allele frequencies among populations, asymmetrical movement of alleles from the centre to the edges of the species range may affect the adaptive capacity of peripheral populations. In southern peripheral populations, the movement of cold-adapted alleles from the north represents a significant impediment to adaptation under climate change, while in the north, movement of warm-adapted alleles from the south may enhance adaptation.     

Motility and chemotactic response of Pseudomonas fluorescens toward chemoattractants present in the exudate of Macrophomina phaseolina

Pseudomonas fluorescens strains (LAM1-hydrophilic) and (LAM2-hydrophobic) showed positive chemotaxis towards attractants (sugars, amino acids, polyols and organic acids) present in the exudate of Macrophomina phaseolina (a soilborne plant pathogenic fungus). The varied response of motility traits such as speed, rate of change in direction (RCDI) and net to gross displacement ratio (NGDR) was observed for different chemoattractants. Swimming speed of the strains was highest in 10-fold diluted exudate or 100–1000 μM strength of different attractants, but further dilutions significantly decreased the swimming speed (P = 0.05). Chemotactic response of P. fluorescens was positively correlated with swimming speed (P = 0.05; r = 0.76). Relative to control, the RCDI values decreased 1.5-fold in amino acids or sugars, and 1.2-fold in polyols or organic acids. With increase in swimming speed, the NGDR of both strains also increased, but the RCDI decreased. Both hydrophilic and hydrophobic strains did not show significant differences in their motility traits. The results demonstrate that M. phaseolina exudate contains chemical attractants that serve as signal for flagellar motility of P. fluorescens. Motile P. fluorescens strains thus may consume fungal exudate as nutrients, and thus spores could offer a niche for these bacteria in soil.     

Influence of genetic architecture on contemporary local evolution in the soapberry bug,Jadera haematoloma: artificial selection on beak length

Little is known about the influence of genetic architecture on local adaptation. We investigated the genetic architecture of the rapid contemporary evolution of mouthparts, the flight polymorphism and life history traits in the soapberry bug Jadera haematoloma (Hemiptera) using laboratory selection. The mouthparts of these seed‐feeding bugs have adapted in 40–50 years by decreasing in length following novel natural selection induced by a host switch to the seeds of an introduced tree with smaller fruits than those of the native host vine. Laboratory selection on beak length in both an ancestral population feeding on the native host and a derived population feeding on the introduced host reveals genetic variance allowing a rapid response (heritabilities of 0.51–0.87) to selection for either longer or shorter beaks. This selection resulted in reverse evolution by restoring long beaks in the derived population and forward evolution by re‐creating short beaks in the ancestral bugs. There were strong genetic correlations (0.68–0.84) in both populations between beak lengths and the frequency of flight morphs, with short beaks associated with short wings. The results reveal a genetically interrelated set of adaptive multivariate traits including both beak length and flight morph. This suite of traits reflects host plant patchiness and seeding phenology. Weaker evidence suggests that egg mass and early egg production may be elements of the same suite. Reversible or forward evolution thus may occur in a broad set of genetically correlated multivariate traits undergoing rapid contemporary adaptation to altered local environments.     

A codon-based model of host-specific selection in parasites,with an application to the influenza A virus

Parasites sometimes expand their host range by acquiring a new host species. After a host change event, the selective regime acting on a given parasite gene may change as a result of host-specific adaptive alterations of protein functionality or host-specific immune-mediated selection. We present a codon-based model that attempts to include these effects by allowing the position-specific substitution process to change in conjunction with a host change event. Following maximum-likelihood parameter estimation, we employ an empirical Bayesian procedure to identify candidate sites potentially involved in host-specific adaptation. We discuss the applicability of the model to the more general problem of ascertaining whether the selective regime differs in two groups of related organisms. The utility of the model is illustrated on a data set of nucleoprotein sequences from the influenza A virus obtained from avian and human hosts.     

Chemical characterization of root exudates from rice (Oryza sativa) and their effects on the chemotactic response of endophytic bacteria

Root exudates represent an important source of nutrients for microorganisms in the rhizosphere and seem to participate in early colonization inducing chemotactic responses of rhizospheric bacteria. We characterized the root exudates collected from rice plantlets cultured under hydroponic conditions and assessed their effects on the chemotaxis of two strains of endophytic bacteria, Corynebacterium flavescens and Bacillus pumilus, collected from the rice rhizosphere. We compared these chemotactic effects on endophytic bacteria with those on two strains of plant-growth-promoting bacteria, Azospirillum brasilense (isolated from the corn rhizosphere) and Bacillus sp. (from the rice rhizosphere). The root exudates were collected at different time intervals. The highest concentration and diversity of amino acids and carbohydrates were found during the first 2 weeks after seeding. Histidine, proline, valine, alanine, and glycine were the main amino acid residues identified during the 4 weeks of culture. The main carbohydrates identified were glucose, arabinose, mannose, galactose, and glucuronic acid. The chemotactic responses of the analyzed endophytic bacteria to root exudates were 3.9 to 5.1 times higher than those of A. brasilense and 2.2 to 2.8 times higher than Bacillus sp. Our results indicate that rice exudates may induce a higher chemotactic response for endophytic bacteria than for other bacterial strains present in the rice rhizosphere.     

Neural network model of the primary visual cortex: From functional architecture to lateral connectivity and back

The role of intrinsic cortical dynamics is a debatable issue. A recent optical imaging study (Kenet et al., 2003) found that activity patterns similar to orientation maps (OMs), emerge in the primary visual cortex (V1) even in the absence of sensory input, suggesting an intrinsic mechanism of OM activation. To better understand these results and shed light on the intrinsic V1 processing, we suggest a neural network model in which OMs are encoded by the intrinsic lateral connections. The proposed connectivity pattern depends on the preferred orientation and, unlike previous models, on the degree of orientation selectivity of the interconnected neurons. We prove that the network has a ring attractor composed of an approximated version of the OMs. Consequently, OMs emerge spontaneously when the network is presented with an unstructured noisy input. Simulations show that the model can be applied to experimental data and generate realistic OMs. We study a variation of the model with spatially restricted connections, and show that it gives rise to states composed of several OMs. We hypothesize that these states can represent local properties of the visual scene. Action Editor: Jonathan D. Victor     

Cell migration and chick limb development: chemotactic action of FGF-4 and the AER.

Experiments have been carried out to investigate the role of the apical ectodermal ridge (AER) and FGF-4 on the control of cell migration during limb bud morphogenesis. By coupling DiI cell labeling with ectopic implantation of FGF-4 microcarrier beads we have found that FGF-4 acts as a potent and specific chemoattractive agent for mesenchymal cells of the limb bud. The response to FGF-4 is dose dependent in both the number of cells stimulated to migrate and the distance migrated. The cell migration response to FGF-4 appears to be independent of the known inductive activity of FGF-4 on Shh gene expression. We investigated the role of the AER in controlling cell migration by characterizing the migration pattern of DiI-labeled subapical cells during normal limb outgrowth and following partial AER removal. Subapical cells within 75 micrometer of the AER migrate to make contact with the AER and are found intermingled with nonlabeled cells. Thus, the progress zone is dynamic with cells constantly altering their neighbor relationships during limb outgrowth. AER removal studies show that cell migration is AER dependent and that subapical cells redirect their path of migration toward a functional AER. These studies indicate that the AER has a chemoattractive function and regulates patterns of cell migration during limb outgrowth. Our results suggest that the chemoattractive activity of the AER is mediated in part by the production of FGF-4.