“Ensemble” iterative relaxation matrix approach: A new NMR refinement protocol applied to the solution structure of crambin

The structure in solution of crambin, a small protein of 46 residues, has been determined from 2D NMR data using an iterative relaxation matrix approach (IRMA) together with distance geometry, distance bound driven dynamics, molecular dynamics, and energy minimization. A new protocol based on an “ensemble” approach is proposed and compared to the more standard initial rate analysis approach and a “single structure” relaxation matrix approach. The effects of fast local motions are included and R-factor calculations are performed on NOE build-ups to describe the quality of agreement between theory and experiment. A new method for stereospecific assignment of prochiral groups, based on a comparison of theoretical and experimental NOE intensities, has been applied. The solution structure of crambin could be determined with a precision (rmsd from the average structure) of 0.7 Å on backbone atoms and 1.1 Å on all heavy atoms and is largely similar to the crystal structure with a small difference observed in the position of the side chain of Tyr-29 which is determined in solution by both J-coupling and NOE data. Regions of higher structural variability (suggesting higher mobility) are found hi the solution structure, in particular for the loop between the two helices (Gly-20 to Pro-22). © 1993 Wiley-Liss, Inc.     

Coherent synthesis of genomic associations with phenotypes and home environments

Local adaptation is often studied via (i) multiple common garden experiments comparing performance of genotypes in different environments and (ii) sequencing genotypes from multiple locations and characterizing geographic patterns in allele frequency. Both approaches aim to characterize the same pattern (local adaptation), yet the complementary information from each has not yet been coherently integrated. Here, we develop a genome‐wide association model of genotype interactions with continuous environmental gradients (G × E), that is reaction norms. We present an approach to impute relative fitness, allowing us to coherently synthesize evidence from common garden and genome–environment associations. Our approach identifies loci exhibiting environmental clines where alleles are associated with higher fitness in home environments. Simulations show our approach can increase power to detect loci causing local adaptation. In a case study on Arabidopsis thaliana, most identified SNPs exhibited home allele advantage and fitness trade‐offs along climate gradients, suggesting selective gradients can maintain allelic clines. SNPs exhibiting G × E associations with fitness were enriched in genic regions, putative partial selective sweeps and associations with an adaptive phenotype (flowering time plasticity). We discuss extensions for situations where only adaptive phenotypes other than fitness are available. Many types of data may point towards the loci underlying G × E and local adaptation; coherent models of diverse data provide a principled basis for synthesis.     

Coastal insect herbivore communities are affected more by local environmental conditions than by plant genotype

Abstract.

• 1 We compared the effects of plant genotype and local environment on population densities of a community of coastal insect herbivores in west-central Florida. Reciprocal transplants of four genotypes of three species of coastal plants, Borrichia frutescens, Iva frutescens and Limbricata, were made in July 1992 between a series of off-shore islands.
• 2 For each plant species, phytophagous insects with a wide range of feeding modes including gall-makers, stem borers, leaf miners and sap suckers were affected more by local environment than by plant genotype. Whereas host genotype had a significant effect on the population densities of gall-makers on B.frutescens in the spring of 1993, no significant effect on the denrities of any other insect species was found and the effect on the gall-makers on Borrichia disappeared in the summer, 1 year after the transplants had been made. In our study, local environment had by far the greatest effect on insect population densities among islands. This is an unusual result because in other studies over 80% of the insect species examined have been affected by plant genotype (Karban, 1992). This result is consistent with that reported by Stiling (1994), who censused populations of two phytophagous insects on reciprocal transplantr ot Borrichia in north Florida.
• 3 Local environment also had an effect on insect population densities within islands. This result contrasts with similar studies performed in north Florida (Stiling, 1994), where population densities did not differ within areas, and underlies how some biotic processes may change with in the same community even over relatively small changes in species range.

     

Whence tit-for-tat?

Summary In theoretical and empirical studies of the evolution of cooperation, the tit-for-tat strategy (i.e. cooperate unless your partner did not cooperate in the previous interaction) is widely considered to be of central importance. Nevertheless, surprisingly little is known about the conditions in which tit-for-tat appears and disappears across generations in a population of interacting individuals. Here, we apply a newly developed classifier-system model (EvA) in addressing this issue when the key features of interactions are caricatured using the iterated prisoner's dilemma game. Our simple representation of behavioural strategies as algorithms composed of two interacting rules allowed us to determine conditions in which tit-for-tat can replace noncooperative strategies and vice versa. Using direct game-theoretic analysis and simulations with the EvA model, we determined that no strategy is evolutionarily stable, but larger population sizes and longer sequences of interactions between individuals can yield transient dominance by tit-for-tat. Genetic drift among behaviourally equivalent strategies is the key mechanism underlying this dominance. Our analysis suggests that tit-for-tat could be important in nature for cognitively simple organisms of limited memory capacity, in strongly kin-selected or group-selected populations, when interaction sequences between individuals are relatively short, in moderate-sized populations of widely interacting individuals and when defectors appear in the population with moderate frequency.     

Genetic variation and phenotypic plasticity in a trophically polymorphic population of pumpkinseed sunfish (Lepomis gibbosus)

Summary Adaptive variation can exist at a variety of scales in biological systems, including among species, among local populations of a single species and among individuals within a single population. Trophic or resource polymorphisms in fishes are a good example of the lowest level of this hierarchy. In lakes without bluegill sunfish (Lepomis macrochirus), pumpkinseed sunfish (Lepomis gibbosus) can be trophically polymorphic, including a planktivorous limnetic form found in the pelagic habitat, in addition to the usual benthic form found in the littoral zone. In this paper we examine the degree to which morphological differences between the two forms are caused by genetic differences versus phenotypic plasticity. Adults from pelagic and littoral sites in Paradox Lake, NY, were bred separately and their progeny were raised in cages both in the open water and shallow water habitats of an artificial pond. The experimental design permitted two tests of genetic differences between the breeding stocks (in open and shallow water cages, respectively) and two tests of phenotypic plasticity (in the limnetic and benthic offspring, respectively). Limnetic progeny were more fusiform than benthic progeny raised in the same habitat. In addition, progeny of both stocks displayed limnetic-type characteristics when raised in the open water and benthic-type characteristics in the shallow water. Thus, genetic differences and phenotypic plasticity both contributed to the trophic polymorphism. Phenotypic plasticity and genetic differentiation accounted for 53 and 14%, respectively, of the variation in morphology. This study addresses the nature of subtle phenotypic differences among individuals from a single population that is embedded within a complex community, a condition that is likely to be the norm for most natural populations, as opposed to very large differences that have evolved in relatively few populations that reside in species-poor environments.     

On the encoding of movement vectors by honeybees. Are distance and direction represented independently?

Honeybees flying repeatedly over the same trajectory link it to an associated visual stimulus such that on viewing the stimulus they perform a trajectory in the habitual direction. To test if trajectory length can also be linked to a visual stimulus, bees were trained to fly through a multi-comparmented maze. Bees flew through a multi-compartmented maze. In one compartment a short trajectory could be linked to a stripe pattern oriented at 45° to the horizontal. In another compartment a longer trajectory could be linked to 135° stripes. Bees made both associations: their trajectories were short when viewing 45° stripes and longer when viewing 135° stripes. 90° stripes evoked trajectories of intermediate length.To test if distance and direction are linked independently to stripe orientation, a bee's trajectory was linked to 135° stripes in one compartment and to 45° stripes in another. These trajectories were the same length but differed in their horizontal direction by 60° or by 120°. 90° stripes evoked trajectories of intermediate direction which were shorter than those elicited by either training pattern. Bees were also trained to generate one long and one short trajectory with directions 120° apart. The trajectories elicited by 90° stripes were then biased towards the direction of the long training vector. Length and direction are not treated separately. The rules for combining trajectories resemble those of vector averaging.     

Analysing the history of the derelomine flower weevil–Carludovica association (Coleoptera: Curculionidae; Cyclanthaceae)

The evolutionary history of the interaction among species of derelomine flower weevils (Coleoptera: Curculionidae: Derelomini) and the Panama-hat palm Carludovica (Cyclanthaceae) is analysed with emphasis on the congruence of (1) topologies and (2) character state transformations in each of the Neotropical clades. For this purpose cladistic analyses are complemented with host plant records, natural history information and selected morphological studies of the associated taxa. The interaction is specialized, involving pollination, oviposition into the inflorescences and the predation of seeds (particularly within Systenotelus ). As results from a range of standard coevolutionary methods of analysis indicate, however, events of colonization, extinction and independent (non-reciprocal) speciation have been abundant throughout the history of the association. At the same time it is possible to specify the homology and succession of characters among species of derelomines and Carludovica and interpret them as reciprocal adaptations to attack and protect the seeds, respectively. It is argued that – in light of the limited evolutionary stability of many insect–plant interactions – the question of coevolution is most effectively addressed by combining information from the character- and topology-based approaches.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 81 , 483–517.     

Divergence of gastropod life history in contrasting thermal environments in a geothermal lake

Experiments using natural populations have provided mixed support for thermal adaptation models, probably because the conditions are often confounded with additional environmental factors like seasonality. The contrasting geothermal environments within Lake Mývatn, northern Iceland, provide a unique opportunity to evaluate thermal adaptation models using closely located natural populations. We conducted laboratory common garden and field reciprocal transplant experiments to investigate how thermal origin influences the life history of Radix balthica snails originating from stable cold (6 °C), stable warm (23 °C) thermal environments or from areas with seasonal temperature variation. Supporting thermal optimality models, warm‐origin snails survived poorly at 6 °C in the common garden experiment and better than cold‐origin and seasonal‐origin snails in the warm habitat in the reciprocal transplant experiment. Contrary to thermal adaptation models, growth rate in both experiments was highest in the warm populations irrespective of temperature, indicating cogradient variation. The optimal temperatures for growth and reproduction were similar irrespective of origin, but cold‐origin snails always had the lowest performance, and seasonal‐origin snails often performed at an intermediate level compared to snails originating in either stable environment. Our results indicate that central life‐history traits can differ in their mode of evolution, with survival following the predictions of thermal optimality models, whereas ecological constraints have shaped the evolution of growth rates in local populations.