Consequences of herbivory in the mountain birch (Betula pubescens ssp tortuosa): importance of the functional organization of the tree

Summary Three types of experiments indicate that the functional organization of the mountain birch may influence the ways in which the tree responds to simulated or natural herbivory. The first experiment showed that herbivory to both short and long shoot leaves affects plant development but, because growth largely proceeds by resources of the previous year, is manifested only in the year following the damage. The second experiment showed that even partial damage to a single long shoot leaf caused the axillary bud of that leaf to produce a shorter shoot the next year. Therefore, the value of a leaf depends also on the organ which it is subtending. In the third experiment we manipulated the apical dominance of shoots in ramets and caused improvement to leaf quality in extant shoots. Ramets within a tree responded individually, probably mediated by disturbance of the hormonal control because removal of apical buds elicited the response although removal of the same number of basal buds did not. Induced amelioration is a different response to induced resistance. The two responses are triggered by different cues and may occur in the same plant. By altering hormonal balance of shoots it is potentially possible for herbivores to induce amelioration of food quality. The ways in which herbivory is simulated may explain variability of results obtained when herbivory-induced responses in plants have been studied.     

Synthetic biology and genetic causation

Synthetic biology research is often described in terms of programming cells through the introduction of synthetic genes. Genetic material is seemingly attributed with a high level of causal responsibility. We discuss genetic causation in synthetic biology and distinguish three gene concepts differing in their assumptions of genetic control. We argue that synthetic biology generally employs a difference-making approach to establishing genetic causes, and that this approach does not commit to a specific notion of genetic program or genetic control. Still, we suggest that a strong program concept of genetic material can be used as a successful heuristic in certain areas of synthetic biology. Its application requires control of causal context, and may stand in need of a modular decomposition of the target system. We relate different modularity concepts to the discussion of genetic causation and point to possible advantages of and important limitations to seeking modularity in synthetic biology systems.     

Consequences of fission in the coral <Emphasis Type="Italic">Siderastrea siderea</Emphasis>: growth rates of small colonies and clonal input to population structure

Colony age and size can be poorly related in scleractinian corals if colonies undergo fission to form smaller independent patches of living tissue (i.e., ramets), but the implications of this life-history characteristic are unclear. This study explored the ecological consequences of the potential discrepancy between size and age for a massive scleractinian, first by testing the effect of colony origin on the growth of small colonies, and second by quantifying the contribution of ramets to population structure. Using Siderastrea siderea in St. John (US Virgin Islands) as an experimental system, the analyses demonstrated that the growth of small colonies derived from sexual reproduction was 2.5-fold greater than that of small ramets which were estimated to be ≈100 years older based on the age of the parent colonies from which they split. Although fission can generate discrete colonies, which in the case of the study reef accounted for 42% of all colonies, it may depress colony success and reef accretion through lowered colony growth rates.     

Splitting the dynamics of large biochemical interaction networks

This article is inscribed in the general motivation of understanding the dynamics on biochemical networks including metabolic and genetic interactions. Our approach is continuous modeling by differential equations. We address the problem of the huge size of those systems. We present a mathematical tool for reducing the size of the model, master-slave synchronization, and fit it to the biochemical context.     

Evolutionary dynamics, epistatic interactions, and biological information

We investigate a definition of biological information that connects population genetics with the tools of information theory by focusing on the distribution of genotypes found in a population. Previous research has treated loci as non-interacting by making specific approximations in the calculation of information-theoretic quantities. We expand earlier mathematical forms to include epistasis, or interactions between mutations at all pairs of loci. Application of our improved measure of biological information to evolution on two-locus, two-allele fitness landscapes demonstrates that mutual information between loci reflects epistatic interaction of mutations. Finally, we consider four-locus, two-allele fitness landscapes with modular structure. As modular interactions are inherently epistatic, we demonstrate that our refined approximation provides insight into the underlying structure of these non-trivial fitness landscapes.     

Quantifying protein modularity and evolvability: A comparison of different techniques

Modularity increases evolvability by reducing constraints on adaptation and by allowing preexisting parts to function in new contexts for novel uses. Protein evolution provides an excellent context to study the causes and consequences of biological modularity. In order to address such questions, however, an index for protein modularity is necessary. This paper proposes a simple index for protein modularity-"module density"-which is the number of evolutionarily independent modules that compose a protein divided by the number of amino acids in the protein. The decomposition of proteins into constituent modules can be accomplished by either of two classes of methods. The first class of methods relies on "suppositional" criteria to assign amino acids to modules, whereas the second class of methods relies on "coevolutionary" criteria for this task. One simple and practical method from the first class consists of approximating the number of modules in a protein as the number of regular secondary structure elements (i.e., helices and sheets). Methods based on coevolutionary criteria require more elaborate data, but they have the advantage of being able to specify modules without prior assumptions about why they exist. Given the increasing availability of datasets sampling protein mutational spectra (e.g., from comparative genomics, experimental evolution, and computational prediction), methods based on coevolutionary criteria will likely become more promising in the near future. The ability to meaningfully quantify protein modularity via simple indices has the potential to aid future efforts to understand protein evolutionary rate determinants, improve molecular evolution models and engineer novel proteins.     

Diet and trophic structure in assemblages of montane frugivorous phyllostomid bats

Neotropical frugivorous bats display a trophic structure composed of bat species with dietary preferences of core plant taxa (Artibeus-Ficus  +  Cecropia, Carollia-Piper, Sturnira- Solanum  +  Piper). This structure is hypothesized to be an ancestral trait, suggesting that similar diets would be observed throughout a species' range. However, most evidence comes from lowlands where data from montane habitats are scarce. In high mountain environments both diversity of bats and plants decreases with altitude; such decline in plant diversity produces less plants to feed from, which should ultimately affect the trophic structure of frugivorous bats in mountain environments. Here, we present a comprehensive review of the diet of frugivorous bats in Neotropical montane environments and evaluate their trophic structure in middle and higher elevations by combining a literature database with field data. We use the concept of modularity to test whether frugivorous montane bats have dietary preferences on core plant taxa. Our database revealed 47 species of montane bats feeding on 211 plant species. We find that the networks are modular, reflecting the trophic structure previously reported. We also found that in highlands the tribe Ectophyllini are Cecropia  +  Cavendishia-specialists rather than Ficus-specialists, and we describe new interactions reflecting 14 species of plants, including three botanical families previously not reported to be consumed by bats.     

Building Developmental Integration into Functional Systems: Function-Induced Integration of Mandibular Shape

The mammalian mandible is a developmentally modular but functionally integrated system. Whether morphological integration can evolve to match the optimal pattern of functional integration may depend on the developmental origin of integration, specifically, on the role that direct epigenetic interactions play in shaping integration. These interactions are hypothesized to integrate modules and also to be highly conservative, potentially constraining the evolution of integration. Using the fox squirrel (Sciurus niger) mandible as a model system, we test five a priori developmental hypotheses that predict mandibular integration and we also explore for correlations between shapes of mandibular regions not anticipated by any of the developmental models. To determine whether direct epigenetic interactions are highly conserved in rodents, we examine the correlation structure of fluctuating asymmetry, and compare integration patterns between fox squirrels and prairie deer mice (Peromyscus maniculatus bairdii). In fox squirrels, we find a correlation structure unanticipated by all a priori developmental models: adjacent parts along the proximodistal jaw axis are correlated whereas more distant ones are not. The most notable exception is that the shape of the anterior incisor alveolus is correlated with the shape of the ramus (FA component) or coronoid (symmetric component). Those exceptions differ between species; in prairie deer mice, the molar alveolus is connected to more parts, and the incisor alveolus to fewer, than in fox squirrels. The structure of integration suggests that the mandible cannot be decomposed into parts but rather is a single connected unit, a result consistent with its functional integration. That match between functional and developmental integration may arise, at least in part, from function-induced growth, building developmental integration into the functional system and enabling direct epigenetic interactions to evolve when function does.     

Quinean social skills: empirical evidence from eye-gaze against information encapsulation

Since social skills are highly significant to the evolutionary success of humans, we should expect these skills to be efficient and reliable. For many Evolutionary Psychologists efficiency entails encapsulation: the only way to get an efficient system is via information encapsulation. But encapsulation reduces reliability in opaque epistemic domains. And the social domain is darkly opaque: people lie and cheat, and deliberately hide their intentions and deceptions. Modest modularity [Currie and Sterelny (2000) Philos Q 50:145–160] attempts to combine efficiency and reliability. Reliability is obtained by placing social skills in un-encapsulated central cognition; efficiency by having the social system sensitive to encapsulated socially tagged cues. In this paper, I argue that this approach fails. I focus on eye-gaze as a plausible example of a socially significant encapsulated cue. I demonstrate contra modest modularity that eye-gaze is subject to influence from central cognition.

Modularity, comparative embryology and evo-devo: Developmental dissection of evolving body plans

Modules can be defined as quasi-autonomous units that are connected loosely with each other within a system. A need for the concept of modularity has emerged as we deal with evolving organisms in evolutionary developmental research, especially because it is unknown how genes are associated with anatomical patterns. One of the strategies to link genotypes with phenotypes could be to relate developmental modules with morphological ones. To do this, it is fundamental to grasp the context in which certain anatomical units and developmental processes are associated with each other specifically. By identifying morphological modularities as units recognized by some categories of general homology as established by comparative anatomy, it becomes possible to identify developmental modules whose genetic components exhibit coextensive expressions. This permits us to distinguish the evolutionary modification in which the identical morphological module simply alters its shape for adaptation, without being decoupled from the functioning gene network (‘coupled modularities’), from the evolution of novelty that involves a heterotopic shift between the anatomical and developmental modules. Using this formulation, it becomes possible, within the realm of Geoffroy's homologous networks, to reduce morphological homologies to developmental mechanistic terms by dissociating certain classes of modules that are often associated with actual shapes and functions.