Combining mechanism and drift in community ecology: a novel statistical mechanics approach

A key challenge for models of community ecology is to combine deterministic mechanism and stochastic drift in a systematic, transparent and tractable manner. Another challenge is to explain and unify different ecological patterns, hitherto modelled in isolation, within a single modelling framework. Here, we show that statistical mechanics provides an effective way to meet both challenges. We apply the statistical principle of maximum entropy (MaxEnt) to a simple resource-based, non-neutral model of a plant community. In contrast to previous ecological applications of MaxEnt, our use of MaxEnt emphasises its theoretical basis in the combinatorics of sampling frequencies, an approach that clarifies its ecological interpretation. In this approach, mechanism and drift are identified, respectively, with ecological resource constraints and entropy maximization. We obtain realistic predictions for species abundance distributions as well as contrasting stability-diversity relationships at community and population levels. The model also predicts critical behaviour that may provide a basis for understanding desertification and other ecological tipping points. Our results complement and extend previous ecological applications of MaxEnt to new areas of community ecology, and further illustrate MaxEnt as a powerful yet simple modelling tool for combining mechanism and drift in a way that unifies disparate ecological patterns.     

Ants and agents: a process algebra approach to modelling ant colony behaviour

Process algebras are widely used in the analysis of distributed computer systems. They allow formal reasoning about how the various components of a system contribute to its overall behaviour. In this paper we show how process algebras can be usefully applied to understanding social insect biology, in particular to studying the relationship between algorithmic behaviour of individual insects and the dynamical behaviour of their colony. We argue that process algebras provide a useful formalism for understanding this relationship, since they combine computer simulation, Markov chain analysis and mean-field methods of analysis. Indeed, process algebras can provide a framework for relating these three methods of analysis to each other and to experiments. We illustrate our approach with a series of graded examples of modelling activity in ant colonies.     

Cell division: Biochemically controlled mechanics

Technical advances are providing new insights into the mechanical properties of cells. Now, by combining genetic and biochemical studies with high-resolution mechanical measurements from atomic force microscopy, the biochemical bases of mechanical processes such as cytokinesis should be discernible.     

Towards a regional approach to cell mechanics

Here we review studies of the physical, material properties of animal cells and their cytoskeleton, such as elastic stiffness and fluid viscosity, that determine how they respond to, and are shaped by, forces inside and out. Currently and historically, most such studies have reported a single value for a cell property and/or propose a single broad structural model based on nonliving materials. We believe that such physical studies would be of more interest to most cell biologists if greater emphasis were placed on the well-established regional differences within a cell and the ability of the cell to quickly change its mechanical behaviors     

Geometry explains the benefits of division of labour in a leafcutter ant

Many ant species have morphologically distinct worker sub-castes. This presumably increases colony efficiency and is thought to be optimized by natural selection. Optimality arguments are, however, often lacking in detail. In ants, the benefits of having workers in a range of sizes have rarely been explained mechanistically. In Atta leafcutter ants, large workers specialize in defence and also cut fruit. Fruit is soft and can be cut by smaller workers. Why, therefore, are large workers involved? According to the geometry hypothesis, cutting large pieces from three-dimensional objects like fruit is enhanced by longer mandibles. By contrast, long mandibles are not needed to cut leaves that are effectively two-dimensional. Our results from Atta laevigata support three predictions from the geometry hypothesis. First, larger workers cut larger fruit pieces. Second, the effect of large size is greater in cutting fruit than leaves. Third, the size of fruit pieces cut increases approximately in proportion to the cube of mandible length. Our results are a novel mechanistic example of how size variation among worker ants enhances division of labour.     

Organization of work in the honeybee: a compromise between division of labour and behavioural flexibility

Although the caste concept has been central to our understanding of the organization of work in social insect colonies, the concept has been the subject of considerable recent criticism. Theoretically, it has been suggested that temporal castes are too inflexible to allow a colony to rapidly reallocate labour in response to changing conditions. In addition, several authors have suggested that task switching is so prevalent that it precludes even the possibility of a rigidly controlled temporal caste system. This study addresses these two criticisms by presenting and testing a revision of the temporal caste concept that recognizes two categories of tasks: those that require a physiological specialization for their efficient performance, and those that all workers are equally able to perform. Only those tasks requiring a physiological specialization are relevant to the temporal caste concept. Two castes of honeybees were shown to vary in response to increased nectar influx, which requires a physiological specialization, but not to heat stress, which requires no specialization. This work suggests that the organization of work in social insect colonies reflects a compromise between selection for the benefits of division of labour and opposing selection for flexibility in task allocation.     

Circular codes revisited: a statistical approach

In 1996 Arquès and Michel [1996. A complementary circular code in the protein coding genes. J. Theor. Biol. 182, 45-58] discovered the existence of a common circular code in eukaryote and prokaryote genomes. Since then, circular code theory has provoked great interest and underwent a rapid development. In this paper we discuss some theoretical issues related to the synchronization properties of coding sequences and circular codes with particular emphasis on the problem of retrieval and maintenance of the reading frame. Motivated by the theoretical discussion, we adopt a rigorous statistical approach in order to try to answer different questions. First, we investigate the covering capability of the whole class of 216 self-complementary, C³ maximal codes with respect to a large set of coding sequences. The results indicate that, on average, the code proposed by Arquès and Michel has the best covering capability but, still, there exists a great variability among sequences. Second, we focus on such code and explore the role played by the proportion of the bases by means of a hierarchy of permutation tests. The results show the existence of a sort of optimization mechanism such that coding sequences are tailored as to maximize or minimize the coverage of circular codes on specific reading frames. Such optimization clearly relates the function of circular codes with reading frame synchronization.     

Developmentally-programmed division of labour in the clonal invader Carpobrotus edulis

Invasive species are one of the main causes for the loss of global biodiversity. However, the mechanisms that explain the success of invasive species remain unsolved. Clonal growth has been pointed out as an attribute that could contribute to the invasiveness of plants, however little research has been conducted to determine the importance of clonal traits in successful invaders. One of the most interesting attributes related to clonal growth is the capacity for division of labour. In this experiment we investigated the capacity for division of labour in the aggressive invader Carpobrotus edulis, and how clonal integration can contribute to the expansion of this species. Division of labour was determined by studying the degree of morphological and physiological specialization of individual ramets to a specific activity: acquisition of soil or aboveground resources and aboveground expansion. Our results showed that there is division of labour in the clonal fragments, with older ramets increasing the biomass allocated to roots (specialization in the uptake of belowground resources) and younger ramets increasing the chlorophyll content and aboveground biomass (specialization in the uptake of aboveground resources). Physiological integration allows division of labour, and as consequence the overall performance of the clonal fragment was enhanced, with connected clonal fragments showing a higher total biomass than severed clonal fragments. Division of labour increased the aboveground growth of apical ramets of C. edulis, and therefore could contribute to an effective colonization of the surrounding area by this aggressive invader. Our study is the first exploring the role of division of labour in the expansion of an invader, and supports the idea that clonal traits could increase the invasiveness of plant species.     

Authenticity of ancient-DNA results: a statistical approach

Although there have been several papers recommending appropriate experimental designs for ancient-DNA studies, there have been few attempts at statistical analysis. We assume that we cannot decide whether a result is authentic simply by examining the sequence (e.g., when working with humans and domestic animals). We use a maximum-likelihood approach to estimate the probability that a positive result from a sample is (either partly or entirely) an amplification of DNA that was present in the sample before the experiment began. Our method is useful in two situations. First, we can decide in advance how many samples will be needed to achieve a given level of confidence. For example, to be almost certain (95% confidence interval 0.96-1.00, maximum-likelihood estimate 1.00) that a positive result comes, at least in part, from DNA present before the experiment began, we need to analyze at least five samples and controls, even if all samples and no negative controls yield positive results. Second, we can decide how much confidence to place in results that have been obtained already, whether or not there are positive results from some controls. For example, the risk that at least one negative control yields a positive result increases with the size of the experiment, but the effects of occasional contamination are less severe in large experiments.     

The evolutionary history of division of labour

Functional specialization, or division of labour (DOL), of parts within organisms and colonies is common in most multi-cellular, colonial and social organisms, but it is far from ubiquitous. Several mechanisms have been proposed to explain the evolutionary origins of DOL; the basic feature common to all of them is that functional differences can arise easily. These mechanisms cannot explain the many groups of colonial and social animals that exhibit no DOL despite up to 500 million years of evolution. Here, I propose a new hypothesis, based on a multi-level selection theory, which predicts that a reproductive DOL is required to evolve prior to subsequent functional specialization. I test this hypothesis using a dataset consisting of the type of DOL for living and extinct colonial and social animals. The frequency distribution of DOL and the sequence of its acquisition confirm that reproductive specialization evolves prior to functional specialization. A corollary of this hypothesis is observed in colonial, social and also within multi-cellular organisms; those species without a reproductive DOL have a smaller range of internal variation, in terms of the number of polymorphs or cell types, than species with a reproductive DOL.     

Spatial division of labour of Schoenoplectus americanus

If connected ramets are growing in heterogeneous environments, Division of Labour (DoL) among ramets potentially will result in more efficient sharing of resources and an overall benefit to the plants. As a result of DoL, connected ramets growing in a heterogeneous environment might achieve more biomass than ramets growing in a homogeneous environment. DoL has been demonstrated to occur in a few clonal plant species, although most studies simply focussed on biomass allocation, not on actual resource capturing such as water and nutrient consumption. The model system for our study is one in which two connected ramet groups of Schoenoplectus americanus were placed into contrasting environments. In one treatment, the connected ramets grew in heterogeneous environments and in the other treatment, the connected ramets grew in the same (i.e. homogeneous) environment. We manipulated two variables (light and salinity) in the experiment. We hypothesized that ramets growing in a shaded and fresh water condition in a heterogeneous environment would use more water than ramets growing in a similar condition but in a homogeneous environment. We further hypothesized that ramets growing in a light and saline condition in a heterogeneous environment would assimilate less water than ramets growing in a similar condition but in a homogeneous environment. These hypotheses are based on the assumption that ramets in a heterogeneous environment would translocate water from ramets growing in a shaded and fresh water condition to ramets growing in a light and saline water condition. We also hypothesized that ramets growing in heterogeneous environments achieve larger biomass than ramets in homogeneous environments. Ramets grown in light and saline conditions in heterogeneous environments allocated more biomass to aboveground parts, had taller shoots, larger Specific Green (leaf) Area and consumed less water than ramets grown in similar conditions but in a homogeneous environment. Results confirm the hypothesis that connected ramets in heterogeneous environments are specialised to capture locally abundant resources and share these with connected ramets growing in other habitats. The result of DoL is that the entire connected ramet system benefits and achieves higher biomass.     

Evolving the division of labour: generalists,specialists and task allocation

The evolutionary dynamics of specialization, in the context of the division of labour, are investigated. Individuals associate in groups in which benefits are shared and costs borne individually; each individual is either a generalist who can perform all the necessary tasks, a specialist who performs a sub-set of the necessary tasks, or a parasite who contributes nothing to the group. The implications of the model are explored analytically and through both numerical and Monte Carlo methods. These methods demonstrate the evolution of populations towards stable arrangements of specialists and generalists. The fittest populations are those that divide tasks fairly and associate in large, highly specialized groups. Generalists have a distinct advantage in small groups, but the presence of generalists, ironically, lowers group fitness. Parasites are able to invade both specialized and non-specialized populations. A basic model for the continuous division of labour is also presented, demonstrating a tendency for populations to evolve increasingly unfair divisions of labour. This last result implies that an evolutionary ratchet favours disparity between the workload of specialist populations.     

Self-assembly,self-organization and division of labour

The prospect of generic principles of biological organization being uncovered through the increasingly broad use of the concepts of ''self-assembly'' and ''self-organization'' in biology will only be fulfilled if students of different levels of biological organization use the same terms with the same meanings. We consider the different ways the terms ''self-assembly'' and ''self-organization'' have been used, from studies of molecules to studies of animal societies. By linking ''self-assembly'' and ''self-organization'' with division of labour, we not only put forward a distinction between the underlying concepts but we are also able to relate them to the question: Why has a certain structure been favoured by natural selection? Using the particularly instructive case of social resilience in ant colonies, we demonstrate that the principle of self-organizing self-assembly may apply to higher levels of biological organization than previously considered. We predict that at the level of interactions among organisms within the most advanced animal societies, specialization through learning has a crucial role to play in re-assembly processes. This review may also help important commonalities and differences to be recognized between ordering mechanisms up to the social level and those further up the biological hierarchy, at the level of ecological communities.