Implications of recurrent disturbance for genetic diversity

Exploring interactions between ecological disturbance, species’ abundances and community composition provides critical insights for ecological dynamics. While disturbance is also potentially an important driver of landscape genetic patterns, the mechanisms by which these patterns may arise by selective and neutral processes are not well‐understood. We used simulation to evaluate the relative importance of disturbance regime components, and their interaction with demographic and dispersal processes, on the distribution of genetic diversity across landscapes. We investigated genetic impacts of variation in key components of disturbance regimes and spatial patterns that are likely to respond to climate change and land management, including disturbance size, frequency, and severity. The influence of disturbance was mediated by dispersal distance and, to a limited extent, by birth rate. Nevertheless, all three disturbance regime components strongly influenced spatial and temporal patterns of genetic diversity within subpopulations, and were associated with changes in genetic structure. Furthermore, disturbance‐induced changes in temporal population dynamics and the spatial distribution of populations across the landscape resulted in disrupted isolation by distance patterns among populations. Our results show that forecast changes in disturbance regimes have the potential to cause major changes to the distribution of genetic diversity within and among populations. We highlight likely scenarios under which future changes to disturbance size, severity, or frequency will have the strongest impacts on population genetic patterns. In addition, our results have implications for the inference of biological processes from genetic data, because the effects of dispersal on genetic patterns were strongly mediated by disturbance regimes.     

Structural basis of hierarchical multiple substates of a protein. I: Introduction

A computer experiment of protein dynamics is carried out, which consists of two steps: (1) A Monte Carlo simulation of thermal fluctuations in the native state of a globular protein, bovine pancreatic trypsin inhibitor; and (2) a simulation of the quick freezing of fluctuating conformations into energy minima by minimization of the energy of a number of conformations sampled in the Monte Carlo simulation. From the analysis of results of the computer experiment is obtained the following picture of protein dynamics: multiple energy minima exist in the native state, and they are distributed in clusters in the conformational space. The dynamics has a hierarchical structure which has at least two levels. In the first level, dynamics is restricted within one of the clusters of minima. In the second, transitions occur among the clusters. Local parts of a protein molecule, side chains and local main chain segments, can take multiple locally stable conformations in the native state. Many minima result from combinations of these multiple local conformations. The hierarchical structure in the dynamics comes from interactions among the local parts. Protein molecules have two types of flexibility, each associated with elastic and plastic deformations, respectively.     

A simulation model of the three-dimensional architecture of the maize root system

In order to study the nutrient and water uptake of rootsin situ, we need a quantitative three-dimensional dynamic model of the root system architecture. The present model takes into account current observations on the morphogenesis of the maize root system. It describes the root system as a set of root axes, characterised by their orders and their inter-node of origin. The evolution of the simulated pattern is achieved by three processes, occuring at each time step: emission of new primary root axes from the shoot, growth and branching of existing root axes. The elongation of an axis depends on its order, inter-node and local growing conditions. Branches appear acropetally at a specified distance from the apex and from former branches, along ranks facing xylem poles, with a branching angle specific to their order and inter-node. From the three-dimensional branched patterns simulated by the model, various outputs, such as root profiles or cross-section maps can be computed, compared to observed data and used as inputs in uptake models. A number of examples of such possible outputs are presented.     

A Simulation Model of Heterodera schachtii Infecting Beta vulgaris

A simulation model of a single sugarbeet, Beta vulgaris L., plant infected by the sugarbeet cyst nematode, Heterodera schachtii Schmidt, was developed using published information. The model is an interactive computer simulation programmed in FORTRAN. Given initial population densities of the nematode at planting, the model simulates nematode population dynamics and the growth of plant tap and fibrous roots. The driving variable for nematode development and plant growth is temperature.     

Generalized finite element solution to one-dimensional flux problems

A finite element numerical solution to the general one-dimensional flow equation is derived in a form that provides a convenient and general means to simulate a wide variety of one-dimensional flow techniques of interest to biological scientists, e.g., ultracentrifugation, electrophoresis, chromatography, etc. Diverse physical models defined in terms of column geometry, solute interactions, and the dependence of transport parameters on column position, time, or concentrations of one or more solutes, can be accommodated. A particularly useful aspect of the formulation is that a wide variety of boundary conditions can be simply applied to the end result, without rederivation of the solution for each new case. The numerical solution is expressed as matrix equations that are sufficiently general so that incorporation of particular models can be effected by substitution of appropriate quantities into the final result.     

Does climatic warming increase the risk of frost damage in northern trees?

Abstract. The effect of climatic warming on the timing of bud burst and the subsequent risk of frost damage on trees in central Finland was assessed with the aid of a computer model, 73 years of temperature data and a climatic scenario corresponding to doubled level of atmospheric CO₂. In general, climatic warming hastened bud burst, due to ontogenetic development during warm spells in autumn, winter and spring. During the years with the warmest winters in the scenario conditions: (a) bud burst took place during mid-winter; and (2) depending on the year, the trees were subsequently exposed to temperatures between −27 and −10°C. This finding suggests that the risk of frost damage to trees will be increased if the predicted climatic warming occurs. Because of the assumptions used in the model, the results are not conclusive, but they do point out the importance of further experimental studies on genetic and environmental regulation of timing of bud burst in trees.     

Evolution vs the number of gene copies per primitive cell

Summary Computer simulations are presented of the rate at which an advantageous mutant would displace the prototype in a replicating system without an accurate segregation mechanism. If the number of gene copies in the system is indefinitely large, Darwinian evolution is essentially stopped because there is no coupling of phenotype with genotype, i.e., there is no growth advantage to the advantageous gene relative to the prototype and therefore no survival of the fittest. The inhibition of evolution due to a number of gene copies<100 would have been not insurmountable. Although the presence of multiple copies would have allowed replacement by an advantageous mutant, it provided a way for the primitive cell to conserve less immediately useful genes that could evolve into different or more effective genes. This possibility was lost as accurate segregation mechanisms evolved and cells with few copies of each gene, such as modern procaryotes, arose.     

Molecular dynamics simulation of crystalline β-cyclodextrin dodecahydrate at 293 K and 120 K

Molecular dynamics (MD) simulations for crystalline -cyclodextrin dodecahydrate (-CD) at two different temperatures, 293 K and 120 K, have been performed using the GROMOS program package. The calculated structural properties are compared to those obtained from neutron diffraction studies of this system at the quoted temperatures. The simulation was carried out over a period of 20 ps on four unit cells containing 8 -CD molecules and 96 water molecules, whereby all atoms were allowed to move.At room temperature, the experimental positions of the (non-hydrogen) glucose atoms are reproduced within 0.034 nm, a value which is smaller than the experimental (0.041 nm) or simulated (0.049 nm) overall root mean square (rms) positional fluctuation. The corresponding numbers for the low temperature study are 0.046 nm, 0.019 nm and 0.022 nm. At both temperatures the experimentally observed degree of anisotropy of the atomic motions is also found in the simulations.The comparison of a variety of structural properties leads to the conclusion that the molecular model and force field used are able to simulate the cyclodextrin system very well. Experimentally observed differences in properties as a function of number of glucose units in the CD molecule (-CD, 6 versus -CD, 7) and as a function of temperature are qualitatively reproduced by the simulations.     

Temporal changes in therophytic communities across the boundary of disturbed-intact ecosystems

External control processes cause continual compositional and structural readjustments of Mediterranean pasture ecosystems. Such control processes include herbivore grazing, meteorological fluctuations and traditional management activities, which determine the stable environment where the succession occurs. Traditional management in this ecosystem frequently involves periodic ploughing or controlled fires.Experimental disturbances were applied to pastures of different maturity. Recovery was studied by relating information gathered for each disturbed system to successional age. The boundary between original systems of differing ages and the newly created systems was studied to compare the space-time evolution of therophytic communities. Permanent transects perpendicular to the disturbance boundaries and containing many small plots were sampled during consecutive years.Sampling plots located on both sides of the boundaries were classified into communities, in order to detect the space-time pasture evolution in successive years. Annual conditional probabilities were calculated for transitions between the recognised communities. During succession different strategies were detected in response to meteorological variations. In pioneer successional stages, substitutions of one community by another in the same space seem to be random. However, greater determinism was detected in more mature pastures, where, in addition, communities' abundance does not respond to meteorological change.Nomenclature follows T. G. Tutin et al. 1964–1980. Flora Europaea. Cambridge University Press, Cambridge.