What drives community dynamics?

The search for general mechanisms of community assembly is a major focus of community ecology. The common practice so far has been to examine alternative assembly theories using dichotomist approaches of the form neutrality versus niche, or compensatory dynamics versus environmental forcing. In reality, all these mechanisms will be operating, albeit with different strengths. While there have been different approaches to community structure and dynamics, including neutrality and niche differentiation, less work has gone into separating out the temporal variation in species abundances into relative contributions from different components. Here we use a refined statistical machinery to decompose temporal fluctuations in species abundances into contributions from environmental stochasticity and inter-/intraspecific interactions, to see which ones dominate. We apply the methodology to community data from a range of taxa. Our results show that communities are largely driven by environmental fluctuations, and that member populations are, to different extents, regulated through intraspecific interactions, the effects of interspecific interactions remaining broadly minor. By decomposing the temporal variation in this way, we have been able to show directly what has been previously inferred indirectly: compensatory dynamics are in fact largely outweighed by environmental forcing, and the latter tends to synchronize the population dynamics.     

What drives plant stress genes?

Currently, there is a lot of interest in the plant stress response. Using large-scale genomics approaches, more and more genes are being identified that are involved in or even regulate this complex process. The recent boost in expression profile analyses for several plant stress responses has enabled the identification of new promoter elements as important factors in establishing the expression regulatory network controlling plant stress response.     

What drives the dynamics of a soil mite population under seasonal flooding? A null model analysis

Floods can inflict high mortality on terrestrial organisms, but may also promote adaptive evolution. In seasonal floodplains, several taxa show flood-related traits that may be important for their long-term persistence, but the available evidence is conflicting. Here, we used a simulation approach to investigate the interplay between seasonal floods and submersion resistance in driving the population dynamics of the parthenogenetic soil mite Rostrozetes ovulum in an Amazonian blackwater floodplain. First, we gathered data from two flood cycles to estimate field survival rate. Next, we used further data from a submersion survival laboratory experiment and a historical flood record to build a null model for R. ovulum’s survival rate under seasonal flooding, and then tested it against field survival estimates. Floods caused marked density declines, but the two estimates of field survival rate were statistically equivalent, suggesting relatively constant survival across years. Submersion survival time varied tenfold among individuals, but its variability was within the range known for life history traits of other asexual invertebrates. Both field survival rates were consistent with the null model, supporting seasonal flooding as the main mortality factor. Surprisingly, though, average flood duration was actually larger than the average mite could survive, suggesting that population persistence relies on relatively rare, super-resistant phenotypes. Overall, the studied R. ovulum population appears to have a mainly density-independent dynamics across years, with its viability depending on mechanisms that buffer flood survival rate against temporal oscillations.     

Cellulose digestion in termites and cockroaches: What role do symbionts play?

• 1.1. Termites and cockroaches are excellent models for studying the role of symbionts in cellulose digestion in insects: they eat cellulose in a variety of forms and may or may not have symbionts.
• 2.2. The wood-eating cockroach, Panesthia cribrata, can be maintained indefinitely, free of microorganisms, on a diet of crystalline cellulose. Under these conditions the RQ is 1, indicating that the cockroach is surviving on glucose produced by endogenous cellulase.
• 3.3. The in vitro rate at which glucose is produced from crystalline cellulose by gut extracts from P. cribrata and Nasutitermes walkeri is comparable to the in vivo production of CO₂ in these insects, clearly indicating that the rate of glucose production from crystalline cellulose is sufficient for their needs.
• 4.4. In all termites and cockroaches examined, cellulase activity was found in the salivary glands and predominantly in the foregut and midgut. These regions are the normal sites of secretion of digestive enzymes and are either devoid of microorganisms (salivary glands) or have very low numbers.
• 5.5. Endogeneous cellulases from termites and cockroaches consist of multiple endo-β-1,4-glucanase (EC 3.2.1.4) and β-1,4-glucosidase (EC 3.2.1.21) components. There is no evidence that an exo-β-1,4-glucanase (cellobiohydrolase) (EC 3.2.1.91) is involved in, or needed for, the production of glucose from crystalline cellulose in termites or cockroaches as the endo-β-1,4-glucanase components are active against both crystalline cellulose and carboxymethylcellulose.
• 6.6. There is no evidence that bacteria are involved in cellulose digestion in termites and cockroaches. The cellulase associated with the fungus garden of M. michaelseni is distinct from that in the midgut; there is little indication that the fungal enzymes are acquired or needed. Lower termites such as Coptotermes lacteus have Protozoa in their hindgut which produce a cellulase(s) quite distinct from that in the foregut and midgut.

     

What drives membrane fusion in eukaryotes?

The fusion of biological membranes is the terminal step of all vesicular trafficking reactions in eukaryotic cells. Therefore, this fusion is fundamental for the transfer of proteins and lipids between different compartments, for exocytosis and for the structural integrity of organelles. In the past decade, many parts of the molecular machinery involved in fusion have been uncovered. Although the mechanisms responsible for mutual recognition and binding of membranes inside eukaryotes are becoming reasonably well known, there is considerable uncertainty as to what causes the actual merging of the lipid bilayer. Two classes of mechanisms have been proposed. Proximity models postulate that very close apposition of membranes suffices to induce fusion. By contrast, pore models propose that continuous proteinaceous pores between apposed membranes could be the basis for fusion.     

What drives invasibility? A multi‐model inference test and spatial modelling of alien plant species richness patterns in northern Portugal

Understanding and predicting biological invasions can focus either on traits that favour species invasiveness or on features of the receiving communities, habitats or landscapes that promote their invasibility. Here, we address invasibility at the regional scale, testing whether some habitats and landscapes are more invasible than others by fitting models that relate alien plant species richness to various environmental predictors. We use a multi‐model information‐theoretic approach to assess invasibility by modelling spatial and ecological patterns of alien invasion in landscape mosaics, and by testing competing hypotheses of environmental factors that may control invasibility. Because invasibility may be mediated by particular characteristics of invasiveness, we classified alien species according to their C‐S‐R plant strategies. We illustrate this approach with a set of 86 alien species in northern Portugal. We first focus on predictors influencing species richness and expressing invasibility, and then evaluate whether distinct plant strategies respond to the same or different groups of environmental predictors. We confirmed climate as a primary determinant of alien invasions, and as a primary environmental gradient determining landscape invasibility. The effects of secondary gradients were detected only when the area was sub‐sampled according to predictions based on the primary gradient. Then, multiple predictor types influenced patterns of alien species richness, with some types (landscape composition, topography and fire regime) prevailing over others. Alien species richness responded most strongly to extreme land management regimes, suggesting that intermediate disturbance induces biotic resistance by favouring native species richness. Land‐use intensification facilitated alien invasion, whereas conservation areas hosted few invaders, highlighting the importance of ecosystem stability in preventing invasions. Plants with different strategies exhibited different responses to environmental gradients, particularly when the variations of the primary gradient were narrowed by sub‐sampling. Such differential responses of plant strategies suggest using distinct control and eradication approaches for different areas and alien plant groups.     

What drives bacteria to produce a biofilm?

Nearly 40 years ago, Dr. R.J. Gibbons made the first reports of the clinical relevance of what we now know as bacterial biofilms when he published his observations of the role of polysaccharide glycocalyx formation on teeth by Streptococcus mutans [Sci. Am. 238 (1978) 86]. As the clinical relevance of bacterial biofilm formation became increasingly apparent, interest in the phenomenon exploded. Studies are rapidly shedding light on the biomolecular pathways leading to this sessile mode of growth but many fundamental questions remain. The intent of this review is to consider the reasons why bacteria switch from a free-floating to a biofilm mode of growth. The currently available wealth of data pertaining to the molecular genetics of biofilm formation in commonly studied, clinically relevant, single-species biofilms will be discussed in an effort to decipher the motivation behind the transition from planktonic to sessile growth in the human body. Four potential incentives behind the formation of biofilms by bacteria during infection are considered: (1) protection from harmful conditions in the host (defense), (2) sequestration to a nutrient-rich area (colonization), (3) utilization of cooperative benefits (community), (4) biofilms normally grow as biofilms and planktonic cultures are an in vitro artifact (biofilms as the default mode of growth).     

Sap feeding by the marsupial Petaurus australis: an enigmatic behaviour?

Summary The Yellow-bellied Glider, Petaurus australis, was observed to feed sporadically but extensively on eucalypt sap. Gliders extracted sap by making incisions into the bark with their procumbent lower incisor teeth and licking the resulting exudate. Less than 1% of possible trees were incised for sap. Sap flow and sap-sugar concentration were estimated for eight sap-site trees and eight non sap-site trees at intervals during an 18 month period. Measurements of sap-sugar concentration differed substantially among trees but fluctuated between sample periods independent of glider use. Sap flow measurements, were always higher for those trees currently in use by gliders, although the particular sap-site trees comprising this group varied between sample periods. The variation in sap flow occurred indenpendent of the incidence of rainfall or the type of microhabitat the tree occupied. Experimental incising of trees, designed to mimic the effects of feeding by gliders, failed to show any effect on sap flow. This suggests that the incidence of sap feeding is determined by a tree's pattern of sap flow and that there may be trees with unusual patterns of sap flow which gliders select as the most favourable trees to incise.     

What happens between an external stimulus and an overt response? A study of covert behavior.

Peripheral components of feedthrough loops were psychophysiologically measured from the brain, both forelimbs, the tongue and the eyes during simple and choice reaction time tasks using linguistic and non-linguistic stimuli. Closing a microswitch with the little finger was the overt response. Covert electromyographic (EMG) responses were computer identified in the following average temporal order: generally, the earliest covert reactions were in the tongue, brain, eyes, and passive arm-hand region. Next were complex EMG events in the active limb. These covert reactions may function in feedthrough loops to generate and transmit codes during internal information processing. The passive arm-hand responses occurred significantly earlier than the onset of the covert EMG burst for closing the microswitch; perhaps there is an inhibitory response "commanding" the passive arm not to respond, before the other (active) limb can overtly respond. Mean response patterns to linguistic and non-linguistic stimuli were almost identical. Reaction time to the onset of the EMG burst for switch closing was from 40 to 95 milliseconds earlier than the usual overt reaction time measure (that to switch closing), suggesting that reaction time studies might be improved by using the onset of EMG increase as the more sensitive and precise measure.     

What does robotics offer animal behaviour?

There is a growing body of robot-based research that makes a serious claim to be a new methodology for biology. Robots can be used as models of specific animal systems to test hypotheses regarding the control of behaviour. At levels from learning algorithms to specific dendritic circuits, implementing a proposed controller in a robotic device tests it against real environments in a way that is difficult to simulate. This often provides insight into the true nature of the problem. It also enforces complete specifications and combines bodies of data. Current work can sometimes be criticized for drawing unjustified conclusions given the limited evaluation and inevitable inaccuracies of robot models. Nevertheless, this approach has led to novel hypotheses for animal behaviour and seems likely to provide fruitful results in the future. Copyright 2000 The Association for the Study of Animal Behaviour.     

What factor drives the fibrillogenic association of beta-sheets?

The identification of the driving factor for fibril formation is paramount to understand the molecular basis of amyloidogenic disease. Recently, an atomic-detail structure of a fibrillogenic aggregate was reported and revealed a tight packing of beta-sheets. However, there is not a single pair-wise interaction of significance between the beta-sheets, no hydrogen bond and no hydrophobic interaction. Instead, there is extensive burial of polar groups at the interface. These observations lead to the question: What factor drives the association of beta-sheets? This issue is addressed by combining all-atom molecular dynamics with an implicit-solvent analysis. The driving force for the association arises from the mechanical equivalent of the dehydration propensity of pre-formed intra-sheet hydrogen bonds and dipole-dipole interactions.     

What positions nucleosomes?--A model

Here we propose a new determinant for localization of nucleosomes along genomic DNA, in addition to sequence-dependent features. The new specific class of chromatin scaling signals involves curved DNA. According to the observed positional distribution of DNA curvature, the new synchronizing signal occurs once per four nucleosomes on average. This new factor in nucleosome positioning should substantially influence the efficiency of biological reactions through regulatory factors microscopically and the entire chromatin structure through the 30 nm fiber structure macroscopically. Allocation of the new type of signals is found to be fixed evolutionarily although they could be shifted in accordance with the hierarchy of functional genomic structures.     

What is an autotroph?

The concept of autotrophy depends on the growth media for pure cultures supplying a single one carbon source for anabolism. Secondary carbon compounds added to the medium as chelators and/or vitamins confuse the meaning. This note suggests a clarification of definition suitable for contemporary biochemical studies of true autotrophs.     

What is an expert? A systems perspective on expertise

Expert knowledge is a valuable source of information with a wide range of research applications. Despite the recent advances in defining expert knowledge, little attention has been given to how to view expertise as a system of interacting contributory factors for quantifying an individual's expertise. We present a systems approach to expertise that accounts for many contributing factors and their inter‐relationships and allows quantification of an individual's expertise. A Bayesian network (BN) was chosen for this purpose. For illustration, we focused on taxonomic expertise. The model structure was developed in consultation with taxonomists. The relative importance of the factors within the network was determined by a second set of taxonomists (supra‐experts) who also provided validation of the model structure. Model performance was assessed by applying the model to hypothetical career states of taxonomists designed to incorporate known differences in career states for model testing. The resulting BN model consisted of 18 primary nodes feeding through one to three higher‐order nodes before converging on the target node (Taxonomic Expert). There was strong consistency among node weights provided by the supra‐experts for some nodes, but not others. The higher‐order nodes, “Quality of work” and “Total productivity”, had the greatest weights. Sensitivity analysis indicated that although some factors had stronger influence in the outer nodes of the network, there was relatively equal influence of the factors leading directly into the target node. Despite the differences in the node weights provided by our supra‐experts, there was good agreement among assessments of our hypothetical experts that accurately reflected differences we had specified. This systems approach provides a way of assessing the overall level of expertise of individuals, accounting for multiple contributory factors, and their interactions. Our approach is adaptable to other situations where it is desirable to understand components of expertise.     

What is an individual organism? A multilevel selection perspective

Most biologists implicitly define an individual organism as "one genome in one body." This definition is based on physiological and genetic criteria, but it is problematic for colonial organisms. We propose a definition based instead on the evolutionary criteria of alignment of fitness, export of fitness by germ-soma specialization, and adaptive functional organization. We consider how these concepts apply to various putative individual organisms. We conclude that complex multicellular organisms and colonies of eusocial insects satisfy these three criteria, but that, in most cases (with at least one notable exception), colonies of modular organisms and genetic chimeras do not. While species do not meet these criteria, they may meet the criteria for a broader concept--that of an evolutionary individual--and sexual reproduction may be a species-level exaptation for enhancing evolvability. We also review the costs and benefits of internal genetic heterogeneity within putative individuals, demonstrating that high relatedness is neither a necessary nor a sufficient condition for individuality, and that, in some cases, genetic variability may have adaptive benefits at the level of the whole.     

What drives the distribution of the bloom-forming cyanobacteria Planktothrix agardhii and Cylindrospermopsis raciborskii?

The cyanobacteria Planktothrix agardhii and Cylindrospermopsis raciborskii are bloom-forming species common in eutrophic freshwaters. These filamentous species share certain physiological traits which imply that they might flourish under similar environmental conditions. We compared the distribution of the two species in a large database (940 samples) covering different climatic regions and the Northern and Southern hemispheres, and carried out laboratory experiments to compare their morphological and physiological responses. The environmental ranges of the two species overlapped with respect to temperature, light and total phosphorus (TP); however, they responded differently to environmental gradients; C.?raciborskii biovolume changed gradually while P. agardhii shifted sharply from being highly dominated to a rare component of the phytoplankton. As expected, P.?agardhii dominates the phytoplankton with high TP and low light availability conditions. Contrary to predictions, C.?raciborskii succeeded in all climates and at temperatures as low as 11?°C. Cylindrospermopsis raciborskii had higher phenotypic plasticity than P.?agardhii in terms of pigments, individual size and growth rates. We conclude that the phenotypic plasticity of C.?raciborskii could explain its ongoing expansion to temperate latitudes and suggest its future predominance under predicted climate-change scenarios.