Barrel-stave model or toroidal model? A case study on melittin pores

Transmembrane pores induced by amphiphilic peptides, including melittin, are often modeled with the barrel-stave model after the alamethicin pore. We examine this assumption on melittin by using two methods, oriented circular dichroism (OCD) for detecting the orientation of melittin helix and neutron scattering for detecting transmembrane pores. OCD spectra of melittin were systematically measured. Melittin can orient either perpendicularly or parallel to a lipid bilayer, depending on the physical condition and the composition of the bilayer. Transmembrane pores were detected when the helices oriented perpendicularly to the plane of the bilayers, not when the helices oriented parallel to the bilayers. The evidence that led to the barrel-stave model for alamethicin and that to the toroidal model for magainin were reviewed. The properties of melittin pores are closely similar to that of magainin but unlike that of alamethicin. We conclude that, among naturally produced peptides that we have investigated, only alamethicin conforms to the barrel-stave model. Other peptides, including magainins, melittin and protegrins, all appear to induce transmembrane pores that conform to the toroidal model in which the lipid monolayer bends continuously through the pore so that the water core is lined by both the peptides and the lipid headgroups.     

Can species distribution modelling provide estimates of population densities? A case study with jaguars in the Neotropics

Aim To test the prediction that environmental suitability derived from species distribution modelling (SDM) could be a surrogate for jaguar local population density estimates. Location Americas. Methods We used 1409 occurrence records of jaguars to model the distribution of the species using 11 SDM methods. We tested whether models’ suitability is linearly correlated with jaguar population densities estimated from 37 different locations. We evaluated whether the relationship between density and suitability forms a constraint envelope, in which higher densities are found mainly in regions with high suitability, whereas low densities can occur in regions with variable suitability. We tested this using heteroscedasticity test and quantile regressions. Results A positive linear relationship between suitability and jaguar density was found only for four methods [bioclimatic envelope (BIOCLIM), genetic algorithm for rule set production (GARP), maximum entropy (Maxent) and generalized boosting models (GBM)], but with weak explanatory power. BIOCLIM showed the strongest relationship. Variance of suitability for lower densities values was larger than for higher values for many of the SDM models used, but the quantile regression was significantly positive only for BIOCLIM and random forests (RF). RF and GBM provided the most accurate models when measured with the standard SDM evaluation metrics, but possess poor relationship with local density estimates. Main conclusions Results indicate that the relationship between density and suitability could be better described as a triangular constraint envelope than by a straight positive relationship, and some of the SDM methods tested here were able to discriminate regions with high or low local population densities. Low jaguar densities can occur in areas with low or high suitability, whereas high values are restricted to areas where the suitability is greater. In high suitability areas but with low jaguar density estimates, we discuss how extrinsic factors driving abundance could act at local scales and then prevent higher densities that would be expected by the favourable regional environmental conditions.     

Why does phenology drive species distribution?

Despite the numerous studies which have been conducted during the past decade on species ranges and their relationship to the environment, our understanding of how environmental conditions shape species distribution is still far from complete. Yet, some process-based species distribution models have been able to simulate plants and insects distribution at a global scale. These models strongly rely on the completion of the annual cycle of the species and therefore on their accomplished phenology. In particular, they have shown that the northern limit of species'' ranges appears to be caused mainly by the inability to undergo full fruit maturation, while the southern limit appears to be caused by the inability to flower or unfold leaves owing to a lack of chilling temperatures that are necessary to break bud dormancy. I discuss here why phenology is a key adaptive trait in shaping species distribution using mostly examples from plant species, which have been the most documented. After discussing how phenology is involved in fitness and why it is an adaptive trait susceptible to evolve quickly in changing climate conditions, I describe how phenology is related to fitness in species distribution process-based models and discuss the fate of species under climate change scenarios using model projections and experimental or field studies from the literature.     

Motorway verges: Paradise for prey species? A case study with the European rabbit

Roads have many effects on the mammal populations of their surroundings. Prey species are thought to establish dense populations in road verges due to a predation release effect, which arise as a side-effect of roadside avoidance by predators and/or predator roadkill. A species that has been suggested to benefit from predation release and attain high densities near roads is the European rabbit, a keystone species in Mediterranean ecosystems. We monitored rabbit relative abundance at three distances from a motorway (50, 450 and 850 m) during a 6 month period, as well as hunting and predator pressures, in a suitable area for rabbits. The lowest rabbit abundance was found next to the motorway (6.76 ± 8.87 pellets/m² per month) and the highest abundance at an intermediate distance (17.65 ± 23.11 pellets/m² per month). Hunting and carnivore pressures were highest at the sampling transect located farthest from the infrastructure. Thus, variability in rabbit abundance did not match the predation release effect found close to the motorway, and some sort of road avoidance or other process must underlie the observed abundance pattern. We advocate for a formal measurement of prey populations response to roads prior to any generalization as, in the case of rabbit, the response to roads and the potential cascading effects on other species may depend on landscape characteristics.     

To model or not to model?

In theory, the combination of mathematical modeling with experimental studies can be a powerful and compelling approach to understanding cell biology. In practice, choosing appropriate problems, identifying willing and able collaborators, and publishing the resulting research can be remarkably challenging. To provide perspective on the question of whether and when to combine modeling and experiments, a panel of experts at the 2010 ASCB Annual Meeting shared their personal experiences and advice on how to use modeling effectively.     

Which are the phenologically flexible species? A case study with common passerine birds

One of the most consensual ecological effects of the current climate warming is the alteration of the environmental timing of ecosystems. Phenological shifts, at different levels of food webs, are predicted to have major effects on species assemblages. Indeed it is unlikely that all species should be able to respond to the phenological shifts of their environment evenly. Yet questions remain about the specific traits that predict the ability of a species to track the temporal fluctuations of its environment. In this study, we use data from the French Constant Effort Site ringing program over a 20 years period (1989–2008) to estimate the ability of 20 common passerine species to adjust their breeding phenology to spring temperature variations. We show that the sensitivity of species breeding phenology to climate relates to species mean migration distance, species’ thermal and habitat niche breadth and brain mass. Species with the broadest ecological and thermal niches, the shortest mean migration distances and the largest brains were most able to adjust their breeding phenology to temperature variations. Our results thus identify long distance migrants and ecological specialists as species that could most suffer from the future expected climate change and suggests phenological adjustment as one possible mechanism underlying the replacement of specialist species by more generalist ones, the so called functional biotic homogenization.     

Spatial distribution of microalgae in marine systems: A reaction–diffusion model

In this paper, we have proposed a reaction–diffusion system of partial differential equations which model the plankton-nutrient interaction mediated by a toxin-determined functional response. It has been established that microalgae, a clean and green source of energy, can be potentially used for carbon capture and sequestration. The common biofuels (bio-diesel and ethanol) are efficiently extracted from microalgae of different shapes and sizes. A spatio-temporal model has been presented to guide exploration and harvesting of microalgae (e.g., dinoflagellates, cilliates, chlorella, etc.). The spatial distribution of the phytoplankton (microalgae) is determined by growth pattern of the biotic subsystem (phytoplankton and zooplankton); e.g., whether it is oscillatory or aperiodic. The model incorporates a toxin-determined functional response of the zooplankton, which can be parametrized for specific phytoplankton–zooplankton combinations in different aquatic bodies such as ponds, seas, and oceans. The present model does not take into account higher zooplankton’s role in maintaining the core subsystem. The temporal model is analytically investigated in terms of the existence criteria and stability analysis (both linear and nonlinear) of the possible equilibria and the spatio-temporal model is studied in terms of global stability, Turing instability and existence of Hopf-bifurcation which help us to explore the dynamical behavior of the spatial model system. Numerical simulations are carried out to support the obtained theoretical results. Simulation experiments and computed densities thereof (equal densities are codes by same color) suggest that the spatial distribution of microalgae is complex; e.g., spatial density of microalgae varies chaotically for certain parameter sets. Harvesting schedule can be designed based on information thus derived. It should be implemented carefully in case the spatial density distribution is chaotic.The sustainability of the marine system for future use has been the prime concern. Parameters of harvesting strategy (time, intensity and technology) are determined in such a way that exploitation causes minimal damage to the environment and the yield of the harvest is maximal. Future studies would consider larger carnivorous fishes (e.g., Squids, Dolphins) on system’s dynamics. The effect of oceanic noise and colloidal swarming of zooplankton in the presence of bacteria will also be incorporated.     

Do species converge during adaptation? A case study in Drosophila

Adaptation to novel environments is a crucial theme in evolutionary biology, particularly because ex situ conservation forces populations to adapt to captivity. Here we analyze the evolution of life-history traits in two closely related species, Drosophila subobscura Collin and Drosophila madeirensis Monclus, during adaptation to the laboratory. Drosophila madeirensis, an endemic species from Madeira, is here shown to have less ability to adapt to the laboratory. Early fecundity was the only trait where this species showed a significant improvement with time. By comparison, D. subobscura improved in most traits, and its early fecundity increased faster than that of D. madeirensis. Our findings suggest that different species, even closely related ones, may adapt at different rates to the same environment.     

Plant intelligence: Why,why not or where?

The concept of plant intelligence, as proposed by Anthony Trewavas, has raised considerable discussion. However, plant intelligence remains loosely defined; often it is either perceived as practically synonymous to Darwinian fitness, or reduced to a mere decorative metaphor. A more strict view can be taken, emphasizing necessary prerequisites such as memory and learning, which requires clarifying the definition of memory itself. To qualify as memories, traces of past events have to be not only stored, but also actively accessed. We propose a criterion for eliminating false candidates of possible plant intelligence phenomena in this stricter sense: an “intelligent” behavior must involve a component that can be approximated by a plausible algorithmic model involving recourse to stored information about past states of the individual or its environment. Re-evaluation of previously presented examples of plant intelligence shows that only some of them pass our test.

“You were hurt?” Kumiko said, looking at the scar.Sally looked down. “Yeah.”“Why didn''t you have it removed?”“Sometimes it''s good to remember.”“Being hurt?”“Being stupid.”—(W. Gibson: Mona Lisa Overdrive)

Key words: intelligence, memory, learning, plant development, mathematical models, plant neurobiology, definition of terms     

Why are Dormice rare? A case study in conservation biology

In the last 100 years, the Dormouse Muscardinus avellcmarius has disappeared from about half its geographical range in Britain. Evidence is presented which indicates that declining range and numbers are due to a complex interplay of factors which include fragmentation, deterioration and loss of specialized habitat. The Dormouse is unusual in being a relatively A-selected small mammal, with exacting ecological requirements which render it very vulnerable, particularly to habitat fragmentation. The Dormouse is also sensitive to climate, both directly and probably indirectly through the effects of weather on the timing and abundance of food (insects, flowers and fruits). Combined with low population density and low intrinsic rate of population increase, this makes the Dormouse highly vulnerable, not just to absolute climatic measures (e.g. temperature, rainfall), but especially to climatic stochasticity, particularly at the edge of its range. There are strong associations between the distribution and changing status of the Dormouse and various climatic parameters, and clear parallels with other climate-sensitive taxa, notably bats and butterflies.
The Dormouse is a very specialized species, highly sensitive to environmental change, resulting in its piecemeal, progressive extinction, particularly in northern counties. It is likely to be a very sensitive indicator species for monitoring future changing environments and an excellent model for studying the effects of habitat fragmentation, climatic shifts and climatic stochasticity.     

Phenotypic plasticity or speciation? A case from a clonal marine organism

Background  

Clonal marine organisms exhibit high levels of morphological variation. Morphological differences may be a response to environmental factors but also they can be attributed to accumulated genetic differences due to disruption of gene flow among populations. In this study, we examined the extensive morphological variation (of 14 characters) in natural populations observed in the gorgonian Eunicea flexuosa, a widely distributed Caribbean octocoral. Eco-phenotypic and genetic effects were evaluated by reciprocal transplants of colonies inhabiting opposite ends of the depth gradient and analysis of population genetics of mitochondrial and nuclear genes, respectively.     

Does reproductive success increase with age or with size in species with indeterminate growth? A case study using sand lizards (Lacerta agilis)

Most data on determinants of reproductive success (RS) and reproductive tactics are correlational in nature, and hence cannot be used to infer causation. Consistent patterns-such as an increase in RS with age, as seen in many types of organisms-may result from diverse underlying mechanisms. Ontogenetic increases in RS in mammals and birds may be due largely to direct effects of age (via learning, etc.) but our analyses show that apparently analogous ontogenetic shifts in reproductive tactics and increases in RS in sand lizards (Lacerta agilis) are actually due to ontogenetic changes in body size. When size effects are removed, age exerts very little effect on either reproductive behaviour or RS in either sex. In many taxa, both age and body size may exert important effects on reproductive biology, and disentangling these effects should be a focus of further research.     

Why flowers close at noon? A case study of an alpine species Gentianopsis paludosa (Gentianaceae)

Repeatable floral closure with diurnal rhythms, that is, flower opening in the morning and closing in the evening, was widely reported. However, the rhythm of flower opening in the morning but closing in the midday received much less attention. Gentianopsis paludosa, Gentianaceae, has an obvious petal movement rhythm opening in the morning and closing at noon at northeast of the Qinghai‐Tibetan Plateau. In this study, we examined the effects of temperature (T), relative humidity (RH), and illumination intensity (II) on G. paludosa''s flower closure. Furthermore, we monitored the environmental changes inside and outside of the flowers, aiming to test the effect of floral closure on the stability of microenvironment inside the flower. Finally, we artificially interrupted temporal petal closure and investigated its effects on reproductive fitness. The results showed that high/low temperature contributed more to the flower closure than low RH, while illumination intensity had no significant effect on it. The medium temperature, relative humidity and illumination intensity (environmental conditions at 10:00) did not delay flower closure when flowers at pre‐closing period or stimulate reopen when flowers full closed. Floral closure provided a stable temperature condition and a higher RH condition inside the flower. Meanwhile, compulsive opening and delayed closure of flowers decreased the seed‐set ratio while no effect was found when flowers were forced to close. We conclude that endogenous rhythm regulates floral closure. The rhythm of petal movement providing a stable microenvironment for G. paludosa, increasing the seed production and saving energy from flower opening maintenance, which might be an adaptive strategy to against unfavorable environmental conditions.     

Colonially breeding seabirds: Predators or prey?

The evolution of aggregation in seabirds is usually attributed to predation pressure, although many authors have argued for the role of foraging constraints to be considered. Discriminating between factors that result in group living and characteristics arising from group living has been regarded as an insoluble problem; yet it is possible to test the predictions of the different models proposed to explain colonial nesting. The resulting explanation suggests that seabird aggregations have evolved in order to utilize a dispersed and unpredictable food supply. As such, colonial nesting leads to increased vulnerability to predation, rather than being a strategy adopted to combat it.     

Equilibrium or not? Modelling potential distribution of invasive species in different stages of invasion

Aim The assumption of equilibrium between organisms and their environment is a standard working postulate in species distribution models (SDMs). However, this assumption is typically violated in models of biological invasions where range expansions are highly constrained by dispersal and colonization processes. Here, we examined how stage of invasion affects the extent to which occurrence data represent the ecological niche of organisms and, in turn, influences spatial prediction of species’ potential distributions. Location Six ecoregions in western Oregon, USA. Methods We compiled occurrence data from 697 field plots collected over a 9‐year period (2001–09) of monitoring the spread of invasive forest pathogen Phytophthora ramorum. Using these data, we applied ecological‐niche factor analysis to calibrate models of potential distribution across different years of colonization. We accounted for natural variation and uncertainties in model evaluation by further investigating three hypothetical scenarios of varying equilibrium in a simulated virtual species, for which the ‘true’ potential distribution was known. Results We confirm our hypothesis that SDMs calibrated in early stages of invasion are less accurate than models calibrated under scenarios closer to equilibrium. SDMs that are developed in early stages of invasion tend to underpredict the potential range compared to models that are built in later stages of invasion. Main conclusions A full environmental niche of invasive species cannot be effectively captured with data from a realized distribution that is restricted by processes preventing full occupancy of suitable habitats. If SDMs are to be used effectively in conservation and management, stage of invasion needs to be considered to avoid underestimation of habitats at risk of invasion.     

Uncoupling proteins: A role in protection against reactive oxygen species—or not?

A physiological function of the original uncoupling protein, UCP1, is well established: UCP1 is the molecular background for nonshivering thermogenesis. The functions of the “novel” UCPs, UCP2 and UCP3, are still not established. Recent discussions imply that all UCPs may play a role in protection against reactive oxygen species (ROS). Here we examine critically the evidence that UCP1, UCP2 and UCP3 are stimulated by ROS (superoxide) or ROS products (4-hydroxy-2-nonenal), and that the UCPs actually diminish oxidative damage. We conclude that, concerning UCP1, it is unlikely that it has such a role; concerning UCP2/UCP3, most evidence for physiologically significant roles in this respect is still circumstantial.     

Why do all host species not show defense against avian brood parasitism: evolutionary lag or equilibrium?

Avian brood parasitism reduces the reproductive success of hosts and is therefore expected to select for host defenses against parasitism, such as an ability to reject parasitic eggs. Field studies have shown that some hosts recognize and reject parasitism, whereas others do not, and the degree of the defense varies from population to population. One long-standing debate concentrates on the differences in the distribution of host defenses observed in hosts parasitized by the brown-headed cowbird and the common cuckoo. The cowbird's hosts show either few or nearly perfect defenses, whereas the cuckoo's hosts have defenses varying from none to complete, with most falling in between the two extremes. To explore the mechanisms underlying this pattern, I constructed a mathematical model in which host defense is assumed to be genetically determined and analyzed how the host defense is established under parasitic pressure. The model shows that differences in the defense-level distribution can be attributed to the difference in the parasite's breeding strategy, generalized or specialized: hosts parasitized by generalists show perfect, none, or intermediate levels of the defense depending on the host abundances, whereas hosts parasitized by specialists always exhibit either none or intermediate levels of the defense if the parasite lacks counter defenses such as egg mimicry. This result provides a testable explanation for the existence of accepter species of the brown-headed cowbird, which might reconcile the previously conflicting hypotheses.