How does feedback from phage infections influence the evolution of phase variation in Campylobacter?

Campylobacter jejuni (C. jejuni) causes gastroenteritis following the consumption of contaminated poultry meat, resulting in a large health and economic burden worldwide. Phage therapy is a promising technique for eradicating C. jejuni from poultry flocks and chicken carcasses. However, C. jejuni can resist infections by some phages through stochastic, phase-variable ON/OFF switching of the phage receptors mediated by simple sequence repeats (SSR). While selection strength and exposure time influence the evolution of SSR-mediated phase variation (PV), phages offer a more complex evolutionary environment as phage replication depends on having a permissive host organism. Here, we build and explore several continuous culture bacteria-phage computational models, each analysing different phase-variable scenarios calibrated to the experimental SSR rates of C. jejuni loci and replication parameters for the F336 phage. We simulate the evolution of PV rates via the adaptive dynamics framework for varying levels of selective pressures that act on the phage-resistant state. Our results indicate that growth reducing counter-selection on a single PV locus results in the stable maintenance of the phage, while compensatory selection between bacterial states affects the evolutionary stable mutation rates (i.e. very high and very low mutation rates are evolutionarily disadvantageous), whereas, in the absence of either selective pressure the evolution of PV rates results in mutation rates below the basal values. Contrastingly, a biologically-relevant model with two phase-variable loci resulted in phage extinction and locking of the bacteria into a phage-resistant state suggesting that another counter-selective pressure is required, instance, the use of a distinct phage whose receptor is an F336-phage-resistant state. We conclude that a delicate balance between counter-selection and phage-attack can result in both the evolution of phase-variable phage receptors and persistence of PV-receptor-specific phage.     

How does temporal variation in habitat connectivity influence metapopulation dynamics?

Metapopulation persistence depends on connectivity between habitat patches. While emphasis has been placed on the spatial dynamics of connectivity, much less has been placed on its short‐term temporal dynamics. In many terrestrial and aquatic ecosystems, however, transient (short‐term) changes in connectivity occur as habitat patches are connected and disconnected due, for example, to climatic or hydrological variability. We evaluated the implications of transient connectivity using a network‐based metapopulation model and a series of scenarios representing temporal changes in connectivity. The transient loss of connectivity can influence metapopulation persistence, and more strongly autocorrelated temporal dynamics affect metapopulation persistence more severely. Given that many ecosystems experience short‐term and temporary loss of habitat connectivity, it is important that these dynamics are adequately represented in metapopulation models; failing to do so may yield overly optimistic‐estimates of metapopulation persistence in fragmented landscapes.     

How does the presence of predators influence the persistence of antipredator behavior?

We developed a virtual world to study the effect of predators on predator recognition. We trained a neural network to discriminate between the shapes of simulated aerial and terrestrial predators and non-predators. Then, the network's weighting values were fixed into the genomes of a set of autonomous agents. These animats were required to eat, avoid death due to starvation, and avoid predation, by fleeing from approaching predators. We systematically varied the predator's lethality, the mutation rate, the cost of fleeing a predator, and the presence or absence of aerial and terrestrial predators. We used ANOVA to analyse the average recognition ability (a measure of directional selection) and the standard deviation of recognition ability (a measure of relaxed selection) after 500 generations of selection. Mutation rate and the cost of flight had the greatest effect on both the average and standard deviation of recognition abilities. The loss of all predators relaxed selection on predator recognition abilities. The loss of specific predators had complex effects on recognition abilities. Persistence is largely influenced by escape costs.     

How does variation in fetal loss affect the distribution of waiting times to conception?

Abstract

Unmeasured variation has long been a concern in analyses of the waiting time to conception. Recent work by Heckman and Walker (1991) and Trussell and Rodriguez (1990) has underscored the fact that statistical considerations alone cannot discriminate among likely models describing the distribution. Here, we specify a single theoretically important source of heterogeneity, namely variability in intrauterine mortality, and assess its effects on the waiting times to a conception which results in a live birth. We find that the effects of variation in fetal loss are confined to the tail of the distribution. Unless variation in fetal loss is extremely large or a substantial proportion of observed waiting times are initiated at late ages, variation in fetal loss does not appear to explain much variation in conception waits. We conclude that heterogeneity in fetal loss does not explain the variation in fecundability that has been observed for first birth intervals. This conclusion supports the hypothesis that at early ages (below age 35) variation in the waiting time to a fertile conception may largely reflect the proportion of nonsusceptible couples in the population. The analyses suggest that for the purposes of testing theoretically motivated models, future efforts should be directed toward examining reproductive experience after age 35 and toward incorporating information on characteristics of the fertile period as it becomes known.     

How does variation in the environment and individual cognition explain the existence of consistent behavioral differences?

According to recent studies on animal personalities, the level of behavioral plasticity, which can be viewed as the slope of the behavioral reaction norm, varies among individuals, populations, and species. Still, it is conceptually unclear how the interaction between environmental variation and variation in animal cognition affect the evolution of behavioral plasticity and expression of animal personalities. Here, we (1) use literature to review how environmental variation and individual variation in cognition explain population and individual level expression of behavioral plasticity and (2) draw together empirically yet nontested, conceptual framework to clarify how these factors affect the evolution and expression of individually consistent behavior in nature. The framework is based on simple principles: first, information acquisition requires cognition that is inherently costly to build and maintain. Second, individual differences in animal cognition affect the differences in behavioral flexibility, i.e. the variance around the mean of the behavioral reaction norm, which defines plasticity. Third, along the lines of the evolution of cognition, we predict that environments with moderate variation favor behavioral flexibility. This occurs since in those environments costs of cognition are covered by being able to recognize and use information effectively. Similarly, nonflexible, stereotypic behaviors may be favored in environments that are either invariable or highly variable, since in those environments cognition does not give any benefits to cover the costs or cognition is not able to keep up with environmental change, respectively. If behavioral plasticity develops in response to increasing environmental variability, plasticity should dominate in environments that are moderately variable, and expression of animal personalities and behavioral syndromes may differ between environments. We give suggestions how to test our hypothesis and propose improvements to current behavioral testing protocols in the field of animal personality.     

How does light intensity influence evening dressing behavior in the cold?

Core temperature (tympanic and rectal temperatures) is lowered for several hours under diurnal bright light exposure and its evening fall is inhibited under evening bright light exposure. Melatonin may be involved in the behavior of these core temperatures. Diurnal bright light exposure for several hours may make dressing behavior and thermal sensibility in the evening cold slower and dull, compared with diurnal dim light exposure. On the contrary, evening bright light exposure for several hours may make the dressing behavior and thermal sensibility in the evening cold quicker and sharper, compared with evening dim light exposure. The underlying physiological mechanisms for these findings are that the thermoregulatory set-point would be reduced more markedly in the evening under the influence of higher elevation of melatonin under the diurnal bright light exposure, and its evening decline would be inhibited by suppression of the nocturnal rise of melatonin under evening bright light exposure.     

How does colony growth influence communication in ants?

Summary. As Lasius niger societies grow from incipient nests to mature colonies, their foraging strategies shift from the individual exploitation of food sources to mass recruitment. Colony size instead of age is the key factor that shapes the exploratory and foraging responses of Lasius niger: a drastic reduction (or increase) of the population elicits an activity profile similar to that observed in younger (or older) societies of the same size. As a colony grows, the proportion of patrollers significantly decreases while the proportion of conveyors remains rather constant. As regards the energetic return, it increases with incipient nest size due to the replacement of minims by ordinary workers of larger crop capacity. We also demonstrate that minims of incipient nests modulate their trail-laying behaviour according to the social context, in this case the colony size. During their ontogenesis, L. niger colonies exhibit a progressive integration of individual foragers into a network of communication, the adaptive significance of which is discussed.     

Do key innovations unlock diversification? A case-study on the morphological and ecological impact of pharyngognathy in acanthomorph fishes

Key innovations may allow lineages access to new resources and facilitate the invasion of new adaptive zones, potentially influencing diversification patterns. Many studies have focused on the impact of key innovations on speciation rates, but far less is known about how they influence phenotypic rates and patterns of ecomorphological diversification. We use the repeated evolution of pharyngognathy within acanthomorph fishes, a commonly cited key innovation, as a case study to explore the predictions of key innovation theory. Specifically, we investigate whether transitions to pharyngognathy led to shifts in the rate of phenotypic evolution, as well as shifts and/or expansion in the occupation of morphological and dietary space, using a dataset of 8 morphological traits measured across 3,853 species of Acanthomorpha. Analyzing the 6 evolutionarily independent pharyngognathous clades together, we found no evidence to support pharyngognathy as a key innovation; however, comparisons between individual pharyngognathous lineages and their sister clades did reveal some consistent patterns. In morphospace, most pharyngognathous clades cluster in areas that correspond to deeper-bodied morphologies relative to their sister clades, while occupying greater areas in dietary space that reflects a more diversified diet. Additionally, both Cichlidae and Labridae exhibited higher univariate rates of phenotypic evolution compared with their closest relatives. However, few of these results were exceptional relative to our null models. Our results suggest that transitions to pharyngognathy may only be advantageous when combined with additional ecological or intrinsic factors, illustrating the importance of accounting for lineage-specific effects when testing key innovation hypotheses. Moreover, the challenges we experienced formulating informative comparisons, despite the ideal evolutionary scenario of multiple independent evolutionary origins of pharyngognathous clades, illustrates the complexities involved in quantifying the impact of key innovations. Given the issues of lineage specific effects and rate heterogeneity at macroevolutionary scales we observed, we suggest a reassessment of the expected impacts of key innovations may be warranted.     

Can spatial variation in epiphyte diversity and community structure be predicted from sampling vascular epiphytes alone?

Aim Non‐vascular epiphytes have been largely ignored in studies examining the biotic and abiotic determinants of spatial variation in epiphyte diversity. Our aim was to test whether the spatial patterning of species richness, biomass and community composition across geographic regions, among trees within regions, and among branches within trees is consistent between the vascular and non‐vascular components of the temperate rain forest flora. Location Coastal lowland podocarp‐broadleaved forests on the west coast of the South Island of New Zealand. Methods We collected single samples (30 × 25 cm) from 96 epiphyte assemblages located on the inner branches of 40 northern rata (Metrosideros robusta) trees. For each sample, branch characteristics such as branch height, branch diameter, branch angle, branch aspect, and minimum and maximum epiphyte mat depth were recorded. The biomass for each individual epiphyte species was determined. Results Northern rata was host to a total of 157 species, comprising 32 vascular and 125 non‐vascular species, with liverworts representing 41% of all species. Within epiphyte mats, the average total organic biomass of 3.5 kg m^?2 of branch surface area consisted largely of non‐living biomass and roots. Vascular and non‐vascular epiphytes showed strikingly different spatial patterns in species richness, biomass and composition between sites, among trees within sites, and among branches within trees, which could not be explained by the branch structural characteristics we measured. The two plant groups had no significant association in community composition (r = 0.04, P = 0.08). However, the species richness of vascular plant seedlings was strongly linked to the presence/absence of lichens. Main conclusions Non‐vascular plants contributed substantially to the high species richness and biomass recorded in this study, which was comparable to that of some tropical rain forests. High variability in community composition among epiphyte mats, and very low correlation with any of the environmental factors measured possibly indicate high levels of stochasticity in seed or spore colonization, establishment success or community assembly among branches in these canopy communities. Although we found some evidence that vascular plant seedling establishment was linked to the presence of lichens and the biomass of non‐living components in the epiphyte mats, there was no correlation in the spatial patterning or determinants of species richness between non‐vascular and vascular plants. Consequently, variation in total epiphyte biodiversity could not be predicted from the measurement of vascular plant diversity alone, which highlights the crucial importance of sampling non‐vascular plants when undertaking epiphyte community studies.     

How does parental role influence the activity and movements of breeding wolves?

We studied the activity and movements of a male and a female wolf during breeding in the Bieszczady Mountains, Poland. The female was less active and mobile and on average closer to the den than the male. The male was less active and mobile when the pack size was seven compared to a year when the pack consisted only of the breeding pair. We conclude that the roles played by breeding males and females rearing pups influence their activity, and that breeding males in larger packs move less during the nursing period because of help by other pack members.     

How does the QB site influence propagate to the QA site in photosystem II?

The redox potential of the primary quinone Q(A) [E(m)(Q(A))] in photosystem II (PSII) is lowered by replacement of the native plastoquinone (PQ) with bromoxynil (BR) at the secondary quinone Q(B) binding site. Using the BR-bound PSII structure presented in the previous Fourier transform infrared and docking calculation studies, we calculated E(m)(Q(A)) considering both the protein environment in atomic detail and the protonation pattern of the titratable residues. The calculated E(m)(Q(A)) shift in response to the replacement of PQ with deprotonated BR at the Q(B) binding site [ΔE(m)(Q(A))(PQ→BR)] was -55 mV when the three regions, Q(A), the non-heme iron complex, and Q(B) (Q(B) = PQ or BR), were treated as a conjugated supramolecule (Q(A)-Fe-Q(B)). The negative charge of BR apparently contributes to the downshift in ΔE(m)(Q(A))(PQ→BR). This downshift, however, is mostly offset by the influence of the residues near Q(B). The charge delocalization over the Q(A)-Fe-Q(B) complex and the resulting H-bond strength change between Q(A) and D2-His214 are crucial factors that yield a ΔE(m)(Q(A))(PQ→BR) of -55 mV by (i) altering the electrostatic influence of the H-bond donor D2-His214 on E(m)(Q(A)) and (ii) suppressing the proton uptake events of the titratable residues that could otherwise upshift ΔE(m)(Q(A))(PQ→BR) during replacement of PQ with BR at the Q(B) site.     

How does the magnitude of genetic variation affect ecological and reproductive character displacement?

While previous studies on character displacement tended to focus on trait divergence and convergence as a result of long-term evolution, recent studies suggest that character displacement can be a special case of evolutionary rescue, where rapid evolution prevents species extinction by weakening interspecific competition. Here we analyzed a simple model to examine how the magnitude of genetic variation affects evolutionary rescue via ecological and reproductive character displacement that weakens interspecific competition in exploitation of shared resources (i.e., resource competition) and in the mating process caused by incomplete species recognition (i.e., reproductive interference), respectively. We found that slow trait divergence due to small genetic variance results in species extinction in reproductive character displacement but not in ecological character displacement. This is because one species becomes rare in slow character displacement, and this causes deterministic extinction due to minority disadvantage of reproductive interference. On the other hand, there is no deterministic extinction in the process of ecological character displacement. Furthermore, species extinction becomes less likely in the case of positive covariance between ecological and reproductive traits as divergence of the ecological trait (e.g., root depths) increases the divergence speed of the reproductive trait (e.g., flower colors) and vice versa. It will be interesting to compare intraspecific genetic (co)variance of ecological and reproductive traits in future studies for understanding how ecological and reproductive character displacement occur without extinction.     

How does modification of adenine by hydroxyl radical influence the stability and the nature of stacking interactions in adenine-cytosine complex?

This study reports on ab initio calculations of adenine - cytosine complexes in two different context alignments appearing in B-DNA. The influence of adenine modification by hydroxyl radical on the stability of the complexes is also discussed. The analysis was performed on over 40 crystallographic structures for each of the sequence contexts. In most cases, modification of adenine by hydroxyl radical leads to less negative intermolecular interaction energies. The issue of the influence of alteration of structural base step parameters on the stability of modified and unmodified adenine - cytosine complexes is also addressed. Analysis of the dependence of intermolecular interaction energy on base step parameters reveals that for twist and shift modification of adenine by hydroxyl radical leads to quite different interaction energy profiles in comparison with unmodified complexes. In order to elucidate the physical origins of this phenomenon, i.e. to analyze how the modification of adenine by hydroxyl radical is reflected in the change of intermolecular interaction energy components, a variational-perturbational decomposition scheme was applied at the MP2/aug-cc-pVDZ level of theory.