Mammalian nonsynonymous sites are not overdispersed: comparative genomic analysis of index of dispersion of mammalian proteins

It is often stated that patterns of nonsynonymous rate variation among mammalian lineages are more irregular than expected or overdispersed under the neutral model, whereas synonymous sites conform to the neutral model. Here we reexamined genome-wide patterns of the variance to mean ratio, or index of dispersion (R), of substitutions in proteins from human, mouse, and dog. Contrary to the prevailing notion, we found that the mean index of dispersion for nonsynonymous sites of mammalian proteins is not significantly different from 1. We propose that earlier analyses were biased because the data included disproportionately more protein hormones, which tend to be more dispersed than genes in other functional categories. Synonymous sites exhibit greater degree of dispersion than nonsynonymous sites, although similar to earlier estimates and potentially due to errors associated with correction for multiple hits. Overall, our analysis identifies strong genome-wide generation-time effect and natural selection as important determinants of among-lineage variation of protein evolutionary rates. Furthermore, patterns of lineage-specific selective constraint are consistent with the nearly neutral model of molecular evolution.     

Engineering proteins with tunable thermodynamic and kinetic stabilities

It is widely recognized that enhancement of protein stability is an important biotechnological goal. However, some applications at least, could actually benefit from stability being strongly dependent on a suitable environment variable, in such a way that enhanced stability or decreased stability could be realized as required. In therapeutic applications, for instance, a long shelf-life under storage conditions may be convenient, but a sufficiently fast degradation of the protein after it has performed the planned molecular task in vivo may avoid side effects and toxicity. Undesirable effects associated to high stability are also likely to occur in food-industry applications. Clearly, one fundamental factor involved here is the kinetic stability of the protein, which relates to the time-scale of the irreversible denaturation processes and which is determined to some significant extent by the free-energy barrier for unfolding (the barrier that "separates" the native state from the highly-susceptible-to-irreversible-alterations nonnative states). With an appropriate experimental model, we show that strong environment-dependencies of the thermodynamic and kinetic stabilities can be achieved using robust protein engineering. We use sequence-alignment analysis and simple computational electrostatics to design stabilizing and destabilizing mutations, the latter introducing interactions between like charges which are screened out at high salt. Our design procedures lead naturally to mutating regions which are mostly unstructured in the transition state for unfolding. As a result, the large salt effect on the thermodynamic stability of our consensus plus charge-reversal variant translates into dramatic changes in the time-scale associated to the unfolding barrier: from the order of years at high salt to the order of days at low salt. Certainly, large changes in salt concentration are not expected to occur in biological systems in vivo. Hence, proteins with strong salt-dependencies of the thermodynamic and kinetic stabilities are more likely to be of use in those cases in which high-stability is required only under storage conditions. A plausible scenario is that inclusion of high salt in liquid formulations will contribute to a long protein shelf-life, while the lower salt concentration under the conditions of the application will help prevent the side effects associated with high-stability which may potentially arise in some therapeutic and food-industry applications. From a more general viewpoint, this work shows that consensus engineering and electrostatic engineering can be readily combined and clarifies relevant aspects of the relation between thermodynamic stability and kinetic stability in proteins.     

A single exposure to immobilization causes long-lasting pituitary-adrenal and behavioral sensitization to mild stressors

We have previously reported that a single exposure to immobilization (IMO) in rats causes a long-term desensitization of the hypothalamic-pituitary-adrenal (HPA) response to the same (homotypic) stressor. Since there are reports showing that a single exposure to other stressors causes sensitization of the HPA response to heterotypic stressors and increases anxiety-like behavior, we studied in the present work the long-term effects of IMO on behavioral and HPA response to mild superimposed stressors. In Experiments 1 and 2, adult male Sprague–Dawley rats were subjected to 2 h of IMO and then exposed for 5 min to the elevated plus-maze (EPM) at 1, 3 or 7 days after IMO. Blood samples were taken at 15 min after initial exposure to the EPM. Increases in anxiety-like behavior and HPA responsiveness to the EPM were found at all times post-IMO. Changes in the resting levels of HPA hormones did not explain the enhanced HPA responsiveness to the EPM (Experiment 3). In Experiments 4 and 5, we studied the effects of a single exposure to a shorter session of IMO (1 h) on behavioral and HPA responses to a brief and mild session of foot-shocks done 10 days after IMO. Neither previous IMO nor exposure to shocks in control rats modified behavior in the EPM. However, a brief session of shocks in previously IMO-exposed rats dramatically increased anxiety in the EPM. HPA and freezing responses to shocks were similar in control and previous IMO groups. Therefore, a single exposure to IMO appears to induce long-lasting HPA and behavioral sensitization to mild superimposed stressors, although the two responses are likely to be at least partially independent. Long-term effects of IMO on the susceptibility to stress-induced endocrine and emotional disturbances may be relevant to the characterization of animal models of post-traumatic stress.     

Yolk testosterone, postnatal growth and song in male canaries

Avian eggs contain substantial amounts of maternal yolk androgens, which have been shown to modulate offspring phenotype. The first studies on the functional consequences of maternal yolk androgens have focused on early life stages and their role in sibling competition. However, recent longitudinal studies reported long-lasting effects of maternal yolk androgens on offspring phenotype, mostly concerning traits that are sensitive to androgens. This suggests that maternal yolk androgens could play an important role in sexual selection, since the expression of many male sexual characters is testosterone-dependent. Using male canaries as a model, we examined the consequences of an experimental elevation of yolk testosterone concentrations on early development as well as long-lasting effects particularly on song, which is one of the most important sexual characters in male songbirds. Elevated yolk testosterone concentrations inhibited male growth, possibly in interaction with an existent ectoparasite exposure. Males hatched from testosterone-treated eggs (T-males) did not have enhanced competitive skills, in contrast to previous studies. The elevation of yolk testosterone concentrations delayed song development but did not affect adult song phenotype. This is intriguing, as yolk testosterone possibly induced developmental stress, which is known to reduce song quality. We hypothesize that yolk testosterone has either no direct effect on adult song phenotype, or that positive effects are merged by the negative effects of developmental stress. Finally, females mated with T-males invested more in their clutch indicating that females either assess T-males as more attractive (differential allocation hypothesis) or compensated for lower offspring viability (compensation hypothesis).     

Intraguild predation in raptor assemblages: a review

Intraguild predation, the killing of species that use similar resources, has been largely overlooked in raptor investigations. To help fill this gap in knowledge, we conducted a literature review, focusing on studies that tested the behavioural and demographic impact of intraguild predation on individuals, populations, and assemblages of diurnal and nocturnal raptorial species. Overall, data were available for 39 empirical and experimental studies on 63 populations belonging to 11 killer species and 15 victim species. An overview of these studies suggested that intraguild predation was a widespread, size-based phenomenon. Results from multiple studies on the same species at different locations were usually consistent across wide geographical areas. Individual-level demographic impacts included reduced site-occupancy, breeding success and survival. Individuals of the prey species responded to predation pressure through direct spatial avoidance, risk-sensitive habitat selection, short-term behavioural avoidance (e.g. reduced vocal activity and escape to refugia after predator detection) and, possibly, temporal segregation. Population-level effects were common but mainly examined as spatio-temporal correlations between the abundance of killer and victim species. Correlative evidence also suggested that intraguild predation may have the potential to structure whole raptor assemblages. More studies on other species and different geographic areas are needed to increase our understanding of the causes and consequences of this widespread interaction. From a conservation point of view, intraguild predation may limit the success of raptor preservation programmes and could be used as a management tool through its effect on mesopredator release and its potentially positive, indirect effects on game species.     

Differential mortality of wintering shorebirds on the Banc d'Arguin, Mauritania, due to predation by large falcons

Predators may influence many aspects of the daily life and seasonal movements of their prey. Here we quantify direct, and evaluate indirect effects of predation by three falcon species (Lanner Falcon Falco biarmicus , Barbary Falcon Falco pelegrinoides and Peregrine Falcon Falco peregrinus ) on coastal shorebirds wintering on the Banc d'Arguin, Mauritania, an area hosting approximately 30% of the East Atlantic Flyway population of shorebirds. On the basis of 754 h of observation over five winters, 97 witnessed attacks and 585 collected prey remains, we show that shorebirds were safer in larger flocks, which tended to be attacked less often. Furthermore, species that forage relatively close to shore and in small flocks were depredated more often than expected from their relative abundance. In three species, Red Knot Calidris canutus canutus , Bar-tailed Godwit Limosa lapponica taymyrensis and Dunlin Calidris alpina , the juveniles were more vulnerable than adults. We estimated that on average 1% of the juvenile and 0.1% of the adult Red Knots present were killed by large falcons each winter. For Red Knots we simultaneously quantified annual survival on the basis of an individual colour-marking programme: mortality due to predation by falcons accounted for an estimated 6.2% (juveniles) and 0.8% (adults) of annual mortality. We suggest that juvenile Red Knots are 10 times as likely to be killed by falcons because they use riskier habitats, i.e. early and late tide foraging areas closer to shores where surprise attacks are both more common and more successful. These results indicate that the strength of indirect effects of predation operating in a shorebird population largely outweigh the effects of mortality per se .     

Sex-related effects of maternal egg investment on offspring in relation to carotenoid availability in the great tit

1. Maternal carotenoids in the egg yolk have been hypothesized to promote maturation of the immune system and protect against free radical damages. Depending on availability, mothers may thus influence offspring quality by depositing variable amounts of carotenoids into the eggs. Sex allocation theory predicts that in good quality environments, females should invest into offspring of the sex that will provide larger fitness return, generally males. 2. In a field experiment we tested whether female great tits bias their investment towards males when carotenoid availability is increased, and whether male offspring of carotenoid-supplemented mothers show higher body condition. We partially cross-fostered hatchlings to disentangle maternal effects from post-hatching effects, and manipulated hen flea Ceratophyllus gallinae infestation to investigate the relationship between carotenoid availability and resistance to ectoparasites. 3. As predicted, we found that carotenoid-supplemented mothers produced males that were heavier than their sisters at hatching, while the reverse was true for control mothers. This suggests that carotenoid availability during egg production affects male and female hatchlings differentially, possibly via a differential allocation to male and female eggs. 4. A main effect of maternal supplementation became visible 14 days after hatching when nestlings hatched from eggs laid by carotenoid-supplemented mothers had gained significantly more mass than control nestlings. Independently of the carotenoid treatment, fleas impaired mass gain of nestlings during the first 9 days in large broods only and reduced tarsus length of male nestlings at an age of 14 days, suggesting a cost to mount a defence against parasites. 5. Overall, our results suggest that pre-laying availability of carotenoids affects nestling condition in a sex-specific way with potentially longer-lasting effects on offspring fitness.     

The effect of vascular plants on carbon turnover and methane emissions from a tundra wetland

This paper investigates how vascular plants affect carbon flow and the formation and emission of the greenhouse gas methane (CH₄) in an arctic wet tundra ecosystem in NE Greenland. We present a field experiment where we studied, in particular, how species‐specific root exudation patterns affect the availability of acetate, a hypothesized precursor of CH₄ formation. We found significantly higher acetate formation rates in the root vicinity of Eriophorum scheuchzeri compared with another dominating sedge in the wetland, i.e. Dupontia psilosantha. Furthermore a shading treatment, which reduced net photosynthesis, resulted in significantly decreased formation rates of acetate. We also found that the potential CH₄ production of the peat profile was highly positively correlated to the concentration of acetate at the respective depths, whereas it was negatively correlated to the concentration of total dissolved organic carbon. This suggests that acetate is a substrate of importance to the methanogens in the studied ecosystem and that acetate concentration in this case can serve as a predictor of substrate quality. To further investigate the importance of acetate as a predecessor to CH₄, we brought an intact peat‐plant monolith system collected at the field site in NE Greenland to the laboratory, sealed it hermetically and studied the decomposition of ¹⁴C‐labelled acetate injected at the depth of methanogenic activity. After 4 h, ¹⁴CH₄ emission from the monolith could be observed. In conclusion, allocation of recently fixed carbon to the roots of certain species of vascular plants affects substrate quality and influence CH₄ formation.     

Neighbourhood effects on the risk of an unpalatable plant being grazed

Most studies on the importance of the neighbourhood on a plant's risk ofherbivory have focused on palatable plants and how they are protected byunpalatable neighbours. This study examined the grazing intensity of arelatively unpalatable shrub, Buxus sempervirens, indifferent neighbours. Exactly 2683 plants of Buxussempervirens (including 172 controls) were sampled in 12 enclosedpastures belonging to 4 sheep farms. The enclosures were grazed at 3 differentseasons (spring, summer and autumn). Plants were divided in 4 age/hight classes(first year, < 4 cm, 4–10 cm, 10–40cm) and into 8 neighbourhoods. The first of these wascharacterisedby the absence of any plants within a radius of 5 cm around theBuxus individual and the 7 others by the identity of thedominant species in contact with the Buxus plant. Theintensity of grazing on the neighbouring plants were also recorded. At the endof one year's monitoring, 26.2% of Buxus sempervirensplants had been grazed. The proportion of plants grazed was significantlyhigherin spring than in the other two seasons. It decreased with increasing plantage.It was higher in neighbourhoods that were intensively grazed than in those withlight grazing. The proportion grazed in the absence of a neighbour plant wasintermediate between the previous two. The probability of a plant of aninvadingspecies being grazed is influenced by factors other than its life-historytraits. Some neighbourhoods consisting of unpalatable plants facilitate theestablishment of Buxus sempervirens by protecting theyoungplants from grazing, whereas other highly palatable neighbourhoods are readilygrazed by sheep, thus indirectly increasing the proportion of Buxussempervirens that are grazed. The young and short (< 4cm in height) Buxus plants, which are lessrecognisable by sheep, are most sensitive to the impact of grazing.     

Responses of ant communities to experimental fire regimes on rangelands in the Victoria River District of the Northern Territory

Abstract Fire is a significant feature of Australia's savannas. Its use is being encouraged for cattle rangeland management, but there is little knowledge of the ecological effects of prescribed fire regimes on native biodiversity. The responses of ant communities to five experimental fire regimes over 2 years are reported from the Victoria River District in the semi‐arid tropics of northern Australia. The experiment was stratified at two levels: soil type (red and black) and fire treatment (unburnt; burnt twice in successive years in early (May) or late (October) dry season and unburnt thereafter; and burnt twice, 3 years apart, in early or late dry season). Ants were sampled twice in April, corresponding with the end of the 1997 and 1998 wet seasons. Ant species richness was not responsive to fire treatment, but reduced with time since fire on black soil. Total ant abundance also reduced with time since fire on the black soil, with significant different abundances in burnt versus unburnt plots in the 1998 sample. Soil type and sampling time had the greatest influence on ant community composition in multivariate analysis than did fire regime, although there were moderate gradients of time since fire with the black soil plots. The abundance of 19 species were significantly different between fire regimes in anova , 13 on red soil and six on black soil. The abundance of eight species (four each on red and black soil) changed significantly with time since fire, with seven promoted by burning. Ant functional group profiles changed little with fire. Total ant abundance and richness had significant relationships with key pasture species and vegetative variables. The responses of ants largely recapitulated those of plants, birds and reptiles on the same plots. It is envisaged that ants will have an important role to play in the sustainable management of Australia's rangelands aiding the off‐reserve conservation of biodiversity.