On itinerant water molecules and detectability of protein-protein interfaces through comparative analysis of homologues

We discuss the question of which residues are sufficiently important for protein-protein interaction to be under notable evolutionary pressure. Its interest stems from the applicability of this knowledge in the reverse direction, to detect a protein-protein interface on a single protomer, starting from the rate of mutation of participating residues. Using the analysis of trajectories produced by the molecular dynamics simulations, we suggest that, in the case of water soluble proteins, a large fraction of evolutionarily privileged residues can be found by considering the dynamic behavior of the protein interface and by looking for residues which exchange water molecules with the bulk of the solvent outstandingly slowly (tentatively termed "dry residues"). We show that the dry interface residues are better conserved across homologues than the generic "geometric footprint" and can be quite reliably detected through comparative analysis of protein homologues, without strong dependence on the choice of method. Furthermore, we show that dry residues distinguish themselves through a set of biophysical properties consistent with the known mechanisms of protein oligomerization: their compositional shift toward nonpolar, overlap, and co-location with residues exhibiting low mobility, their two- to threefold increased propensity over the rest of the geometric footprint to form hydrogen bonds, and four- to almost tenfold increased likelihood to participate in formation of salt bridges. These properties, consistently, help understand the observed increase in the evolutionary pressure that dry residues experience.     

Prediction of mean adult survival rates of southern African birds from demographic and ecological covariates

Estimates of annual survival rates of birds are valuable in a wide range of studies of population ecology and conservation. These include modelling studies to assess the impacts of climatic change or anthropogenic mortality for many species for which no reliable direct estimates of survival are available. We evaluate the performance of regression models in predicting adult survival rates of birds from values of demographic and ecological covariates available from textbooks and databases. We estimated adult survival for 67 species using dead recoveries of birds ringed in southern Africa and fitted regression models using five covariates: mean clutch size, mean body mass, mean age at first breeding, diet and migratory tendency. Models including these explanatory variables performed well in predicting adult survival in this set of species, both when phylogenetic relatedness of the species was taken into account using phylogenetic generalized least squares (51% of variation in logit survival explained) and when it was not (48%). Two independent validation tests also indicated good predictive power, as indicated by high correlations of observed with expected values in a leave‐one‐out cross validation test performed using data from the 67 species (35% of variation in logit survival explained), and when annual survival rates from independent mark–recapture studies of 38 southern African species were predicted from covariates and the regression using dead recoveries (48%). Clutch size and body mass were the most influential covariates, both with and without the inclusion of phylogenetic effects, and a regression model including only these two variables performed well in both of the validation tests (39 and 48% of variation in logit survival explained). Our regression models, including the version with only clutch size and body mass, are likely to perform well in predicting adult survival rate for southern African species for which direct survival estimates are not available.     

BIODIVERSITY RESEARCH: Soil moisture limits foraging: a possible mechanism for the range dynamics of the hadeda ibis in southern Africa

Aim Climate limits the ranges of many animals, but the mechanism whereby it does so remains poorly understood. One explanation is that climate (e.g. temperature or rainfall) affects energy expenditure, eventually limiting where a species can occur. We propose that climate can also affect energy uptake through its effect on foraging efficiency. We examined this idea for the case of the hadeda ibis (Bostrychia hagedash) which has considerably expanded its range in southern Africa over the past 80 years. Hadedas forage mainly by extracting earthworms and other invertebrates from soft soil. Soil moisture, in the absence of irrigation largely determined by climate and soil composition, may therefore be a factor limiting feeding efficiency in hadedas. Location We tested this hypothesis by observing foraging hadedas in Cape Town, South Africa. Results We found that soil moisture limited the rate at which hadedas caught prey items, with an optimum on relatively moist ground. We further measured the energy content of the hadedas’ main prey, earthworms. Using published physiological relationships, we estimated that hadedas need to forage for about 6.3 h to meet their daily energy requirements under optimal soil moisture conditions. On dry soils, they need to forage for >12 h, thus showing that soil moisture has the potential to limit the range of this species. Main conclusions Hadedas originally only occurred in the wettest parts of South Africa, but gradually colonized drier areas, and are now absent only from the driest parts of the country. Our results support the view that climate (determining soil moisture) originally limited the hadedas range and that irrigation has been an important factor facilitating their range expansion. The hadeda is an example for a species whose range expansion is driven by interactions between climate and land‐use change.     

Character and evolution of protein-protein interfaces

Protein-protein interactions create the macromolecular assemblies and sequential signaling pathways essential for cell function. Their number far exceeds the number of proteins themselves and their experimental characterization, while improving, remains relatively slow. For these reasons, novel computational methods have important roles to play in understanding the physical basis of protein interactions, and in constraining the molecular basis of their specificity. This paper discusses methods based on multiple sequence alignments of protein homologues and phylogenetic trees.     

Effectiveness of protected areas for bird conservation depends on guild

Aim

Protected areas are key conservation tools intended to increase biodiversity and reduce extinction risks of species and populations. However, the degree to which protected areas achieve their conservation goals is generally unknown for many protected areas worldwide. We assess the effect of protected areas on the abundance of 196 common, resident bird species. If protected areas were beneficial to avian biodiversity, we expect landscapes with a higher proportion of protected areas will have higher densities of species compared to landscapes with no protection.

Location

Greater Gauteng region, South Africa.

Methods

We analysed bird survey data collected over regular grid cells across the study area. We estimated bird abundance in relation to the proportion of a grid cell that was protected with the Royle–Nichols model and fitted the model once for each of the species. We examined variation in estimated abundance as a function of avian guild (defined by the type of food a species preferentially ate and its foraging mode) with a regression tree analysis.

Results

Abundance was significantly positively related to the proportion of protected areas in grid cells for 26% of the species, significantly negatively related in 15%, and not significantly related in 59% species. We found three distinct guild groups which differed in their average abundance, after accounting for associated variance. Group 1 consisted of guilds frugivores, ground‐feeders, hawkers, predators, and vegivores and average abundance was strongly positively related to the proportion of protected areas. Group 2 included granivores, and average abundance was strongly negatively related to proportion of protected areas. Group 3 included gleaners only, and average abundance was not related to proportion of protected areas.

Main conclusion

We conclude that the network of protected areas within the greater Gauteng region sustained relatively higher abundances of common birds and thus perform an important conservation role.

     

Geographic variation in reproduction and survival of kelp gulls Larus dominicanus vetula in southern Africa

Different populations of a species tend to vary in survival and reproduction, but the extent and scale of such spatial variation are poorly known. We estimated survival and clutch size of kelp gulls Larus dominicanus vetula across their entire African range. At this large geographic scale, we found no evidence for spatial variation in survival, and there was no variation in clutch size. However, there was considerable variation in clutch size among colonies within regions. Over the whole study, mean annual survival of juvenile and adult birds was 0.44 and 0.84, and mean clutch size was 2.2 eggs. A matrix population model showed that population growth was least sensitive to variation in clutch size, and the observed variation in clutch size could not fully account for the observed variation in population growth among colonies and regions. Our results thus suggest that dispersal and/or variation in survival (including egg/nestling survival) at a small spatial scale are also important for the spatial pattern of kelp gull population dynamics. These results are consistent with a metapopulation approach to spatial population dynamics.     

Imperfect detection distorts depth‐related trends in marine macrofaunal species richness

Ecology and biodiversity research are underpinned by species richness patterns and their environmental drivers. However, a key topic in this discussion is the accuracy of these patterns which are greatly dependent on species detection probabilities. Due to variations in detection of species, true ecological patterns may be distorted. This is particularly true for subtidal macro‐infaunal communities. We tested three hypothesized relationships between marine benthic macrofaunal diversity and depth using species richness per site estimated with a capture–recapture heterogeneity model that accounts for variable detection probabilities. These metrics were based on data from 42 replicated sites across the continental shelf of the Southern Benguela. Average detection probability decreased with greater depth but species richness increased along the same depth gradient. The conflation of these trends in observed diversity data resulted in a positively near‐linear depth–diversity relationship, while accounting for variable species detection revealed a much stronger relationship. Ignoring species detection in ecosystems with imperfect detection could therefore distort species richness patterns, which has implications for ecological theory, management and conservation.     

Phenotypic selection and covariation in the life‐history traits of elephant seals: heavier offspring gain a double selective advantage

Early developmental conditions contribute to individual heterogeneity of both phenotypic traits and fitness components, ultimately affecting population dynamics. Although the demographic consequences of ontogenic growth are best quantified using an integrated measure of fitness, most analyses to date have instead studied individual fitness components in isolation. Here, we estimated phenotypic selection on weaning mass in female southern elephant seals Mirounga leonina by analyzing individual‐based data collected between 1986 and 2016 with capture–recapture and matrix projection models. In support of a hypothesis predicting a gradual decrease of weaning mass effects with time since weaning (the replacement hypothesis), we found that the estimated effects of weaning mass on future survival and recruitment probability was of intermediate duration (rather than transient or permanent). Heavier female offspring had improved odds of survival in early life and a higher probability to recruit at an early age. The positive link between weaning mass and recruitment age is noteworthy, considering that pre‐recruitment mortality already imposed a strong selective filter on the population, leaving only the most ‘robust’ individuals to reproduce. The selection gradient on asymptotic population growth rate, a measure of mean absolute fitness, was weaker than selection on first‐year survival and recruitment probabilities. Weaker selection on mean fitness occurs because weaning mass has little impact on adult survival, the fitness component to which the population growth of long‐lived species is most sensitive. These results highlight the need to interpret individual variation in phenotypic traits in a context that considers the demographic pathways between the trait and an inclusive proxy of individual fitness. Although variation in weaning mass do not translate to permanent survival differences among individuals in adulthood, it explains heterogeneity and positive covariation between survival and breeding in early life, which contribute to between‐individual variation in fitness.     

ICDs at higher age and clinical risk factors

Background

The implantable cardioverter defibrillator (ICD) is effective in preventing sudden cardiac death. However, in elderly patients (aged 75 years or older) the role of ICDs is still not well-defined and controversial.

Methods

We retrospectively analysed all clinical and survival data of all ICD patients who were ≥75 years at the date of implantation in the Erasmus MC, Rotterdam, the Netherlands and the University Hospital, Basel, Switzerland. Kaplan-Meier survival analysis was performed, and mortality predictors were identified. Mortality of the cohort was compared with a random sample of patients aged 60–70 years originating from the same database and to an age- and sex-matched cohort of Dutch persons.

Results

The study cohort consisted of 179 patients aged 75 years or older who were implanted between February 1999 and July 2008. The median follow-up time was 2.0 (IQR 2.8) years. Survival rates after 1, 2 and 3 years were 87, 82, 75 %, respectively. Survival was similar for primary and secondary prevention. Mortality in this study population could be predicted by combining four clinical risk factors: QRS duration >120 ms, NYHA class > II, renal failure and atrial fibrillation (AF). Survival was worse compared with the group of ICD patients aged 60–70 years and to the age- and sex-matched group of elderly persons. However, survival was not significantly worse when comparing elderly ICD patients without additional risk factors to the general population.

Conclusions

Elderly patients still have an acceptable survival probability independent of prevention indication, certainly if there are no additional clinical risk factors. The presence or absence of additional clinical risk factors should be taken into account when making the decision for implantation, since they strongly correlate with survival.