Experimental evidence of long‐term reproductive costs in a colonial nesting seabird

Trade‐offs between current and future reproduction are central to the evolution of life histories. Experiments that manipulate brood size provide an effective approach to investigating future costs of current reproduction. Most manipulative studies to date, however, have addressed only the short‐term effects of brood size manipulation. Our goal was to determine whether survival or breeding costs of reproduction in a long‐lived species manifest beyond the subsequent breeding season. To this end, we investigated long‐term survival and breeding effects of a multi‐year reproductive cost experiment conducted on black‐legged kittiwakes Rissa tridactyla, a long‐lived colonial nesting seabird. We used multi‐state capture–recapture modeling to assess hypotheses regarding the role of experimentally reduced breeding effort and other factors, including climate phase and colony size and productivity, on future survival and breeding probabilities during the 16‐yr period following the experiment. We found that forced nest failures had a positive effect on breeding probability over time, but had no effect on long‐term survival. This apparent canalization of survival suggests that adult survival is the most important parameter influencing fitness in this long‐lived species, and that adults should pay reproductive costs in ways that do not compromise this critical life history parameter. When declines in adult survival rate are observed, they may indicate populations of conservation concern.     

Maintenance of body‐size variation and host range in the orange‐tip butterfly: evidence for a trade‐off between adult life‐history traits

1. The evolution of host range and preference in phytophagous insects is driven by a female's oviposition choice impacting her offspring's fitness. Analysis of the fitness of progeny on different host plants has commonly been restricted to the performance of immature stages. However, since host use can affect adult size, it is important to measure the ongoing effects of host choice on the resulting imagines. 2. The orange‐tip butterfly, Anthocharis cardamines, shows a strong preference for two host plants in Britain, Alliaria petiolata and Cardamine pratensis, which affect body size. Whilst females exhibit a strong positive size–fecundity relation, the impact of body‐size alteration is unknown in males. In this study, fitness effects of host plant choice for male A. cardamines were examined. 3. Males reared on C. pratensis were smaller and emerged earlier than those reared on A. petiolata, and early‐season males were smaller than late‐season ones in the field. Interestingly, regression analysis indicated that the earlier emergence of small males was a host‐mediated rather than a size‐mediated effect. Small size was associated with reduced male dispersal in a semi‐isolated wild population over a 3‐year period. 4. It is proposed that the earlier emergence associated with C. pratensis has evolved in response to depressed dispersal in isolated/semi‐isolated populations associated with this patchily distributed host. We suggest that adult life‐history traits are important for the maintenance of host range in this species, and offer a critique of Courtney's earlier hypothesis that host range is maintained by time‐limited oviposition behaviour.     

Combining point‐process and landscape vegetation models to predict large herbivore distributions in space and time—A case study of Rupicapra rupicapra

Aim

When modelling the distribution of animals under current and future conditions, both their response to environmental constraints and their resources’ response to these environmental constraints need to be taken into account. Here, we develop a framework to predict the distribution of large herbivores under global change, while accounting for changes in their main resources. We applied it to Rupicapra rupicapra, the chamois of the European Alps.

Location

The Bauges Regional Park (French Alps).

Methods

We built sixteen plant functional groups (PFGs) that account for the chamois’ diet (estimated from sequenced environmental DNA found in the faeces), climatic requirements, dispersal limitations, successional stage and interaction for light. These PFGs were then simulated using a dynamic vegetation model, under current and future climatic conditions up to 2100. Finally, we modelled the spatial distribution of the chamois under both current and future conditions using a point‐process model applied to either climate‐only variables or climate and simulated vegetation structure variables.

Results

Both the climate‐only and the climate and vegetation models successfully predicted the current distribution of the chamois species. However, when applied into the future, the predictions differed widely. While the climate‐only models predicted an 80% decrease in total species occupancy, including vegetation structure and plant resources for chamois in the model provided more optimistic predictions because they account for the transient dynamics of the vegetation (?20% in species occupancy).

Main conclusions

Applying our framework to the chamois shows that the inclusion of ecological mechanisms (i.e., plant resources) produces more realistic predictions under current conditions and should prove useful for anticipating future impacts. We have shown that discounting the pure effects of vegetation on chamois might lead to overpessimistic predictions under climate change. Our approach paves the way for improved synergies between different fields to produce biodiversity scenarios.

     

A cost–benefit analysis of the environmental taxation policy in China: A frontier analysis‐based environmentally extended input–output optimization method

China's high‐speed economic development and reliance on overconsumption of natural resources have led to serious environmental pollution. Environmental taxation is seen as an effective economic tool to help mitigate air pollution. In order to assess the effects of different scenarios of environmental taxation policies, we propose a frontier‐based environmentally extended input–output optimization model with explicit emission abatement sectors to reflect the inputs and benefits of abatement. Frontier analysis ensures policy scenarios are assessed under the same technical efficiency benchmark, while input–output analysis depicts the wide range of economic transactions among sectors of an economy. Four scenarios are considered in this study, which are increasing specific tax rates of SO₂, NO_x, and soot and dust separately and increasing all three tax rates simultaneously. Our estimation results show that: raising tax rates of SO₂, NO_x, and soot and dust simultaneously would have the highest emission reduction effects, with the SO₂ tax rate making the greatest contribution to emission reduction. Raising the soot and dust tax rate is the most environmentally friendly strategy due to its highest abatement to welfare through avoided health costs. The combination of frontier analysis and input–output analysis provides policy makers a comprehensive and sectoral approach to assess costs and benefits of environmental taxation.     

Role of tyrosine hot‐spot residues at the interface of colicin E9 and immunity protein 9: A comparative free energy simulation study

The endonuclease activity of the bacterial colicin 9 enzyme is controlled by the specific and high‐affinity binding of immunity protein 9 (Im9). Molecular dynamics simulation studies in explicit solvent were used to investigate the free energy change associated with the mutation of two hot‐spot interface residues [tyrosine (Tyr): Tyr54 and Tyr55] of Im9 to Ala. In addition, the effect of several other mutations (Leu33Ala, Leu52Ala, Val34Ala, Val37Ala, Ser48Ala, and Ile53Ala) with smaller influence on binding affinity was also studied. Good qualitative agreement of calculated free energy changes and experimental data on binding affinity of the mutations was observed. The simulation studies can help to elucidate the molecular details on how the mutations influence protein–protein binding affinity. The role of solvent and conformational flexibility of the partner proteins was studied by comparing the results in the presence or absence of solvent and with or without positional restraints. Restriction of the conformational mobility of protein partners resulted in significant changes of the calculated free energies but of similar magnitude for isolated Im9 and for the complex and therefore in only modest changes of binding free energy differences. Although the overall binding free energy change was similar for the two Tyr–Ala mutations, the physical origin appeared to be different with solvation changes contributing significantly to the Tyr55Ala mutation and to a loss of direct protein–protein interactions dominating the free energy change due to the Tyr54Ala mutation. Proteins 2013. © 2012 Wiley Periodicals, Inc.     

Structural insight for the roles of fas death domain binding to fadd and oligomerization degree of the fas–fadd complex in the death‐inducing signaling complex formation: A computational study

Fas binding to Fas‐associated death domain (FADD) activates FADD–caspase‐8 binding to form death‐inducing signaling complex (DISC) that triggers apoptosis. The Fas–Fas association exists primarily as dimer in the Fas–FADD complex, and the Fas–FADD tetramer complexes have the tendency to form higher order oligomer. The importance of the oligomerized Fas–FADD complex in DISC formation has been confirmed. This study sought to provide structural insight for the roles of Fas death domain (Fas DD) binding to FADD and the oligomerization of Fas DD–FADD complex in activating FADD–procaspase‐8 binding. Results show Fas DD binding to FADD stabilized the FADD conformation, including the increased stability of the critical residues in FADD death effector domain (FADD DED) for FADD–procaspase‐8 binding. Fas DD binding to FADD resulted in the decreased degree of both correlated and anticorrelated motion of the residues in FADD and caused the reversed correlated motion between FADD DED and FADD death domain (FADD DD). The exposure of procaspase‐8 binding residues in FADD that allows FADD to interact with procaspase‐8 was observed with Fas DD binding to FADD. We also observed different degrees of conformational and motion changes of FADD in the Fas DD–FADD complex with different degrees of oligomerization. The increased conformational stability and the decreased degree of correlated motion of the residues in FADD in Fas DD–FADD tetramer complex were observed compared to those in Fas DD–FADD dimer complex. This study provides structural evidence for the roles of Fas DD binding to FADD and the oligomerization degree of Fas DD–FADD complex in DISC formation to signal apoptosis. Proteins 2013. © 2012 Wiley Periodicals, Inc.     

Large scale conformational transitions in β‐structural motif of gramicidin A: kinetic analysis based on CD and FT‐IR data

Gramicidin A (gA) is a polypeptide antibiotic, which forms dimeric channels specific for monovalent cations in artificial and biological membranes. It is a polymorphic molecule that adopts a unique variety of helical conformations, including antiparallel double‐stranded ↑↓β5.6 or ↑↓β7.2 helices (number of residues per turn) and a single‐stranded β6.3 helix (the ‘channel form’). The behavior of gA‐Cs⁺ complex in the micelles of TX‐100 was studied in this work. Transfer of the complex into the micelles activates a cascade of sequential conformational transitions monitored by CD and FT‐IR spectroscopy: At the first step after Cs⁺ removal, the RH ↑↓β5.6 helix is formed, which has been discussed so far only hypothetically. Kinetics of the transitions was measured, and the activation parameters were determined. The activation energies of the ↑↓β5.6 → β‐helical monomer transition in dioxane and dioxane/water solutions were also measured for comparison. The presence of water raises the transition rate constant ~10³ times but does not lead to crucial fall of the activation energy. All activation energies were found in the 20–25 kcal/mol range, i.e. much lower than would be expected for unwinding of the double helix (when 28 H‐bonds are broken simultaneously). These results can be accounted for in the light of local unfolding (or ‘cracking’) model for large scale conformational transitions developed by the P. G.Wolynes team [Miyashita O, Onuchic JN, Wolynes PG. Proc. Natl. Acad. Sci. USA 2003; 100: 12570‐12575.]. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd.     

A method for reverse interactome analysis: High‐resolution mapping of interdomain interaction network in Dam1 complex and its specific disorganization based on the interaction domain expression

An experimental methodology that facilitates functional analysis of numerous protein–protein interactions, which have been found in genome‐wide interactome researches, has long been awaited. We propose herein an antagonistic inhibition‐based approach. The antagonizing polypeptide is generated in the course of interaction domain mapping based on yeast 2‐hybrid (Y2H) screening coupled with in vitro convergence of the Y2H‐selected fragments, which is performed in a formatted procedure. Using the coupled methodology, we first performed a high‐resolution mapping of an interdomain interaction network within budding yeast's Dam1 complex. Dam1 complex is a kinetochore protein complex composed of 10 essential subunits including Spc34p and Spc19p. The high‐resolution mapping revealed the overall network structure within the complex for the first time: Dam1 components form into two separated subnetworks on N‐terminal scaffolding domains of Spc34p and Spc19p, and the coiled‐coil interaction in their C‐terminal domains connects the subnetworks. Secondly, we show that the domain fragments converged in the high‐resolution mapping acted as potent inhibitors for the endogenous interactions when episomally overexpressed. The in vivo Dam1 interaction targeting with the fragments conferred a similar phenotype on the host cells; a critical and irreversible damage, which was accompanied with disturbed budding and chromosome mis‐segregation as a result of disorganized spindle. These phenotypes were strongly related to the cellular function of the Dam1 complex. The results and approach we demonstrated herein not only shed light on the Dam1 molecular architecture but also pave the road to reverse‐interactome analysis and discoveries of novel drugs that target disease‐related protein–protein interactions. © 2010 American Institute of Chemical Engineers Biotechnol. Prog., 2010     

Contrasting responses to Pleistocene climate changes: a case study of two sister species Allium cyathophorum and A. spicata (Amaryllidaceae) distributed in the eastern and western Qinghai–Tibet Plateau

It has been hypothesized that species occurring in the eastern and the western Qinghai–Tibet Plateau (QTP) responded differently to climate changes during the Pleistocene. Here, we test this hypothesis by phylogeographic analysis of two sister species, Allium cyathophorum and A. spicata. We sequenced two chloroplast DNA (cpDNA) fragments (accD‐psaI and the rpl16 intron) of 150 individuals, and the nuclear (ITS) region of 114 individuals, from 19 populations throughout the distributional ranges of these species. The divergence between the two species was dated at 779 ‐ 714 thousand years before the present and was likely initiated by the most major glaciation in the QTP. Analysis of chlorotype diversity showed that A. spicata, the species occurring in the western QTP, contains much lower genetic diversity (0.25) than A. cyathophorum (0.93), which is distributed in the eastern QTP. Moreover, multiple independent tests suggested that the A. spicata population had expanded recently, while no such expansion was detected in A. cyathophorum, indicating a contrasting pattern of responses to Pleistocene climate changes. These findings highlight the importance of geographical topography in determining how species responded to the climate changes that took place in the QTP during the Pleistocene.     

Spatial sampling bias and model complexity in stream‐based species distribution models: A case study of Paddlefish (Polyodon spathula) in the Arkansas River basin,USA

Leveraging existing presence records and geospatial datasets, species distribution modeling has been widely applied to informing species conservation and restoration efforts. Maxent is one of the most popular modeling algorithms, yet recent research has demonstrated Maxent models are vulnerable to prediction errors related to spatial sampling bias and model complexity. Despite elevated rates of biodiversity imperilment in stream ecosystems, the application of Maxent models to stream networks has lagged, as has the availability of tools to address potential sources of error and calculate model evaluation metrics when modeling in nonraster environments (such as stream networks). Herein, we use Maxent and customized R code to estimate the potential distribution of paddlefish (Polyodon spathula) at a stream‐segment level within the Arkansas River basin, USA, while accounting for potential spatial sampling bias and model complexity. Filtering the presence data appeared to adequately remove an eastward, large‐river sampling bias that was evident within the unfiltered presence dataset. In particular, our novel riverscape filter provided a repeatable means of obtaining a relatively even coverage of presence data among watersheds and streams of varying sizes. The greatest differences in estimated distributions were observed among models constructed with default versus AIC_C‐selected parameterization. Although all models had similarly high performance and evaluation metrics, the AIC_C‐selected models were more inclusive of westward‐situated and smaller, headwater streams. Overall, our results solidified the importance of accounting for model complexity and spatial sampling bias in SDMs constructed within stream networks and provided a roadmap for future paddlefish restoration efforts in the study area.