Topological effects of network structure on long‐term social network dynamics in a wild mammal

Social structure influences ecological processes such as dispersal and invasion, and affects survival and reproductive success. Recent studies have used static snapshots of social networks, thus neglecting their temporal dynamics, and focused primarily on a limited number of variables that might be affecting social structure. Here, instead we modelled effects of multiple predictors of social network dynamics in the spotted hyena, using observational data collected during 20 years of continuous field research in Kenya. We tested the hypothesis that the current state of the social network affects its long‐term dynamics. We employed stochastic agent‐based models that allowed us to estimate the contribution of multiple factors to network changes. After controlling for environmental and individual effects, we found that network density and individual centrality affected network dynamics, but that social bond transitivity consistently had the strongest effects. Our results emphasise the significance of structural properties of networks in shaping social dynamics.     

A specific role for Arabidopsis TRAPPII in post-Golgi trafficking that is crucial for cytokinesis and cell polarity

Cytokinesis and cell polarity are supported by membrane trafficking from the trans-Golgi network (TGN), but the molecular mechanisms that promote membrane trafficking from the TGN are poorly defined in plant cells. Here we show that TRAPPII in Arabidopsis regulates the post-Golgi trafficking that is crucial for assembly of the cell plate and cell polarity. Disruptions of AtTRS120 or AtTRS130, two genes encoding two key subunits of TRAPPII, result in defective cytokinesis and cell polarity in embryogenesis and seedling development. In attrs120 and attrs130, the organization and trafficking in the endoplasmic reticulum (ER)-Golgi interface are normal. However, post-Golgi trafficking to the cell plate and to the cell wall, but not to the vacuole, is impaired. Furthermore, TRAPPII is required for the selective transport of PIN2, but not PIN1, to the plasma membrane. We revealed that AtTRS130 is co-localized with RAB-A1c. Expression of constitutively active RAB-A1c partially rescues attrs130. RAB-A1c, which resides at the TGN, is delocalized to the cytosol in attrs130. We propose that TRAPPII in Arabidopsis acts upstream of Rab-A GTPases in post-Golgi membrane trafficking in plant cells.     

Triggering dissymmetry in achiral dye molecules by chiral solvents: Circular dichroism experiments and DFT calculations

The electronic circular dichroism spectra of achiral product “Lumogen F Red” (ROT‐300) in four different chiral solvents are recorded at different temperatures. DFT calculations allow to identify two enantiomeric conformers for ROT‐300. In vacuo they are equally populated; in chiral solvents one enantiomer prevails. Thermodynamic quantities involved in the chiral preference are derived. Chirality, 2011. © 2011 Wiley‐Liss, Inc.     

Decoding the genome beyond sequencing: the new phase of genomic research

While our understanding of gene-based biology has greatly improved, it is clear that the function of the genome and most diseases cannot be fully explained by genes and other regulatory elements. Genes and the genome represent distinct levels of genetic organization with their own coding systems; Genes code parts like protein and RNA, but the genome codes the structure of genetic networks, which are defined by the whole set of genes, chromosomes and their topological interactions within a cell. Accordingly, the genetic code of DNA offers limited understanding of genome functions. In this perspective, we introduce the genome theory which calls for the departure of gene-centric genomic research. To make this transition for the next phase of genomic research, it is essential to acknowledge the importance of new genome-based biological concepts and to establish new technology platforms to decode the genome beyond sequencing.     

Effects of the landscape on boreal toad gene flow: does the pattern–process relationship hold true across distinct landscapes at the northern range margin?

Understanding the impact of natural and anthropogenic landscape features on population connectivity is a major goal in evolutionary ecology and conservation. Discovery of dispersal barriers is important for predicting population responses to landscape and environmental changes, particularly for populations at geographic range margins. We used a landscape genetics approach to quantify the effects of landscape features on gene flow and connectivity of boreal toad (Bufo boreas) populations from two distinct landscapes in south-east Alaska (Admiralty Island, ANM, and the Chilkat River Valley, CRV). We used two common methodologies for calculating resistance distances in landscape genetics studies (resistance based on least-cost paths and circuit theory). We found a strong effect of saltwater on genetic distance of CRV populations, but no landscape effects were found for the ANM populations. Our discordant results show the importance of examining multiple landscapes that differ in the variability of their features, to maximize detectability of underlying processes and allow results to be broadly applicable across regions. Saltwater serves as a physiological barrier to boreal toad gene flow and affects populations on a small geographic scale, yet there appear to be few other barriers to toad dispersal in this intact northern region.     

Niche diversification follows key innovation in Antarctic fish radiation

Antarctic notothenioid fishes provide a fascinating evolutionary laboratory for the study of adaptive radiation, as their diversification is linked to both isolation in an extreme environment and a key innovation that allows them to exploit it. In this issue of Molecular Ecology, Rutschmann et al. (2011) evaluate how dietary niche differences have evolved in notothenioids: rarely, or repeatedly in multiple lineages. The authors use stable isotopes to measure species’ use of benthic vs. pelagic resources and map resource use onto a molecular phylogeny. Their findings indicate that pelagic diets have evolved in multiple lineages in at least two families, indicating that dietary niche diversification has occurred repeatedly and in parallel.     

Bats are able to maintain long-term social relationships despite the high fission-fusion dynamics of their groups

Elephants, dolphins, as well as some carnivores and primates maintain social links despite their frequent splitting and merging in groups of variable composition, a phenomenon known as fission-fusion. Information on the dynamics of social links and interactions among individuals is of high importance to the understanding of the evolution of animal sociality, including that of humans. However, detailed long-term data on such dynamics in wild mammals with fully known demography and kin structures are scarce. Applying a weighted network analysis on 20,500 individual roosting observations over 5 years, we show that in two wild Bechstein's bat colonies with high fission-fusion dynamics, individuals of different age, size, reproductive status and relatedness maintain long-term social relationships. In the larger colony, we detected two stable subunits, each comprising bats from several family lineages. Links between these subunits were mainly maintained by older bats and persisted over all years. Moreover, we show that the full details of the social structure become apparent only when large datasets are used. The stable multi-level social structures in Bechstein's bat colonies resemble that of elephants, dolphins and some primates. Our findings thus may shed new light on the link between social complexity and social cognition in mammals.     

An ANN-GA model based promoter prediction in Arabidopsis thaliana using tilling microarray data

Identification of promoter region is an important part of gene annotation. Identification of promoters in eukaryotes is important as promoters modulate various metabolic functions and cellular stress responses. In this work, a novel approach utilizing intensity values of tilling microarray data for a model eukaryotic plant Arabidopsis thaliana, was used to specify promoter region from non-promoter region. A feed-forward back propagation neural network model supported by genetic algorithm was employed to predict the class of data with a window size of 41. A dataset comprising of 2992 data vectors representing both promoter and non-promoter regions, chosen randomly from probe intensity vectors for whole genome of Arabidopsis thaliana generated through tilling microarray technique was used. The classifier model shows prediction accuracy of 69.73% and 65.36% on training and validation sets, respectively. Further, a concept of distance based class membership was used to validate reliability of classifier, which showed promising results. The study shows the usability of micro-array probe intensities to predict the promoter regions in eukaryotic genomes.     

Determinants of age-dependent change in a secondary sexual character

Many secondary sexual characters vary in a systematic way with the age of individuals, with young and old individuals displaying at lower levels than individuals of intermediate age. Analyses quantifying the within-individual and among-individual components of phenotypic variation can help partition effects of phenotypic plasticity and selective mortality. We analysed phenotypic variation in the expression of a secondary sexual character, tail length, in male and female barn swallows Hirundo rustica from four European populations studied during 11-26 years, using linear mixed effect models to describe age-related expression. Tail length increased from yearlings to intermediate aged birds with a subsequent decrease at old age. In males, this age-related pattern was because of both within-subject and between-subject effects, with no difference among populations. Males having longer lifespan had shorter tails when young than those having shorter lifespan. Females showed similar patterns of age-related variation as males, with no difference among populations. The major difference between sexes was that the between-subject effects (i.e. disappearance effects or selection) were much more important for males compared to females for which lifetime variation in tail length was mainly because of a within-subject effect (i.e., a plastic response). These findings suggest that whereas males trade greater expression of the secondary sexual character at young age against longevity, that was not the case for females. This is consistent with tail length being more costly in males than in females, with the cost of long tails potentially being offset by elevated mating success, whereas that is not the case in females.     

Multimodel inference in ecology and evolution: challenges and solutions

Information theoretic approaches and model averaging are increasing in popularity, but this approach can be difficult to apply to the realistic, complex models that typify many ecological and evolutionary analyses. This is especially true for those researchers without a formal background in information theory. Here, we highlight a number of practical obstacles to model averaging complex models. Although not meant to be an exhaustive review, we identify several important issues with tentative solutions where they exist (e.g. dealing with collinearity amongst predictors; how to compute model-averaged parameters) and highlight areas for future research where solutions are not clear (e.g. when to use random intercepts or slopes; which information criteria to use when random factors are involved). We also provide a worked example of a mixed model analysis of inbreeding depression in a wild population. By providing an overview of these issues, we hope that this approach will become more accessible to those investigating any process where multiple variables impact an evolutionary or ecological response.