What happens below the canopy? Direct and indirect influences of the dominant species on forest vertical layers

Temperate forests are one of the most important ecosystems in the world, and thus disentangling the factors that drive diversity within these ecosystems is of major concern. However, due to the complex interactions among forests layers, topography and soil factors, discovering the drivers of diversity is often complicated. In this study, we tested three a priori hypotheses about the effect of the dominant competitor (Pinus koraiensis) on the different forest layers in a 25 ha full mapped plot of temperate forest in the Changbai Mountain of northeastern China. Structural equation modelling (SEM) was used to study the direct and indirect interactions between four vertical forest layers (dominant competitor, canopy composition, sub‐canopy diversity and shrub diversity), topographic factors, edaphic factors to discover sub‐canopy and shrub diversity drivers. Our results suggest that the dominant competitor (Pinus koraiensis) is a key factor explaining canopy variation, and sub‐canopy diversity and shrub diversity, and that this competitor can act directly (through shading) and indirectly (through the modification of the soil). Topographic heterogeneity also had significant effects on the soil variation and the diversity of the sub‐canopy and shrub layers. Finally our results indicate that the influence of canopy composition on the diversity of the rest of forest layers is indirect and positive, suggesting that the dominant competitor is the main factor limiting diversity. In conclusion, we have found strong evidence that the dominant species of the canopy can influence, both directly and indirectly, the diversity of the different vertical forest layers. Patterns of diversity in forests are driven by a multiplicity of factors that are inherently related.     

What influences the worldwide genetic structure of sperm whales (Physeter macrocephalus)?

The interplay of natural selection and genetic drift, influenced by geographic isolation, mating systems and population size, determines patterns of genetic diversity within species. The sperm whale provides an interesting example of a long‐lived species with few geographic barriers to dispersal. Worldwide mtDNA diversity is relatively low, but highly structured among geographic regions and social groups, attributed to female philopatry. However, it is unclear whether this female philopatry is due to geographic regions or social groups, or how this might vary on a worldwide scale. To answer these questions, we combined mtDNA information for 1091 previously published samples with 542 newly obtained DNA profiles (394‐bp mtDNA, sex, 13 microsatellites) including the previously unsampled Indian Ocean, and social group information for 541 individuals. We found low mtDNA diversity (π = 0.430%) reflecting an expansion event <80 000 years bp, but strong differentiation by ocean, among regions within some oceans, and among social groups. In comparison, microsatellite differentiation was low at all levels, presumably due to male‐mediated gene flow. A hierarchical amova showed that regions were important for explaining mtDNA variance in the Indian Ocean, but not Pacific, with social group sampling in the Atlantic too limited to include in analyses. Social groups were important in partitioning mtDNA and microsatellite variance within both oceans. Therefore, both geographic philopatry and social philopatry influence genetic structure in the sperm whale, but their relative importance differs by sex and ocean, reflecting breeding behaviour, geographic features and perhaps a more recent origin of sperm whales in the Pacific. By investigating the interplay of evolutionary forces operating at different temporal and geographic scales, we show that sperm whales are perhaps a unique example of a worldwide population expansion followed by rapid assortment due to female social organization.     

Are phylogenies resolved at the genus level appropriate for studies on phylogenetic structure of species assemblages?

Phylogenies are essential to studies investigating the effect of evolutionary history on assembly of species in ecological communities and geographical and ecological patterns of phylogenetic structure of species assemblages. Because phylogenies well resolved at the species level are lacking for many major groups of organisms such as vascular plants, researchers often generate a species-level phylogenies using a phylogeny well resolved at the genus level as a backbone and attaching species to their respective genera in the phylogeny as polytomies or by using a megaphylogeny well resolved at the genus level as a backbone and adding additional species to the megaphylogeny as polytomies of their respective genera. However, whether the result of a study using species-level phylogenies generated in these ways is robust, compared to that based on phylogenies fully resolved at the species level, has not been assessed. Here, we use 1093 angiosperm tree assemblages (each in a 110 × 110 km quadrat) in North America as a model system to address this question, by examining six commonly used metrics of phylogenetic structure (phylogenetic diversity and phylogenetic relatedness) and six climate variables commonly used in ecology. Our results showed that (1) the scores of phylogenetic metrics derived from species-level phylogenies resolved at the genus level with species being attached to their respective genera as polytomies are very strongly or perfectly correlated to those derived from a phylogeny fully resolved at the species level (the mean of correlation coefficients is 0.973), and (2) the relationships between the scores of phylogenetic metrics and climate variables are consistent between the two sets of analyses based on the two types of phylogeny. Our study suggests that using species-level phylogenies resolved at the genus level with species being attached to their genera as polytomies is appropriate in studies exploring patterns of phylogenetic structure of species in ecological communities across geographical and ecological gradients.     

What controls the distribution of tropical forest and savanna?

Forest and savanna biomes dominate the tropics, yet factors controlling their distribution remain poorly understood. Climate is clearly important, but extensive savannas in some high rainfall areas suggest a decoupling of climate and vegetation. In some situations edaphic factors are important, with forest often associated with high nutrient availability. Fire also plays a key role in limiting forest, with fire exclusion often causing a switch from savanna to forest. These observations can be captured by a broad conceptual model with two components: (1) forest and savanna are alternative stable states, maintained by tree cover-fire feedbacks, (2) the interaction between tree growth rates and fire frequency limits forest development; any factor that increases growth (e.g. elevated availability of water, nutrients, CO(2)), or decreases fire frequency, will favour canopy closure. This model is consistent with the range of environmental variables correlated with forest distribution, and with the current trend of forest expansion, likely driven by increasing CO(2) concentrations. Resolving the drivers of forest and savanna distribution has moved beyond simple correlative studies that are unlikely to establish ultimate causation. Experiments using Dynamic Global Vegetation Models, parameterised with measurements from each continent, provide an important tool for understanding the controls of these systems.     

Are the assemblages of tree pollination modes being recovered by tropical forest restoration?

Questions

Do the assemblages of pollination modes in restored (tree plantings) and secondary (naturally regenerated) forests change in comparison to primary forests, and how do these assemblages relate to species turnover at regional scale?

Location

Southeast region of Brazil.

Methods

We classified tree species found in a total of 40 forest sites (18 primary, 11 restored, 11 secondary) according to pollination mode, based on the literature. We calculated and compared functional dissimilarity distances, amounts of species and accumulated abundance of pollination modes, and functional indices of richness and evenness between forest types.

Results

Functional dissimilarity distances were much smaller than species dissimilarity distances within forest types (mean <20%, >80%, respectively), indicating a small variation in pollination modes between sites. Functional indices of richness and evenness did not differ between forest types. However, significant changes were found in the species and abundance proportions of several pollination modes. Primary forests were characterized by the predominance of generalized insect‐pollinated species, followed by secondary proportions of bee, wind and moth pollination; other pollination modes were underrepresented. In restored forests, reductions were found in generalized insect, moth, wind, fly, pollen‐consuming insect and very‐small insect pollination, whereas the species pollinated by bees and bats more than doubled. Smaller changes were found among secondary forests, including reductions in moth, fly and fig‐wasp pollination, whereas there were incremental changes in bee, beetle, big animal and small insect pollination.

Conclusions

Our results indicate a rather stable assemblage of pollination modes and also high ecological redundancy among trees regardless of the species replacement at the regional scale. Major changes among restored forests are probably in response to larger disturbance effects and/or restoration practices conducted in these sites. In contrast, smaller changes among secondary forests could be in response to smaller disturbance effects and natural selection processes, and also seem to suggest that highly resilient degraded areas are more likely to recuperate their functional diversity through natural regeneration alone. In both cases, however, efforts to recover such patterns should be encouraged to avoid possible negative effects in plant–pollinator interactions.     

What is the real crystallographic structure of the L photointermediate of bacteriorhodopsin?

In the last few years, three laboratories have reported three entirely different crystallographic models for the L photointermediate of bacteriorhodopsin. All are from X-ray diffraction of illuminated crystals that contain L in photostationary states created at similar cryogenic temperatures. This article compares the models and their implications, the crystallographic statistics and the methods used to derive them, as well as their agreement with non-crystallographic information.     

What governs the functional diversity patterns of fishes in the headwater streams of the humid forest enclaves: environmental conditions,taxonomic diversity or biotic interactions?

The relationship between functional and taxonomic diversity is a major issue in ecology. Biodiversity in aquatic environments is strongly influenced by environmental gradients that act as dispersion and niche barriers. Environmental conditions act as filters to select functional traits, but biotic interactions also play a role in assemblage structure. In headwater streams, the relationship between functional and taxonomic diversity remains unclear. In this study we investigated how environmental conditions, taxonomic diversity and biotic interactions influence the spatial distribution of traits and functional diversity in stream fish species. Standardized sampling of fish species was carried out in 50 m sections of 16 streams located in rainforest enclaves in a semiarid region of Brazil (Caatinga biome). The functional diversity indices displayed different responses to the predictor variables used. Functional richness was mainly influenced by environmental conditions, while functional evenness was mostly determined by taxonomic diversity. On the other hand, functional dispersion was explained by a combination of environmental conditions and taxonomic diversity. The spatial distribution of fish species with the same functional traits was random, indicating that biotic interactions are not a strong predictor in these ecosystems. Channel width, pH and substrate were the most important variables in the spatial distribution of the functional traits of the fish species. Our results suggest that the functional structure of fish assemblages in headwater streams depends mainly on environmental conditions and taxonomic diversity.     

Do isolation and local habitat jointly limit the structure of stream invertebrate assemblages?

1. Both local and regional processes simultaneously control species assemblages depending on spatial habitat configuration. In dendritic networks like streams, the unique spatial arrangement of habitats produces various combinations of local habitat size and isolation. Stream invertebrate assemblages could therefore be controlled by different combinations of local and regional processes, depending on their location in the network. 2. Using quantile regression, we investigated how local habitat size, local environmental conditions and spatial isolation influenced variation in assemblage composition. Adult Trichoptera and benthic macroinvertebrate assemblages were represented by non‐metric multidimensional scaling (NMDS) ordination scores, as were local environmental conditions, in four headwater stream networks in New Zealand. 3. With increasing local habitat size, there was a decrease in variation in assemblage composition (NMDS scores) of both adult Trichoptera and benthic macroinvertebrates. This relationship between habitat size and assemblage variation was related to local habitat conditions at the upper limit of assemblage variability and spatial isolation at the lower limit of assemblage variability, for both adult Trichoptera and benthic assemblages, indicating joint local and regional controls on stream invertebrate assemblages. 4. The relationships between local assemblages and their neighbours, based on community similarity scores, differed between benthic macroinvertebrates and adult Trichoptera. For benthic assemblages, the larger the stream, the more similar assemblages were to neighbouring assemblages, whereas there was no consistent relationship between assemblage similarity and stream size for adult Trichoptera. This difference in structuring could be attributed to contrasting spatial influences linked to the different dispersal modes of adults and larvae. However, because adult and benthic assemblages are not independent, the influence of life stage on spatial distribution is difficult to determine (i.e. it is essentially a ‘chicken and egg’ argument). 5. Overall, our approach using quantile regression to evaluate limit responses, rather than regressions on means, has highlighted the joint importance of local habitat and spatial processes in structuring stream invertebrate assemblages. Furthermore, we have provided evidence for the importance of the spatial network arrangement and interactions between life stages and dispersal processes, in structuring stream assemblages.     

What is the shape of the distribution of protein conformations at equilibrium?

According to the thermodynamic hypothesis, the native state of proteins is that in which the free energy of the system is at its lowest, so that at normal temperature and pressure, proteins evolve to that state. We selected four proteins representative of each of the four classes, and for each protein make four simulations, one starting from the native structure and the other three starting from the structure obtained by threading the sequence of one protein onto the native backbone fold of the other three proteins. Because of their large conformational distances with respect to the native structure, the three alternative initial structures cannot be considered as local minima within the native ensemble of the corresponding protein. As expected, the initial native states are preserved in the .5?μs simulations performed here and validate the simulations. On the other hand, when the initial state is not native, an analysis of the trajectories does not reveal any evolution towards the native state, during that time. These results indicate that the distribution of protein conformations is multipeak shaped, so that apart from the peak corresponding to the native state, there are other peaks associated with average structures that are very different from the native and that can last as long as the native state.     

What causes population cycles of forest Lepidoptera?

Hypotheses for the causes of regular cycles in populations of forest Lepidoptera have invoked pathogen-insect or foliage-insect interactions. However, the available data suggest that forest caterpillar cycles are more likely to be the result of interactions with insect parasitoids, an old argument that seems to have been neglected in recent years.     

Evaluating detectability of freshwater fish assemblages in tropical streams: Is hand-seining sufficient?

Unprecedented threats to natural ecosystems mean that accurate quantification of biodiversity is a priority, particularly in the tropics which are underrepresented in monitoring schemes. Data from a freshwater fish assemblage in Trinidad were used to evaluate the effectiveness of hand-seining as a survey method in tropical streams. We uncovered large differences in species detectability when hand-seining was used alone, in comparison with when hand-seining and electrofishing were used together. The addition of electrofishing increased the number of individuals caught threefold, and increased the biomass fivefold. Some species were never detected using hand-seining, resulting in significant underestimates of species richness; rarefaction curves suggest that even when hand-seining effort increases, species richness is still underestimated. Diversity indices (Shannon and Simpson index) reveal that diversity was also significantly lower for hand-seined samples. Furthermore, the results of multivariate analyses investigating assemblage structure also differed significantly depending on whether they were based on hand-seined data alone, or a combination of hand-seining and electrofishing. Despite the extra equipment and maintenance required, these findings underline the value of including electrofishing when sampling tropical freshwater streams.     

What shapes cerambycid beetle communities in a tropical forest mosaic? Assessing the effects of host tree identity,forest structure,and vertical stratification

Due to anthropogenic activities, tropical rain forests face many challenges in sustaining biodiversity and maintaining global climates. This study explores how forest successional stage, tree composition, and stratum affect communities of saproxylic cerambycid beetles—concealed feeders that play important roles in forest nutrient cycling. Forty trees in five families (Fabaceae, Lecythidaceae, Malvaceae, Moraceae, and Sapotaceae) were sampled in a mosaic of old‐growth and secondary forest on the Osa Peninsula, Costa Rica. Bait branches yielded 3549 cerambycid individuals in 49 species. Species richness was almost identical in old‐growth and secondary forest, and both yielded specialists, but abundance was higher in old‐growth forest. Overall community structure was most strongly influenced by host plant species; within most plant families it was also impacted by forest successional status. Moraceae was the exception, presumably because the focal tree species was abundant in both old‐growth and secondary forest. Several host and old‐growth specialist species reached high densities within patches of old‐growth forest, but seldom colonized apparently suitable trees within secondary forest. This suggests that even small areas of old‐growth forest can act as refuges, but that secondary forest may act as a barrier to dispersal. The vulnerability of specialized saproxylic insects to land use change will be linked to the ability of their preferred hosts to disperse to and persist in successional habitats; rearing studies may provide the most accurate method to monitor community changes over time.     

Spider diversity in epiphytes: Can shade coffee plantations promote the conservation of cloud forest assemblages?

Cloud forests (CF) are disappearing due to anthropogenic causes such as cultivation. A characteristic feature of the CF is that a high proportion of its biomass occurs in the form of epiphytes, which are vital microhabitats to canopy dwelling arthropods. Coffee plantations overlap with CF and replace them. Epiphytes are abundant in shade coffee (SC) plantations and therefore these plants are an appropriate background for comparing the diversity between these systems. Spiders are understudied in canopies, and since they are major predators and their communities are highly sensitive to environmental changes, they can be used to test the similarity between habitats. We conducted a diversity assay of spiders living in epiphytes in cloud forest fragments and SC plantations, to test the hypothesis that SC plantations function as refugia. We manually sampled epiphytes within the canopy of two coffee plantations and two fragments of cloud forest in central Veracruz, Mexico. Our results show that SC plantations account for higher spider abundance and species richness than cloud forest fragments, there is little overlap between the species found in both systems, and the range of distribution and the guild structure of the spider assemblages between both systems is similar. As there were no significant differences between cloud forest fragments and SC plantations in terms of spider species assemblages, species distribution and guild structure the epiphytes from the SC plantations can be consider a refuge for the spider fauna from the surrounding cloud forest fragments. Epiphyte load and tree height are important factors driving the differentiation at community level, between sites and habitats. Bromeliads harbored more spiders than the other types of epiphytes, and since these plants are frequently removed by farmers or extracted for commercial and religious purposes, we suggest that preserving epiphytes in coffee plantations and cloud forest fragments could aid in the conservation of spiders.     

Can differences in the structure of larval,juvenile and adult coral‐reef fish assemblages be detected at the family level?

Processes occurring at the end of the larval stage are of major importance in shaping spatial structure of fish assemblages in coral reefs. However, because of the difficulty in identifying larvae to species, many studies dealing with these stages are limited to the family level. It remains unknown if variation in the spatial structure of coral‐reef fish assemblages across life stages can be detected at such a coarse taxonomic level. Two different surveys conducted in a similar area of New Caledonia, Southwest Pacific, provided the opportunity to compare the structure of coral‐reef fish assemblages collected as pre‐settlement larvae, juveniles and adults along a coast to barrier reef gradient. Adult and juvenile fish were sampled using underwater visual counts (UVC) during the warm seasons of 2004 and 2005. Pre‐settlement larvae were sampled with light‐traps during the same seasons. In order to standardize data between sampling methods, analyses were conducted on the relative abundance (for larvae) and density (for juveniles and adults) of 21 families commonly collected with both methods. Relative abundances/densities of families were analysed as a function of life stage (larvae, juveniles or adults), large‐scale spatial location (coast, lagoon or barrier) and years (2004, 2005) using non‐parametric multidimensional scaling (nMDS) and permutational multivariate analysis of variance (permanova ). Kruskal–Wallis tests were then used to examine differences among life stages and locations for individual families. Different levels of spatial and temporal variability characterized fish assemblages from different life stages, and differences among life stages were detected at all locations and years. Differences among life stages were also significant at the level of individual families. Overall results indicate that studies conducted at the family level may efficiently reveal changes in coral‐reef fish spatial structure among successive life stages when large spatial scales are considered.     

Visualization of the interactome: What are we looking at?

Network visualization of the interactome has been become routine in systems biology research. Not only does it serve as an illustration on the cellular organization of protein-protein interactions, it also serves as a biological context for gaining insights from high-throughput data. However, the challenges to produce an effective visualization have been great owing to the fact that the scale, biological context and dynamics of any given interactome are too large and complex to be captured by a single visualization. Visualization design therefore requires a pragmatic trade-off between capturing biological concept and being comprehensible. In this review, we focus on the biological interpretation of different network visualizations. We will draw on examples predominantly from our experiences but elaborate them in the context of the broader field. A rich variety of networks will be introduced including interactomes and the complexome in 2D, interactomes in 2.5D and 3D and dynamic networks.     

Does environmental disturbance also influence within-stream beta diversity of macroinvertebrate assemblages in tropical streams?

Riparian deforestation is a major threat to the ecological integrity of streams and aquatic biodiversity, influencing microhabitat availability and susceptibility to disturbances. Here we tested if riparian deforestation of tropical streams influenced beta diversity of macroinvertebrate assemblages, by comparing indices that weighted differentially rare and dominant taxa, and testing if nestedness in community composition increased in deforested streams. Within-stream beta diversity was higher in deforested than forested streams, mainly due to taxon loss and higher dominance. In disturbed streams, higher sedimentation in pool mesohabitats resulted in larger differences in community composition, whereas mesohabitats in forested streams were more stable.     

Does microhabitat structure affect foliar mite assemblages?

1. Habitat structure is an important factor influencing population dynamics and trophic organisation of terrestrial invertebrates. The phylloplane zone on vascular plant leaves is topographically complex, containing a multitude of microhabitats such as leaf hairs, lesions, and structural refugia such as domatia, which may modify interactions between resident invertebrate communities, colonisers, and subsequent trophic relationships. Leaf domatia are small indentations on the underside of leaves and are often inhabited by potentially beneficial mites and other arthropods. 2. This study investigated the relationship between domatia availability and foliar mite assemblages in contrasting habitats (native forest, plantation forest, and pasture) using a standard test plant (the endemic New Zealand shrub Coprosma lucida, J.R. & G. Forst.). 3. Diverse woody native vegetation types supported higher numbers of mite species than either plantation forest or pastoral grasses. The highest number of mite species occurred in the native forest (63%), plantation forest (38%), and pastoral grasses (25%). In the native vegetation type, experimental C. lucida leaves with domatia supported higher mite densities, greater colonisation success, and more diverse mite assemblages than those without domatia. Mite assemblages within the pastoral site were significantly different from the other two vegetation types. Only one fungivorous mite species, Orthotydeus californicus, occurred compared to five mite species in native and plantation forests. 4. This study indicated that foliar mite assemblages in native vegetation on experimental C. lucida shrubs are influenced by domatia availability, resident foliar mites, and local mite assemblages.     

What is the function of receptor and membrane endocytosis at the postsynaptic neuron?

This paper explores the implications of certain new developments in cell biology upon neuroscience. Until recently it was thought that neurotransmitters and neuromodulators had only one function, which was to stimulate their specific receptors at the cell surface. From here on, all activity was supposed to be effected by postsynaptic cascades. The discovery that membrane components, particularly G-protein-linked receptors, are not static but are subject to a massive and complex process of continual endocytosis, processing in the endosome system and recycling back to the external membrane, raises the question of its functional significance. In addition, it has been found that many neuromodulators such as polypeptides have their main locus of action inside the postsynaptic neuron. This review covers the role of the endocytic mechanism on receptor desensitization and resensitization, synaptic reorganization and plasticity synaptic scaling and the possible repair of oxidative damage. The possible involvement of this system in Alzheimer's disease is discussed.