How well do the existing and proposed reserve networks represent vertebrate species in Chile?

Increasingly, biogeographical knowledge and analysis are playing a fundamental role in assessing the representativeness of biodiversity in protected areas, and in identifying critical areas for conservation. With almost 20% of the country assigned to protected areas, Chile is well above the conservation target (i.e. 10–12%) proposed by many international conservation organizations. Moreover, the Chilean government has recently proposed new conservation priority sites to improve the current protected area network. Here, we used all 653 terrestrial vertebrate species present in continental Chile to assess the performance of the existing and proposed reserve networks. Using geographical information systems, we overlaid maps of species distribution, current protected areas, and proposed conservation priority sites to assess how well each species is represented within these networks. Additionally, we performed a systematic reserve selection procedure to identify alternative conservation areas for expanding the current reserve system. Our results show that over 13% of the species are not covered by any existing protected area, and that 73% of Chilean vertebrate species can be considered partial gaps, with only a small fraction of their geographical ranges currently under protection. The coverage is also deficient for endemic (species confined to Chile) and threatened species. While the proposed priority sites do increase coverage, we found that there are still several gaps and these are not the most efficient choices. Both the gap analysis and the reserve selection analysis identified important areas to be added to the existing reserve system, mostly in northern and central Chile. This study underscores the need for a systematic conservation planning approach to redefine the conservation priority sites in order to maximize the representation of species, particularly endemic and threatened species.     

How well do we understand the clusters found in microarray data?

We wished to quantify the state-of-the-art of our understanding of clusters in microarray data. To do this we systematically compared the clusters produced on sets of microarray data using a representative set of clustering algorithms (hierarchical, k-means, and a modified version of QT_CLUST) with the annotation schemes MIPS, GeneOntology and GenProtEC. We assumed that if a cluster reflected known biology its members would share related ontological annotations. This assumption is the basis of "guilt-by-association" and is commonly used to assign the putative function of proteins. To statistically measure the relationship between cluster and annotation we developed a new predictive discriminatory measure. We found that the clusters found in microarray data do not in general agree with functional annotation classes. Although many statistically significant relationships can be found, the majority of clusters are not related to known biology (as described in annotation ontologies). This implies that use of guilt-by-association is not supported by annotation ontologies. Depending on the estimate of the amount of noise in the data, our results suggest that bioinformatics has only codified a small proportion of the biological knowledge required to understand microarray data.     

How well do reduced models capture the dynamics in models of interacting neurons?

This paper introduces a class of stochastic models of interacting neurons with emergent dynamics similar to those seen in local cortical populations. Rigorous results on existence and uniqueness of nonequilibrium steady states are proved. These network models are then compared to very simple reduced models driven by the same mean excitatory and inhibitory currents. Discrepancies in firing rates between network and reduced models are investigated and explained by correlations in spiking, or partial synchronization, working in concert with “nonlinearities” in the time evolution of membrane potentials. The use of simple random walks and their first passage times to simulate fluctuations in neuronal membrane potentials and interspike times is also considered.

     

How do painters represent motion in garments? Graphic invariants across centuries

Western visual art has radically changed throughout the centuries: different techniques, interest in the representation of reality, and use of graphic signs. Indeed, only a few pictorial cues have retained the same meaning and use. These kinds of graphic invariants may play a key role not only in a comparative study of art history, but also for discovering underlying common perceptual mechanisms. Here the aim is to show that western painters use the same graphic solutions to represent motion in garments, across countries and centuries. A pilot experiment, using 160 paintings representative of all main western European art movements from the thirteenth to the twentieth century, shows that different artists represented the motion of garments with the same orientation, curvature and convergence of lines. Experiment 1 demonstrates, with a smaller sample of paintings (16, i.e. two per century) that the relationship between orientation, curvature and convergence of lines is a good predictor of perceived motion. Experiment 2 shows how the same garments, isolated from the context of the paintings, still give different dynamic impressions according to the same rules. Finally, Experiment 3 confirmed the same results, whilst patterns previously used are simplified to their geometrical structure. These results call for an underlying perceptual mechanism that specifically recognizes orientation, curvature and parallelism levels as cues of motion in a static pattern.     

Invertebrates in the canopy of tropical rain forests How much do we really know?

The current state of knowledge of canopy invertebrates in tropical rain forests is reviewed using data drawn, without bias toward taxon, collecting method or biogeographical region, from 89 studies concerned with mass-collecting (>1000 individuals). The review is intended to identify the most serious gaps and biases in the distribution of higher taxa among forest types and biogeographical regions. With respect to knowledge, biogeographical regions can be ranked as Neotropical > Australian > Oriental > Afrotropical. The canopy of lowland wet and subtropical forests has been studied in greater detail, whereas the canopy of lowland dry and montane forests is much less well known. Collecting techniques influence greatly the present knowledge of canopy invertebrates. Invertebrates other than arthropods, often abundant in epiphytic habitats, phytotelmata and perched litter, are virtually unknown. The abundance of several groups, such as Acari, Collembola and Isoptera, is almost certainly seriously underestimated. Densities of invertebrate individuals in the canopy of tropical rain forests appear to be lower than in temperate forests, although invertebrate abundance is dissipated by the high standing-biomass of rain forests. Coleoptera, particularly Staphylinidae, Curculionidae and Chrysomelidae, along with Hymenoptera, Lepidoptera and Araneae appear to be the most speciose taxa in the canopy, and it is probable that this reflects their range of feeding habits and exploitation of rain forests habitats. The distribution of individuals among the major arthropod orders and across the studies examined is complex and depends on many factors. The amount of variance that can be directly explained by biogeography, forest types (subtropical, wet, dry or montane), or collecting methods appears to be about 11%. The explained variance increases when considering major families of Coleoptera (28%) or subfamilies of Chrysomelidae (40%). In all cases, the variance explained by the type of forest is much higher than by that explained by biogeography. These conclusions are similar when considering various prey-predator relationships in the canopy. This suggests that, at the higher taxa level, the composition of the invertebrate fauna in the canopy may vary comparatively more across forest types than across biogeographical regions and this is discussed briefly from a conservation viewpoint.     

How much do we know about the breeding biology of bird species in the world?

Knowledge on species’ breeding biology is the building blocks of avian life history theory. A review for the current status of the knowledge at a global scale is needed to highlight the priority for future research. We collected all available information on three critical nesting parameters (clutch size, incubation period and nestling period) for the close to 10 000 bird species in the world and identified taxonomic, geographic and habitat gaps in the distribution of knowledge on avian breeding biology. The results show that only one third of all extant species are well known regarding the three nesting parameters analyzed, while the rest are partly or poorly known. Most data deficient taxonomic groups are tropical forest nesters, particularly from the Amazon basin, southeast Asia, Equatorial Africa and Madagascar – the places that harbor the world's highest bird diversity. These knowledge gaps could be hampering our understanding of avian life histories. Ornithologists are encouraged to pay more efforts to explore the breeding biology of those poorly‐known species.     

How do invasive species travel to and through urban environments?

Globalisation has resulted in the movement of organisms outside their natural range, often with negative ecological and economic consequences. As cities are hubs of anthropogenic activities, with both highly transformed and disturbed environments, these areas are often the first point of entry for alien species. We compiled a global database of cities with more than one million inhabitants that data had on alien species occurrence. We then identified the most prominent pathways of introduction and vectors of spread of alien species in these cities. Most species were intentionally introduced to cities and were released or escaped from confinement. The majority of alien species then spread within cities through natural means (primarily unaided dispersal). Pathway prominence varied across the taxonomic groups of alien species: the most prominent pathway for plants and vertebrates was the escape pathway; for invertebrates the stowaway and contaminant pathways were most likely to facilitate introductions. For some organisms, pathway prominence varied with the geographical and climatic characteristics of the city. The characteristics of the cities also influenced the prominence of vectors of spread for alien species. Preventing the natural spread of alien species within cities, and into adjacent natural environments will be, at best, difficult. To prevent invasions, both the intentional and unintentional introduction of potentially harmful alien species to cities must be prevented. The pathways of introduction and vectors of spread identified here should be prioritised for management.     

How do climate warming and species richness affect CO2 fluxes in experimental grasslands?

This paper presents the results of 2 yr of CO(2) flux measurements on grassland communities of varying species richness, exposed to either the current or a warmer climate. We grew experimental plant communities containing one, three or nine grassland species in 12 sunlit, climate-controlled chambers. Half of these chambers were exposed to ambient air temperatures, while the other half were warmed by 3 degrees C. Equal amounts of water were added to heated and unheated communities, implying drier soils if warming increased evapotranspiration. Three main CO(2) fluxes (gross photosynthesis, above-ground and below-ground respiration) were measured multiple times per year and reconstructed hourly or half-hourly by relating them to their most important environmental driver. While CO(2) outputs through respiration were largely unchanged under warming, CO(2) inputs through photosynthesis were lowered, especially in summer, when heat and drought stress were higher. Above-ground CO(2) fluxes were significantly increased in multispecies communities, as more complementary resource use stimulated productivity. Finally, effects of warming appeared to be smallest in monocultures. This study shows that in a future warmer climate the CO(2) sink capacity of temperate grasslands could decline, and that such adverse effects are not likely to be mitigated by efforts to maintain or increase species richness.     

How do climate warming and plant species richness affect water use in experimental grasslands?

Climate warming and plant species richness loss have been the subject of numerous experiments, but studies on their combined impact are lacking. Here we studied how both warming and species richness loss affect water use in grasslands, while identifying interactions between these global changes. Experimental ecosystems containing one, three or nine grassland species from three functional groups were grown in 12 sunlit, climate-controlled chambers (2.25 m² ground area) in Wilrijk, Belgium. Half of these chambers were exposed to ambient air temperatures (unheated), while the other half were warmed by 3°C (heated). Equal amounts of water were added to heated and unheated communities, so that warming would imply drier soils if evapotranspiration (ET) was higher. After an initial ET increase in response to warming, stomatal regulation and lower above-ground productivity resulted in ET values comparable with those recorded in the unheated communities. As a result of the decreased biomass production, water use efficiency (WUE) was reduced by warming. Higher complementarity and the improved competitive success of water-efficient species in mixtures led to an increased WUE in multi-species communities as compared to monocultures, regardless of the induced warming. However, since the WUE of individual species was affected in different ways by higher temperatures, compositional changes in mixtures seem likely under climatic change due to shifts in competitiveness. In conclusion, while increased complementarity and selection of water-efficient species ensured more efficient water use in mixtures than monocultures, global warming will likely decrease this WUE, and this may be most pronounced in species-rich communities.     

How do predators and scavengers locate resource hotspots within a tropical forest?

In many parts of the world, wildlife species congregate at ‘hotspot’ locations that offer feeding opportunities unmatched in the wider landscape. But to exploit those resource‐rich sites, animals must first locate them. In tropical Australia, predators and scavengers (especially dingos, scrub turkeys, snakes, and invasive toads) gather beneath large canopy‐emergent trees that house breeding colonies of metallic starlings (Aplonis metallica). Some wildlife species feed on fallen nestlings whereas others consume the rich insect fauna supported by bird detritus, or the other species attracted to those resources. Those congregations largely cease as soon as colony trees fall, suggesting that wildlife aggregations are responses to bird‐associated cues rather than to specific locations. To identify the proximate cues that elicit congregation of wildlife under such trees, we deployed sound cues (starling‐chatter) and two types of scent cues (soil from beneath a starling tree, and complete nests on broken branches). We recorded visitations by animals with camera‐traps. Starling‐chatter did not attract significant numbers of animals, but soil from beneath colony trees attracted many animals (mostly scrub turkeys). Complete nests attracted nest‐predators (dingos, snakes). Our experiments suggest that faunal aggregations beneath colony trees are driven by proximate responses to distinctive scent cues in the soil, especially for species that obtain their food from that bird‐fertilized substrate; but predators that feed directly on fallen nestlings key in specifically on that resource.     

How do floating aquatic weeds affect wetland conservation and development? How can these effects be minimised?

The most important floating aquatic weeds (FAWs) are Eichhornia crassipes, Salvinia molesta and Pistia stratiotes. E. crassipes and P. stratiotes reproduce sexually. All three species reproduce asexually. E. crassipes and S. molesta have particularly high growth rates. All can form dense mats and growth rates are increased by high nutrient levels and temperatures. Spread between continents and watersheds is largely the result of human activities. Spread within watersheds is mostly via floating propagules. FAWs are known to affect water resource management, the continued existence of human riverine and wetland communities, and conservation of biodiversity. Waterways can be blocked, and the efficiency of irrigation and hydro generation impaired. People are affected by reduction of the fish catch, inability to travel by boat and consequent isolation from gardens, markets and health services, and also changes in populations of vectors of human and animal diseases. Biodiversity can be reduced and conservation value affected. It is proposed that rational application of physical, chemical and biological control of FAWs, and reduction of nutrient input should be part of every strategy for the sustainable management of wetlands.     

Pound-wise but penny-foolish: How well do micromolecules fare in macromolecular refinement?

For the refinement of protein and nucleic acid structures, high-quality geometric restraint libraries are available. Unfortunately, for other compounds, such as physiological ligands, lead compounds, substrate analogs, etc., the situation is not as favorable. As a result, the structures of small molecules found in complexes with biomacromolecules are often less reliable than those of the surrounding amino or nucleic acids. Here, we briefly review the use of geometric restraints in structure refinement (be it against X-ray crystallographic or NMR-derived data) and simulation. In addition, we discuss methods to generate both restraint libraries and (idealized) coordinates for small molecules and provide some practical advice.     

How do flies tolerate microorganisms in the gut?

Although gut epithelia are in constant contact with a large number of microbe-derived immune elicitors such as peptidoglycan, they do not mount an intense immune response. In this issue of Cell Host & Microbe, Lhocine et al. (2008) report that the PIMS gene product induces immune tolerance by reducing the availability of the peptidoglycan receptor in the plasma membrane. These findings provide a novel insight into the molecular mechanisms by which the host gut maintains balanced host-microbe interactions.     

How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels

The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study ‘replicated’ instances of secondary contact between closely related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry‐informative panel of such SNPs. We then compared their frequencies in newly sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi‐stable variants (Dobzhansky‐Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact.     

Artificial substrata in a shallow sublittoral habitat: do they adequately represent natural habitats or the local species pool?

Artificial substrata have been advocated as tools which have considerable potential for monitoring both natural and anthropogenic effects on invertebrate communities of shallow coastal environments. In this experiment, community structure was compared between two dominant natural algal habitats (kelp holdfasts and algal turf) and artificial substratum units (ASUs; nests of pan scourers) deployed in close contact with, and 20 cm above the substratum. Univariate and multivariate statistical analyses were applied to the data to determine the similarity of community structure between the four different habitats. In addition, recently developed measures of taxonomic distinctness were applied to the data from both sets of artificial substrata to determine if they provided a representative sample of the local epifaunal species pool and thus have the potential to be used as surrogate samples for this important faunal group. There were marked differences between community structure in each of the habitats. Both sets of artificial substrata were dominated by tubicolous polychaetes with abundances that were more than an order of magnitude greater than in the holdfast and turf samples. The fauna recruiting to the artificial substrata deployed above the substratum showed the lowest values in the univariate summaries of diversity and evenness and were unrepresentative of the local species pool. Artificial samples deployed in contact with the substratum showed greater diversity and evenness but were still mostly unrepresentative of the local species pool. The tendency for both sets of artificial substrata to under-sample amphipods and to be dominated by suspension-feeding polychaetes suggests that methods using these units may be relatively insensitive to the effects of anthropogenic impacts (e.g. sewage outfalls) where shifts in community structure including increased dominance of suspension-feeders and polychaetes and a reduced dominance of amphipods have been observed. Further studies, including the evaluation of temporal variation in community structure related to the time at which the ASUs are deployed and duration of deployment, are needed to test the wider utility of artificial substrata as tools for monitoring shallow, sublittoral, epifaunal communities.     

How do biodiversity and conservation values relate to landscape preferences? A case study from the Swiss Alps

The importance of the values underlying different concepts of biodiversity conservation and landscape planning is increasingly recognised, and yet these value judgements of the public and of experts are still poorly understood. Although landscape and conservation management are closely interrelated and measures in one field are likely to have effects on the other, the relationship between biodiversity and conservation values on the one hand, and landscape preferences on the other hand, has been hardly explored so far. This study represents a first attempt to empirically examine this relationship from an integrated perspective, considering philosophical, ecological and economic aspects and using items focused on biodiversity. We used a quantitative survey of the general Swiss population with visualisations of potential landscape developments in the Swiss Alps and items related to biodiversity- and conservation-values. Our research shows that respondents who prefer reforested landscapes tend to be more concerned about the conservation of species, landscapes, and natural processes than people preferring cultural landscapes. Respondents who prefer cultural landscapes are more oriented towards utilitarian values and are overrepresented in mountain areas as compared to the lowlands, thus in areas that are more likely to become the target of conservation measures. Our findings have practical implications for conservation in Switzerland and other mountainous areas, particularly in times of agricultural decline and land abandonment and their associated changes in landscape and biodiversity.