Does the uniform packing of sand in a cylinder provide a uniform penetration resistance?

Sand packed to a constant dry bulk density, is frequently used as an artificial growth medium in which to simulate the effects of a constant mechanical impedance on root growth. This research aimed to determine whether conventional packing resulted in constant mechanical impedance and to test alternative packing regimes. Perspex cylinders 300 mm tall with a 49 mm internal diameter were packed with moist sand to uniform and varying bulk densities to examine which type of packing gave the greatest uniformity of penetration resistance (PR) with depth. The cylinders packed to a constant bulk density (1.48, 1.55, and 1.6 Mg m^-3) all had measured PR profiles which increased markedly with depth by approximately 1, 1.5 and 3 MPa, respectively, within the top 100 mm. Between 100–300 mm depth, these same cylinders showed reductions in PR of up to 1, 2 and 2 MPa respectively. These results show that sand packed to a constant bulk density with depth would not provide a uniform mechanical impedance to plant roots.By packing sand to different bulk densities at different depths, we obtained packed cylinders that had much more uniform PR profiles (with average values of 0.25, 1.40 and 2.30 MPa). Below a depth of 50 mm, the coefficients of variation for replicate cylinders packed in this way were 12%, 5% and 18% for the 0.25, 1.40, and 2.30 MPa treatments respectively. For experiments with single plants, the lower PR values that were unavoidable near to the surface (< 50 mm) can be avoided by sowing seeds at the base of a funnel inserted into the cylinder. Treatments such as these can provide reproducible growth media, with adequate water/nutrient and aeration status for the study of plant response to uniform mechanical impedance.     

Does local habitat fragmentation affect large‐scale distributions? The case of a specialist grassland bird

Aim

Although the negative effects of habitat fragmentation have been widely documented at the landscape scale, much less is known about its impacts on species distributions at the biogeographical scale. We hypothesize that fragmentation influences the large‐scale distribution of area‐ and edge‐sensitive species by limiting their occurrence in regions with fragmented habitats , despite otherwise favourable environmental conditions. We test this hypothesis by assessing the interplay of climate and landscape factors influencing the distribution of the calandra lark, a grassland specialist that is highly sensitive to habitat fragmentation.

Location

Iberia Peninsula, Europe.

Methods

Ecological niche modelling was used to investigate the relative influence of climate/topography, landscape fragmentation and spatial structure on calandra lark distribution. Modelling assumed explicitly a hierarchically structured effect among explanatory variables, with climate/topography operating at broader spatial scales than landscape variables. An eigenvector‐based spatial filtering approach was used to cancel bias introduced by spatial autocorrelation. The information theoretic approach was used in model selection, and variation partitioning was used to isolate the unique and shared effects of sets of explanatory variables.

Results

Climate and topography were the most influential variables shaping the distribution of calandra lark, but incorporating landscape metrics contributed significantly to model improvement. The probability of calandra lark occurrence increased with total habitat area and declined with the number of patches and edge density. Variation partitioning showed a strong overlap between variation explained by climate/topography and landscape variables. After accounting for spatial structure in species distribution, the explanatory power of environmental variables remained largely unchanged.

Main conclusions

We have shown here that landscape fragmentation can influence species distributions at the biogeographical scale. Incorporating fragmentation metrics into large‐scale ecological niche models may contribute for a better understanding of mechanism driving species distributions and for improving predictive modelling of range shifts associated with land use and climate changes.

     

What's in a name? The case of cyanobacteria

A redefinition of the cyanobacterial lineage has been proposed based on phylogenomic analysis of distantly related nonphototrophic lineages. We define Cyanobacteria here as “Organisms in the domain bacteria able to carry out oxygenic photosynthesis with water as an electron donor and to reduce carbon dioxide as a source of carbon, or those secondarily evolved from such organisms.”     

Does the skeleton of a sponge provide a defense against predatory reef fish?

Sponge tissue often contains two structural components in high concentrations: spicules of silica, and refractory fibers of protein (spongin). Some terrestrial plants contain analogous structures, siliceous inclusions and refractory lignins, that have been demonstrated to deter herbivory. We performed feeding experiments with predatory reef fish to assess the deterrent properties of the structural components of three common Caribbean demosponges, Agelas clathrodes, Ectyoplasia ferox, and Xestospongia muta. The concentrations of spicules and spongin in the tissues varied widely between the three species, but when assayed at their natural volumetric concentrations, neither spicules (all three species assayed) nor the intact spiculated spongin skeleton (A. clathrodes and X. muta assayed) deterred feeding by reef fish in aquarium or field assays using prepared foods of a nutritional quality similar to, or higher than, that of sponge tissue. Spicules deterred feeding in aquarium assays when incorporated into prepared foods of a nutritional quality lower than that of sponge tissue (15–19 times less protein), but spiculated spongin skeleton was still palatable, even in prepared foods devoid of measurable protein, and even though spicules embedded in spongin were oriented in their natural conformation. Based on comparisons of the nutritional qualities of the tissues of the three sponge species and of the prepared foods, sponge tissue would have to be much lower in food value (5 times less protein or lower) for spicules to provide an effective defense, and spicules in combination with the spongin skeleton would be unlikely to provide an effective defense regardless of the nutritional quality of the tissue. Unlike terrestrial plants, marine sponges may use silica and refractory fibers solely for structural purposes.     

Dynamics in Central European near‐natural Abies‐Fagus forests: Does the mosaic‐cycle approach provide an appropriate model?

Question: The mosaic‐cycle concept of forest dynamics dominates in Central Europe. According to this concept intermediate‐scale disturbances only accelerate the forest break‐up under existing cycles of forest development. Is such an approach correct, or should new developmental cycles be elaborated for intermediate‐scale disturbances? Location: Near‐natural Abies alba ‐ Fagus sylvatica forests in the ?wiétokrzyski National Park in Central Poland. In these forests intermediate‐scale disturbances occurred between 1970 and 1990. Methods: Data were collected twice in areas surrounding 212 permanent sample points (in 1994 and 2004). Two increment cores were taken from 259 sample Abies trees. The effect of intermediate‐scale disturbances on radial increment of Abies was assessed. Probabilities of stand transition during a 10‐year period between individual stages and phases of development of the mixed forest were calculated. The development stages and phases were arranged into hypothetical succession series of successive changes. Results: In 1994 70 stands and in 2004, 47 stands representing stages and phases containing the older generation formed by trees > 100–150 years were found. Also, in 1994 142 and in 2004, 165 stands representing stages and phases containing the younger generations only, formed by trees < 100‐150 years, were recorded. Stages and phases containing only younger generations do not occur in the existing forest development cycle which does not consider the influence of intermediate‐scale disturbances separately. Two developmental cycles, which take into account the presence of the older generation and the younger generations only (under conditions of the occurrence of intermediate‐scale disturbances), are proposed. Conclusion: The mosaic‐cycle concept of forest dynamics can be used to analyse the dynamics of Central European near‐natural mixed‐species forests, but new developmental cycles should be elaborated for intermediate‐scale disturbances.     

What is the advantage of a transient precursor in autophagosome biogenesis?

We have recently proposed that some autophagosomes are formed within omegasomes, membrane sites connected to the endoplasmic reticulum and enriched in phosphatidylinositol 3-phosphate. In order to understand if there is any biological advantage to having such a precursor in autophagosome biogenesis, we generated a simple computer program that simulates omegasome and autophagosome formation under a variety of conditions. We concluded from running this simulation that having a transient precursor permits a bigger dynamic range of the autophagic response and allows a more efficient approach to steady state after autophagy stimulation.     

Genomic‐scale comparison of sequence‐ and structure‐based methods of function prediction: Does structure provide additional insight?

A function annotation method using the sequence-to-structure-to-function paradigm is applied to the identification of all disulfide oxidoreductases in the Saccharomyces cerevisiae genome. The method identifies 27 sequences as potential disulfide oxidoreductases. All previously known thioredoxins, glutaredoxins, and disulfide isomerases are correctly identified. Three of the 27 predictions are probable false-positives. Three novel predictions, which subsequently have been experimentally validated, are presented. Two additional novel predictions suggest a disulfide oxidoreductase regulatory mechanism for two subunits (OST3 and OST6) of the yeast oligosaccharyltransferase complex. Based on homology, this prediction can be extended to a potential tumor suppressor gene, N33, in humans, whose biochemical function was not previously known. Attempts to obtain a folded, active N33 construct to test the prediction were unsuccessful. The results show that structure prediction coupled with biochemically relevant structural motifs is a powerful method for the function annotation of genome sequences and can provide more detailed, robust predictions than function prediction methods that rely on sequence comparison alone.     

Does an ecological advantage produce the asymmetric lineage ratio in a harvester ant population?

In dependent-lineage harvester ant populations, two lineages interbreed but are genetically distinct. The offspring of a male and queen of the same lineage are female reproductives; the offspring of a male and queen of different lineages are workers. Geographic surveys have shown asymmetries in the ratio of the two lineages in many harvester ant populations, which may be maintained by an ecological advantage to one of the lineages. Using census data from a long-term study of a dependent-lineage population of the red harvester ant, Pogonomyrmex barbatus, we identified the lineage of 130 colonies sampled in 1997–1999, ranging in age from 1 to 19 years when collected, and 268 colonies sampled in 2010, ranging in age from 1 to 28 years when collected. The ratio of lineages in the study population is similar across an 11-year interval, 0.59 J2 in 1999 and 0.66 J2 in 2010. The rare lineage, J1, had a slightly but significantly higher number of mates of the opposite lineage than the common lineage, J2, and, using data from previous work on reproductive output, higher male production. Mature colonies of the two lineages did not differ in nest mound size, foraging activity, or the propensity to relocate their nests. There were no strong differences in the relative recruitment or survivorship of the two lineages. Our results show no ecological advantage for either lineage, indicating that differences between the lineages in sex ratio allocation may be sufficient to maintain the current asymmetry of the lineage ratio in this population.     

Mating in the pseudogamic apomictic Anemopaegma acutifolium DC: another case of pseudo‐self‐compatibility in Bignoniaceae?

Self‐compatibility in apomictic pseudogamic species is considered fundamental to assure reproduction by seeds in extreme situations, making apomictic species more advantageous than sexual ones in these scenarios. Anemopaegma acutifolium is a polyploidy, apomictic sporophytic species with no endosperm development in ovules of unpollinated pistils, which indicates obligate pseudogamy. Thus, the aim of the present work is to study the breeding system and post‐pollination events to test if there is similar pseudogamous development irrespective of pollination treatment. We analysed fruit and seed set obtained in controlled experimental pollinations, as well as embryo number per seed, and the progress of ovule penetration, fertilisation and early endosperm development between self‐ and cross‐pollinated pistils. We found that the species is self‐fertile and that spontaneous selfing fruit set is also possible, although emasculated flowers never form fruits. Selfed pistils were as efficient as crossed ones for all parameters analysed, except for a delay in endosperm development observed in the former that may be an effect of the late‐acting self‐incompatibility. Therefore, the avoidance of selfed pistil abortion seems to be promoted by the presence of adventitious embryos and a normal endosperm. We conclude that A. acutifolium shows apomixis‐related pseudo‐self‐compatibility, as in other self‐fertile apomictic species of Bignoniaceae, which confer reproductive assurance and increases fruit‐set and persistence ability in fast‐changing tropical habitats.     

The multistemmed structure of Juniperus thurifera: adaptive advantage in a severe environment?

A comparative study of radial growth and biomass between multistemmed trees with variable number of stems and single-stemmed trees was carried out to better understand determinism and organisation of multicaulis structure of a juniper species (Juniperus thurifera L.) growing in high Mediterranean mountains (High Atlas, Morocco). It appears that all the stems of the same tree have similar ages and so simultaneous development. Their mean annual radial increments show significant differences because of probable competition for water and nutrient supply and obvious physical competition for space. The multistemmed trees characterized by low number of stems have the same mean annual radial growth as single-stemmed trees and more generally all multistemmed junipers have a higher biomass. The multicaulis structure of Juniperus thurifera thus could be considered as an adaptation to severe environment, characterized not only by hard topographical, edaphic and climatic conditions, but by strong human pressure too.     

Does nest predation risk affect the frequency of extra‐pair paternity in a socially monogamous passerine?

While considerable variations in both the frequency of extra‐pair paternity (EPP) and the behavioral events that produce it are recognized among species, populations, individuals, and breeding attempts, the determinants of these variations are surprisingly difficult to establish. Nest predation may be one such determinant, since it is the most important source of reproductive failure, and past studies have suggested a variety of reproductive flexibilities under nest predation risk. However, despite its potentially significant effect on mating behaviors, nest predation risk has rarely been discussed in association with variations in intraspecific EPP patterns. Here, we examined the effect of naturally occurring nest predation, which varied between sites, years, and breeding attempts, on patterns of EPP in 92 broods (132 adults and 710 nestlings) of the Japanese great tit Parus major minor. We found that the frequency of extra‐pair offspring was positively correlated with the nest predation rate, along with a correlation to breeding attempts in a season, but not with other factors such as individual quality or breeding density. Under high nest‐predation risk, it may be adaptive for males to search for additional extra‐pair copulation to spread the risk of losing all offspring and to invest less in mate‐guarding, which also enables females to seek additional extra‐mating. The results of this study suggest that nest predation risk, among other factors, may significantly influence paternity allocation in birds.     

Does the speed of shortening affect steady-state force depression in cat soleus muscle?

It has been stated repeatedly for the past 50 years that the steady-state force depression following shortening of an activated muscle depends on the speed of shortening. However, these statements were based on results from experiments in which muscles were shortened at different speeds but identical activation levels. Therefore, the force during shortening was changed in accordance with the force-velocity relationship of muscles: that is, increasing speeds of shortening were associated with decreasing forces, and vice versa. Consequently, it is not possible at present to distinguish whether force depression is caused by the changes in speed, as frequently stated, or the associated changes in force, or both. The purpose of this study was to test if force depression depends on the speed of shortening. We hypothesized that force depression was dependent on the force but not the speed of contraction. Our prediction is that the amount of force depression after shortening contractions at different speeds could be similar if the force during contraction was controlled at a similar level. Cat soleus muscles (n=7) were shortened by 9 or 12 mm at speeds of 3, 9, and 27 mm/s, first with a constant activation during shortening (30Hz), then with activation levels that were reduced (<30Hz) for the slow speeds (3 and 9 mm/s) to approximate the shortening forces of the fast speed contractions (27 mm/s). If done properly, force depression could be precisely matched at the three different speeds, indicating that force depression was related to the force during the shortening contraction but not to the speed. However, in order to match force depression, the forces during shortening had to be systematically greater for the slow compared to the fast speeds of shortening, suggesting that force depression also depends on the level of activation, as force depression at constant activation levels can only be matched if the force during shortening, evaluated by the mechanical work, is identical. Therefore, we conclude that force depression depends on the force and activation level during shortening, but does not depend on the speed of shortening as has been assumed for half a century. These results support, but do not prove, the current hypothesis that force depression is caused by a stress-related cross-bridge inhibition in the actin-myosin overlap zone that is newly formed during muscle shortening.     

Built to bite? Differences in cranial morphology and bite performance between narrow‐ and broad‐headed European glass eels

The presence of two phenotypes in a single species is a widespread phenomenon, also observed in European eel (Anguilla anguilla). This dimorphism has been related to dietary differences in the subadult elver and yellow eel stages, with broad‐heads generally feeding on harder and/or larger‐bodied prey items than narrow‐heads. Nevertheless, both broad‐ and narrow‐headed phenotypes can already be found among glass eels, the stage preceding the elver eel stage. As these glass eels are considered nonfeeding, we investigate here to what degree the observed variation in head width is reflected in variation in the musculoskeletal feeding system, as well as whether this reflects the same variation observed in the older, dimorphic yellow eels. Additionally, we investigate whether musculoskeletal differences between broad‐ and narrow‐headed glass eels have implications on their feeding performance and could thus impact prey preference when eels start feeding. Therefore, we compared the cranial musculoskeletal system of five broad‐ and narrow‐headed glass eels using 3D‐reconstructions and simulated the glass eel's bite force using the data of the muscle reconstructions. We found that the variation in the musculoskeletal system of glass eels indeed reflects that of the yellow eels. Broader heads were related to larger jaw muscles, responsible for mouth closure. Accordingly, broad‐heads could generate higher bite forces than narrow‐headed glass eels. In addition, broader heads were associated with higher coronoid processes and shorter hyomandibulae, beneficial for dealing with higher mechanical loadings and consequently, harder prey. We, thus, show that head width variation in glass eels is related to musculoskeletal differences which, in turn, can affect feeding performance. As such, differences in prey preference can already take place the moment the eels start feeding, potentially leading to the dimorphism observed in the elver and yellow eel stage.     

Does lethal control of top‐predators release mesopredators? A re‐evaluation of three Australian case studies

Top‐predators can sometimes be important for structuring fauna assemblages in terrestrial ecosystems. Through a complex trophic cascade, the lethal control of top‐predators has been predicted to elicit positive population responses from mesopredators that may in turn increase predation pressure on prey species of concern. In support of this hypothesis, many relevant research papers, opinion pieces and literature reviews identify three particular case studies as supporting evidence for top‐predator control‐induced release of mesopredators in Australia. However, many fundamental details essential for supporting this hypothesis are missing from these case studies, which were each designed to investigate alternative aims. Here, we re‐evaluate the strength of evidence for top‐predator control‐induced mesopredator release from these three studies after comprehensive analyses of associated unpublished correlative and experimental data. Circumstantial evidence alluded to mesopredator releases of either the European Red Fox (Vulpes vulpes) or feral Cat (Felis catus) coinciding with Dingo (Canis lupus dingo) control in each case. Importantly, however, substantial limitations in predator population sampling techniques and/or experimental designs preclude strong assertions about the effect of lethal control on mesopredator populations from these studies. In all cases, multiple confounding factors and plausible alternative explanations for observed changes in predator populations exist. In accord with several critical reviews and a growing body of demonstrated experimental evidence on the subject, we conclude that there is an absence of reliable evidence for top‐predator control‐induced mesopredator release from these three case studies. Well‐designed and executed studies are critical for investigating potential top‐predator control‐induced mesopredator release.     

Does selective logging change ground‐dwelling beetle assemblages in a subtropical broad‐leafed forest of China?

Selective logging with natural regeneration is advocated as a near‐to‐nature strategy and has been implemented in many forested systems during the last decades. However, the efficiency of such practices for the maintenance of forest species are poorly understood. We compared the species richness, abundance and composition of ground‐dwelling beetles between selectively logged and unlogged forests to evaluate the possible effects of selective logging in a subtropical broad‐leafed forest in southeastern China. Using pitfall traps, beetles were sampled in two naturally regenerating stands after clearcuts (ca. 50 years old, stem‐exclusion stage: selectively logged 20 years ago) and two mature stands (> 80 years old, understory re‐initiation stage: selectively logged 50 years ago) during 2009 and 2010. Overall, selective logging had no significant effects on total beetle richness and abundance, but saproxylic species group and some abundant forest species significantly decreased in abundance in selectively logged plots compared with unlogged plots in mature stands. Beetle assemblages showed significant differences between selectively logged and unlogged plots in mature stands. Some environmental characteristics associated with selective logging (e.g., logging strategy, stand age, and cover of shrub and moss layers) were the most important variables explaining beetle assemblage structure. Our results conclude that selective logging has no significant impacts on overall richness and abundance of ground‐dwelling beetles. However, the negative effects of selective logging on saproxylic species group and some unlogged forest specialists highlight the need for large intact forested areas for sustaining the existence of forest specialist beetles.     

Does Bt rice pose risks to non‐target arthropods? Results of a meta‐analysis in China

Transgenic Bt rice expressing the insecticidal proteins derived from Bacillus thuringiensis Berliner (Bt) has been developed since 1989. Their ecological risks towards non‐target organisms have been investigated; however, these studies were conducted individually, yielding uncertainty regarding potential agroecological risks associated with large‐scale deployment of Bt rice lines. Here, we developed a meta‐analysis of the existing literature to synthesize current knowledge of the impacts of Bt rice on functional arthropod guilds, including herbivores, predators, parasitoids and detritivores in laboratory and field studies. Laboratory results indicate Bt rice did not influence survival rate and developmental duration of herbivores, although exposure to Bt rice led to reduced egg laying, which correctly predicted their reduced abundance in Bt rice agroecosystems. Similarly, consuming prey exposed to Bt protein did not influence survival, development or fecundity of predators, indicating constant abundances of predators in Bt rice fields. Compared to control agroecosystems, parasitoid populations decreased slightly in Bt rice cropping systems, while detritivores increased. We draw two inferences. One, laboratory studies of Bt rice showing effects on ecological functional groups are mainly either consistent with or more conservative than results of field studies, and two, Bt rice will pose negligible risks to the non‐target functional guilds in future large‐scale Bt rice agroecosystems in China.     

Olfactory morphology of carcharhinid and sphyrnid sharks: Does the cephalofoil confer a sensory advantage?

Many hypotheses have been advanced to explain the adaptive significance of the sphyrnid cephalofoil, including potential advantages of spacing the olfactory organs at the distal tips of the broad surface. We employed comparative morphology to test whether the sphyrnid cephalofoil provides better stereo-olfaction, increases olfactory acuity, and samples a greater volume of the medium compared to the situation in carcharhiniform sharks. The broadly spaced nares provide sphyrnid species with a significantly greater separation between the olfactory rosettes, which could lead to an enhanced ability to resolve odor gradients. In addition, most sphyrnid species possess prenarial grooves that greatly increase the volume of water sampled by the nares and thus increase the probability of odorant encounter. However, despite a much greater head width, and a significantly greater number of olfactory lamellae, scalloped hammerhead sharks do not possess a greater amount of olfactory epithelial surface area than the carcharhiniform sandbar sharks. Therefore, sphyrnid sharks might not possess any greater olfactory acuity than carcharhinids. Despite this, there are clear olfactory advantages to the cephalofoil head morphology that could have led to its evolution, persistence, and diversification. persistence, and diversification.