What drives the positive correlation between human population density and bird species richness in Australia?

Aim To test six hypotheses that could explain or mediate the positive correlation between human population density (HPD) and bird species richness while controlling for biased sampling effort. These hypotheses were labelled as follows: productivity (net primary productivity, NPP); inherent heterogeneity (diversity of vegetation types); anthropogenic heterogeneity (diversity of land uses); conservation policy (proportion of conservation land); increased productivity (human‐induced productivity increases); and the reduced‐slope hypothesis (which predicts that humans have a negative impact on species numbers across the full range of variation in HPD). Location Australia. Methods All data were collected at a spatial resolution of 1° across mainland Australia. Bird species richness was from 2007 atlas data and random subsampling was used to account for biased sampling effort. HPD was from the 2006 census. All other data were from government produced geographic information system layers. The most important biotic or abiotic factors influencing patterns in both species richness and HPD were assessed using simultaneous autoregressive models and an information theoretic approach. Results NPP appeared to be one of the main factors driving spatial congruence between bird species richness and HPD. Inherent habitat heterogeneity was weakly related to richness and HPD, although an interaction between heterogeneity and NPP indicated that the former may be an important determinant of species richness in low‐productivity regions. There was little evidence that anthropogenic landscape heterogeneity or human‐induced changes in productivity influenced the relationship between species richness and HPD, but conservation policy appeared to act as an important mediating factor and species richness was positively related to the proportion of conservation land only in regions of high HPD. Main conclusions The spatial congruence between bird species richness and HPD occurs because both respond positively to productivity and, in certain circumstances, habitat heterogeneity. Our results suggest that conservation policy could mediate this relationship, but further research is required to determine the importance of conservation reserves in supporting species in regions densely populated by humans.     

Does the effect of flowering time on biomass allocation across latitudes differ between invasive and native salt marsh grass Spartina alterniflora?

1. Parallel latitudinal clines in flowering time have been documented in both the invasive and native ranges of plants. Furthermore, flowering time has been found to affect biomass at maturity. Therefore, understanding how these flowering times affect biomass accumulation across latitudes is essential to understanding plant adaptations and distributions.
2. We investigated and compared trends in first flowering day (FFD), aboveground biomass (AGB), belowground biomass (BGB), and BGB:AGB ratio of the salt marsh grass Spartina alterniflora along latitudinal gradients from the invasive (China, 19–40°N) and native range (United States, 27–43°N) in a greenhouse common garden experiment, and tested whether FFD would drive these divergences between invasive and native ranges.
3. The invasive populations produced more (~20%, ~19%) AGB and BGB than native populations, but there were no significant differences in the FFD and BGB:AGB ratio. We found significant parallel latitudinal clines in FFD in both invasive and native ranges. In addition, the BGB:AGB ratio was negatively correlated with the FFD in both the invasive and native ranges but nonsignificant in invasive populations. In contrast, AGB and BGB increased with latitude in the invasive range, but declined with latitude in the native range. Most interestingly, we found AGB and BGB positively correlated with the FFD in the native range, but no significant relationships in the invasive range.
4. Our results indirectly support the evolution of increased competitive ability hypothesis (EICA) that S. alterniflora has evolved to produce greater AGB and BGB in China, but the flowering and allocation pattern of native populations is maintained in the invasive range. Our results also suggest that invasive S. alterniflora in China is not constrained by the trade‐off of earlier flowering with smaller size, and that flowering time has played an important role in biomass allocation across latitudes.

     

What is going on with the hormonal control of flowering in plants?

Molecular genetic studies using Arabidopsis thaliana as a model system have overwhelmingly revealed many important molecular mechanisms underlying the control of various biological events, including floral induction in plants. The major genetic pathways of flowering have been characterized in-depth, and include the photoperiod, vernalization, autonomous and gibberellin pathways. In recent years, novel flowering pathways are increasingly being identified. These include age, thermosensory, sugar, stress and hormonal signals to control floral transition. Among them, hormonal control of flowering except the gibberellin pathway is not formally considered a major flowering pathway per se, due to relatively weak and often pleiotropic genetic effects, complex phenotypic variations, including some controversial ones. However, a number of recent studies have suggested that various stress signals may be mediated by hormonal regulation of flowering. In view of molecular diversity in plant kingdoms, this review begins with an assessment of photoperiodic flowering, not in A. thaliana, but in rice (Oryza sativa); rice is a staple crop for human consumption worldwide, and is a model system of short-day plants, cereals and breeding crops. The rice flowering pathway is then compared with that of A. thaliana. This review then aims to update our knowledge on hormonal control of flowering, and integrate it into the entire flowering gene network.     

Does fitness erode in the absence of selection? An experimental test with Tribolium

In the absence of natural selection, average fitness in the population is expected to decline due to the accumulation of deleterious mutations. Replicate populations of flour beetles (Tribolium confusum) were maintained for 22 generations in the virtual absence of selection (random mating, favorable environment, excess of food, and mortality of only 3%). Larva-to-adult survivorship rates were similar in the stock population and selection-free populations. In contrast, starvation resistance of adult beetles from selection-free populations was significantly reduced (by more than 2% per generation). When tested in the favorable environment, beetles in one selection-free population had significantly slower development and smaller sizes of females than beetles from the stock population. Since such changes in these fitness components are usually maladaptive, they indicate possible erosion of fitness under relaxed selection at the rate of 0.1-0.2% per generation. No fitness erosion was detectable in the second selection-free population.     

What factor drives the fibrillogenic association of beta-sheets?

The identification of the driving factor for fibril formation is paramount to understand the molecular basis of amyloidogenic disease. Recently, an atomic-detail structure of a fibrillogenic aggregate was reported and revealed a tight packing of beta-sheets. However, there is not a single pair-wise interaction of significance between the beta-sheets, no hydrogen bond and no hydrophobic interaction. Instead, there is extensive burial of polar groups at the interface. These observations lead to the question: What factor drives the association of beta-sheets? This issue is addressed by combining all-atom molecular dynamics with an implicit-solvent analysis. The driving force for the association arises from the mechanical equivalent of the dehydration propensity of pre-formed intra-sheet hydrogen bonds and dipole-dipole interactions.     

What drives the distribution of the bloom-forming cyanobacteria Planktothrix agardhii and Cylindrospermopsis raciborskii?

The cyanobacteria Planktothrix agardhii and Cylindrospermopsis raciborskii are bloom-forming species common in eutrophic freshwaters. These filamentous species share certain physiological traits which imply that they might flourish under similar environmental conditions. We compared the distribution of the two species in a large database (940 samples) covering different climatic regions and the Northern and Southern hemispheres, and carried out laboratory experiments to compare their morphological and physiological responses. The environmental ranges of the two species overlapped with respect to temperature, light and total phosphorus (TP); however, they responded differently to environmental gradients; C.?raciborskii biovolume changed gradually while P. agardhii shifted sharply from being highly dominated to a rare component of the phytoplankton. As expected, P.?agardhii dominates the phytoplankton with high TP and low light availability conditions. Contrary to predictions, C.?raciborskii succeeded in all climates and at temperatures as low as 11?°C. Cylindrospermopsis raciborskii had higher phenotypic plasticity than P.?agardhii in terms of pigments, individual size and growth rates. We conclude that the phenotypic plasticity of C.?raciborskii could explain its ongoing expansion to temperate latitudes and suggest its future predominance under predicted climate-change scenarios.     

Volatilisation of metals and metalloids: An inherent feature of methanoarchaea?

As shown by recent studies, anaerobic members of Archaea and Bacteria are involved in processes that transform ionic species of metals and metalloids (arsenic, antimony, bismuth, selenium, tellurium and mercury) into volatile and mostly toxic derivatives (mainly methyl derivatives or hydrides). Since the fact that these transformations proceed in both environmental settings and in parts of the human body, we have to consider that these processes also interfere directly with human health. The diversity of the volatile derivatives produced and their emission rates were significantly higher in methanoarchaeal than in bacterial strains, which supports the pivotal role of methanoarchaea in transforming metals and metalloids (metal(loid)s) into their volatile derivatives. Compared with methanoarchaea, 14 anaerobic bacterial strains showed a significantly restricted spectrum of volatilised derivatives and mostly lower production rates of volatile bismuth and selenium derivatives. Since methanoarchaea isolated from the human gut (Methanosphaera stadtmanae, Methanobrevibacter smithii) showed a higher potential for metal(loid) derivatisation compared to bacterial gut isolates, we assume that methanoarchaea in the human gut are mainly responsible for the production of these volatile derivatives. The observation that trimethylbismuth ((CH(3))(3)Bi), the main volatile derivative of bismuth produced in human feces, inhibited growing cultures of Bacteroides thetaiotaomicron, a representative member of the human physiological gut flora, suggests that these volatiles exert their toxic effects on human health not only by direct interaction with host cells but also by disturbing the physiological gut microflora.     

Mapping QTL associated with photoperiod sensitivity and assessing the importance of QTL×environment interaction for flowering time in maize

Background

An understanding of the genetic determinism of photoperiod response of flowering is a prerequisite for the successful exchange of germplasm across different latitudes. In order to contribute to resolve the genetic basis of photoperiod sensitivity in maize, a set of 201 recombinant inbred lines (RIL), derived from a temperate and tropical inbred line cross were evaluated in 5 field trials spread in short- and long-day environments.

Methodology/Principal Findings

Firstly, QTL analyses for flowering time and photoperiod sensitivity in maize were conducted in individual photoperiod environments separately, and then, the total genetic effect was partitioned into additive effect (A) and additive-by-environment interaction effect (AE) by using a mixed-model-based composite interval mapping (MCIM) method.

Conclusions/Significance

Seven putative QTL were found associated with DPS thermal time based on the data estimated in individual environments. Nine putative QTL were found associated with DPS thermal time across environments and six of them showed significant QTL×enviroment (QE) interactions. Three QTL for photoperiod sensitivity were identified on chromosome 4, 9 and 10, which had the similar position to QTL for DPS thermal time in the two long-day environment. The major photoperiod sensitive loci qDPS10 responded to both short and long-day photoperiod environments and had opposite effects in different photoperiod environment. The QTL qDPS3, which had the greatest additive effect exclusively in the short-day environment, were photoperiod independent and should be classified in autonomous promotion pathway.     

Environment characterisation for the interpretation of environmental effect and genotype × environment interaction

Increasing attention is being paid to environment characterisation as a means of identifying the environmental factors determining grain protein content (GPC) in durum wheat. New insights in crop physiology and agronomy have led to the development of crop simulation models. Those models can reconstruct plant development for past cropping seasons. One major advantage of these models is that they can also indicate the intensity of limiting factors affecting plants during particular developmental stages. The main environmental factors determining GPC in durum wheat can be investigated by introducing the intensity of limiting factors into genotype × environment (G×E) models. In our case, limiting factors corresponding to water deficit and nitrogen availability were calculated for the development period between booting and heading. These variables were then introduced into a clustering model. This model is an extension of factorial regression applied to discrete environment and genotypic variables. This procedure effectively described the environment main effect: around 30.9% of the sum of squares of the environment main effect was accounted for, using less than 33% of the degrees of freedom. It also partially accounted for G×E interaction. Our methodology, coupling the use of crop simulation and G×E analysis models, is of potential value for improving our understanding of the main development stages and identification of environmental limiting factors for the development of GPC.     

What is the relationship between the global structures of apo and holo proteins?

It is well known that ligand binding and release may induce a wide range of structural changes in a receptor protein, varying from small movements of loops or side chains in the binding pocket to large‐scale domain hinge‐bending and shear motions or even partial unfolding that facilitates the capture and release of a ligand. An interesting question is what in general are the conformational changes triggered by ligand binding? The aim of this work is analyze the magnitude of structural changes in a protein resulting from ligand binding to assess if the state of ligand binding needs to be included in template‐based protein structure prediction algorithms. To address this issue, a nonredundant dataset of 521 paired protein structures in the ligand‐free and ligand‐bound form was created and used to estimate the degree of both local and global structure similarity between the apo and holo forms. In most cases, the proteins undergo relatively small conformational rearrangements of their tertiary structure upon ligand binding/release (most root‐mean‐square‐deviations from native, RMSD, are <1 Å). However, a clear difference was observed between single‐ and multiple‐domain proteins. For the latter, RMSD changes greater than 1 Å and sometimes larger were found for almost 1/3 of the cases; these are mainly associated with large‐scale hinge‐bending movements of entire domains. The changes in the mutual orientation of individual domains in multiple‐domain proteins upon ligand binding were investigated using a mechanistic model based on mass‐weighted principal axes as well as interface buried surface calculations. Some preferences toward the anticipated mechanism of protein domain movements are predictable based on the examination of just the ligand‐free structural form. These results have applications to protein structure prediction, particularly in the context of protein domain assembly, if additional information concerning ligand binding is exploited. Proteins 2008. © 2007 Wiley‐Liss, Inc.     

Phenotypic selection on floral scent: trade-off between attraction and deterrence?

Flowers emit a large variety of floral signals that play a fundamental role in the communication of plants with their mutualists and antagonists. We investigated phenotypic selection on floral scent and floral display using the rewarding orchid species Gymnadenia odoratissima. We found positive directional selection on inflorescence size, as well as positive and negative selection on floral scent compounds. Structural equation modeling showed that “active” compounds, i.e. those that were shown in earlier investigations to be detected by pollinator insects, were positively linked to fitness, whereas “non-active” were negatively linked to fitness. Our results suggest that different patterns of selection impact on different scent compounds, which may relate to the functions of compounds for attracting/deterring insects.     

What drives proteins into the major or minor grooves of DNA?

The energetic profiles of a significant number of protein-DNA systems at 20 °C reveal that, despite comparable Gibbs free energies, association with the major groove is primarily an enthalpy-driven process, whereas binding to the minor groove is characterized by an unfavorable enthalpy that is compensated by favorable entropic contributions. These distinct energetic signatures for major versus minor groove binding are irrespective of the magnitude of DNA bending and/or the extent of binding-induced protein refolding. The primary determinants of their different energetic profiles appear to be the distinct hydration properties of the major and minor grooves; namely, that the water in the A+T-rich minor groove is in a highly ordered state and its removal results in a substantial positive contribution to the binding entropy. Since the entropic forces driving protein binding into the minor groove are a consequence of displacing water ordered by the regular arrangement of polar contacts, they cannot be regarded as hydrophobic.     

Is time on our side? Strengthening the link between field efforts and conservation needs

The collection and organization of distributional data is the first crucial stage of any conservation planning action: therefore the decline in field research has implications in both the systematic, floristic and conservation fields. The aim of this paper is to analyze the effects of data updating on conservation planning and priorities. Focusing on the short time frame ranging from 2006 to 2011, we present a case study showing the rate of increase of collected data (taxa and records) and the consequential effects on the definition of areas of priority interest for plant conservation (Important Plant Areas—IPAs). We gathered data on a total of 193 taxa and 849 records with a mean rate of increase of +97 % for taxa and +166 % for records (2006/2011). This increase caused a positive rate of change in high ranking cells (+78 %) defining IPAs, while the number of low ranking cells and no data cells slightly decreased (?12 and ?8 %, respectively). Our results suggest that specific investment to complete the knowledge on the distribution of selected taxa (e.g. 193 taxa represent the 7.5 % of the total vascular flora of Sardinia) would dramatically reduce both the Linnean and Wallacean shortfalls and would allow robust conservation programs to preserve the diversity of the island. Updating the IPAs on a regular basis is a good example of a process that has a low impact as well as a big potential gain especially when field research can only be performed with low intensity and small monetary investments.