Are QST–FST comparisons for natural populations meaningful?

Comparisons between putatively neutral genetic differentiation amongst populations, F_ST, and quantitative genetic variation, Q_ST, are increasingly being used to test for natural selection. However, we find that approximately half of the comparisons that use only data from wild populations confound phenotypic and genetic variation. We urge the use of a clear distinction between narrow‐sense Q_ST, which can be meaningfully compared with F_ST, and phenotypic divergence measured between populations, P_ST, which is inadequate for comparisons in the wild. We also point out that an unbiased estimate of Q_ST can be found using the so‐called ‘animal model’ of quantitative genetics.     

Triathlon for energy functions: Who is the winner for design of protein–protein interactions?

Computational prediction of stabilizing mutations into monomeric proteins has become an almost ordinary task. Yet, computational stabilization of protein–protein complexes remains a challenge. Design of protein–protein interactions (PPIs) is impeded by the absence of an energy function that could reliably reproduce all favorable interactions between the binding partners. In this work, we present three energy functions: one function that was trained on monomeric proteins, while the other two were optimized by different techniques to predict side-chain conformations in a dataset of PPIs. The performances of these energy functions are evaluated in three different tasks related to design of PPIs: predicting side-chain conformations in PPIs, recovering native binding-interface sequences, and predicting changes in free energy of binding due to mutations. Our findings show that both functions optimized on side-chain repacking in PPIs are more suitable for PPI design compared to the function trained on monomeric proteins. Yet, no function performs best at all three tasks. Comparison of the three energy functions and their performances revealed that (1) burial of polar atoms should not be penalized significantly in PPI design as in single-protein design and (2) contribution of electrostatic interactions should be increased several-fold when switching from single-protein to PPI design. In addition, the use of a softer van der Waals potential is beneficial in cases when backbone flexibility is important. All things considered, we define an energy function that captures most of the nuances of the binding energetics and hence, should be used in future for design of PPIs.     

A simple framework for a complex problem? Predicting wildlife–vehicle collisions

Collisions of vehicles with wildlife kill and injure animals and are also a risk to vehicle occupants, but preventing these collisions is challenging. Surveys to identify problem areas are expensive and logistically difficult. Computer modeling has identified correlates of collisions, yet these can be difficult for managers to interpret in a way that will help them reduce collision risk. We introduce a novel method to predict collision risk by modeling hazard (presence and movement of vehicles) and exposure (animal presence) across geographic space. To estimate the hazard, we predict relative traffic volume and speed along road segments across southeastern Australia using regression models based on human demographic variables. We model exposure by predicting suitable habitat for our case study species (Eastern Grey Kangaroo Macropus giganteus) based on existing fauna survey records and geographic and climatic variables. Records of reported kangaroo–vehicle collisions are used to investigate how these factors collectively contribute to collision risk. The species occurrence (exposure) model generated plausible predictions across the study area, reducing the null deviance by 30.4%. The vehicle (hazard) models explained 54.7% variance in the traffic volume data and 58.7% in the traffic speed data. Using these as predictors of collision risk explained 23.7% of the deviance in incidence of collisions. Discrimination ability of the model was good when predicting to an independent dataset. The research demonstrates that collision risks can be modeled across geographic space with a conceptual analytical framework using existing sources of data, reducing the need for expensive or time‐consuming field data collection. The framework is novel because it disentangles natural and anthropogenic effects on the likelihood of wildlife–vehicle collisions by representing hazard and exposure with separate, tunable submodels.     

Cold stress and acclimation – what is important for metabolic adjustment?

As sessile organisms, plants are unable to escape from the many abiotic and biotic factors that cause a departure from optimal conditions of growth and development. Low temperature represents one of the most harmful abiotic stresses affecting temperate plants. These species have adapted to seasonal variations in temperature by adjusting their metabolism during autumn, increasing their content of a range of cryo‐protective compounds to maximise their cold tolerance. Some of these molecules are synthesised de novo. The down‐regulation of some gene products represents an additional important regulatory mechanism. Ways in which plants cope with cold stress are described, and the current state of the art with respect to both the model plant Arabidopsis thaliana and crop plants in the area of gene expression and metabolic pathways during low‐temperature stress are discussed.     

Fadenwürmer – fade Würmer?

Nematodes – there is more to it … Nematodes play a central role – not only in a negative way as dreaded parasites of humans, animals and plants, where they may be harmful in terms of health and economy. The majority of nematodes turn out to be highly beneficial: Firstly, they are a vital part of the food web and by this indispensably involved in nutrient cycles. On the other hand, we increasingly make use of nematodes in biological control of pest organisms, in the ecotoxicological assessment of soils and sediments and as excellent model organisms in a broad range of different research fields.     

Structural (UV) and carotenoid‐based plumage coloration – signals for parental investment?

Parental care increases parental fitness through improved offspring condition and survival but comes at a cost for the caretaker(s). To increase life‐time fitness, caring parents are, therefore, expected to adjust their reproductive investment to current environmental conditions and parental capacities. The latter is thought to be signaled via ornamental traits of the bearer. We here investigated whether pre‐ and/or posthatching investment of blue tit (Cyanistes caeruleus) parents was related to ornamental plumage traits (UV crown coloration and carotenoid‐based plumage coloration) expressed by either the individual itself (i.e. “good parent hypothesis”) or its partner (i.e. “differential allocation hypothesis”). Our results show that neither prehatching (that is clutch size and offspring begging intensity) nor posthatching parental investment (provisioning rate, offspring body condition at fledging) was related to an individual's UV crown coloration or to that of its partner. Similar observations were made for carotenoid‐based plumage coloration, except for a consistent positive relationship between offspring begging intensity and maternal carotenoid‐based plumage coloration. This sex‐specific pattern likely reflects a maternal effect mediated via maternally derived egg substances, given that the relationship persisted when offspring were cross‐fostered. This suggests that females adjust their offspring's phenotype toward own phenotype, which may facilitate in particular mother‐offspring co‐adaptation. Overall, our results contribute to the current state of evidence that structural or pigment‐based plumage coloration of blue tits are inconsistently correlated with central life‐history traits.     

High host‐plant nitrogen content: a prerequisite for the evolution of ant–caterpillar mutualism?

The amount of nitrogen required to complete an insect's life cycle may vary greatly among species that have evolved distinct life history traits. Myrmecophilous caterpillars in the Lycaenidae family produce nitrogen-rich exudates from their dorsal glands to attract ants for protection, and this phenomenon has been postulated to shape the caterpillar's host-plant choice. Accordingly, it was postulated that evolution towards myrmecophily in Lycaenidae is correlated with the utilization of nitrogen-rich host plants. Although our results were consistent with the evolutionary shifts towards high-nutrient host plants serving as exaptation for the evolution of myrmecophily in lycaenids, the selection of nitrogen-rich host plants was not confined to lycaenids. Butterfly species in the nonmyrmecophilous family Pieridae also preferred nitrogen-rich host plants. Thus, we conclude that nitrogen is an overall important component in the caterpillar diet, independent of the level of myrmecophily, as nitrogen can enhance the overall insect fitness and survival. However, when nitrogen can be obtained through alternative means, as in socially parasitic lycaenid species feeding on ant brood, the selective pressure for maintaining the use of nutrient-rich host plants is relaxed, enabling the colonization of nitrogen-poor host plants.     

Fishing for Accessory Binding Sites at GPCRs with ‘Loop‐Hooks’ – An Approach towards Selectivity? Part I

Receptor‐subtype selectivity is an important issue in medicinal chemistry and can become very difficult to achieve if the actual binding pockets of the respective receptors are highly conserved. For such cases, known unselective ligands could be equipped with a spacer that sticks outside the actual orthosteric binding pocket towards the extracellular loops. The end of the spacer bears certain functional groups to enable specific or unspecific interactions with the receptor residues outside the binding cavity. Our experiments indicated that it is possible to achieve selectivity within the dopamine D1 family with such ‘loop‐hooks’.     

Will a 385 million year‐struggle for light become a struggle for water and for carbon? – How trees may cope with more frequent climate change‐type drought events

Trees are exceptional organisms that have evolved over some 385 million years and have overtaken other plants in order to harvest light first. However, this advantage comes with a cost: trees must transport water all the way up to their crowns and inherent physical limitations make them vulnerable to water deficits. Because climate change scenarios predict more frequent extreme drought events, trees will increasingly need to cope with water stress. Recent occurrences of climate change‐type droughts have had severe impacts on several forest ecosystems. Initial experimental studies have been undertaken and show that stomatal control of water loss hinders carbon assimilation and could lead to starvation during droughts. Other mechanisms of drought‐induced mortality are catastrophic xylem dysfunction, impeded long‐distance transport of carbohydrates (translocation) and also symplastic failure (cellular breakdown). However, direct empirical support is absent for either hypothesis. More experimental studies are necessary to increase our understanding of these processes and to resolve the mystery of drought‐related tree mortality. Instead of testing the validity of particular hypothesis as mechanisms of drought‐induced tree mortality, future research should aim at revealing the temporal dynamics of these mechanisms in different species and over a gradient of environmental conditions. Only such studies will reveal whether the struggle for light will become a struggle for water and/or for carbon in drought‐affected areas.     

Breaking the Social–Non‐social Dichotomy: A Role for Reptiles in Vertebrate Social Behavior Research?

Although social behavior in vertebrates spans a continuum from solitary to highly social, taxa are often dichotomized as either ‘social’ or ‘non‐social’. We argue that this social dichotomy is overly simplistic, neglects the diversity of vertebrate social systems, impedes our understanding of the evolution of social behavior, and perpetuates the erroneous belief that one group—the reptiles—is primarily ‘non‐social’. This perspective essay highlights the diversity and complexity of reptile social systems, briefly reviews reasons for their historical neglect in research, and indicates how reptiles can contribute to our understanding of the evolution of vertebrate social behavior. Although a robust review of social behavior across vertebrates is lacking, the repeated evolution of social systems in multiple independent lineages enables investigation of the factors that promote shifts in vertebrate social behavior and the paraphyly of reptiles reinforces the need to understand reptile social behavior.     

Non‐equilibrium in plant distribution models – only an issue for introduced or dispersal limited species?

Species distribution models rely on the assumption that species' distributions are at equilibrium with environmental conditions within a region – i.e. they occur in all suitable habitats. If this assumption holds, species occurrence should be predictable from measures of the environment. Introduced species may be poor candidates for distribution models due to their presumed lack of equilibrium within the landscapes they occupy, although predicting their potential distributions is often of critical importance to natural resource managers. We determined if the accuracy of species distribution models differed between 17 native and 17 introduced riparian plant species in the western United States. We also assessed if model accuracy was associated with both environmental and biological factors that can influence dispersal. We used Random Forests to model species distributions and linear regression to determine if model accuracy was associated with dispersal‐related traits. Model accuracy for introduced species was higher than that for native species. Dispersal‐related traits did not affect model accuracy or improvement, though two other traits, family affiliation and rarity on the landscape, did have an effect. Distance‐based measures of dispersal potential improved model fit equally for both native and introduced species and for species with a variety of dispersal traits, suggesting that the importance of regional propagule pressure is relatively constant across species with different dispersal opportunities. Several lines of future questioning are suggested by our results, including why introduced species may in some cases produce more accurate distribution models than native species and how species dispersal traits relate to distribution model accuracy at different spatial scales.     

Biometry of Cenomanian–Turonian placoliths: a proxy for changes of fertility and surface‐water temperature?

Most publications discussing Cenomanian–Turonian calcareous nannofossils focus on abundance fluctuations across the boundary interval. So far, there have been no studies that deal with the influence of palaeoenvironmental changes on the size of common Cenomanian–Turonian nannofossil taxa. The genera Biscutum, Broinsonia, Prediscosphaera, Retecapsa and Watznaueria have therefore been analysed from 19 samples of Cenomanian–Turonian age from the Goban Spur, northeast Atlantic. The genus Biscutum shows a slight decrease of mean length from 4.14 μm in the Cenomanian to 3.94 μm in the Turonian. Broinsonia is marked by a decrease from 6.07 μm in the Cenomanian to 5.64 μm in the Turonian. On the other hand, Prediscospheara increases in size from 4.98 μm in the Cenomanian to 5.61 μm in the Turonian. Two genera (Retecapsa, Watznaueria) show no significant changes in their mean length. The mean size of Biscutum is perhaps controlled by nutrients, where larger specimens may have preferred the more fertile palaeoenvironment of the Late Cenomanian. The size decrease of Biscutum in the Turonian is probably related to reduced nutrient availability. The genus Prediscosphaera spp., may have favoured low‐fertility conditions, as its mean size increases in the Turonian. A worldwide decline of the frequency of Broinsonia spp. during the Cenomanian–Turonian transition implies that this genus is not solely controlled by the nutrient content. The size of Broinsonia spp. may have been therefore influenced by the latest Cenomanian warming event. The increase in sea‐surface temperature may have been unfavourable for Broinsonia spp. as reflected by decreasing mean size and frequency. □Calcareous nannofossils, biometry, morphometry, Oceanic Anoxic Event 2.     

Aquakultur – quo vadis?!

Aquaculture – quo vadis? Aquaculture is more than just fish production; it is a globally active sector of the food production industry. The production methods interact in different degrees with the environment, resulting in possible negative impact. Through enhancement of the production systems as well as utilized resources, such influence can be controlled and minimized. This includes the amount of water consumption, nutrient efficiency and thus nutrient excretion from the production systems. An optimization of the culture conditions has direct benefits for animal welfare, diseases resistance, product quality and consequently supporting the productivity of the aquaculture enterprises. Further support and networking of the stakeholders involved in education, research and private companies within the respective fields is required to reach the overall goal of an ecologically and economically sustainable aquaculture.     

Adipositas – eine Bürde der Evolution?

Obesity – a consequence of evolution? The high obesity rates are the result of a dramatic mismatch between current environment and a human body evolved in the environment of our evolutionary adaptedness. Various evolutionary hypotheses try to explain this relationship. Natural and sexual selection shaped our gene pool towards an optimal adaptation to these environments and life circumstances. Our recent obesogenic environment differs dramatically from that in which we evolved.     

Lipopolysaccharide‐induced increase in signalling in hippocampus is abrogated by IL‐10 – a role for IL‐1β?

Parenterally administered lipopolysaccharide (LPS) increases the concentration of the pro-inflammatory cytokine interleukin-1beta (IL-1beta) in the rat hippocampus and evidence suggests that this effect plays a significant role in inhibiting long-term potentiation (LTP). The anti-inflammatory cytokine IL-10, antagonizes certain effects of IL-1beta, so if the effects of LPS are mediated through an increase in IL-1beta, it might be predicted that IL-10 would also abrogate the effect of LPS. Here, we report that IL-10 reversed the inhibitory effect of LPS on LTP and the data couple this with an inhibitory effect on the LPS-induced increase in IL-1beta. LPS treatment increased hippocampal expression of IL-1 receptor Type I protein. Consistent with the LPS-induced increases in IL-1beta concentration and receptor expression, were downstream changes which included enhanced phosphorylation of IRAK and the stress-activated kinases, JNK and p38; these LPS-induced changes were reversed by IL-10, which concurs with the idea that these events are triggered by increased activation of IL-1RI by IL-1beta. We provide evidence which indicates that LPS treatment leads to evidence of cell death and this was reversed in hippocampus prepared from LPS-treated rats which received IL-10. The evidence is therefore consistent with the idea that IL-10 acts to protect neuronal tissue from the detrimental effects induced by LPS.