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Homotherium was a genus of large-bodied scimitar-toothed cats, morphologically distinct from any extant felid species, that went extinct at the end of the Pleistocene [1-4]. They possessed large, saber-form serrated canine teeth, powerful forelimbs, a sloping back, and an enlarged optic bulb, all of which were key characteristics for predation on Pleistocene megafauna [5]. Previous mitochondrial DNA phylogenies suggested that it was a highly divergent sister lineage to all extant cat species [6-8]. However, mitochondrial phylogenies can be misled by hybridization [9], incomplete lineage sorting (ILS), or sex-biased dispersal patterns [10], which might be especially relevant for Homotherium since widespread mito-nuclear discrepancies have been uncovered in modern cats [10]. To examine the evolutionary history of Homotherium, we generated a -7x nuclear genome and a similar to 38x exome from H. latidens using shotgun and target-capture sequencing approaches. Phylogenetic analyses reveal Homotherium as highly divergent (similar to 22.5 Ma) from living cat species, with no detectable signs of gene flow. Comparative genomic analyses found signatures of positive selection in several genes, including those involved in vision, cognitive function, and energy consumption, putatively consistent with diurnal activity, well-developed social behavior, and cursorial hunting [5]. Finally, we uncover relatively high levels of genetic diversity, suggesting that Homotherium may have been more abundant than the limited fossil record suggests [3, 4, 11-14]. Our findings complement and extend previous inferences from both the fossil record and initial molecular studies, enhancing our understanding of the evolution and ecology of this remarkable lineage.
As the Arctic coast erodes, it drains thermokarst lakes, transforming them into lagoons, and, eventually, integrates them into subsea permafrost. Lagoons represent the first stage of a thermokarst lake transition to a marine setting and possibly more saline and colder upper boundary conditions. In this research, borehole data, electrical resistivity surveying, and modeling of heat and salt diffusion were carried out at Polar Fox Lagoon on the Bykovsky Peninsula, Siberia. Polar Fox Lagoon is a seasonally isolated water body connected to Tiksi Bay through a channel, leading to hypersaline waters under the ice cover. The boreholes in the center of the lagoon revealed floating ice and a saline cryotic bed underlain by a saline cryotic talik, a thin ice-bearing permafrost layer, and unfrozen ground. The bathymetry showed that most of the lagoon had bedfast ice in spring. In bedfast ice areas, the electrical resistivity profiles suggested that an unfrozen saline layer was underlain by a thick layer of refrozen talik. The modeling showed that thermokarst lake taliks can refreeze when submerged in saltwater with mean annual bottom water temperatures below or slightly above 0 degrees C. This occurs, because the top-down chemical degradation of newly formed ice-bearing permafrost is slower than the refreezing of the talik. Hence, lagoons may precondition taliks with a layer of ice-bearing permafrost before encroachment by the sea, and this frozen layer may act as a cap on gas migration out of the underlying talik.
Objectives: In this work, a simple and rapid liquid chromatographic method for the simultaneous determination of irbesartan (IRBE) and hydrochlorothiazide (HCT) was developed and validated by reverse phase high performance liquid chromatography (RP-HPLC). <br /> Materials and Methods: Experimental conditions such as different buffer solutions, various pH values, temperature, composition of the mobile phase, and the effect of flow rate were optimized. <br /> Results: The developed RP-HPLC method for these antihypertensive agents was wholly validated and IRBE was detected in the linear range of 0.1-25 mu g mL(-1) and HCT was detected in the linear range of 0.25-25 mu g mL(-1). Moreover, the suggested chromatographic technique was successfully applied for the determination of the drugs in human serum and pharmaceutical dosage forms with limit of detection values of 0.008 mu g mL(-1) for IRBE and 0.012 mu g mL(-1) for HCT. <br /> Conclusion: The proposed rapid analysis method of these antihypertensive drugs can be easily used and applied by pharmaceutical companies for which the analysis time is important.
Large-scale crop yield failures are increasingly associated with food price spikes and food insecurity and are a large source of income risk for farmers. While the evidence linking extreme weather to yield failures is clear, consensus on the broader set of weather drivers and conditions responsible for recent yield failures is lacking. We investigate this for the case of four major crops in Germany over the past 20 years using a combination of machine learning and process-based modelling. Our results confirm that years associated with widespread yield failures across crops were generally associated with severe drought, such as in 2018 and to a lesser extent 2003. However, for years with more localized yield failures and large differences in spatial patterns of yield failures between crops, no single driver or combination of drivers was identified. Relatively large residuals of unexplained variation likely indicate the importance of non-weather related factors, such as management (pest, weed and nutrient management and possible interactions with weather) explaining yield failures. Models to inform adaptation planning at farm, market or policy levels are here suggested to require consideration of cumulative resource capture and use, as well as effects of extreme events, the latter largely missing in process-based models. However, increasingly novel combinations of weather events under climate change may limit the extent to which data driven methods can replace process-based models in risk assessments.
Impacts of extreme weather events on bacterial community composition of a temperate humic lake
(2020)
Extreme weather events are projected to increase in frequency and intensity as climate change continues. Heterotrophic bacteria play a critical role in lake ecosystems, yet little research has been done to determine how they are affected by such extremes. The purpose of this study was to use high-throughput sequencing to explore the bacterial community composition of a humic oligotrophic lake on the North Atlantic Irish coast and to assess the impacts on composition dynamics related to extreme weather events. Samples for sequencing were collected from Lough Feeagh on a fortnightly basis from April to November 2018. Filtration was used to separate free-living and particle-associated bacterial communities and amplicon sequencing was performed for the 16S rRNA V4 region. Two named storms, six high discharge events, and one drought period occurred during the sampling period. These events had variable, context-dependent effects on bacterial communities in Lough Feeagh. The particle-associated community was found to be more likely to respond to physical changes, such as mixing, while the free-living population responded to changes in nutrient and carbon concentrations. Generally, however, the high stability of the bacterial community observed in Lough Feeagh suggests that the bacterial community is relatively resilient to extreme weather events.
A fundamental focus of current ecological and evolutionary research is to illuminate the drivers of animals' success in coping with human-induced rapid environmental change (HIREC). Behavioural adaptations are likely to play a major role in coping with HIREC because behaviour largely determines how individuals interact with their surroundings. A substantial body of research reports behavioural modifications in urban dwellers compared to rural conspecifics. However, it is often unknown whether the observed phenotypic divergence is due to phenotypic plasticity or the product of genetic adaptations. Here, we aimed at investigating (a) whether behavioural differences arise also between rural and urban populations of non-commensal rodents; and (b) whether these differences result from behavioural flexibility or from intrinsic behavioural characteristics, such as genetic or maternal effects. We captured and kept under common environment conditions 42 rural and 52 urban adult common voles (Microtus arvalis) from seven subpopulations along a rural-urban gradient. We investigated individual variation in behavioural responses associated with risk-taking and exploration, in situ at the time of capture in the field and ex situ after 3 months in captivity. Urban dwellers were bolder and more explorative than rural conspecifics at the time of capture in their respective sites (in situ). However, when tested under common environmental conditions ex situ, rural individuals showed little change in their behavioural responses whereas urban individuals altered their behaviour considerably and were consistently shyer and less explorative than when tested in situ. The combination of elevated risk-taking and exploration with high behavioural flexibility might allow urban populations to successfully cope with the challenges of HIREC. Investigating whether the observed differences in behavioural flexibility are adaptive and how they are shaped by additive and interactive effects of genetic make-up and past environmental conditions will help illuminate eco-evolutionary dynamics under HIREC and predict persistence of populations under urban conditions.
Coarse-grained molecular model for the Glycosylphosphatidylinositol anchor with and without protein
(2020)
Glycosylphosphatidylinositol (GPI) anchors are a unique class of complex glycolipids that anchor a great variety of proteins to the extracellular leaflet of plasma membranes of eukaryotic cells. These anchors can exist either with or without an attached protein called GPI-anchored protein (GPI-AP) both in vitro and in vivo. Although GPIs are known to participate in a broad range of cellular functions, it is to a large extent unknown how these are related to GPI structure and composition. Their conformational flexibility and microheterogeneity make it difficult to study them experimentally. Simplified atomistic models are amenable to all-atom computer simulations in small lipid bilayer patches but not suitable for studying their partitioning and trafficking in complex and heterogeneous membranes. Here, we present a coarse-grained model of the GPI anchor constructed with a modified version of the MARTINI force field that is suited for modeling carbohydrates, proteins, and lipids in an aqueous environment using MARTINI's polarizable water. The nonbonded interactions for sugars were reparametrized by calculating their partitioning free energies between polar and apolar phases. In addition, sugar-sugar interactions were optimized by adjusting the second virial coefficients of osmotic pressures for solutions of glucose, sucrose, and trehalose to match with experimental data. With respect to the conformational dynamics of GPI-anchored green fluorescent protein, the accessible time scales are now at least an order of magnitude larger than for the all-atom system. This is particularly important for fine-tuning the mutual interactions of lipids, carbohydrates, and amino acids when comparing to experimental results. We discuss the prospective use of the coarse-grained GPI model for studying protein-sorting and trafficking in membrane models.
We expressed Dictyostelium lamin (NE81) lacking both a functional nuclear localization signal and a CAAX-box for C-terminal lipid modification. This lamin mutant assembled into supramolecular, three-dimensional clusters in the cytosol that disassembled at the onset of mitosis and re-assembled in late telophase, thus mimicking the behavior of the endogenous protein. As disassembly is regulated by CDK1-mediated phosphorylation at serine 122, we generated a phosphomimetic S122E mutant called GFP-NE81-S122E-∆NLS∆CLIM. Surprisingly, during imaging, the fusion protein assembled into cytosolic clusters, similar to the protein lacking the phosphomimetic mutation. Clusters disassembled again in the darkness. Assembly could be induced with blue but not green or near ultraviolet light, and it was independent of the fusion tag. Assembly similarly occurred upon cell flattening. Earlier reports and own observations suggested that both blue light and cell flattening could result in a decrease of intracellular pH. Indeed, keeping the cells at low pH also reversibly induced cluster formation. Our results indicate that lamin assembly can be induced by various stress factors and that these are transduced via intracellular acidification. Although these effects have been shown in a phosphomimetic CDK1 mutant of the Dictyostelium lamin, they are likely relevant also for wild-type lamin.
Island disharmony refers to the biased representation of higher taxa on islands compared to their mainland source regions and represents a central concept in island biology. Here, we develop a generalizable framework for approximating these source regions and conduct the first global assessment of island disharmony and its underlying drivers. We compiled vascular plant species lists for 178 oceanic islands and 735 mainland regions. Using mainland data only, we modelled species turnover as a function of environmental and geographic distance and predicted the proportion of shared species between each island and mainland region. We then quantified the over- or under-representation of families on individual islands (representational disharmony) by contrasting the observed number of species against a null model of random colonization from the mainland source pool, and analysed the effects of six family-level functional traits on the resulting measure. Furthermore, we aggregated the values of representational disharmony per island to characterize overall taxonomic bias of a given flora (compositional disharmony), and analysed this second measure as a function of four island biogeographical variables. Our results indicate considerable variation in representational disharmony both within and among plant families. Examples of generally over-represented families include Urticaceae, Convolvulaceae and almost all pteridophyte families. Other families such as Asteraceae and Orchidaceae were generally under-represented, with local peaks of over-representation in known radiation hotspots. Abiotic pollination and a lack of dispersal specialization were most strongly associated with an insular over-representation of families, whereas other family-level traits showed minor effects. With respect to compositional disharmony, large, high-elevation islands tended to have the most disharmonic floras. Our results provide important insights into the taxon- and island-specific drivers of disharmony. The proposed framework allows overcoming the limitations of previous approaches and provides a quantitative basis for incorporating functional and phylogenetic approaches into future studies of island disharmony.
Anthropogenic changes in climate, land use, and disturbance regimes, as well as introductions of non-native species can lead to the transformation of many ecosystems. The resulting novel ecosystems are usually characterized by species assemblages that have not occurred previously in a given area. Quantifying the ecological novelty of communities (i.e., biotic novelty) would enhance the understanding of environmental change. However, quantification remains challenging since current novelty metrics, such as the number and/or proportion of non-native species in a community, fall short of considering both functional and evolutionary aspects of biotic novelty. Here, we propose the Biotic Novelty Index (BNI), an intuitive and flexible multidimensional measure that combines (a) functional differences between native and non-native introduced species with (b) temporal dynamics of species introductions. We show that the BNI is an additive partition of Rao's quadratic entropy, capturing the novel interaction component of the community's functional diversity. Simulations show that the index varies predictably with the relative amount of functional novelty added by recently arrived species, and they illustrate the need to provide an additional standardized version of the index. We present a detailed R code and two applications of the BNI by (a) measuring changes of biotic novelty of dry grassland plant communities along an urbanization gradient in a metropolitan region and (b) determining the biotic novelty of plant species assemblages at a national scale. The results illustrate the applicability of the index across scales and its flexibility in the use of data of different quality. Both case studies revealed strong connections between biotic novelty and increasing urbanization, a measure of abiotic novelty. We conclude that the BNI framework may help building a basis for better understanding the ecological and evolutionary consequences of global change.