Simulated effects of low atmospheric CO2 on structure and composition of North American vegetation at the Last Glacial Maximum

1. Physiological experiments have indicated that the lower CO₂ levels of the last glaciation (200 μmol mol^?1) probably reduced plant water-use efficiency (WUE) and that they combined with increased aridity and colder temperatures to alter vegetation structure and composition at the Last Glacial Maximum (LGM). 2. The effects of low CO₂ on vegetation structure were investigated using BIOME3 simulations of leaf area index (LAI), and a two-by-two factorial experimental design (modern/LGM CO₂, modern/LGM climate).3. Using BIOME3, and a combination of lowered CO₂ and simulated LGM climate (from the NCAR-CCM1 model), results in the introduction of additional xeric vegetation types between open woodland and closed-canopy forest along a latitudinal gradient in eastern North America.4. The simulated LAI of LGM vegetation was 25–60% lower in many regions of central and eastern United States relative to modern climate, indicating that glacial vegetation was much more open than today.5. Comparison of factorial simulations show that low atmospheric CO₂ has the potential to alter vegetation structure (LAI) to a greater extent than LGM climate.6. If the magnitude of LAI reductions simulated for glacial North America were global, then low atmospheric CO₂ may have promoted atmospheric warming and increased aridity, through alteration of rates of water and heat exchange with the atmosphere.     

Modelling the effect of temperature, water activity and pH on the growth of Serpula lacrymans

Aims: To predict the risk factors for building infestation by Serpula lacrymans, which is one of the most destructive fungi causing timber decay in buildings. Methods and Results: The growth rate was assessed on malt extract agar media at temperatures between 1·5 and 45°C, at water activity (a_w) over the range of 0·800–0·993 and at pH ranges from 1·5 to 11·0. The radial growth rate (μ) and the lag phase (λ) were estimated from the radial growth kinetics via the plots radius vs time. These parameters were then modelled as a function of the environmental factors tested. Models derived from the cardinal model (CM) were used to fit the experimental data and allowed an estimation of the optimal and limit values for fungal growth. Optimal growth rate occurred at 20°C, at high a_w level (0·993) and at a pH range between 4·0 and 6·0. The strain effect on the temperature parameters was further evaluated using 14 strains of S. lacrymans. The robustness of the temperature model was validated on data sets measured in two different wood‐based media (Quercus robur L. and Picea abies). Conclusions: The two‐step procedure of exponential model with latency followed by the CM with inflection gives reliable predictions for the growth conditions of a filamentous fungus in our study. The procedure was validated for the study of abiotic factors on the growth rate of S. lacrymans. Significance and Impact of the Study: This work describes the usefulness of evaluating the effect of physico‐chemical factors on fungal growth in predictive building mycology. Consequently, the developed mathematical models for predicting fungal growth on a macroscopic scale can be used as a tool for risk assessment of timber decay in buildings.     

4.4 Å cryo-EM structure of an enveloped alphavirus Venezuelan equine encephalitis virus

Venezuelan equine encephalitis virus (VEEV), a member of the membrane‐containing Alphavirus genus, is a human and equine pathogen, and has been developed as a biological weapon. Using electron cryo‐microscopy (cryo‐EM), we determined the structure of an attenuated vaccine strain, TC‐83, of VEEV to 4.4 Å resolution. Our density map clearly resolves regions (including E1, E2 transmembrane helices and cytoplasmic tails) that were missing in the crystal structures of domains of alphavirus subunits. These new features are implicated in the fusion, assembly and budding processes of alphaviruses. Furthermore, our map reveals the unexpected E3 protein, which is cleaved and generally thought to be absent in the mature VEEV. Our structural results suggest a mechanism for the initial stage of nucleocapsid core formation, and shed light on the virulence attenuation, host recognition and neutralizing activities of VEEV and other alphavirus pathogens.     

Broad-scale habitat use by red-legged partridge <Emphasis Type="Italic">(Alectoris rufa</Emphasis>) in a low-density area in northwestern Spain

We developed broad-scale habitat selection models for the distribution of red-legged partridge Alectoris rufa in a low-density area in northwestern Spain, the Baixa-Limia site of community importance (SCI). The fieldwork consisted of ground surveys in 1 × 1 km squares. For habitat selection analysis, we used a 2 × 2 km grid integrating the information obtained in the 1 × 1 km squares. As predictors we used environmental variables measured on digital 1:50,000 scale cartography using a geographical information system (GIS). The red-legged partridge was scarce in the study area. The logistic regression analysis carried out on data from the squares with probable and confirmed breeding included the area of scrubland and pastureland with a positive sign. Using the breeding index category (BIC) three variables produced a slightly positive response: area of scrubland and pastureland, length of border between scrublands and forests, and length of border between forests and dams. The difficulty for modelling the habitat selection of this species could be due to human activities (hunting, habitat loss, restocking of hunt species), and may have modified their habitat preferences. Furthermore, the occupation of suboptimal habitats would distort the real habitat preferences.     

Mountain summer farms in Røldal,western Norway –; vegetation classification and patterns in species turnover and richness

This paper discusses vegetation types and diversity patterns in relation to environment and land-use at summer farms, a characteristic cultural landscape in the Norwegian mountains. Floristic data (189 taxa) were collected in 130 4-m² sample plots within 12 summer farms in Røldal, western Norway. The study was designed to sample as fully as possible the range of floristic, environmental, and land-use conditions. Vegetation types delimited by two-way indicator species analysis were consistent with results from earlier phytosociological studies. Detrended correspondence analysis and canonical correspondence analysis show that rather than being distinct vegetation types, the major floristic variation is structured along a spatial gradient from summer farm to the surrounding heathland vegetation. Species richness (alpha diversity) was modelled against environmental variables by generalized linear modelling and compositional turnover (beta diversity) by canonical correspondence analysis. Most environmental factors made significant contributions, but the spatial distance-to-farm gradient was the best predictor of both species richness and turnover. While summer farms reduce mean species richness at the plot scale, the compositional heterogeneity of the upland landscapes is increased, thereby creating ‘ecological room’ for additional vegetation types and species. Within an overall similarity across scales, soil variables (pH, base saturation, LOI, phosphate and nitrogen) differed considerably in their explanatory power for richness and turnover. A difference between ‘productivity limiting’ factors and ‘environmental sieves’ is proposed as an explanation. Species turnover with altitude is relatively low in grasslands as compared to heaths.     

Quantitative palaeobiogeography: GIS, phylogenetic biogeographical analysis, and conservation insights

Aim  The utility of GIS-based and phylogenetic biogeographical analysis in palaeobiogeography is reviewed with reference to its ability to elucidate patterns of interest for modern conservation biology, specifically the long-term effects of invasive species.
Location  Emphasis is on biogeographical patterns in the Appalachian basin and mid-continent of North America during the Devonian. Global palaeobiogeographical patterns of the Cambrian are also considered.
Methods  Palaeobiogeographical patterns are assessed within a GIS framework, including both direct range reconstruction and niche modelling methods, and within phylogenetic biogeographical analysis. Biogeographical patterns are considered within multiple clades of fossil invertebrates, including trilobites, crustaceans, brachiopods, and bivalves.
Results  GIS-based analysis (including niche modelling methods) of Devonian invertebrates demonstrates a tightly correlated relationship between sea-level rises and range expansion, dispersal events, and species invasions. The predominance of range expansion and species invasions during the Late Devonian reduced opportunities for vicariant speciation during this interval. Comparison of phylogenetic biogeographical patterns between Cambrian and Devonian trilobites allows discernment of the relative roles of tectonics and eustacy in driving biogeographical patterns.
Main conclusions  GIS analysis and phylogenetic biogeography are powerful tools for analysing the coevolution of the Earth and its biota. Analyses can identify episodes of vicariance and geo-dispersal and produce testable hypotheses for further analysis within the fossil record.     

Phosphorus eutrophication in the SW Frisian lake district 2. Phosphorus balances and simulation of reduction scenarios

The lakes and interconnecting canals in the S.W. Frisian lake district are highly eutrophic. In the mid-1980's a project on eutrophication and lake restoration research was started. This project was aimed at modelling water transport and phosphorus (P) dynamics and at simulating management scenarios. A simple dynamic P-balance model was used to calculate total phosphorus (TP) balances and to simulate three TP reduction scenarios in each of three lakes: Tjeukemeer, Groote Brekken and Slotermeer. The model covered three periods in 1985, 1986 and 1987. The external loads to Tjeukemeer were highest, moderate to Groote Brekken, and lowest to Slotermeer. The major P sources in the area were discharges from the surrounding polders, used mainly for agriculture, and from IJsselmeer.Despite a 75% TP-reduction in water from the surrounding polders the 0.07 mg l^–1 target level could be reached only occasionally in Tjeukemeer, while in the other two lakes this level was not even approached. The effect of a 75% reduction in water from IJsselmeer was greatest in Groote Brekken (but again approached the target only occasionally), moderate in Tjeukemeer and least in Slotermeer. The simulations showed that only a 75% reduction in both external loads (from polders and from IJsselmeer) will lead to achieving the target level in Tjeukemeer and Groote Brekken during the summer periods. In Slotermeer, a relatively isolated lake, other measures are necessary to reach the target level. The results are confirmed by an approximate theoretical analysis of the effects of load reduction.     

Global patterns in the shape of species geographical ranges reveal range determinants

Aim Do species range shapes follow general patterns? If so, what mechanisms underlie those patterns? We show for 11,582 species from a variety of taxa across the world that most species have similar latitudinal and longitudinal ranges. We then seek to disentangle the roles of climate, extrinsic dispersal limitation (e.g. barriers) and intrinsic dispersal limitation (reflecting a species’ ability to disperse) as constraints of species range shape. We also assess the relationship between range size and shape. Location Global. Methods Range shape patterns were measured as the slope of the regression of latitudinal species ranges against longitudinal ranges for each taxon and continent, and as the coefficient of determination measuring the degree of scattering of species ranges from the 1:1 line (i.e. latitudinal range = longitudinal range). Two major competing hypotheses explaining species distributions (i.e. dispersal or climatic determinism) were explored. To this end, we compared the observed slopes and coefficients of determination with those predicted by a climatic null model that estimates the potential range shapes in the absence of dispersal limitation. The predictions compared were that species distribution shapes are determined purely by (1) intrinsic dispersal limitation, (2) extrinsic dispersal limitations such as topographic barriers, and (3) climate. Results  Using this methodology, we show for a wide variety of taxa across the globe that species generally have very similar latitudinal and longitudinal ranges. However, neither neutral models assuming random but spatially constrained dispersal, nor models assuming climatic control of species distributions describe range shapes adequately. The empirical relationship between the latitudinal and longitudinal ranges of species falls between the predictions of these competing models. Main conclusions We propose that this pattern arises from the combined effect of macroclimate and intrinsic dispersal limitation, the latter being the major determinant among restricted‐range species. Hence, accurately projecting the impact of climate change onto species ranges will require a solid understanding of how climate and dispersal jointly control species ranges.     

Identification of the PcrA DNA helicase reaction pathway by applying advanced targeted molecular dynamic simulations

PcrA DNA helicase uses the free energy of hydrolysis and binding of ATP to unwind double-stranded DNA (ds-DNA). There are two states of PcrA, termed the substrate and product complexes and, through the conformational changes between these two states, PcrA moves along ds-DNA and separates the two strands. In this study, two different methods, namely chain minimisation (CM, less reliable method) and auto targeted molecular dynamic (TMD) simulation (more reliable), were performed to generate two different initial reaction pathways between these two states, and then fixed root mean square distance (RMSD) TMD simulation was performed to optimise these two initial pathways. In general, the two optimised pathways share very similar major conformational changes, but are different in the minor motions. The potential energy profiles of the two improved pathways are generally similar, but the one generated by the improved TMD path is slightly lower. Considering the poor reliability of the initial path generated by CM and insignificant improvements of the auto-TMD path, our study suggests that fixed RMSD TMD simulation can generate reliable reaction pathways, but the different initial paths still have some influence on the detailed conformational analysis.     

Particle size influences decay rates of environmental DNA in aquatic systems

Environmental DNA (eDNA) analysis is a powerful tool for remote detection of target organisms. However, obtaining quantitative and longitudinal information from eDNA data is challenging, requiring a deep understanding of eDNA ecology. Notably, if the various size components of eDNA decay at different rates, and we can separate them within a sample, their changing proportions could be used to obtain longitudinal dynamics information on targets. To test this possibility, we conducted an aquatic mesocosm experiment in which we separated fish-derived eDNA components using sequential filtration to evaluate the decay rate and changing proportion of various eDNA particle sizes over time. We then fit four alternative mathematical decay models to the data, building towards a predictive framework to interpret eDNA data from various particle sizes. We found that medium-sized particles (1–10 μm) decayed more slowly than other size classes (i.e., <1 and > 10 μm), and thus made up an increasing proportion of eDNA particles over time. We also observed distinct eDNA particle size distribution (PSD) between our Common carp and Rainbow trout samples, suggesting that target-specific assays are required to determine starting eDNA PSDs. Additionally, we found evidence that different sizes of eDNA particles do not decay independently, with particle size conversion replenishing smaller particles over time. Nonetheless, a parsimonious mathematical model where particle sizes decay independently best explained the data. Given these results, we suggest a framework to discern target distance and abundance with eDNA data by applying sequential filtration, which theoretically has both metabarcoding and single-target applications.