Model‐specification uncertainty in future forest pest outbreak

Climate change will modify forest pest outbreak characteristics, although there are disagreements regarding the specifics of these changes. A large part of this variability may be attributed to model specifications. As a case study, we developed a consensus model predicting spruce budworm (SBW, Choristoneura fumiferana [Clem.]) outbreak duration using two different predictor data sets and six different correlative methods. The model was used to project outbreak duration and the uncertainty associated with using different data sets and correlative methods (=model‐specification uncertainty) for 2011–2040, 2041–2070 and 2071–2100, according to three forcing scenarios (RCP 2.6, RCP 4.5 and RCP 8.5). The consensus model showed very high explanatory power and low bias. The model projected a more important northward shift and decrease in outbreak duration under the RCP 8.5 scenario. However, variation in single‐model projections increases with time, making future projections highly uncertain. Notably, the magnitude of the shifts in northward expansion, overall outbreak duration and the patterns of outbreaks duration at the southern edge were highly variable according to the predictor data set and correlative method used. We also demonstrated that variation in forcing scenarios contributed only slightly to the uncertainty of model projections compared with the two sources of model‐specification uncertainty. Our approach helped to quantify model‐specification uncertainty in future forest pest outbreak characteristics. It may contribute to sounder decision‐making by acknowledging the limits of the projections and help to identify areas where model‐specification uncertainty is high. As such, we further stress that this uncertainty should be strongly considered when making forest management plans, notably by adopting adaptive management strategies so as to reduce future risks.     

Distribution of cuticular proteins in different structures of adult Anopheles gambiae

Anopheles gambiae devotes over 2% (295) of its protein coding genes to structural cuticular proteins (CPs) that have been classified into 13 different families plus ten low complexity proteins not assigned to families. Small groups of genes code for identical proteins reducing the total number of unique cuticular proteins to 282. Is the large number because different structures utilize different CPs, or are all of the genes widely expressed? We used LC-MS/MS to learn how many products of these genes were found in five adult structures: Johnston's organs, the remainder of the male antennae, eye lenses, legs, and wings. Data were analyzed against both the entire proteome and a smaller database of just CPs. We recovered unique peptides for 97 CPs and shared peptides for another 35. Members of 11 of the 13 families were recovered as well as some unclassified. Only 11 CPs were present exclusively in only one structure while 43 CPs were recovered from all five structures. A quantitative analysis, using normalized spectral counts, revealed that only a few CPs were abundant in each structure. When the MS/MS data were run against the entire proteome, the majority of the top hits were to CPs, but peptides were recovered from an additional 467 proteins. CP peptides were frequently recovered from chitin-binding domains, confirming that protein-chitin interactions are not mediated by covalent bonds. Comparison with three other MS/MS analyses of cuticles or cuticle-rich structures augmented the current analysis. Our findings provide new insights into the composition of different mosquito structures and reveal the complexity of selection and utilization of genes coding for structural cuticular proteins.     

The human RD protein is closely related to nuclear RNA-binding proteins and has been highly conserved

We have isolated cDNA clones encoding the human RD protein, which is closely related to several known nuclear RNA-binding proteins. The RD protein contains a 60-amino acid (aa) tract almost entirely of alternating basic and acidic aa, (RD)_n, primarily arginine (Arg; R) and aspartic acid (Asp; D). The protein also contains an ‘RNP sequence domain’. Arg-rich tracts and the RNP sequence domain are both features of nuclear RNA-binding proteins. However, we have been unable to detect RNA-binding by the human RD protein. The very strong evolutionary conservation of the mammalian RD protein as sequence suggests that it plays an important role in the cell.     

Predictable cholesterol binding sites in GPCRs lack consensus motifs

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Biogeographical analysis of rodent endemism and distributional congruence in the southern–central Andes (north‐western Argentina)

The recognition of areas of endemism (AEs) is important for conservation biology and biogeographical regionalization. Our objective was to quantitatively identify AEs and distributional congruence patterns of native rodents at the tropical/temperate transition in the central Andes. We analysed 6200 geo‐referenced distributional records of 80 species in north‐western Argentina using NDM/VNDM software. We found 20 AEs defined by 22 endemic species (27% of the total rodent fauna) and 34 patterns of distributional congruence in non‐endemic rodents. Geographical range congruence follows two main patterns running parallel along the Andes. One is related to the humid eastern slopes of the Andes (Argentinean Yungas forest) and the other to the high Andes (Argentinean Puna plateau). Endemism was mainly restricted to the southernmost part of the Yungas forest and adjacent dryer valleys (Monte desert). Species diversity was highest in the northern sector of the Argentinean Yungas forest, where several species reach their southern distributional range. This incongruence among hotspots of diversity and endemism has also been also noted in diversity studies at continental and global scales. Our results provide a starting point for conservation planning in the southernmost Central Andes, which combines the taper of tropical diversity and range‐restricted species endemic to the tropical–temperate transition. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 112 , 163–179.     

DarkDivNet – A global research collaboration to explore the dark diversity of plant communities

DarkDivNet is a global research collaboration which explores dark diversity — the set of species that are absent from a site despite being suitable under the site conditions and present in the region. Participants of the network survey vascular plant diversity both at local (10  m × 10 m) and regional scales (radius 10 km) using a standardized approach. They also measure simple plant traits and collect soil samples. Observed and dark diversity together form the site‐specific species pool, and the ratio of observed diversity and dark diversity describes community completeness. We shall explore how observed and dark diversity, site‐specific species pool and community completeness vary across natural and anthropogenic gradients. We link plant diversity measures to the information obtained from environmental DNA: soil biota and plant taxa that occurred at the site before. We will refine existing dark diversity methods and use large vegetation databases to infer species habitat suitability. We expand the dark diversity concept from a purely taxonomy‐based approach to include the functional and phylogenetic aspects of diversity. DarkDivNet currently includes 161 planned sampling areas globally, but new participants are welcome. The main vegetation sampling period is scheduled until September 2020, with the first research papers being produced after that.     

Pollution,food safety,and the distribution of knowledge

Human perceptions of the relationship between pollution and food safety are often haphazard and contradictory, based on a variety of sources of information. Recent media events concerning seafood and coastal pollution have generated concern that an otherwise healthy food— fish and shellfish—has become dangerous. We assess consumer knowledge about seafood safety and coastal pollution using several methods, including tests of cultural consensus. We find that consumers view seafood as far more threatened by pollution than scientific analysis suggests, due in part to their perceptions about the dynamics of the marine environment. Finding variation in perceptions within our population based on income and other factors, we explore the use of the cultural consensus approach in large and heterogeneous populations.     

The C-Terminal Domain of RNA Polymerase II Is a Multivalent Targeting Sequence that Supports Drosophila Development with Only Consensus Heptads

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