Cardinal temperatures variability within a tropical japonica rice diversity panel

Air temperature is one of the most critical climatic factors controlling rice growth, development, and production in current and future climatic scenarii predicting increasingly frequent situations of extreme and/or fluctuating temperatures. With its large spectrum of geographical origins and cropping areas, one can credit tropical japonica rice subspecies of a probable genetic diversity of its response to air temperature, which is of major interest for the breeding of better adapted rice varieties. A panel of 195 rice accessions (175 japonica plus 20 reference cultivars) was studied in controlled environment to estimate cardinal (base, optimum, and maximum) temperatures based on the monitoring of the elongation rate (LERmax) of the sixth leaf on the main stem in response to six fixed thermal treatments ranging from 16 to 35 °C. A dedicated statistical framework was elaborated for estimating LERmax, cardinal temperature and related uncertainties. Developed statistical framework enhanced the precision of cardinal temperatures estimated compared to previously reported methods, especially for base temperature. Maximum temperature was trickier to estimate and will require further studies. A significant genotypic variability for base and optimal temperature was pointed out, suggesting tropical japonica subspecies represents a relevant genetic pool to breed for rice genotypes adapted to various thermal situations. These results also suggested that using genotype-dependent cardinal temperature values should enhance the way crop growth models account for genotype?×?environment interactions hence their predictive value in current and future climatic conditions.     

Post‐capture survival of whale sharks encircled in tuna purse‐seine nets: tagging and safe release methods

1. Whale shark, the world's largest fish, is believed to be particularly vulnerable owing to its biological characteristics (slow growth, late maturation, great longevity) and is listed as Vulnerable by IUCN and included in Appendix II of CITES. 2. Whale sharks are occasionally encircled in tropical tuna purse‐seine nets, throughout this global fishery. Although apparent immediate survival rates following encirclement and release have recently been assessed through scientific onboard observer programmes, a more rigorous methodology is still required for studying post‐released survival. 3. This work provides a method for applying pop‐up satellite tags and reports an enhanced release procedure for whale sharks. The first assessment of survival after release from purse‐seine nets involved six whale sharks tagged between May and September 2014 in the eastern tropical Atlantic Ocean. Five tags transmitted data: three popped up as programmed (after 30 days), while two surfaced prematurely (one after 21 and the other after 71 days (programmed to pop off after 30 and 90 days, respectively)) but showed no sign of unusual behaviour. 4. Overall, whale sharks survived at least 21 days (one at least 71 days) after release from purse‐seine nets. These observations based on five large individuals (total length > 8 m), suggest that whale sharks have a good chance of survival when released with the proposed method. 5. Additional tagging in this and other oceans, especially of juveniles which may be more sensitive to encirclement and release operations, is essential to further assess whale shark post‐release survival rates in tuna purse‐seine fisheries. Copyright © 2016 John Wiley & Sons, Ltd.     

Evidence of differential spreading events of grapevine pinot Gris virus in Italy using datamining as a tool

European Journal of Plant Pathology - Since its identification in 2003, grapevine Pinot gris virus (GPGV, Trichovirus) has now been detected in most grape-growing countries. So far, little is known...     

A general framework for modeling memory in capture—Recapture data

In classical multisite capture-recapture (CR) models, the probability of moving to a new location depends only on the current site occupied. Yet, it is known that some species, such as Canada geese (Branta Canadensis), have a strong tendency to return to sites visited earlier during their life. To account for this “phenomenon of memory,” several authors have considered CR models in which transition probabilities depend not only on the current location of the individuals but also on the sites previously visited. In this article, we clarify the differences between these previous “memory” models and provide a general framework for the study of memory using CR data. We illustrate this study with the reanalysis of the movements of Canada geese among three wintering sites. This article has supplementary material online.     

Global analysis of the protection status of the world’s forests

This study presents a global analysis of forest cover and forest protection. An updated Global Forest Map (using MODIS2005) provided a current assessment of forest cover within 20 natural forest types. This map was overlaid onto WWF realms and ecoregions to gain additional biogeographic information on forest distribution. Using the 2008 World Database on Protected Areas, percentage forest cover protection was calculated globally, within forest types, realms and ecoregions, and within selected areas of global conservation importance. At the 10% tree cover threshold, global forest cover was 39 million km². Of this, 7.7% fell within protected areas under IUCN management categories I–IV. With the inclusion of IUCN categories V and VI, the level of global forest protection increased to 13.5%. Percentage forest protection (IUCN I–IV) varied greatly between realms from 5.5% (Palearctic) to 13.4% (Australasia), and for forest types from 3.2% (temperate freshwater swamp forest) to 28% (temperate broadleaf evergreen forest). Median protection of forest cover in 670 ecoregions (forest above a specified threshold) was 5.9% (IUCN I–IV); at IUCN I–VI, 46% of the ecoregions had less than 10% forest protection. Considering their biodiversity importance, forest protection within global priority areas was insufficient, e.g., median protection of 8.4% in biodiversity hotspots (IUCN I–IV). Results have policy relevance in terms of the target of the Convention on Biological Diversity (CBD), reconfirmed in 2008, to effectively conserve “at least 10% of each of the world’s forest types”. Regular updates of these analyses would allow progress towards achieving that target to be monitored.     

Environmental factors and megafauna spatio‐temporal co‐occurrence with purse‐seine fisheries

Tropical tuna purse‐seine fisheries spatially co‐occur with various megafauna species, such as whale sharks, dolphins and baleen whales in all oceans of the world. Here, we analyzed a 10‐year (2002–2011) dataset from logbooks of European tropical tuna purse‐seine vessels operating in the tropical Eastern Atlantic and Western Indian Oceans, with the aim of identifying the principle environmental variables under which such co‐occurrence appear. We applied a Delta‐model approach using Generalized Additive Models (GAM) and Boosted Regression Trees (BRT) models, accounting for spatial autocorrelation using a contiguity matrix based on a residuals autocovariate (RAC) approach. The variables that contributed most in the models were chlorophyll‐a concentration in the Atlantic Ocean, as well as depth and monsoon in the Indian Ocean. High co‐occurrence between whale sharks, baleen whales and tuna purse‐seine fisheries were mostly observed in productive areas during particular seasons. In light of the lack of a full coverage scientific observer on board program, the large, long‐term dataset obtained from logbooks of tuna purse‐seine vessels is highly important for identifying seasonal and spatial co‐occurrence between the distribution of fisheries and megafauna, and the underlying environmental variables. This study can help to design conservation management measures for megafauna species within the framework of spatial fishery management strategies.     

Benefits,concerns, and solutions of fishing for tunas with drifting fish aggregation devices

Drifting fish aggregating devices (dFADs) are human-made floating objects widely used by tropical tuna purse seine (PS) fisheries to increase catch of target species. However, dFAD use has several negative impacts, including increased potential for overfishing, higher juvenile tuna catch, higher bycatch compared to other PS fishing modes, ghost-fishing, and generation of marine litter. Based on these impacts, some stakeholders, especially environmental non-governmental organizations and other competing fishing industries, suggest that dFADs should be completely banned. We list the pros and cons of dFAD fishing; address how to improve current management; and suggest solutions for the sustainability of dFAD fishing in the long term. A dFAD ban would lead to major changes in the availability and sourcing of tuna for human consumption and decrease the licensing revenue received by many developing states. Most importantly, we argue that tools exist today to manage for, reduce or eliminate most of the negative impacts of dFADs (e.g., bans on discards, limits on active dFADs, biodegradable non-entangling constructions, time-area deployment closures, recovery programs, and full data transparency, among others). Management decisions based on sound scientific reasoning are needed to address the legitimate concerns surrounding dFAD use and ensure the sustainability of both pelagic and coastal ecosystems and tropical tuna PS fisheries.     

A bacterial protein targets the BAHD1 chromatin complex to stimulate type III interferon response

Intracellular pathogens such as Listeria monocytogenes subvert cellular functions through the interaction of bacterial effectors with host components. Here we found that a secreted listerial virulence factor, LntA, could target the chromatin repressor BAHD1 in the host cell nucleus to activate interferon (IFN)-stimulated genes (ISGs). IFN-λ expression was induced in response to infection of epithelial cells with bacteria lacking LntA; however, the BAHD1-chromatin associated complex repressed downstream ISGs. In contrast, in cells infected with lntA-expressing bacteria, LntA prevented BAHD1 recruitment to ISGs and stimulated their expression. Murine listeriosis decreased in BAHD1(+/-) mice or when lntA was constitutively expressed. Thus, the LntA-BAHD1 interplay may modulate IFN-λ-mediated immune response to control bacterial colonization of the host.     

Developmental Dynamics and Early Growth Vigour in Rice 2. Modelling Genetic Diversity Using Ecomeristem

Early vigour is an important objective in rice breeding. A previous study reported strong positive effects of development rate (DR, 1/phyllochron) on early growth vigour in two rice panels. This study provided a model‐based analysis of DR effects on rice early vigour and underlying source–sink processes during exponential growth, using Ecomeristem model. Relevant model parameters were fitted to panel observations, and their effect on early vigour was quantified. A sensitivity analysis was performed to quantify the impact of model parameters on simulation outputs. The simulated behaviour of a population of virtual genotypes defined by the combination of model parameter values was compared with that of diversity panel. Finally, a simulation experiment was conducted to analyse source–sink adjustments constituting early vigour across a range of DR. Parameters governing structural development, particularly DR, had greater impact on vigour than parameters for resource acquisition. High DR was associated with rapid dry weight accumulation and low transitory carbohydrate reserves in both real and virtual populations. Genotypic DR is thus a major driver of early vigour in rice under stress‐free conditions. To evaluate traits contributing to vigour, the capacity of crop models to simulate interactions between structural development and resource acquisition must be improved.