Repetitive DNA Restructuring Across Multiple Nicotiana Allopolyploidisation Events Shows a Lack of Strong Cytoplasmic Bias in Influencing Repeat Turnover.

Allopolyploidy is acknowledged as an important force in plant evolution. Frequent allopolyploidy in Nicotiana across different timescales permits the evaluation of genome restructuring and repeat dynamics through time. Here we use a clustering approach on high-throughput sequence reads to identify the main classes of repetitive elements following three allotetraploid events, and how these are inherited from the closest extant relatives of the maternal and paternal subgenome donors. In all three cases, there was a lack of clear maternal, cytoplasmic bias in repeat evolution, i.e., lack of a predicted bias towards maternal subgenome-derived repeats, with roughly equal contributions from both parental subgenomes. Different overall repeat dynamics were found across timescales of <0.5 (N. rustica L.), 4 (N. repanda Willd.) and 6 (N. benthamiana Domin) Ma, with nearly additive, genome upsizing, and genome downsizing, respectively. Lower copy repeats were inherited in similar abundance to the parental subgenomes, whereas higher copy repeats contributed the most to genome size change in N. repanda and N. benthamiana. Genome downsizing post-polyploidisation may be a general long-term trend across angiosperms, but at more recent timescales there is species-specific variance as found in Nicotiana

Nitrogen and phosphorus interactions at a 21 nitrogen:1 phosphorus Redfield-like ratio impact growth and seed yield in wheat (Triticum aestivum L.)

Efficient use of nitrogen (N) and phosphorus (P) is essential to reduce fertilizer costs and nutrient pollution and to lower the carbon footprint of agriculture. This requires a better understanding of N and P limitations on photosynthesis and biomass generation in one of the world's most important crops, wheat (Triticum aestivum). In a fully factorial nutrient experiment, we find that the limiting nutrient, N or P, at a Redfield-like N:P ratio (21N:1P molar) produces the ‘effective dose of fertilizer’ for the generation of above-ground biomass (seed or vegetative). Best-fit structural equation models showed that neither N nor P applied in excess of 21N:1P led to any increase in biomass. The light (qP, NPQ) and dark (Amax, Vcmax, Jmax) reactions of photosynthesis are also constrained by the limiting nutrient at the 21N:1P Redfield-like ratio. Beyond this ratio, ‘excess N’ or ‘excess P’ had no effects. The direct effects of the ‘effective dose of fertilizer’ on the accumulation of biomass were stronger than its indirect effects via photosynthesis, likely driven by the N and P costs in building nucleic acids needed for cell division, cell maintenance and RNA transcription. Modern composite fertilizers are typically provided at a much higher P content than a 21N:1P ratio, potentially resulting in a huge global wastage of P, a finite resource, with all the concomitant costs to the farmer, consumer and the environment

Down, then up: non-parallel genome size changes and a descending chromosome series in a recent radiation of the Australian allotetraploid plant species, Nicotiana section Suaveolentes (Solanaceae)

Background and aims: The extent to which genome size and chromosome numbers evolve in concert is little understood, particularly after polyploidy (whole-genome duplication), when a genome returns to a diploid-like condition (diploidisation). We study this phenomenon in 46 species of allotetraploid Nicotiana section Suaveolentes (Solanaceae), which formed less than six million years ago and radiated in the arid centre of Australia.Methods: We analysed newly assessed genome sizes and chromosome numbers within the context of a restriction site-associated nuclear DNA (RADseq) phylogenetic framework.Key results: RADseq generated a well-supported phylogenetic tree, in which multiple accessions from each species formed unique genetic clusters. Chromosome numbers and genome sizes vary from n = 2x = 15-24 and 2.7-5.8 pg/1 C nucleus, respectively. Decreases in both genome size and chromosome number occur, although neither consistently nor in parallel. Species with the lowest chromosome numbers (n = 15-18) do not possess the smallest genome sizes, and although N. heterantha has retained the ancestral chromosome complement, n = 2x = 24, it nonetheless has the smallest genome size, even smaller than that of the modern representatives of ancestral diploids.Conclusions: The results indicate that decreases in genome size and chromosome number occur in parallel down to a chromosome number threshold, n = 20, below which genome size increases, a phenomenon potentially explained by decreasing rates of recombination over fewer chromosomes. We hypothesize that, more generally in plants, major decreases in genome size post-polyploidization take place while chromosome numbers are still high because in these stages elimination of retrotransposons and other repetitive elements is more efficient. Once such major genome size change has been accomplished, then dysploid chromosome reductions take place to reorganize these smaller genomes, producing species with small genomes and low chromosome numbers such as those observed in many annual angiosperms, including Arabidopsis. Mark W Chase, Rosabelle Samuel, Andrew R Leitch, Maïté S Guignard, John G Conran, Felipe Nollet, Paul Fletcher, Aljaž Jakob, Luiz A Cauz-Santos, Gabriel Vignolle, Steven Dodsworth, Maarten J M Christenhusz, Maria Teresa Buril, Ovidiu Pau

Large-scale unit commitment under uncertainty: an updated literature survey

The Unit Commitment problem in energy management aims at finding the optimal production schedule of a set of generation units, while meeting various system-wide constraints. It has always been a large-scale, non-convex, difficult problem, especially in view of the fact that, due to operational requirements, it has to be solved in an unreasonably small time for its size. Recently, growing renewable energy shares have strongly increased the level of uncertainty in the system, making the (ideal) Unit Commitment model a large-scale, non-convex and uncertain (stochastic, robust, chance-constrained) program. We provide a survey of the literature on methods for the Uncertain Unit Commitment problem, in all its variants. We start with a review of the main contributions on solution methods for the deterministic versions of the problem, focussing on those based on mathematical programming techniques that are more relevant for the uncertain versions of the problem. We then present and categorize the approaches to the latter, while providing entry points to the relevant literature on optimization under uncertainty. This is an updated version of the paper "Large-scale Unit Commitment under uncertainty: a literature survey" that appeared in 4OR 13(2), 115--171 (2015); this version has over 170 more citations, most of which appeared in the last three years, proving how fast the literature on uncertain Unit Commitment evolves, and therefore the interest in this subject

Climate change impacts on a sedimentary coast—a regional synthesis from genes to ecosystems

AbstractClimate change effects on coastal ecosystems vary on large spatial scales, but can also be highly site dependent at the regional level. The Wadden Sea in the south-eastern North Sea is warming faster than many other temperate coastal areas, with surface seawater temperature increasing by almost 2 °C over the last 60 years, nearly double the global ocean mean increase. Climate warming is accompanied by rising sea levels, which have increased by approximately 2 mm yr−1 over the last 120 years. For this sedimentary coast, the predicted acceleration of sea-level rise will have profound effects on tidal dynamics and bathymetry in the area. This paper synthesises studies of the effects of ocean warming and sea level rise in the northern Wadden Sea, largely based on research conducted at the Wadden Sea Station Sylt of the Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research. An increasing rate of sea level rise above a critical threshold will lead to coastal erosion and changes in sediment composition, and may cause the transition from a tidal to lagoon-like environment as tidal flats submerge. This involves changes to coastal morphology, and the decline of important habitats such as muddy tidal flats, salt marshes and seagrass meadows, as well as their ecological services (e.g. carbon sequestration). Ocean warming affects plankton dynamics and phenology, as well as benthic community structure by hampering cold-adapted but facilitating warm-adapted species. The latter consist mostly of introduced non-native species originating from warmer coasts, with some epibenthic species acting as ecosystem engineers that create novel habitats on the tidal flats. Warming also changes interactions between species by decoupling existing predator–prey dynamics, as well as forming new interactions in which mass mortalities caused by parasites and pathogens can play an understudied but essential role. However, Wadden Sea organisms can adapt to changing abiotic and biotic parameters via genetic adaptation and phenotypic plasticity, which can also be inherited across generations (transgenerational plasticity), enabling faster plastic responses to future conditions. Important research advances have been made using next-generation molecular tools (-omics), mesocosm experiments simulating future climate scenarios, modelling approaches (ecological network analysis), and internet-based technologies for data collection and archiving. By synthesising these climate change impacts on multiple levels of physical and biological organisation in the northern Wadden Sea, we reveal knowledge gaps that need to be addressed by future investigations and comparative studies in other regions in order to implement management, mitigation and restoration strategies to preserve the uniqueness of this ecosystem of global importance.</jats:p