Hybridization selects for prime‐numbered life cycles in Magicicada: An individual‐based simulation model of a structured periodical cicada population

We investigate competition between separate periodical cicada populations each possessing different life‐cycle lengths. We build an individual‐based model to simulate the cicada life cycle and allow random migrations to occur between patches inhabited by the different populations. We show that if hybridization between different cycle lengths produces offspring that have an intermediate life‐cycle length, then predation acts disproportionately to select against the hybrid offspring. This happens because they emerge in low densities without the safety‐in‐numbers provided by either parent population. Thus, prime‐numbered life cycles that can better avoid hybridization are favored. However, we find that this advantage of prime‐numbered cycles occurs only if there is some mechanism that can occasionally synchronize emergence between local populations in sufficiently many patches.     

Population genetics of Setaria viridis,a new model system

An extensive survey of the standing genetic variation in natural populations is among the priority steps in developing a species into a model system. In recent years, green foxtail (Setaria viridis), along with its domesticated form foxtail millet (S. italica), has rapidly become a promising new model system for C₄ grasses and bioenergy crops, due to its rapid life cycle, large amount of seed production and small diploid genome, among other characters. However, remarkably little is known about the genetic diversity in natural populations of this species. In this study, we survey the genetic diversity of a worldwide sample of more than 200 S. viridis accessions, using the genotyping‐by‐sequencing technique. Two distinct genetic groups in S. viridis and a third group resembling S. italica were identified, with considerable admixture among the three groups. We find the genetic variation of North American S. viridis correlates with both geography and climate and is representative of the total genetic diversity in this species. This pattern may reflect several introduction/dispersal events of S. viridis into North America. We also modelled demographic history and show signal of recent population decline in one subgroup. Finally, we show linkage disequilibrium decay is rapid (<45 kb) in our total sample and slow in genetic subgroups. These results together provide an in‐depth understanding of the pattern of genetic diversity of this new model species on a broad geographic scale. They also provide key guidelines for on‐going and future work including germplasm preservation, local adaptation, crossing designs and genomewide association studies.     

Glucose metabolism down‐regulates the uptake of 6‐(N‐(7‐nitrobenz‐2‐oxa‐1,3‐diazol‐4‐yl)amino)‐2‐deoxyglucose (6‐NBDG) mediated by glucose transporter 1 isoform (GLUT1): theory and simulations using the symmetric four‐state carrier model

The non‐metabolizable fluorescent glucose analogue 6‐(N‐(7‐nitrobenz‐2‐oxa‐1,3‐diazol‐4‐yl)amino)‐2‐deoxyglucose (6‐NBDG) is increasingly used to study cellular transport of glucose. Intracellular accumulation of exogenously applied 6‐NBDG is assumed to reflect concurrent gradient‐driven glucose uptake by glucose transporters (GLUTs). Here, theoretical considerations are provided that put this assumption into question. In particular, depending on the microscopic parameters of the carrier proteins, theory proves that changes in glucose transport can be accompanied by opposite changes in flow of 6‐NBDG. Simulations were carried out applying the symmetric four‐state carrier model on the GLUT1 isoform, which is the only isoform whose kinetic parameters are presently available. Results show that cellular 6‐NBDG uptake decreases with increasing rate of glucose utilization under core‐model conditions, supported by literature, namely where the transporter is assumed to work in regime of slow reorientation of the free‐carrier compared with the ligand–carrier complex. To observe an increase of 6‐NBDG uptake with increasing rate of glucose utilization, and thus interpret 6‐NBDG increase as surrogate of glucose uptake, the transporter must be assumed to operate in regime of slow ligand–carrier binding, a condition that is currently not supported by literature. Our findings suggest that the interpretation of data obtained with NBDG derivatives is presently ambiguous and should be cautious because the underlying transport kinetics are not adequately established.     

A metabolic signature for long life in the Caenorhabditis elegans Mit mutants

Mit mutations that disrupt function of the mitochondrial electron transport chain can, inexplicably, prolong Caenorhabditis elegans lifespan. In this study we use a metabolomics approach to identify an ensemble of mitochondrial‐derived α‐ketoacids and α‐hydroxyacids that are produced by long‐lived Mit mutants but not by other long‐lived mutants or by short‐lived mitochondrial mutants. We show that accumulation of these compounds is dependent on concerted inhibition of three α‐ketoacid dehydrogenases that share dihydrolipoamide dehydrogenase (DLD) as a common subunit, a protein previously linked in humans with increased risk of Alzheimer's disease. When the expression of DLD in wild‐type animals was reduced using RNA interference we observed an unprecedented effect on lifespan – as RNAi dosage was increased lifespan was significantly shortened, but, at higher doses, it was significantly lengthened, suggesting that DLD plays a unique role in modulating length of life. Our findings provide novel insight into the origin of the Mit phenotype.     

Evaluation of the ECOSSE model for simulating soil organic carbon under Miscanthus and short rotation coppice‐willow crops in Britain

In this paper, we focus on the impact on soil organic carbon (SOC) of two dedicated energy crops: perennial grass Miscanthus x Giganteus (Miscanthus) and short rotation coppice (SRC)‐willow. The amount of SOC sequestered in the soil is a function of site‐specific factors including soil texture, management practices, initial SOC levels and climate; for these reasons, both losses and gains in SOC were observed in previous Miscanthus and SRC‐willow studies. The ECOSSE model was developed to simulate soil C dynamics and greenhouse gas emissions in mineral and organic soils. The performance of ECOSSE has already been tested at site level to simulate the impacts of land‐use change to short rotation forestry (SRF) on SOC. However, it has not been extensively evaluated under other bioenergy plantations, such as Miscanthus and SRC‐willow. Twenty‐nine locations in the United Kingdom, comprising 19 paired transitions to SRC‐willow and 20 paired transitions to Miscanthus, were selected to evaluate the performance of ECOSSE in predicting SOC and SOC change from conventional systems (arable and grassland) to these selected bioenergy crops. The results of the present work revealed a strong correlation between modelled and measured SOC and SOC change after transition to Miscanthus and SRC‐willow plantations, at two soil depths (0–30 and 0–100 cm), as well as the absence of significant bias in the model. Moreover, model error was within (i.e. not significantly larger than) the measurement error. The high degrees of association and coincidence with measured SOC under Miscanthus and SRC‐willow plantations in the United Kingdom, provide confidence in using this process‐based model for quantitatively predicting the impacts of future land use on SOC, at site level as well as at national level.     

The role of ABC genes in shaping perianth phenotype in the basal angiosperm Magnolia

It is generally accepted that the genus Magnolia is characterised by an undifferentiated perianth, typically organised into three whorls of nearly identical tepals. In some species, however, we encountered interesting and significant perianth modifications. In Magnolia acuminata, M. liliiflora and M. stellata the perianth elements of the first whorl are visually different from the others. In M. stellata the additional, spirally arranged perianth elements are present above the first three whorls, which suggests that they have been formed within the domain of stamen primordia. In these three species, we analysed expression patterns of the key flower genes (AP1, AGL6, AP3, PI, AG) responsible for the identity of flower elements and correlated them with results of morphological and anatomical investigations. In all studied species the elements of the first whorl lacked the identity of petals (lack of AP3 and PI expression) but also that of leaves (presence of AGL6 expression), and this seems to prove their sepal character. The analysis of additional perianth elements of M. stellata, spirally arranged on the elongated floral axis, revealed overlapping and reduced activity of genes involved in specification of the identity of the perianth (AGL6) but also of generative parts (AG), even though no clear gradient of morphological changes could be observed. In conclusion, Magnolia genus is capable of forming, in some species, a perianth differentiated into a calyx (sepals) and corolla (petals). Spirally arranged, additional perianth elements of M. stellata, despite activity of AG falling basipetally, resemble petals.     

Modification,Biological Evaluation and SAR Studies of Novel 1H‐Pyrazol Derivatives Containing N,N′‐Disubstituted Urea Moiety as Potential Anti‐melanoma Agents

Malignant melanomas are amongst the most aggressive cancers. BRAF Inhibitors have exhibited therapeutic effects against BRAF‐mutant melanoma. In continuation of our earlier studies on anti‐melanoma agents based on 1H‐pyrazole skeleton, two sets of novel compounds that include 1H‐pyrazole‐4‐amines FA 1 – FA13 and corresponding urea derivatives FN 1 – FN13 have been synthesized and evaluated for their BRAF^V600E inhibitory and antiproliferation activities. Compound FN 10 displayed the most potent biological activity against BRAF^V600E (IC₅₀ = 0.066 μm ) and the A375 human melanoma cell line (GI₅₀ = 0.81 μm ), which was comparable to the positive control vemurafenib, and more potent than our previously reported 1H‐pyrazole‐3‐amines and their urea derivatives. The results of SAR studies and molecular docking can guide further optimization and may help to improve potency of these pyrazole‐based anti‐melanoma agents.     

SNP development from RNA‐seq data in a nonmodel fish: how many individuals are needed for accurate allele frequency prediction?

Single nucleotide polymorphisms (SNPs) are rapidly becoming the marker of choice in population genetics due to a variety of advantages relative to other markers, including higher genomic density, data quality, reproducibility and genotyping efficiency, as well as ease of portability between laboratories. Advances in sequencing technology and methodologies to reduce genomic representation have made the isolation of SNPs feasible for nonmodel organisms. RNA‐seq is one such technique for the discovery of SNPs and development of markers for large‐scale genotyping. Here, we report the development of 192 validated SNP markers for parentage analysis in Tripterygion delaisi (the black‐faced blenny), a small rocky‐shore fish from the Mediterranean Sea. RNA‐seq data for 15 individual samples were used for SNP discovery by applying a series of selection criteria. Genotypes were then collected from 1599 individuals from the same population with the resulting loci. Differences in heterozygosity and allele frequencies were found between the two data sets. Heterozygosity was lower, on average, in the population sample, and the mean difference between the frequencies of particular alleles in the two data sets was 0.135 ± 0.100. We used bootstrap resampling of the sequence data to predict appropriate sample sizes for SNP discovery. As cDNA library production is time‐consuming and expensive, we suggest that using seven individuals for RNA sequencing reduces the probability of discarding highly informative SNP loci, due to lack of observed polymorphism, whereas use of more than 12 samples does not considerably improve prediction of true allele frequencies.     

Multilocus patterns of genetic variation across Cryptosporidium species suggest balancing selection at the gp60 locus

Cryptosporidium is an apicomplexan protozoan that lives in most vertebrates, including humans. Its gp60 gene is functionally involved in its attachment to host cells, and its high level of genetic variation has made it the reference marker for sample typing in epidemiological studies. To understand the origin of such high diversity and to determine the extent to which this classification applies to the rest of the genome, we analysed the patterns of variation at gp60 and nine other nuclear loci in isolates of three Cryptosporidium species. Most loci showed low genetic polymorphism (π_S <1%) and similar levels of between‐species divergence. Contrastingly, gp60 exhibited very different characteristics: (i) it was nearly ten times more variable than the other loci; (ii) it displayed a significant excess of polymorphisms relative to between‐species differences in a maximum‐likelihood Hudson–Kreitman–Aguadé test; (iii) gp60 subtypes turned out to be much older than the species they were found in; and (iv) showed a significant excess of polymorphic variants shared across species from random expectations. These observations suggest that this locus evolves under balancing selection and specifically under negative frequency‐dependent selection (FDS). Interestingly, genetic variation at the other loci clusters very well within the groups of isolates defined by gp60 subtypes, which may provide new tools to understand the genome‐wide patterns of genetic variation of the parasite in the wild. These results suggest that gp60 plays an active and essential role in the life cycle of the parasite and that genetic variation at this locus might be essential for the parasite's long‐term success.     

RAD‐sequencing for estimating genomic relatedness matrix‐based heritability in the wild: A case study in roe deer

Estimating the evolutionary potential of quantitative traits and reliably predicting responses to selection in wild populations are important challenges in evolutionary biology. The genomic revolution has opened up opportunities for measuring relatedness among individuals with precision, enabling pedigree‐free estimation of trait heritabilities in wild populations. However, until now, most quantitative genetic studies based on a genomic relatedness matrix (GRM) have focused on long‐term monitored populations for which traditional pedigrees were also available, and have often had access to knowledge of genome sequence and variability. Here, we investigated the potential of RAD‐sequencing for estimating heritability in a free‐ranging roe deer (Capreolous capreolus) population for which no prior genomic resources were available. We propose a step‐by‐step analytical framework to optimize the quality and quantity of the genomic data and explore the impact of the single nucleotide polymorphism (SNP) calling and filtering processes on the GRM structure and GRM‐based heritability estimates. As expected, our results show that sequence coverage strongly affects the number of recovered loci, the genotyping error rate and the amount of missing data. Ultimately, this had little effect on heritability estimates and their standard errors, provided that the GRM was built from a minimum number of loci (above 7,000). Genomic relatedness matrix‐based heritability estimates thus appear robust to a moderate level of genotyping errors in the SNP data set. We also showed that quality filters, such as the removal of low‐frequency variants, affect the relatedness structure of the GRM, generating lower h² estimates. Our work illustrates the huge potential of RAD‐sequencing for estimating GRM‐based heritability in virtually any natural population.     

Estimation of vegetation photosynthetic capacity from space‐based measurements of chlorophyll fluorescence for terrestrial biosphere models

Photosynthesis simulations by terrestrial biosphere models are usually based on the Farquhar's model, in which the maximum rate of carboxylation (V_cmax) is a key control parameter of photosynthetic capacity. Even though V_cmax is known to vary substantially in space and time in response to environmental controls, it is typically parameterized in models with tabulated values associated to plant functional types. Remote sensing can be used to produce a spatially continuous and temporally resolved view on photosynthetic efficiency, but traditional vegetation observations based on spectral reflectance lack a direct link to plant photochemical processes. Alternatively, recent space‐borne measurements of sun‐induced chlorophyll fluorescence (SIF) can offer an observational constraint on photosynthesis simulations. Here, we show that top‐of‐canopy SIF measurements from space are sensitive to V_cmax at the ecosystem level, and present an approach to invert V_cmax from SIF data. We use the Soil‐Canopy Observation of Photosynthesis and Energy (SCOPE) balance model to derive empirical relationships between seasonal V_cmax and SIF which are used to solve the inverse problem. We evaluate our V_cmax estimation method at six agricultural flux tower sites in the midwestern US using spaced‐based SIF retrievals. Our V_cmax estimates agree well with literature values for corn and soybean plants (average values of 37 and 101 μmol m^?2 s^?1, respectively) and show plausible seasonal patterns. The effect of the updated seasonally varying V_cmax parameterization on simulated gross primary productivity (GPP) is tested by comparing to simulations with fixed V_cmax values. Validation against flux tower observations demonstrate that simulations of GPP and light use efficiency improve significantly when our time‐resolved V_cmax estimates from SIF are used, with R² for GPP comparisons increasing from 0.85 to 0.93, and for light use efficiency from 0.44 to 0.83. Our results support the use of space‐based SIF data as a proxy for photosynthetic capacity and suggest the potential for global, time‐resolved estimates of V_cmax.     

The use of CO2 flux time series for parameter and carbon stock estimation in carbon cycle research

Data assimilation (DA) is increasingly being employed to estimate the parameters and states of terrestrial ecosystem models from eddy covariance measurements of net carbon (C) fluxes. The length of the observation time series used varies for each study. The impact of these differences has not been quantified explicitly. Therefore, in this study, we investigate the importance of the time series length relative to observation noise and data gaps. Different length synthetic time series are used to determine the parameter and C stocks of a simple ecosystem C model. Two commonly used DA schemes are tested: the sequential Ensemble Kalman Filter (EnKF) and a batch Metropolis Markov chain Monte Carlo algorithm. Longer time series improve both the parameter and C pool estimates of the EnKF, while adversely affecting those of the Metropolis algorithm. For both DA approaches, the length of the time series has more influence on the parameter and pool estimates than the level of random noise or amount of data. In this study, the EnKF provides more robust parameter and C pool estimates than the Metropolis algorithm. Optimized parameters and states are often used as the basis for forecasting future responses. Despite having better parameter and C pool estimates, EnKF forecasts estimates have much larger uncertainties than the Metropolis algorithm forecast estimates. Finally, we suggest that the structure of simple box models, as used in this study, introduces a large degree of equifinality into DA. Neither DA scheme correctly accounts for the equifinality, but our results suggest that it is particularly problematic for the batch Metropolis algorithm.     

Combining hyperspectral imaging and chemometrics to assess and interpret the effects of environmental stressors on zebrafish eye images at tissue level

Changes on an organism by the exposure to environmental stressors may be characterized by hyperspectral images (HSI), which preserve the morphology of biological samples, and suitable chemometric tools. The approach proposed allows assessing and interpreting the effect of contaminant exposure on heterogeneous biological samples monitored by HSI at specific tissue levels. In this work, the model example used consists of the study of the effect of the exposure of chlorpyrifos‐oxon on zebrafish tissues. To assess this effect, unmixing of the biological sample images followed by tissue‐specific classification models based on the unmixed spectral signatures is proposed. Unmixing and classification are performed by multivariate curve resolution‐alternating least squares (MCR‐ALS) and partial least squares‐discriminant analysis (PLS‐DA), respectively. Crucial aspects of the approach are: (1) the simultaneous MCR‐ALS analysis of all images from 1 population to take into account biological variability and provide reliable tissue spectral signatures, and (2) the use of resolved spectral signatures from control and exposed populations obtained from resampling of pixel subsets analyzed by MCR‐ALS multiset analysis as information for the tissue‐specific PLS‐DA classification models. Classification results diagnose the presence of a significant effect and identify the spectral regions at a tissue level responsible for the biological change.      

Engineering fire blight resistance into the apple cultivar ‘Gala’ using the FB_MR5 CC‐NBS‐LRR resistance gene of Malus × robusta 5

The fire blight susceptible apple cultivar Malus × domestica Borkh. cv. ‘Gala’ was transformed with the candidate fire blight resistance gene FB_MR5 originating from the crab apple accession Malus × robusta 5 (Mr5). A total of five different transgenic lines were obtained. All transgenic lines were shown to be stably transformed and originate from different transgenic events. The transgenic lines express the FB_MR5 either driven by the constitutive CaMV 35S promoter and the ocs terminator or by its native promoter and terminator sequences. Phenotyping experiments were performed with Mr5‐virulent and Mr5‐avirulent strains of Erwinia amylovora, the causal agent of fire blight. Significantly less disease symptoms were detected on transgenic lines after inoculation with two different Mr5‐avirulent E. amylovora strains, while significantly more shoot necrosis was observed after inoculation with the Mr5‐virulent mutant strain ZYRKD3_1. The results of these experiments demonstrated the ability of a single gene isolated from the native gene pool of apple to protect a susceptible cultivar from fire blight. Furthermore, this gene is confirmed to be the resistance determinant of Mr5 as the transformed lines undergo the same gene‐for‐gene interaction in the host–pathogen relationship Mr5–E. amylovora.     

Bacterial iturins mediate biocontrol activity of Bacillus sp. against postharvest pear fruit‐rotting fungi

A potential antagonist, Bacillus sp. LYLB4 isolated from pear fruits, was tested for its antifungal activity against postharvest pear pathogens. LYLB4 had a remarkable antifungal effect on Botryosphaeria dothidea. Although it showed a weak inhibition effect on the growth of Rhizopus stolonifer on potato dextrose agar (PDA) plates, LYLB4 almost completely destroyed R. stolonifer during direct contact in potato dextrose broth (PDB). LYLB4 treatment was able to significantly reduce disease incidence (by 68.9% and 100%, respectively) and lesion diameter (by 68.7% and 100%, respectively) of ring rot caused by B. dothidea and soft rot caused by R. stolonifer in pears. LYLB4 also suppressed several other phytopathogens in vitro, suggesting a broad‐spectrum antagonistic activity against fungal pathogens. 16S rRNA and gyrA sequence analysis indicated that LYLB4 is closely related to B. velezensis. Genome mining indicated that LYLB4 had 11 secondary metabolites encoding clusters, but that the surfactin and fengycin gene clusters may not be functional because of a large deletion. Matrix‐assisted laser desorption ionization‐time of flight mass spectra (MALDI‐TOF‐MS) demonstrated that iturins were the major lipopeptides, and that C₁₆/C₁₇ Bacillomycin D synthesis was stimulated when LYLB4 was co‐cultured with B. dothidea compared to the control. Overall, these results demonstrate that the main biocontrol mechanism adopted by LYLB4 could be through the production of toxic metabolites and direct contact with pathogens.     

How climate,migration ability and habitat fragmentation affect the projected future distribution of European beech

Recent efforts to incorporate migration processes into species distribution models (SDMs) are allowing assessments of whether species are likely to be able to track their future climate optimum and the possible causes of failing to do so. Here, we projected the range shift of European beech over the 21st century using a process‐based SDM coupled to a phenomenological migration model accounting for population dynamics, according to two climate change scenarios and one land use change scenario. Our model predicts that the climatically suitable habitat for European beech will shift north‐eastward and upward mainly because (i) higher temperature and precipitation, at the northern range margins, will increase survival and fruit maturation success, while (ii) lower precipitations and higher winter temperature, at the southern range margins, will increase drought mortality and prevent bud dormancy breaking. Beech colonization rate of newly climatically suitable habitats in 2100 is projected to be very low (1–2% of the newly suitable habitats colonised). Unexpectedly, the projected realized contraction rate was higher than the projected potential contraction rate. As a result, the realized distribution of beech is projected to strongly contract by 2100 (by 36–61%) mainly due to a substantial increase in climate variability after 2050, which generates local extinctions, even at the core of the distribution, the frequency of which prevents beech recolonization during more favourable years. Although European beech will be able to persist in some parts of the trailing edge of its distribution, the combined effects of climate and land use changes, limited migration ability, and a slow life‐history are likely to increase its threat status in the near future.