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Climate extremes cause significant winter wheat yield loss and can cause much greater impacts than single extremes in isolation when multiple extremes occur simultaneously. Here we show that compound hot-dry-windy events (HDW) significantly increased in the U.S. Great Plains from 1982 to 2020. These HDW events were the most impactful drivers for wheat yield loss, accounting for a 4% yield reduction per 10 h of HDW during heading to maturity. Current HDW trends are associated with yield reduction rates of up to 0.09 t ha -1 per decade and HDW variations are atmospheric-bridged with the Pacific Decadal Oscillation. We quantify the "yield shock", which is spatially distributed, with the losses in severely HDW-affected areas, presumably the same areas affected by the Dust Bowl of the 1930s. Our findings indicate that compound HDW, which traditional risk assessments overlooked, have significant implications for the U.S. winter wheat production and beyond., (© 2022. The Author(s).)

Advances in spectroscopy have the potential to improve our understanding of agricultural processes and associated trace gas emissions. We implement field-deployed, open-path dual-comb spectroscopy (DCS) for precise multispecies emissions estimation from livestock. With broad atmospheric dual-comb spectra, we interrogate upwind and downwind paths from pens containing approximately 300 head of cattle, providing time-resolved concentration enhancements and fluxes of CH 4 , NH 3 , CO 2 , and H 2 O. The methane fluxes determined from DCS data and fluxes obtained with a colocated closed-path cavity ring-down spectroscopy gas analyzer agree to within 6%. The NH 3 concentration retrievals have sensitivity of 10 parts per billion and yield corresponding NH3 fluxes with a statistical precision of 8% and low systematic uncertainty. Open-path DCS offers accurate multispecies agricultural gas flux quantification without external calibration and is easily extended to larger agricultural systems where point-sampling-based approaches are insufficient, presenting opportunities for field-scale biogeochemical studies and ecological monitoring., (Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).)

Contrary to previous assumptions that most mutations are deleterious, there is increasing evidence for persistence of large-effect mutations in natural populations. A possible explanation for these observations is that mutant phenotypes and fitness may depend upon the specific environmental conditions to which a mutant is exposed. Here, we tested this hypothesis by growing large-effect flowering time mutants of Arabidopsis thaliana in multiple field sites and seasons to quantify their fitness effects in realistic natural conditions. By constructing environment-specific fitness landscapes based on flowering time and branching architecture, we observed that a subset of mutations increased fitness, but only in specific environments. These mutations increased fitness via different paths: through shifting flowering time, branching, or both. Branching was under stronger selection, but flowering time was more genetically variable, pointing to the importance of indirect selection on mutations through their pleiotropic effects on multiple phenotypes. Finally, mutations in hub genes with greater connectedness in their regulatory networks had greater effects on both phenotypes and fitness. Together, these findings indicate that large-effect mutations may persist in populations because they influence traits that are adaptive only under specific environmental conditions. Understanding their evolutionary dynamics therefore requires measuring their effects in multiple natural environments., Competing Interests: The authors declare no conflict of interest., (Copyright © 2019 the Author(s). Published by PNAS.)

Ecophysiological crop models encode intra-species behaviors using parameters that are presumed to summarize genotypic properties of individual lines or cultivars. These genotype-specific parameters (GSP's) can be interpreted as quantitative traits that can be mapped or otherwise analyzed, as are more conventional traits. The goal of this study was to investigate the estimation of parameters controlling maize anthesis date with the CERES-Maize model, based on 5,266 maize lines from 11 plantings at locations across the eastern United States. High performance computing was used to develop a database of 356 million simulated anthesis dates in response to four CERES-Maize model parameters. Although the resulting estimates showed high predictive value (R2 = 0.94), three issues presented serious challenges for use of GSP's as traits. First (expressivity), the model was unable to express the observed data for 168 to 3,339 lines (depending on the combination of site-years), many of which ended up sharing the same parameter value irrespective of genetics. Second, for 2,254 lines, the model reproduced the data, but multiple parameter sets were equally effective (equifinality). Third, parameter values were highly dependent (p<10-6919) on the sets of environments used to estimate them (instability), calling in to question the assumption that they represent fundamental genetic traits. The issues of expressivity, equifinality and instability must be addressed before the genetic mapping of GSP's becomes a robust means to help solve the genotype-to-phenotype problem in crops.

In Chernobyl, chronic exposure to radioactive contaminants has a variety of deleterious effects on exposed organisms, including genetic damage and mutation accumulation. However, the potential for such effects to be transmitted to the next generation is poorly understood. We captured lesser marsh grasshoppers (Chorthippus albomarginatus) in the Chernobyl Exclusion Zone from sites varying in levels of environmental radiation by more than three orders of magnitude. We then raised their offspring in a common garden experiment in order to assess the effects of parental exposure to radiation on offspring development and DNA damage. Offspring that reached maturity at a younger age had higher levels of DNA damage. Contrary to our hypothesis, parental exposure to radioactive contamination did not affect DNA damage in their offspring possibly because of intervening adaptation or parental compensatory mechanisms. Our results suggest a trade-off between developmental rate and resistance to DNA damage, whereby offspring developing at faster rates do so at the cost of damaging their DNA. This result is consistent with and extends findings in other species, suggesting that faster growth rates cause increased oxidative damage and stress. We propose that growth rates are subject to stabilizing selection balancing the benefits of fast development and the competing need of buffering its damaging effects to macromolecules and tissues.

Circadian clocks have evolved independently in all three domains of life, suggesting that internal mechanisms of time-keeping are adaptive in contemporary populations. However, the performance consequences of either discrete or quantitative clock variation have rarely been tested in field settings. Clock sensitivity of diverse segregating lines to the environment remains uncharacterized as do the statistical genetic parameters that determine evolutionary potential. In field studies with Arabidopsis thaliana, we found that major perturbations to circadian cycle length (referred to as clock period) via mutation reduce both survival and fecundity. Subtler adjustments via genomic introgression of naturally occurring alleles indicated that clock periods slightly >24 hr were adaptive, consistent with prior models describing how well the timing of biological processes is adjusted within a diurnal cycle (referred to as phase). In segregating recombinant inbred lines (RILs), circadian phase varied up to 2 hr across months of the growing season, and both period and phase expressed significant genetic variances. Performance metrics including developmental rate, size and fruit set were described by principal components (PC) analyses and circadian parameters correlated with the first PC, such that period lengths slightly >24 hr were associated with improved performance in multiple RIL sets. These experiments translate functional analyses of clock behaviour performed in controlled settings to natural ones, demonstrating that quantitative variation in circadian phase is highly responsive to seasonally variable abiotic factors. The results expand upon prior studies in controlled settings, showing that discrete and quantitative variation in clock phenotypes correlates with performance in nature., (© 2017 John Wiley & Sons Ltd.)

The genetic basis of growth and development is often studied in constant laboratory environments; however, the environmental conditions that organisms experience in nature are often much more dynamic. We examined how daily temperature fluctuations, average temperature, day length and vernalization influence the flowering time of 59 genotypes of Arabidopsis thaliana with allelic perturbations known to affect flowering time. For a subset of genotypes, we also assessed treatment effects on morphology and growth. We identified 17 genotypes, many of which have high levels of the floral repressor FLOWERING LOCUS C (FLC), that bolted dramatically earlier in fluctuating - as opposed to constant - warm temperatures (mean = 22°C). This acceleration was not caused by transient VERNALIZATION INSENSITIVE 3-mediated vernalization, differential growth rates or exposure to high temperatures, and was not apparent when the average temperature was cool (mean = 12°C). Further, in constant temperatures, contrary to physiological expectations, these genotypes flowered more rapidly in cool than in warm environments. Fluctuating temperatures often reversed these responses, restoring faster bolting in warm conditions. Independently of bolting time, warm fluctuating temperature profiles also caused morphological changes associated with shade avoidance or 'high-temperature' phenotypes. Our results suggest that previous studies have overestimated the effect of the floral repressor FLC on flowering time by using constant temperature laboratory conditions., (© 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.)

Unlabelled: In evaluating conservation and management options for species, practitioners might consider surrogate habitats at multiple scales when estimating available habitat or modeling species' potential distributions based on suitable habitats, especially when native environments are rare. Species' dependence on surrogates likely increases as optimal habitat is degraded and lost due to anthropogenic landscape change, and thus surrogate habitats may be vital for an imperiled species' survival in highly modified landscapes. We used spatial habitat models to examine a potential surrogate habitat for an imperiled ambush predator (eastern diamondback rattlesnake, Crotalus adamanteus; EDB) at two scales. The EDB is an apex predator indigenous to imperiled longleaf pine ecosystems (Pinus palustris) of the southeastern United States. Loss of native open-canopy pine savannas and woodlands has been suggested as the principal cause of the species' extensive decline. We examined EDB habitat selection in the Coastal Plain tidewater region to evaluate the role of marsh as a potential surrogate habitat and to further quantify the species' habitat requirements at two scales: home range (HR) and within the home range (WHR). We studied EDBs using radiotelemetry and employed an information-theoretic approach and logistic regression to model habitat selection as use vs., Availability: We failed to detect a positive association with marsh as a surrogate habitat at the HR scale; rather, EDBs exhibited significantly negative associations with all landscape patches except pine savanna. Within home range selection was characterized by a negative association with forest and a positive association with ground cover, which suggests that EDBs may use surrogate habitats of similar structure, including marsh, within their home ranges. While our HR analysis did not support tidal marsh as a surrogate habitat, marsh may still provide resources for EDBs at smaller scales.

Locally adapted genotypes have higher fitness in their native site in comparison to foreign genotypes. Recent studies have demonstrated both local adaptation to and genomic associations with a range of climate variables. For climate adaptation, the most common genomic pattern is conditional neutrality, as proven by weak across-environment correlations, frequent SNP×environment interactions, and the topology of some developmental and physiological pathways potentially involved in local adaptation. Genomic association approaches readily translate to non-model systems, and genetically explicit climate envelope models will predict future species' distributions under changing climates. Here, we review recent evidence for local adaptation to climate, focusing primarily on the model system, Arabidopsis thaliana, and on studies incorporating genomic tools into field studies or climate analyses., (Published by Elsevier Ltd.)

Groundwater provides a reliable tap to sustain agricultural production, yet persistent aquifer depletion threatens future sustainability. The High Plains Aquifer supplies 30% of the nation's irrigated groundwater, and the Kansas portion supports the congressional district with the highest market value for agriculture in the nation. We project groundwater declines to assess when the study area might run out of water, and comprehensively forecast the impacts of reduced pumping on corn and cattle production. So far, 30% of the groundwater has been pumped and another 39% will be depleted over the next 50 y given existing trends. Recharge supplies 15% of current pumping and would take an average of 500-1,300 y to completely refill a depleted aquifer. Significant declines in the region's pumping rates will occur over the next 15-20 y given current trends, yet irrigated agricultural production might increase through 2040 because of projected increases in water use efficiencies in corn production. Water use reductions of 20% today would cut agricultural production to the levels of 15-20 y ago, the time of peak agricultural production would extend to the 2070s, and production beyond 2070 would significantly exceed that projected without reduced pumping. Scenarios evaluate incremental reductions of current pumping by 20-80%, the latter rate approaching natural recharge. Findings substantiate that saving more water today would result in increased net production due to projected future increases in crop water use efficiencies. Society has an opportunity now to make changes with tremendous implications for future sustainability and livability.

Selection on quantitative trait loci (QTL) may vary among natural environments due to differences in the genetic architecture of traits, environment-specific allelic effects or changes in the direction and magnitude of selection on specific traits. To dissect the environmental differences in selection on life history QTL across climatic regions, we grew a panel of interconnected recombinant inbred lines (RILs) of Arabidopsis thaliana in four field sites across its native European range. For each environment, we mapped QTL for growth, reproductive timing and development. Several QTL were pleiotropic across environments, three colocalizing with known functional polymorphisms in flowering time genes (CRY2, FRI and MAF2-5), but major QTL differed across field sites, showing conditional neutrality. We used structural equation models to trace selection paths from QTL to lifetime fitness in each environment. Only three QTL directly affected fruit number, measuring fitness. Most QTL had an indirect effect on fitness through their effect on bolting time or leaf length. Influence of life history traits on fitness differed dramatically across sites, resulting in different patterns of selection on reproductive timing and underlying QTL. In two oceanic field sites with high prereproductive mortality, QTL alleles contributing to early reproduction resulted in greater fruit production, conferring selective advantage, whereas alleles contributing to later reproduction resulted in larger size and higher fitness in a continental site. This demonstrates how environmental variation leads to change in both QTL effect sizes and direction of selection on traits, justifying the persistence of allelic polymorphism at life history QTL across the species range., (© 2013 John Wiley & Sons Ltd.)

This paper describes a new computational method to make predictions on the outcome of pair-wise crosses of plant lines limiting expensive laboratory breeding experiments to carry out crosses of the most promising pairs of lines. Compared to the well-known marker assisted breeding, the proposed approach approximates plant gene regulatory networks to estimate outcomes of all possible crossovers, thereby taking into account epistatic relationships between alleles. The proposed method is tested and compare with various breeding approaches on artificial NK landscape models and an extensive synthetic model of Arabidopsis plant's flowering time system. The results show our method outperforms other breeding strategies.

Mutagenic and epigenetic effects of environmental stressors and their transgenerational consequences are of interest to evolutionary biologists because they can amplify natural genetic variation. We studied the effect of parental exposure to radioactive contamination on offspring development in lesser marsh grasshopper Chorthippus albomarginatus. We used a geometric morphometric approach to measure fluctuating asymmetry (FA), wing shape and wing size. We measured time to sexual maturity to check whether parental exposure to radiation influenced offspring developmental trajectory and tested effects of radiation on hatching success and parental fecundity. Wings were larger in early maturing individuals born to parents from high radiation sites compared to early maturing individuals from low radiation sites. As time to sexual maturity increased, wing size decreased but more sharply in individuals from high radiation sites. Radiation exposure did not significantly affect FA or shape in wings nor did it significantly affect hatching success and fecundity. Overall, parental radiation exposure can adversely affect offspring development and fitness depending on developmental trajectories although the cause of this effect remains unclear. We suggest more direct measures of fitness and the inclusion of replication in future studies to help further our understanding of the relationship between developmental instability, fitness and environmental stress., (© 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.)

• In this study, we used a combination of theoretical (models) and experimental (field data) approaches to investigate the interaction between light and temperature signalling in the control of Arabidopsis flowering. • We utilised our recently published phenology model that describes the flowering time of Arabidopsis grown under a range of field conditions. We first examined the ability of the model to predict the flowering time of field plantings at different sites and seasons in light of the specific meteorological conditions that pertained. • Our analysis suggested that the synchrony of temperature and light cycles is important in promoting floral initiation. New features were incorporated into the model that improved its predictive accuracy across seasons. Using both laboratory and field data, our study has revealed an important seasonal effect of night temperatures on flowering time. Further model adjustments to describe phytochrome (phy) mutants supported our findings and implicated phyB in the temporal gating of temperature-induced flowering. • Our study suggests that different molecular pathways interact and predominate in natural environments that change seasonally. Temperature effects are mediated largely during the photoperiod during spring/summer (long days) but, as days shorten in the autumn, night temperatures become increasingly important., (© 2012 The Authors. New Phytologist © 2012 New Phytologist Trust.)

Preventable venous thromboembolism (VTE) and "appropriate" type, dose, and duration of prophylaxis are emerging concepts. Contemporary definitions by key quality organisations, including the World Health Organization, have shifted towards "preventable" VTE being considered an adverse event or adverse drug event. A decision tree and cost model were developed to estimate the United States health care costs for total deep-vein thrombosis (DVT), total hospital-acquired DVT, and total "preventable" DVT. Annual cost ranges were obtained in 2010 US dollars for total ($7.5 to $39.5 billion), hospital-acquired ($5 to $26.5 billion), and preventable ($2.5 to $19.5 billion) DVT costs. When the sensitivity analysis was applied--taking into consideration higher incidence rates and costs - annual US total, hospital-acquired, and "preventable" DVT costs ranged from $9.8 to $52 billion, $6.8 to $36 billion, and $3.4 to $27 billion, respectively.

The iPlant Collaborative (iPlant) is a United States National Science Foundation (NSF) funded project that aims to create an innovative, comprehensive, and foundational cyberinfrastructure in support of plant biology research (PSCIC, 2006). iPlant is developing cyberinfrastructure that uniquely enables scientists throughout the diverse fields that comprise plant biology to address Grand Challenges in new ways, to stimulate and facilitate cross-disciplinary research, to promote biology and computer science research interactions, and to train the next generation of scientists on the use of cyberinfrastructure in research and education. Meeting humanity's projected demands for agricultural and forest products and the expectation that natural ecosystems be managed sustainably will require synergies from the application of information technologies. The iPlant cyberinfrastructure design is based on an unprecedented period of research community input, and leverages developments in high-performance computing, data storage, and cyberinfrastructure for the physical sciences. iPlant is an open-source project with application programming interfaces that allow the community to extend the infrastructure to meet its needs. iPlant is sponsoring community-driven workshops addressing specific scientific questions via analysis tool integration and hypothesis testing. These workshops teach researchers how to add bioinformatics tools and/or datasets into the iPlant cyberinfrastructure enabling plant scientists to perform complex analyses on large datasets without the need to master the command-line or high-performance computational services.

A liquid nitrogen jet-cooled thermal modulator dedicated to comprehensive two-dimensional gas chromatography has been mounted in a GC oven coupled to a high resolution magnetic sector mass spectrometry instrument. The data acquisition parameters of the slow double-focusing magnetic sector MS instrument have been optimized to accommodate the description of the narrow modulated GC peaks. Acquisition rates were increased to 20Hz, while maintaining high mass resolution. Selected ion monitoring (SIM) descriptors, typically including several ions for both native and labeled analytes, were thus reduced to one or two to ensure enough MS cycle time. For maximization of the sensitivity enhancement due to cryogenic zone compression (CZC), the entire GC peak of interest was trapped and remobilized in one event. Optimization of the method resulted in the ability to detect low attogram (ag) amounts of 2,3,7,8-tetrachlorodibenzo-p-dioxin (2,3,7,8-TCDD) (313ag gives a S/N of 400:1), a level that had not yet been attained using classical GC-HRMS. An isotope-dilution calibration curve was constructed using (13)C(12)-2,3,7,8-TCDD as the internal standard over the range of 500ag/μL to 35,000ag/μL (R(2)=0.9953). Analyses of a standard natural human reference serum-matrix NIST SRM 1589a containing 223ag of 1,2,3,7,8-pentachlorodibenzo-p-dioxin (1,2,3,7,8-PeCDD) (70% recovery rate assumed) resulted in a peak with a S/N of 188:1 (4 sigma, m/z=355.8546). Measurement of 2,2-bis (4-chlorophenyl-1,1,1-trichloroethane) (DDE) and 2,2',4,4',5,5'-hexabromobiphenyl (BB-153) in human dried-blood spot (DBS) samples is also reported to illustrate the usefulness of such a sensitive technique. Finally, some of the challenges related to sample preparation, blank levels, and to the fact of measuring of such a limited number of molecules (less than 600,000 TCDD molecules) are discussed., (Copyright © 2010 Elsevier B.V. All rights reserved.)

We are now reaching the stage at which specific genetic factors with known physiological effects can be tied directly and quantitatively to variation in phenology. With such a mechanistic understanding, scientists can better predict phenological responses to novel seasonal climates. Using the widespread model species Arabidopsis thaliana, we explore how variation in different genetic pathways can be linked to phenology and life-history variation across geographical regions and seasons. We show that the expression of phenological traits including flowering depends critically on the growth season, and we outline an integrated life-history approach to phenology in which the timing of later life-history events can be contingent on the environmental cues regulating earlier life stages. As flowering time in many plants is determined by the integration of multiple environmentally sensitive gene pathways, the novel combinations of important seasonal cues in projected future climates will alter how phenology responds to variation in the flowering time gene network with important consequences for plant life history. We discuss how phenology models in other systems--both natural and agricultural--could employ a similar framework to explore the potential contribution of genetic variation to the physiological integration of cues determining phenology.

Like many species, the model plant Arabidopsis thaliana exhibits multiple different life histories in natural environments. We grew mutants impaired in different signaling pathways in field experiments across the species' native European range in order to dissect the mechanisms underlying this variation. Unexpectedly, mutational loss at loci implicated in the cold requirement for flowering had little effect on life history except in late-summer cohorts. A genetically informed photothermal model of progression toward flowering explained most of the observed variation and predicted an abrupt transition from autumn flowering to spring flowering in late-summer germinants. Environmental signals control the timing of this transition, creating a critical window of acute sensitivity to genetic and climatic change that may be common for seasonally regulated life history traits.

This paper presents a hybrid algorithm based on Genetic Programming (GP) and Particle Swarm Optimisation (PSO) for the automated recovery of gene network structure. It uses gene expression time series data as well as phenotypic data pertaining to plant flowering time as its input data. The algorithm then attempts to discover simple structures to approximate the plant gene regulatory networks that produce model gene expressions and flowering times that closely resemble the input data. To show the efficacy of the proposed approach, simulation results applied to flowering time control in Arabidopsis thaliana are demonstrated and discussed.

Considerable effort has been invested in determining traits underlying invasiveness. Yet, identifying a set of traits that commonly confers invasiveness in a range of species has proven elusive, and almost nothing is known about genetic loci affecting invasive success. Incorporating genetic model organisms into ecologically relevant studies is one promising avenue to begin dissecting the genetic underpinnings of invasiveness. Molecular biologists are rapidly characterizing genes mediating developmental responses to diverse environmental cues, i.e., genes for plasticity, as well as to environmental factors likely to impose strong selection on invading species, e.g., resistance to herbivores and competitors, coordination of life-history events with seasonal changes, and physiological tolerance of heat, drought, or cold. Here, we give an overview of molecular genetic tools increasingly used to characterize the genetic basis of adaptation and that may be used to begin identifying genetic mechanisms of invasiveness. Given the divergent traits that affect invasiveness, "invasiveness genes" common to many clades are unlikely, but the combination of developmental genetic advances with further evolutionary studies and modeling may provide a framework for identifying genes that account for invasiveness in related species.

Caves have been used in the ancient past as shelter or habitat by many organisms (including humans). Since antiquity, humans have explored caves for the minerals they contain and sometimes for ceremonial purposes. Over the past century, caves have become the target of increasing exploration, scientific research, and recreation. The use of caves on extraterrestrial bodies for human habitation has been suggested by several investigators. Lunar lava tube bases received early attention because lava tubes were clearly visible in lunar images from the Apollo Era. More recently, Mars Observer Camera data has shown us clear evidence of large tubes visible in a number of volcanic regions on Mars. The budding field of cave geomicrobiology has direct application to questions about subsurface life on other planets. Caves contain many unusual organisms making their living from unlikely materials like manganese, iron, and sulfur. This makes caves and other subsurface habitats prime targets for astrobiological missions to Mars and possibly other bodies. We present the results of a completed Phase I and on-going Phase II NASA Institute for Advanced Concepts (NIAC) study that intensively examines the possibilities of using extraterrestrial caves as both a resource for human explorers and as a highly promising scientific target for both robotic and future human missions to Mars and beyond.

Rotating disk electrode (RDE) voltammetry was used to examine the effect of N-methyl-D-aspartate (NMDA) on the initial velocity of dopamine (DA) uptake in suspensions of rat striatal tissue. Transport velocities were determined by measuring the rate of clearance of 2 microM DA added to the tissue suspension. NMDA (200 microM) was found to increase the initial velocity of DA transport from 548 +/- 28 to 803 +/- 63 pmol/s per g tissue (mean +/- SEM; P < 0.005). The increase was reversed by the competitive NMDA antagonist AP5, and thus appears to be receptor-mediated. In a separate experiment, lower concentrations of NMDA (20-100 microM) yielded a high correlation (r = 0.96; P < 0.05) of velocity versus concentration. Kainic acid (10 microM) also was found to increase the initial rate of uptake, from 505 +/- 34 to 702 +/- 71 pmol/s per g (P < 0.05). The results of this study indicate that the rate of DA uptake in the striatum can be modulated in vitro by presynaptic ionotropic glutamate receptors.