Global Institute for Water Security

An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage-related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.

This planetary boundaries framework update finds that six of the nine boundaries are transgressed, suggesting that Earth is now well outside of the safe operating space for humanity. Ocean acidification is close to being breached, while aerosol loading regionally exceeds the boundary. Stratospheric ozone levels have slightly recovered. The transgression level has increased for all boundaries earlier identified as overstepped. As primary production drives Earth system biosphere functions, human appropriation of net primary production is proposed as a control variable for functional biosphere integrity. This boundary is also transgressed. Earth system modeling of different levels of the transgression of the climate and land system change boundaries illustrates that these anthropogenic impacts on Earth system must be considered in a systemic context.

, water, and energy exchange between the biosphere and the atmosphere, and other meteorological and biological measurements, from 212 sites around the globe (over 1500 site-years, up to and including year 2014). These sites, independently managed and operated, voluntarily contributed their data to create global datasets. Data were quality controlled and processed using uniform methods, to improve consistency and intercomparability across sites. The dataset is already being used in a number of applications, including ecophysiology studies, remote sensing studies, and development of ecosystem and Earth system models. FLUXNET2015 includes derived-data products, such as gap-filled time series, ecosystem respiration and photosynthetic uptake estimates, estimation of uncertainties, and metadata about the measurements, presented for the first time in this paper. In addition, 206 of these sites are for the first time distributed under a Creative Commons (CC-BY 4.0) license. This paper details this enhanced dataset and the processing methods, now made available as open-source codes, making the dataset more accessible, transparent, and reproducible.

The Prediction in Ungauged Basins (PUB) initiative of the International Association of Hydrological Sciences (IAHS), launched in 2003 and concluded by the PUB Symposium 2012 held in Delft (23-25 October 2012), set out to shift the scientific culture of hydrology towards improved scientific understanding of hydrological processes, as well as associated uncertainties and the development of models with increasing realism and predictive power. This paper reviews the work that has been done under the six science themes of the PUB Decade and outlines the challenges ahead for the hydrological sciences community.

This paper is the outcome of a community initiative to identify major unsolved scientific problems in hydrology motivated by a need for stronger harmonisation of research efforts. The procedure involved a public consultation through online media, followed by two workshops through which a large number of potential science questions were collated, prioritised, and synthesised. In spite of the diversity of the participants (230 scientists in total), the process revealed much about community priorities and the state of our science: a preference for continuity in research questions rather than radical departures or redirections from past and current work. Questions remain focused on the process-based understanding of hydrological variability and causality at all space and time scales. Increased attention to environmental change drives a new emphasis on understanding how change propagates across interfaces within the hydrological system and across disciplinary boundaries. In particular, the expansion of the human footprint raises a new set of questions related to human interactions with nature and water cycle feedbacks in the context of complex water management problems. We hope that this reflection and synthesis of the 23 unsolved problems in hydrology will help guide research efforts for some years to come.

The coordinated expression of highly related homoeologous genes in polyploid species underlies the phenotypes of many of the world's major crops. Here we combine extensive gene expression datasets to produce a comprehensive, genome-wide analysis of homoeolog expression patterns in hexaploid bread wheat. Bias in homoeolog expression varies between tissues, with ~30% of wheat homoeologs showing nonbalanced expression. We found expression asymmetries along wheat chromosomes, with homoeologs showing the largest inter-tissue, inter-cultivar, and coding sequence variation, most often located in high-recombination distal ends of chromosomes. These transcriptionally dynamic genes potentially represent the first steps toward neo- or subfunctionalization of wheat homoeologs. Coexpression networks reveal extensive coordination of homoeologs throughout development and, alongside a detailed expression atlas, provide a framework to target candidate genes underpinning agronomic traits in wheat.

Time-resolved satellite gravimetry has revolutionized understanding of mass transport in the Earth system. Since 2002, the Gravity Recovery and Climate Experiment (GRACE) has enabled monitoring of the terrestrial water cycle, ice sheet and glacier mass balance, sea level change and ocean bottom pressure variations, as well as understanding responses to changes in the global climate system. Initially a pioneering experiment of geodesy, the time-variable observations have matured into reliable mass transport products, allowing assessment and forecast of a number of important climate trends, and improvements in service applications such as the United States Drought Monitor. With the successful launch of the GRACE Follow-On mission, a multi-decadal record of mass variability in the Earth system is within reach. The Gravity Recovery and Climate Experiment (GRACE) mission, launched in 2002, allows monitoring of changes in hydrology and the cryosphere with terrestrial and ocean applications. This Review Article focuses on its contribution to the detection and quantification of climate change signals.

Abstract Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat ( Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome 1 , and the lack of genome-assembly data for multiple wheat lines 2,3 . Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses 4,5 . We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm1 6 , a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars.

Climate extremes threaten human health, economic stability, and the well-being of natural and built environments (e.g., 2003 European heat wave). As the world continues to warm, climate hazards are expected to increase in frequency and intensity. The impacts of extreme events will also be more severe due to the increased exposure (growing population and development) and vulnerability (aging infrastructure) of human settlements. Climate models attribute part of the projected increases in the intensity and frequency of natural disasters to anthropogenic emissions and changes in land use and land cover. Here, we review the impacts, historical and projected changes,and theoretical research gaps of key extreme events (heat waves, droughts, wildfires, precipitation, and flooding). We also highlight the need to improve our understanding of the dependence between individual and interrelated climate extremes because anthropogenic-induced warming increases the risk of not only individual climate extremes but also compound (co-occurring) and cascading hazards. ▪ Climate hazards are expected to increase in frequency and intensity in a warming world. ▪ Anthropogenic-induced warming increases the risk of compound and cascading hazards. ▪ We need to improve our understanding of causes and drivers of compound and cascading hazards.

Genomics and domestication of wheat Modern wheat, which underlies the diet of many across the globe, has a long history of selection and crosses among different species. Avni et al. used the Hi-C method of genome confirmation capture to assemble and annotate the wild allotetraploid wheat ( Triticum turgidum ). They then identified the putative causal mutations in genes controlling shattering (a key domestication trait among cereal crops). They also performed an exome capture–based analysis of domestication among wild and domesticated genotypes of emmer wheat. The findings present a compelling overview of the emmer wheat genome and its usefulness in an agricultural context for understanding traits in modern bread wheat. Science , this issue p. 93

The domestication of wild emmer wheat led to the selection of modern durum wheat, grown mainly for pasta production. We describe the 10.45 gigabase (Gb) assembly of the genome of durum wheat cultivar Svevo. The assembly enabled genome-wide genetic diversity analyses revealing the changes imposed by thousands of years of empirical selection and breeding. Regions exhibiting strong signatures of genetic divergence associated with domestication and breeding were widespread in the genome with several major diversity losses in the pericentromeric regions. A locus on chromosome 5B carries a gene encoding a metal transporter (TdHMA3-B1) with a non-functional variant causing high accumulation of cadmium in grain. The high-cadmium allele, widespread among durum cultivars but undetected in wild emmer accessions, increased in frequency from domesticated emmer to modern durum wheat. The rapid cloning of TdHMA3-B1 rescues a wild beneficial allele and demonstrates the practical use of the Svevo genome for wheat improvement.

Abstract Global warming is expected to change the regime of extreme precipitation. Physical laws translate increasing atmospheric heat into increasing atmospheric water content that drives precipitation changes. Within the literature, general agreement is that extreme precipitation is changing, yet different assessment methods, data sets, and study periods may result in different patterns and rates of change. Here we perform a global analysis of 8,730 daily precipitation records focusing on the 1964–2013 period when the global warming accelerates. We introduce a novel analysis of the N largest extremes in records having N complete years within the study period. Based on these extremes, which represent more accurately heavy precipitation than annual maxima, we form time series of their annual frequency and mean annual magnitude. The analysis offers new insights and reveals (1) global and zonal increasing trends in the frequency of extremes that are highly unlikely under the assumption of stationarity and (2) magnitude changes that are not as evident. Frequency changes reveal a coherent spatial pattern with increasing trends being detected in large parts of Eurasia, North Australia, and the Midwestern United States. Globally, over the last decade of the studied period we find 7% more extreme events than the expected number. Finally, we report that changes in magnitude are not in general correlated with changes in frequency.

Sensitivity analysis (SA) is en route to becoming an integral part of mathematical modeling. The tremendous potential benefits of SA are, however, yet to be fully realized, both for advancing mechanistic and data-driven modeling of human and natural systems, and in support of decision making. In this perspective paper, a multidisciplinary group of researchers and practitioners revisit the current status of SA, and outline research challenges in regard to both theoretical frameworks and their applications to solve real-world problems. Six areas are discussed that warrant further attention, including (1) structuring and standardizing SA as a discipline, (2) realizing the untapped potential of SA for systems modeling, (3) addressing the computational burden of SA, (4) progressing SA in the context of machine learning, (5) clarifying the relationship and role of SA to uncertainty quantification, and (6) evolving the use of SA in support of decision making. An outlook for the future of SA is provided that underlines how SA must underpin a wide variety of activities to better serve science and society.

Abstract Risk management has reduced vulnerability to floods and droughts globally 1,2 , yet their impacts are still increasing 3 . An improved understanding of the causes of changing impacts is therefore needed, but has been hampered by a lack of empirical data 4,5 . On the basis of a global dataset of 45 pairs of events that occurred within the same area, we show that risk management generally reduces the impacts of floods and droughts but faces difficulties in reducing the impacts of unprecedented events of a magnitude not previously experienced. If the second event was much more hazardous than the first, its impact was almost always higher. This is because management was not designed to deal with such extreme events: for example, they exceeded the design levels of levees and reservoirs. In two success stories, the impact of the second, more hazardous, event was lower, as a result of improved risk management governance and high investment in integrated management. The observed difficulty of managing unprecedented events is alarming, given that more extreme hydrological events are projected owing to climate change 3 .

Key Points Celerity is faster than velocity Watershed models are evaluated only against celerity Velocity must be addressed in future watershed models

Winter conditions are rapidly changing in temperate ecosystems, particularly for those that experience periods of snow and ice cover. Relatively little is known of winter ecology in these systems, due to a historical research focus on summer 'growing seasons'. We executed the first global quantitative synthesis on under-ice lake ecology, including 36 abiotic and biotic variables from 42 research groups and 101 lakes, examining seasonal differences and connections as well as how seasonal differences vary with geophysical factors. Plankton were more abundant under ice than expected; mean winter values were 43.2% of summer values for chlorophyll a, 15.8% of summer phytoplankton biovolume and 25.3% of summer zooplankton density. Dissolved nitrogen concentrations were typically higher during winter, and these differences were exaggerated in smaller lakes. Lake size also influenced winter-summer patterns for dissolved organic carbon (DOC), with higher winter DOC in smaller lakes. At coarse levels of taxonomic aggregation, phytoplankton and zooplankton community composition showed few systematic differences between seasons, although literature suggests that seasonal differences are frequently lake-specific, species-specific, or occur at the level of functional group. Within the subset of lakes that had longer time series, winter influenced the subsequent summer for some nutrient variables and zooplankton biomass.

Abstract Groundwater recharged by meteoric water supports human life by providing two billion people with drinking water and by supplying 40% of cropland irrigation. While annual groundwater recharge rates are reported in many studies, fewer studies have explicitly quantified intra‐annual (i.e., seasonal) differences in groundwater recharge. Understanding seasonal differences in the fraction of precipitation that recharges aquifers is important for predicting annual recharge groundwater rates under changing seasonal precipitation and evapotranspiration regimes in a warming climate, for accurately interpreting isotopic proxies in paleoclimate records, and for understanding linkages between ecosystem productivity and groundwater recharge. Here we determine seasonal differences in the groundwater recharge ratio, defined here as the ratio of groundwater recharge to precipitation, at 54 globally distributed locations on the basis of 18 O/ 16 O and 2 H/ 1 H ratios in precipitation and groundwater. Our analysis shows that arid and temperate climates have wintertime groundwater recharge ratios that are consistently higher than summertime groundwater recharge ratios, while tropical groundwater recharge ratios are at a maximum during the wet season. The isotope‐based recharge ratio seasonality is consistent with monthly outputs from a global hydrological model (PCR‐GLOBWB) for most, but not all locations. The pronounced seasonality in groundwater recharge ratios shown in this study signifies that, from the point of view of predicting future groundwater recharge rates, a unit change in winter (temperate and arid regions) or wet season (tropics) precipitation will result in a greater change to the annual groundwater recharge rate than the same unit change to summer or dry season precipitation.

Sequence assembly of large and repeat-rich plant genomes has been challenging, requiring substantial computational resources and often several complementary sequence assembly and genome mapping approaches. The recent development of fast and accurate long-read sequencing by circular consensus sequencing (CCS) on the PacBio platform may greatly increase the scope of plant pan-genome projects. Here, we compare current long-read sequencing platforms regarding their ability to rapidly generate contiguous sequence assemblies in pan-genome studies of barley (Hordeum vulgare). Most long-read assemblies are clearly superior to the current barley reference sequence based on short-reads. Assemblies derived from accurate long reads excel in most metrics, but the CCS approach was the most cost-effective strategy for assembling tens of barley genomes. A downsampling analysis indicated that 20-fold CCS coverage can yield very good sequence assemblies, while even five-fold CCS data may capture the complete sequence of most genes. We present an updated reference genome assembly for barley with near-complete representation of the repeat-rich intergenic space. Long-read assembly can underpin the construction of accurate and complete sequences of multiple genomes of a species to build pan-genome infrastructures in Triticeae crops and their wild relatives.

Abstract Groundwater provides critical freshwater supply, particularly in dry regions where surface water availability is limited. Climate change impacts on GWS (groundwater storage) could affect the sustainability of freshwater resources. Here, we used a fully-coupled climate model to investigate GWS changes over seven critical aquifers identified as significantly distressed by satellite observations. We assessed the potential climate-driven impacts on GWS changes throughout the 21 st century under the business-as-usual scenario (RCP8.5). Results show that the climate-driven impacts on GWS changes do not necessarily reflect the long-term trend in precipitation; instead, the trend may result from enhancement of evapotranspiration, and reduction in snowmelt, which collectively lead to divergent responses of GWS changes across different aquifers. Finally, we compare the climate-driven and anthropogenic pumping impacts. The reduction in GWS is mainly due to the combined impacts of over-pumping and climate effects; however, the contribution of pumping could easily far exceed the natural replenishment.

N-(1,3-Dimethylbutyl)-N′-phenyl-p-phenylenediamine-quinone (6PPD-quinone), a transformation product of the rubber tire antioxidant 6PPD, has recently been identified as the chemical responsible for urban runoff mortality syndrome in coho salmon, with a median lethal concentration (LC50) of <0.1 μg/L. Subsequent studies have failed to confirm comparable sensitivity in other fish species. Here, we investigated the acute toxicity of 6PPD-quinone to rainbow trout, brook trout, Arctic char, and white sturgeon. Fish were exposed under static renewal conditions, and exposure concentrations were verified analytically. Mortalities in brook trout occurred between 1.2 and 20 h, while mortalities began after 7 h and spanned 60 h in rainbow trout. The LC50s in brook trout (24 h) and rainbow trout (72 h) were 0.59 and 1.00 μg/L, respectively. Both species showed characteristic symptoms (increased ventilation, gasping, spiraling, and loss of equilibrium) shortly before death. No mortalities were observed after exposure of either char or sturgeon for 96 h at measured concentrations as high as 14.2 μg/L. This is the first study to demonstrate the acute toxicity of 6PPD-quinone to other fishes of commercial, cultural, and ecological importance at environmentally relevant concentrations and provides urgently needed information for environmental risk assessments of this contaminant of emerging concern.