Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2.

DNA rearrangements resulting in human genome structural variants (SVs) are caused by diverse mutational mechanisms. We used long- and short-read sequencing technologies to investigate end products of de novo chromosome 17p11.2 rearrangements and query the molecular mechanisms underlying both recurrent and non-recurrent events. Evidence for an increased rate of clustered single-nucleotide variant (SNV) mutation in cis with non-recurrent rearrangements was found. Indel and SNV formation are associated with both copy-number gains and losses of 17p11.2, occur up to ∼1 Mb away from the breakpoint junctions, and favor C > G transversion substitutions; results suggest that single-stranded DNA is formed during the genesis of the SV and provide compelling support for a microhomology-mediated break-induced replication (MMBIR) mechanism for SV formation. Our data show an additional mutational burden of MMBIR consisting of hypermutation confined to the locus and manifesting as SNVs and indels predominantly within genes.

Membrane Lipids Augment Cell Envelope Stress Signaling via the MadRS System to Defend Against Antimicrobial Peptides and Antibiotics in Enterococcus faecalis.

Enterococci have evolved resistance mechanisms to protect their cell envelopes against bacteriocins and host cationic antimicrobial peptides (CAMPs) produced in the gastrointestinal environment. Activation of the membrane stress response has also been tied to resistance to the lipopeptide antibiotic daptomycin. However, the actual effectors mediating resistance have not been elucidated. Here, we show that the MadRS (formerly YxdJK) membrane antimicrobial peptide defense system controls a network of genes, including a previously uncharacterized three gene operon (madEFG) that protects the E. faecalis cell envelope from antimicrobial peptides. Constitutive activation of the system confers protection against CAMPs and daptomycin in the absence of a functional LiaFSR system and leads to persistence of cardiac microlesions in vivo. Moreover, changes in the lipid cell membrane environment alter CAMP susceptibility and expression of the MadRS system. Thus, we provide a framework supporting a multilayered envelope defense mechanism for resistance and survival coupled to virulence.

In pursuit of a better world: crop improvement and the CGIAR.

The CGIAR crop improvement (CI) programs, unlike commercial CI programs, which are mainly geared to profit though meeting farmers' needs, are charged with meeting multiple objectives with target populations that include both farmers and the community at large. We compiled the opinions from >30 experts in the private and public sector on key strategies, methodologies, and activities that could the help CGIAR meet the challenges of providing farmers with improved varieties while simultaneously meeting the goals of: (i) nutrition, health, and food security; (ii) poverty reduction, livelihoods, and jobs; (iii) gender equality, youth, and inclusion; (iv) climate adaptation and mitigation; and (v) environmental health and biodiversity. We review the crop improvement processes starting with crop choice, moving through to breeding objectives, production of potential new varieties, selection, and finally adoption by farmers. The importance of multidisciplinary teams working towards common objectives is stressed as a key factor to success. The role of the distinct disciplines, actors, and their interactions throughout the process from crop choice through to adoption by farmers is discussed and illustrated.

Increases in extreme heat stress in domesticated livestock species during the twenty-first century.

Anthropogenic climate change is expected to have major impacts on domesticated livestock, including increased heat stress in animals in both intensive and extensive livestock systems. We estimate the changes in the number of extreme heat stress days per year for animals raised outdoors that can be expected in the major domesticated animal species (cattle, sheep, goats, poultry, and pigs) across the globe during this century. We used the temperature humidity index as a proxy for heat stress, calculated using temperature and relative humidity data collated from an ensemble of CMIP6 climate model output for mid and end century. We estimate changes in the proportions of different livestock species that may be at increased risk of extreme heat stress under two contrasting greenhouse gas emission scenarios. Results are discussed in relation to changes in the suitability of different climate conditions for domesticated livestock during the current century. We find that by end century, extreme heat stress risk is projected to increase for all livestock species in many parts of the tropics and some of the temperate zones, and to become climatically more widespread, compared to 2000. Although adaptation options exist for both intensive and extensive livestock production systems, the increasing pervasiveness of extreme heat stress risk in the future will seriously challenge the viability of outdoor livestock keeping, particularly in the lower latitudes in lower and middle-income countries where the costs of adaptation may be challenging to address.

Multiple cropping systems of the world and the potential for increasing cropping intensity.

Multiple cropping, defined as harvesting more than once a year, is a widespread land management strategy in tropical and subtropical agriculture. It is a way of intensifying agricultural production and diversifying the crop mix for economic and environmental benefits. Here we present the first global gridded data set of multiple cropping systems and quantify the physical area of more than 200 systems, the global multiple cropping area and the potential for increasing cropping intensity. We use national and sub-national data on monthly crop-specific growing areas around the year 2000 (1998-2002) for 26 crop groups, global cropland extent and crop harvested areas to identify sequential cropping systems of two or three crops with non-overlapping growing seasons. We find multiple cropping systems on 135 million hectares (12% of global cropland) with 85 million hectares in irrigated agriculture. 34%, 13% and 10% of the rice, wheat and maize area, respectively are under multiple cropping, demonstrating the importance of such cropping systems for cereal production. Harvesting currently single cropped areas a second time could increase global harvested areas by 87-395 million hectares, which is about 45% lower than previous estimates. Some scenarios of intensification indicate that it could be enough land to avoid expanding physical cropland into other land uses but attainable intensification will depend on the local context and the crop yields attainable in the second cycle and its related environmental costs.

Climate change and variability impacts on grazing herds: Insights from a system dynamics approach for semi-arid Australian rangelands.

Grazing livestock are an important source of food and income for millions of people worldwide. Changes in mean climate and increasing climate variability are affecting grasslands' carrying capacity, thus threatening the livelihood of millions of people as well as the health of grassland ecosystems. Compared with cropping systems, relatively little is known about the impact of such climatic changes on grasslands and livestock productivity and the adaptation responses available to farmers. In this study, we analysed the relationship between changes in mean precipitation, precipitation variability, farming practices and grazing cattle using a system dynamics approach for a semi-arid Australian rangeland system. We found that forage production and animal stocking rates were significantly affected by drought intensities and durations as well as by long-term climate trends. After a drought event, herd size recovery times ranged from years to decades in the absence of proactive restocking through animal purchases. Decreases in the annual precipitation means or increases in the interannual (year-to-year) and intra-annual (month-to-month) precipitation variability, all reduced herd sizes. The contribution of farming practices versus climate effect on herd dynamics varied depending on the herd characteristics considered. Climate contributed the most to the variance in stocking rates, followed by forage productivity levels and feeding supplementation practices (with or without urea and molasses). While intensification strategies and favourable climates increased long-term herd sizes, they also resulted in larger reductions in animal numbers during droughts and raised total enteric methane emissions. In the face of future climate trends, the grazing sector will need to increase its adaptability. Understanding which farming strategies can be beneficial, where, and when, as well as the enabling mechanisms required to implement them, will be critical for effectively improving rangelands and the livelihoods of pastoralists worldwide.

Oxygen and RNA in stress-induced mutation.

Mechanisms of mutation upregulated by stress responses have been described in several organisms from bacteria to human. These mechanisms might accelerate genetic change specifically when cells are maladapted to their environment. Stress-induced mutation mechanisms differ in their genetic requirements from mutation in growing cells, occurring by different mechanisms in different assay systems, but having in common a requirement for the induction of stress-responses. Here, we review progress in two areas relevant to stress-response-dependent mutagenic DNA break repair mechanisms in Escherichia coli. First, we review evidence that relates mutation to transcription. This connection might allow mutagenesis in transcribed regions, including those relevant to any stress being experienced, opening the possibility that mutations could be targeted to regions where mutation might be advantageous under conditions of a specific stress. We review the mechanisms by which replication initiated by transcription can lead to mutation. Second, we review recent findings that, although stress-induced mutation does not require exogenous DNA-damaging agents, it does require the presence of damaged bases in DNA. For starved E. coli, endogenous oxygen radicals cause these altered bases. We postulate that damaged bases stall the replisome, which, we suggest, is required for DNA-polymerase exchange, allowing the action of low-fidelity DNA polymerases that promote mutation.

Climate change impacts on selected global rangeland ecosystem services.

Rangelands are Earth's dominant land cover and are important providers of ecosystem services. Reliance on rangelands is projected to grow, thus understanding the sensitivity of rangelands to future climates is essential. We used a new ecosystem model of moderate complexity that allows, for the first time, to quantify global changes expected in rangelands under future climates. The mean global annual net primary production (NPP) may decline by 10 g C m-2  year-1 in 2050 under Representative Concentration Pathway (RCP) 8.5, but herbaceous NPP is projected to increase slightly (i.e., average of 3 g C m-2  year-1 ). Responses vary substantially from place-to-place, with large increases in annual productivity projected in northern regions (e.g., a 21% increase in productivity in the US and Canada) and large declines in western Africa (-46% in sub-Saharan western Africa) and Australia (-17%). Soil organic carbon is projected to increase in Australia (9%), the Middle East (14%), and central Asia (16%) and decline in many African savannas (e.g., -18% in sub-Saharan western Africa). Livestock are projected to decline 7.5 to 9.6%, an economic loss of from $9.7 to $12.6 billion. Our results suggest that forage production in Africa is sensitive to changes in climate, which will have substantial impacts on the livelihoods of the more than 180 million people who raise livestock on those rangelands. Our approach and the simulation tool presented here offer considerable potential for forecasting future conditions, highlight regions of concern, and support analyses where costs and benefits of adaptations and policies may be quantified. Otherwise, the technical options and policy and enabling environment that are needed to facilitate widespread adaptation may be very difficult to elucidate.

Agricultural diversification as an important strategy for achieving food security in Africa.

Farmers in Africa have long adapted to climatic and other risks by diversifying their farming activities. Using a multi-scale approach, we explore the relationship between farming diversity and food security and the diversification potential of African agriculture and its limits on the household and continental scale. On the household scale, we use agricultural surveys from more than 28,000 households located in 18 African countries. In a next step, we use the relationship between rainfall, rainfall variability, and farming diversity to determine the available diversification options for farmers on the continental scale. On the household scale, we show that households with greater farming diversity are more successful in meeting their consumption needs, but only up to a certain level of diversity per ha cropland and more often if food can be purchased from off-farm income or income from farm sales. More diverse farming systems can contribute to household food security; however, the relationship is influenced by other factors, for example, the market orientation of a household, livestock ownership, nonagricultural employment opportunities, and available land resources. On the continental scale, the greatest opportunities for diversification of food crops, cash crops, and livestock are located in areas with 500-1,000 mm annual rainfall and 17%-22% rainfall variability. Forty-three percent of the African cropland lacks these opportunities at present which may hamper the ability of agricultural systems to respond to climate change. While sustainable intensification practices that increase yields have received most attention to date, our study suggests that a shift in the research and policy paradigm toward agricultural diversification options may be necessary.

Linking regional stakeholder scenarios and shared socioeconomic pathways: Quantified West African food and climate futures in a global context.

The climate change research community's shared socioeconomic pathways (SSPs) are a set of alternative global development scenarios focused on mitigation of and adaptation to climate change. To use these scenarios as a global context that is relevant for policy guidance at regional and national levels, they have to be connected to an exploration of drivers and challenges informed by regional expertise. In this paper, we present scenarios for West Africa developed by regional stakeholders and quantified using two global economic models, GLOBIOM and IMPACT, in interaction with stakeholder-generated narratives and scenario trends and SSP assumptions. We present this process as an example of linking comparable scenarios across levels to increase coherence with global contexts, while presenting insights about the future of agriculture and food security under a range of future drivers including climate change. In these scenarios, strong economic development increases food security and agricultural development. The latter increases crop and livestock productivity leading to an expansion of agricultural area within the region while reducing the land expansion burden elsewhere. In the context of a global economy, West Africa remains a large consumer and producer of a selection of commodities. However, the growth in population coupled with rising incomes leads to increases in the region's imports. For West Africa, climate change is projected to have negative effects on both crop yields and grassland productivity, and a lack of investment may exacerbate these effects. Linking multi-stakeholder regional scenarios to the global SSPs ensures scenarios that are regionally appropriate and useful for policy development as evidenced in the case study, while allowing for a critical link to global contexts.

Climate change mitigation through livestock system transitions.

Livestock are responsible for 12% of anthropogenic greenhouse gas emissions. Sustainable intensification of livestock production systems might become a key climate mitigation technology. However, livestock production systems vary substantially, making the implementation of climate mitigation policies a formidable challenge. Here, we provide results from an economic model using a detailed and high-resolution representation of livestock production systems. We project that by 2030 autonomous transitions toward more efficient systems would decrease emissions by 736 million metric tons of carbon dioxide equivalent per year (MtCO2e⋅y(-1)), mainly through avoided emissions from the conversion of 162 Mha of natural land. A moderate mitigation policy targeting emissions from both the agricultural and land-use change sectors with a carbon price of US$10 per tCO2e could lead to an abatement of 3,223 MtCO2e⋅y(-1). Livestock system transitions would contribute 21% of the total abatement, intra- and interregional relocation of livestock production another 40%, and all other mechanisms would add 39%. A comparable abatement of 3,068 MtCO2e⋅y(-1) could be achieved also with a policy targeting only emissions from land-use change. Stringent climate policies might lead to reductions in food availability of up to 200 kcal per capita per day globally. We find that mitigation policies targeting emissions from land-use change are 5 to 10 times more efficient--measured in "total abatement calorie cost"--than policies targeting emissions from livestock only. Thus, fostering transitions toward more productive livestock production systems in combination with climate policies targeting the land-use change appears to be the most efficient lever to deliver desirable climate and food availability outcomes.

Reducing emissions from agriculture to meet the 2 °C target.

More than 100 countries pledged to reduce agricultural greenhouse gas (GHG) emissions in the 2015 Paris Agreement of the United Nations Framework Convention on Climate Change. Yet technical information about how much mitigation is needed in the sector vs. how much is feasible remains poor. We identify a preliminary global target for reducing emissions from agriculture of ~1 GtCO2 e yr-1 by 2030 to limit warming in 2100 to 2 °C above pre-industrial levels. Yet plausible agricultural development pathways with mitigation cobenefits deliver only 21-40% of needed mitigation. The target indicates that more transformative technical and policy options will be needed, such as methane inhibitors and finance for new practices. A more comprehensive target for the 2 °C limit should be developed to include soil carbon and agriculture-related mitigation options. Excluding agricultural emissions from mitigation targets and plans will increase the cost of mitigation in other sectors or reduce the feasibility of meeting the 2 °C limit.

Biomass use, production, feed efficiencies, and greenhouse gas emissions from global livestock systems.

We present a unique, biologically consistent, spatially disaggregated global livestock dataset containing information on biomass use, production, feed efficiency, excretion, and greenhouse gas emissions for 28 regions, 8 livestock production systems, 4 animal species (cattle, small ruminants, pigs, and poultry), and 3 livestock products (milk, meat, and eggs). The dataset contains over 50 new global maps containing high-resolution information for understanding the multiple roles (biophysical, economic, social) that livestock can play in different parts of the world. The dataset highlights: (i) feed efficiency as a key driver of productivity, resource use, and greenhouse gas emission intensities, with vast differences between production systems and animal products; (ii) the importance of grasslands as a global resource, supplying almost 50% of biomass for animals while continuing to be at the epicentre of land conversion processes; and (iii) the importance of mixed crop­livestock systems, producing the greater part of animal production (over 60%) in both the developed and the developing world. These data provide critical information for developing targeted, sustainable solutions for the livestock sector and its widely ranging contribution to the global food system.

Addressing uncertainty in adaptation planning for agriculture.

We present a framework for prioritizing adaptation approaches at a range of timeframes. The framework is illustrated by four case studies from developing countries, each with associated characterization of uncertainty. Two cases on near-term adaptation planning in Sri Lanka and on stakeholder scenario exercises in East Africa show how the relative utility of capacity vs. impact approaches to adaptation planning differ with level of uncertainty and associated lead time. An additional two cases demonstrate that it is possible to identify uncertainties that are relevant to decision making in specific timeframes and circumstances. The case on coffee in Latin America identifies altitudinal thresholds at which incremental vs. transformative adaptation pathways are robust options. The final case uses three crop-climate simulation studies to demonstrate how uncertainty can be characterized at different time horizons to discriminate where robust adaptation options are possible. We find that impact approaches, which use predictive models, are increasingly useful over longer lead times and at higher levels of greenhouse gas emissions. We also find that extreme events are important in determining predictability across a broad range of timescales. The results demonstrate the potential for robust knowledge and actions in the face of uncertainty.

Mapping global cropland and field size.

A new 1 km global IIASA-IFPRI cropland percentage map for the baseline year 2005 has been developed which integrates a number of individual cropland maps at global to regional to national scales. The individual map products include existing global land cover maps such as GlobCover 2005 and MODIS v.5, regional maps such as AFRICOVER and national maps from mapping agencies and other organizations. The different products are ranked at the national level using crowdsourced data from Geo-Wiki to create a map that reflects the likelihood of cropland. Calibration with national and subnational crop statistics was then undertaken to distribute the cropland within each country and subnational unit. The new IIASA-IFPRI cropland product has been validated using very high-resolution satellite imagery via Geo-Wiki and has an overall accuracy of 82.4%. It has also been compared with the EarthStat cropland product and shows a lower root mean square error on an independent data set collected from Geo-Wiki. The first ever global field size map was produced at the same resolution as the IIASA-IFPRI cropland map based on interpolation of field size data collected via a Geo-Wiki crowdsourcing campaign. A validation exercise of the global field size map revealed satisfactory agreement with control data, particularly given the relatively modest size of the field size data set used to create the map. Both are critical inputs to global agricultural monitoring in the frame of GEOGLAM and will serve the global land modelling and integrated assessment community, in particular for improving land use models that require baseline cropland information. These products are freely available for downloading from the http://cropland.geo-wiki.org website.

Climate variability and vulnerability to climate change: a review.

The focus of the great majority of climate change impact studies is on changes in mean climate. In terms of climate model output, these changes are more robust than changes in climate variability. By concentrating on changes in climate means, the full impacts of climate change on biological and human systems are probably being seriously underestimated. Here, we briefly review the possible impacts of changes in climate variability and the frequency of extreme events on biological and food systems, with a focus on the developing world. We present new analysis that tentatively links increases in climate variability with increasing food insecurity in the future. We consider the ways in which people deal with climate variability and extremes and how they may adapt in the future. Key knowledge and data gaps are highlighted. These include the timing and interactions of different climatic stresses on plant growth and development, particularly at higher temperatures, and the impacts on crops, livestock and farming systems of changes in climate variability and extreme events on pest-weed-disease complexes. We highlight the need to reframe research questions in such a way that they can provide decision makers throughout the food system with actionable answers, and the need for investment in climate and environmental monitoring. Improved understanding of the full range of impacts of climate change on biological and food systems is a critical step in being able to address effectively the effects of climate variability and extreme events on human vulnerability and food security, particularly in agriculturally based developing countries facing the challenge of having to feed rapidly growing populations in the coming decades.

Enabling food system innovation: accelerators for change.

It is widely accepted that current food systems are not on a trajectory for achieving the Sustainable Development Goals by the end of the decade. Technological innovation will have a considerable role to play in different parts of the food system; many promising options exist or are in the pipeline, some of which may be highly disruptive to existing value chains. Scaling up the innovations required, at the same time as protecting those who may lose out in the short term, will require a strong enabling environment. Here we apply an existing framework of eight change accelerators to six case studies of historical agricultural innovation. We estimated the degree to which each accelerator had been addressed at some stage in the innovation process, as a measure of the gap between what was needed and what was achieved. For the innovations that are being taken to scale and widely utilized, these accelerator gaps are small. Uptake of other innovations is stalled, and for these we found large gaps for one or more of the eight accelerators. Impactful innovation processes address all eight change accelerators at some point, with different phasing of the accelerators depending on the nature of the technology and on the impact pathway being pursued. This simple framework, when used in combination with narratives of uptake based on theories of change and impact pathways, may provide an effective means of screening future innovation processes to help prioritize and guide investment that can lead to more resilient, sustainable and equitable food systems.

A global clustering of terrestrial food production systems.

Food production is at the heart of global sustainability challenges, with unsustainable practices being a major driver of biodiversity loss, emissions and land degradation. The concept of foodscapes, defined as the characteristics of food production along biophysical and socio-economic gradients, could be a way addressing those challenges. By identifying homologues foodscapes classes possible interventions and leverage points for more sustainable agriculture could be identified. Here we provide a globally consistent approximation of the world's foodscape classes. We integrate global data on biophysical and socio-economic factors to identify a minimum set of emergent clusters and evaluate their characteristics, vulnerabilities and risks with regards to global change factors. Overall, we find food production globally to be highly concentrated in a few areas. Worryingly, we find particularly intensively cultivated or irrigated foodscape classes to be under considerable climatic and degradation risks. Our work can serve as baseline for global-scale zoning and gap analyses, while also revealing homologous areas for possible agricultural interventions.

Potential for reduced methane and carbon dioxide emissions from livestock and pasture management in the tropics.

We estimate the potential reductions in methane and carbon dioxide emissions from several livestock and pasture management options in the mixed and rangeland-based production systems in the tropics. The impacts of adoption of improved pastures, intensifying ruminant diets, changes in land-use practices, and changing breeds of large ruminants on the production of methane and carbon dioxide are calculated for two levels of adoption: complete adoption, to estimate the upper limit to reductions in these greenhouse gases (GHGs), and optimistic but plausible adoption rates taken from the literature, where these exist. Results are expressed both in GHG per ton of livestock product and in Gt CO(2)-eq. We estimate that the maximum mitigation potential of these options in the land-based livestock systems in the tropics amounts to approximately 7% of the global agricultural mitigation potential to 2030. Using historical adoption rates from the literature, the plausible mitigation potential of these options could contribute approximately 4% of global agricultural GHG mitigation. This could be worth on the order of $1.3 billion per year at a price of $20 per t CO(2)-eq. The household-level and sociocultural impacts of some of these options warrant further study, however, because livestock have multiple roles in tropical systems that often go far beyond their productive utility.

Impacts of heat stress on global cattle production during the 21st century: a modelling study.

BACKGROUND: Heat stress in animals is one of the major climate change impacts on domesticated livestock raised in both intensive and extensive production systems. At temperatures higher than an animal's thermoneutral zone, heat stress can affect liveweight gain, milk yield, and fertility. Animal welfare may also be negatively affected by heat stress even in the absence of effects on productivity, at least in the short term. METHODS: We estimated the comparative statics change in the value of cattle milk and meat production from heat stress-induced losses at the global level, using climate scenario outputs for the middle (2045) and end of the century (2085). The loss estimates are based on bioenergetic equations that relate changes in dry matter intake (DMI) to both cold and hot, humid weather. DMI changes were estimated using CMIP6 climate data and linked to a global dataset containing information on livestock production systems, animal numbers, and region-specific and system-specific animal diets. Changes in DMI were converted to changes in milk and meat production and valued using early 20th century world prices (ie, constant 2005 US dollars). FINDINGS: For a high greenhouse-gas emission scenario (SSP5-8.5), production losses from heat stress were estimated to amount to $39·94 billion (95% CI 34·39-45·49 billion) per year by the end of the century, or 9·8% of the value of production of meat and milk from cattle in 2005. For a low emission scenario (SSP1-2.6), the value of production losses was $14·89 billion (12·62-16·95 billion) per year, or 3·7% of 2005 value. In both scenarios, losses in most tropical regions were projected to be far greater than they were in temperate regions. INTERPRETATION: Our results highlight the potential magnitude and extent of the adaptation efforts that will be necessary to combat the effects of increasing heat stress on cattle production during this century if food security challenges are to be minimised. Adaptations include switching to more heat-tolerant breeds and provision of shade, ventilation, and cooling systems. FUNDING: CGIAR Trust Fund and bilateral donors.