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cellSTAAR advances noncoding rare variant association analysis by integrating single-cell genomics data.

A study of over 36,000 villages in Indonesia shows that palm oil eco-certification reduces poverty in market-oriented villages but increases it in subsistence villages.

MultiSTAAR provides a general and flexible statistical framework for functionally informed multi-trait rare variant analysis of biobank-scale sequencing studies by jointly analyzing multiple traits and incorporating annotation information.

Genome-wide ancient DNA data from individuals from the Middle Bronze Age to Iron Age documents large-scale movement of people from the European continent between 1300 and 800 bc that was probably responsible for spreading early Celtic languages to Britain.

China’s agricultural output is growing rapidly, but the environmental impacts are unclear. This study finds this impact has risen, but much more slowly than output due to improved farm management, though ongoing shifts in cropland location may challenge this development.

This research quantifies the role of zero deforestation policies and potential leakages in Brazilian soybean production, the third major driver of deforestation globally. Here the authors provide the first estimates of net global avoided soy-driven deforestation from zero-deforestation import restrictions and find that such restrictions could help avoid ~40% of deforestation for soy cultivation in Brazil and ~2% of global deforestation.

The goals, resources and design of the NHLBI Trans-Omics for Precision Medicine (TOPMed) programme are described, and analyses of rare variants detected in the first 53,831 samples provide insights into mutational processes and recent human evolutionary history.

A dataset of 3D images from more than 200,000 human induced pluripotent stem cells is used to develop a framework to analyse cell shape and the location and organization of major intracellular structures.

Indonesia accounts for a large proportion of the oil palm plantation expansion occurring globally. However, Indonesia’s mixed forests (and associated carbon stocks) complicate estimation of the contribution of oil palm agriculture to global carbon budgets. Remotely sensed land-cover classification combined with carbon flux estimates are now used to develop high-resolution estimates of carbon flux from Kalimantan plantations for the period 1990–2010.

Genome-wide association analyses based on whole-genome sequencing and imputation identify 40 new risk variants for colorectal cancer, including a strongly protective low-frequency variant at CHD1 and loci implicating signaling and immune function in disease etiology.

Dysregulation of ribonucleoprotein complex granules, previously implicated in neuromuscular disease, can drive pathogenesis in a genetic form of dilated cardiomyopathy, as shown in gene-edited pigs and patient-derived cardiomyocytes.

Ancient DNA reveals genetic differences between stone-tool users and people associated with ceramic technology in the Caribbean and provides substantially lower estimates of population sizes in the region before European contact.

The blooming alga Emiliania huxleyi and its viruses are a model for density-dependent virulent dynamics. However, Knowles et al. show that this host–virus system exhibits temperate dynamics at natural host densities, in a manner dependent on host physiology.

Genome-wide data from 166 East Asian individuals dating to between 6000 bc and ad 1000 and from 46 present-day groups provide insights into the histories of mixture and migration of human populations in East Asia.

The potential for enhanced sediment delivery to the Ganges-Brahmaputra delta exists, but it alone is insufficient to sustain the system. The delta may be resilient to climate change, but only in the absence of dam construction and water diversions.

A global model finds that the environmental impacts of the food system could increase by 60–90% by 2050, and that dietary changes, improvements in technologies and management, and reductions in food loss and waste will all be needed to mitigate these impacts.

Analysis of whole-genome sequences of 25,465 individuals of European ancestry shows that rare variants contribute substantially to the heritability of height and body mass index.

Pecan is an important specialty crop that has experienced extensive interspecific hybridization and nearly-obligate outcrossing. Here, the authors assemble diploid genomes of four outbred genotypes, identify interspecific introgressions through comparative genomics analyses, and map QTLs associated with pest resistance.

STAARpipeline is a comprehensive framework for flexible and scalable rare-variant association analysis using whole-genome sequencing data and annotation information.

Genetic analyses of ancestrally diverse populations show evidence of heterogeneity across ancestries and provide insights into clinical implications, highlighting the importance of including ancestrally diverse populations to maximize genetic discovery and reduce health disparities.

Independent smallholder farmers without exclusive contracts with specific mills were underrepresented at certified palm oil mills, and they contributed one-third of regional oil palm production, according to an analysis using a conceptual model of market participation and palm oil data.

Primary production and degradative processes impact the carbon to nitrogen ratio of particulate organic matter with depth, according to analysis of seawater samples from the northwest Sargasso Sea.

Global high-resolution crop-specific estimates of greenhouse gas emissions intensity (in 2000) reveal that certain cropping practices contribute disproportionately to emissions, making them suitable targets for climate mitigation policies.

STAAR is a powerful rare variant association test that incorporates variant functional categories and complementary functional annotations using a dynamic weighting scheme based on annotation principal components. STAAR accounts for population structure and relatedness and is scalable for analyzing large whole-genome sequencing studies.

Analysis of fecal samples from patients and mice, shows that chronic multisymptom illness which affects a subsection of elderly and war Veterans, is associated with alteration in genes related to antibiotic resistance.

A comprehensive overview of how oil palm expansion and production has impacted forests on an international scale.

In this Perspective, private company supply-chain initiatives designed to reduce deforestation are assessed. Public–private policy mixes are advocated to increase their efficacy.

Predatory niche and ecological trait space analyses identify modern humans as unique predators of vertebrates.