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Abstract In heterozygous genomes, allele-specific measurements can reveal biologically significant differences in DNA methylation between homologous alleles associated with local changes in genetic sequence. Current approaches for detecting such events from whole-genome bisulfite sequencing (WGBS) data perform statistically independent marginal analysis at individual cytosine-phosphate-guanine (CpG) sites, thus ignoring correlations in the methylation state, or carry-out a joint statistical analysis of methylation patterns at four CpG sites producing unreliable statistical evidence. Here, we employ the one-dimensional Ising model of statistical physics and develop a method for detecting allele-specific methylation (ASM) events within segments of DNA containing clusters of linked single-nucleotide polymorphisms (SNPs), called haplotypes. Comparisons with existing approaches using simulated and real WGBS data show that our method provides an improved fit to data, especially when considering large haplotypes. Importantly, the method employs robust hypothesis testing for detecting statistically significant imbalances in mean methylation level and methylation entropy, as well as for identifying haplotypes for which the genetic variant carries significant information about the methylation state. As such, our ASM analysis approach can potentially lead to biological discoveries with important implications for the genetics of complex human diseases. 

Atmospheric deposition is a major source of the nutrients sulfur and selenium to agricultural soils. Air pollution control and cleaner energy production have reduced anthropogenic emissions of sulfur and selenium, which has led to lower atmospheric deposition fluxes of these elements. Here, we use a global aerosol-chemistry-climate model to map recent (2005–2009) sulfur and selenium deposition, and project future (2095–2099) changes under two socioeconomic scenarios. Across the Northern Hemisphere, we find substantially decreased deposition to agricultural soils, by 70 to 90% for sulfur and by 55 to 80% for selenium. Recent trends in sulfur and selenium concentrations in USA streams suggest that catchment mass balances of these elements are already changing due to the declining atmospheric supply. Sustainable fertilizer management strategies will need to be developed to offset the decrease in atmospheric nutrient supply and ensure future food security and nutrition, while avoiding consequences for downstream aquatic ecosystems.