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Spatially separate populations may exhibit synchronised dynamics as a result of correlated environmental influences. Here, Massie et al. show that this phenomenon, known as the Moran effect, can be enhanced if the environmental signals experienced by two populations differ in their noise colour.

Individuals with schizophrenia show reduced structural similarity in temporal, cingulate, and insular lobes, especially those with worse cognition and symptoms, affecting late maturing association areas with low metabolism and high neurotransmission.

Simultaneous profiling of spatial transcriptomics (ST) and metabolomics (SM) offers a novel way to decode tissue microenvironment heterogeneity. Here, the authors present SpatialMETA, a conditional variational autoencoder-based framework designed for the integration of ST and SM data.

The identification of top spatially variable genes is a key step in the analysis of spatially-resolved transcriptomics data. Here, the authors develop a scalable method based on nearest-neighbor Gaussian processes and evaluate performance compared to existing and baseline methods.

Access to green space has been a critical, and contentious, issue for neighbourhood inequality and health outcomes. This Analysis looks at how the COVID-19 pandemic interacts with availability of nature for urban residents.

uMAIA is an analytical framework designed to enable the construction of metabolic atlases at high resolution using mass spectrometry imaging data.

Cardiomyocytes are the dominant initiators of a type I interferon response in the infarct borderzone.

Machine-learning algorithms trained on 25,000 geolocated soil samples are used to create high-resolution global maps of mycorrhizal fungi, revealing that less than 10% of their biodiversity hotspots are in protected areas.

Wu, Zhang and colleagues introduce ‘compare and contrast spatial transcriptomics’ (CoCo-ST), a graph contrastive learning-based method for spatial transcriptomics analysis that detects low-variance structures.

The traditional structural transformation narrative emphasizes intersectoral labour reallocation out of agriculture. This study presents ten stylized facts about how employment and compensation evolve within agrifood value chains amid structural transformation, offering insights into post-farmgate dynamics and gender pay inequality.

Ritter et al. present a spatial transcriptomics and deep learning-based approach named NePSTA (neuropathology spatial transcriptomic analysis) and leverage it to improve neuropathological diagnostics and enhance central nervous system tumor subtype classification.

Analyses of soil microbiomes across the United States reveal pervasive multidimensional specialization and generalization across prokaryotic communities impacting evolutionary trajectories, microbial dominance and community roles.

Malaria infection risk is complex to quantify, partly because polyclonal as well as asymptomatic infections are common. Here, the authors use parasite genotyping data from a prospective cohort study in Mali to estimate infection incidence at the strain level and explore risk factors associated with heterogeneous infection rates.

Spapros is a probe set selection pipeline for targeted spatial transcriptomics that optimizes for both transcriptional and within-cell type variation.

Phylogenetic analysis of trait heritability (PATH) applies phylogenetic correlations to single-cell lineage tracing data, quantifying cell state plasticity and transition probabilities. PATH offers insights into cell state heritability and transition dynamics in cancers.

Evolutionary models can help understand how the spatial arrangement of a population shapes its evolutionary dynamics. This study presents such a method and shows that the spatial architectures of stem cell populations in bone marrow are suppressors of selection, hinting at a potential evolutionary design.

Multimodal DNA methylation and transcriptome profiling of single glioma cells links tumor cell transcriptional states to epigenetics via interaction with PRC2 and shows that these states are heritable and important for tumor plasticity.

Ultrasensitive, spatially-resolved proteomics techniques allow mapping the organisation of healthy and diseased tissues. Here, the authors develop a workflow for spatially-resolved, quantitative tissue proteomics with spatially aware statistics and clustering, with which they characterise a human atypical teratoid-rhabdoid tumour at different spatial resolutions.

TopoVelo infers cell differentiation stages and rate parameters of gene expression using spatially coupled differential equations.

A consumption-based carbon accounting method that takes into account how national policy changes affect emissions redraws the global emissions map.

The quark structure of the f₀(980) hadron is still unknown after 50 years of its discovery. Here, the CMS Collaboration reports a measurement of the elliptic flow of the f₀(980) state in proton-lead collisions at a nucleon-nucleon centre-of-mass energy of 8.16 TeV, providing strong evidence that the state is an ordinary meson.

Here, Schuldt et al. collate data from two long-term grassland and forest biodiversity experiments to ask how plant diversity facets affect the diversity of higher trophic levels. The results show that positive effects of plant diversity on consumer diversity are mediated by plant structural and functional diversity, and vary across ecosystems and trophic levels.

The role of developmental pathways in medulloblastoma tumours (MB) with sonic hedgehog (SHH) activation remains to be explored. Here, the authors perform multi-omic analysis and characterise the key transcriptomic and metabolic patterns of highly differentiated cells in SHH MBs.

This study presents a global map of predicted insect mitochondrial genetic diversity from cytochrome c oxidase subunit 1 sequences. From over 2 million mtDNA sequences, they find a negative quadratic latitudinal gradient in genetic diversity evenness, peaking in the subtropics and correlating with hot, stable environments.

Spatial visualization of metabolites in tissues via mass spectrometry imaging can be prone to user perception bias. Here, the authors report the computational framework moleculaR that introduces probabilistic data-dependent molecular mapping of nonrandom spatial patterns of metabolite signals.

Geographic location can be a key determinant of human health outcomes. Here, the authors show that in large-scale trials, randomization that is pair matched by geography can lead to substantial improvements in statistical efficiency and enable insights into spatially varying intervention effects.

Digitisation of vast archives of histology slides provides opportunities to use machine learning to identify specific tissue substructures associated with disease. Here the authors use self-supervised learning on 1.7 million histology images from 23 human tissues. The model segments tissues, detects pathologies and predicts RNA expression, linking morphology and gene expression.

Perineural invasion and cancer-induced nerve injury of tumour-associated nerves are associated with poor response to anti-PD-1 therapy, which can be reversed by combining anti-PD-1 therapy with anti-inflammatory interventions.

Differentiating neutrophil functional states is difficult. Here the authors show, using single cell RNA-sequencing and trajectory analyses, that mouse neutrophils can be presented as a transcriptome continuum rather than discrete subsets, but are affected by inflammation to express distinct transcriptional states.

Spatial omics reveal tissue structures and can aid patient stratification. The authors present a method to identify patterns in tissue patches, enabling analysis of disease progression and treatment response, while providing insights into spatial coordination at the cell-type or marker level.

Analysis of eight taxonomic groups across 186 islands and 423 mainland regions reveals that those with the greatest gross domestic product per capita, human population density and area have the highest established alien species richness, with the strongest effects on islands.

The physical organization of the genome in non-bilaterian animals and their closest unicellular relatives is characterized; comparative analysis shows chromatin looping is a conserved feature of genome architecture and spatial genome regulation emerged early in animal evolution.

Analysis of ground-sourced and satellite-derived models reveals a global forest carbon potential of 226 Gt outside agricultural and urban lands, with a difference of only 12% across these modelling approaches.

The long-term effectiveness of assisted gene flow of trees could be jeopardised by rapid climate change. Here the authors analyse a large dataset of relocated black spruce populations in Canada, finding that local adaptation to climate of origin improved NPP responses, but only for up to ~15 years after planting.

A common but untested expectation is that nutrient enrichment causes biotic homogenization. However, a globally standardized nutrient addition experiment in grasslands shows proportionally similar species loss across scales and no biotic homogenization after up to 14 years of treatment.

Biogeographic patterns of genetic diversity are poorly documented, especially for fish species. Here the authors show that (mitochondrial) genetic diversity has global spatial organization patterns with different environmental drivers for marine and freshwater fishes, where genetic diversity is only partly congruent with species richness.

Leroi et al. argue that neutral models, which are evolutionary models that do not involve a process of natural selection, must be applied with care, and that alternative methods are often needed to conclusively explain the diversity of variants.

This study presents a comprehensive evaluation of Xenium In Situ datasets and provides recommendations on analysis workflows.

Springtails are omnipresent soil arthropods, vital for ecosystems. In the first global assessment of springtails, this study shows a 20-fold biomass difference between the tundra and the tropics, with distinct temperature-related patterns for diversity and metabolism that suggest climate change may restructure the functioning of soil biodiversity.

Using prey size measurements from ten Southern Ocean lanternfish species sampled across >10° of latitude, this study shows that higher temperatures were associated with smaller fish and an overall decrease in the size of fish relative to their prey. Ocean warming may therefore alter the diversity and size structuring of trophic interactions, reducing the stability of marine ecosystems.