Science

Reconstructing clonal relationships among human cells is fundamental to understanding development, aging, and disease. Somatic mitochondrial DNA (mtDNA) mutations act as endogenous single-cell barcodes measurable alongside cell-state profiles, but lineage tracing has traditionally focused on high-heteroplasmy variants, which are easier to detect but few and potentially shaped by selection. Whether the more abundant lower-heteroplasmy variants encode bona fide lineage information has not been tested against an independent clonal reference. Using lentiviral barcoding of human hematopoietic cells to establish ground-truth clone identities, we show that after stringent molecule-level error filtering, mutation calls below 10% per-cell heteroplasmy account for roughly half of all lineage-informative calls. Retaining the full heteroplasmy spectrum approximately doubled the clonal-assignment area under the precision-recall curve relative to a >10% cutoff, and single-molecule-supported calls improved recovery when retained collectively. These findings establish lower-heteroplasmy mtDNA mutations as an abundant, bona fide record of clonal history, substantially expanding the clonal resolution attainable in human tissues without genetic engineering.

The steroid hormone 20-hydroxyecdysone (20E) controls molting and metamorphosis in arthropods, yet it also accumulates in plants, where its biosynthesis has remained unknown. We show that quinoa (Chenopodium quinoa) produces 20E through a seven-gene biosynthetic cluster encoding five cytochrome P450s, a fatty acid hydroxylase-like enzyme (FAH), and a 2-oxoglutarate-dependent dioxygenase (2OGD). Distinct mutant alleles, complementation crosses, and chemical rescue established FAH as essential for pathway entry, whereas natural accessions carrying a large cluster deletion lacked 20E and all detectable intermediates. Heterologous reconstruction in Nicotiana benthamiana demonstrated that the cluster is sufficient to convert lathosterol to 20E through an unusual FAH-catalyzed C6 oxidation and 2OGD-mediated C5 epimerization. Plants and arthropods therefore evolved distinct enzymatic routes to the same molecule. This pathway provides a blueprint for engineering 20E and defining its broader ecological functions.

Plasmodium cynomolgi is the closest relative of P. vivax and the primary experimental model for relapsing malaria, hypnozoite biology, and blood-stage drug susceptibility. Yet existing reference genomes remain fragmented, leaving structurally complex, AT-rich regions largely unresolved. We generated a chromosome-scale genome assembly for the K4-A7 cloned line of P. cynomolgi Berok by combining Hi-C chromosome conformation capture, Oxford Nanopore long reads, PacBio, and Illumina sequencing. The assembly spans 14 chromosomes plus mitochondrial and apicoplast genomes, with only seven unplaced minor contigs, the fewest for any non-P. falciparum Plasmodium genome, and an N50 of 3.06 Mb. Critically, this hybrid strategy resolved approximately 8 Mb of extremely AT-rich (~20% GC) sequence onto chromosomes 4, 8, and 13, anchoring what were previously unplaced or absent contigs into a continuous chromosomal framework. These subtelomere-like expansions (SLEs) constitute ~26.5% of the chromosomal genome and are enriched for PIR/VIR, STP1, variable surface antigen, and methyltransferase pseudogene families. Despite low gene density, SLE-encoded genes are transcriptionally active and show stage-specific expression across the erythrocytic cycle. Integrated lifecycle transcriptomics across 7,006 genes revealed a ~54-hour erythrocytic cycle with a "just-in-time" transcriptional cascade closely resembling that of P. vivax. Phylogenomic analyses and pairwise amino acid comparisons across more than 2,600 single-copy orthologs show that Berok forms a deeply diverged P. cynomolgi lineage, suggesting a distinct subspecies. This assembly establishes a high-resolution genomic foundation for comparative malaria biology, drug discovery, and the study of subtelomeric architecture, host adaptation, and lineage boundaries in primate Plasmodium.

South central Africa, between the Congo Basin, the Great Lakes, and southern Africa, has long served as a corridor for human movement. Yet, it remains unclear whether there is genetic continuity between pre-Iron Age foragers and later Bantu-associated populations and whether the settlement of this region reflects multiple Bantu-associated migrations rather than the simpler serial founder model suggested by existing genomic data. To do so, we generated genome-wide ancient DNA from 71 Iron Age and historical individuals from present-day Zambia and Malawi, and analyzed these genomes alongside published data from present-day Africans. One late Iron Age individual (16th-17th century) from Kalala Island in the Kafue River, Zambia, carries 40% non Bantu related ancestry that closely matches local Later Stone Age foragers. Admixture for this individual is estimated to be 850 years ago, several centuries earlier than reported for present day BaTwa from the same region. Focusing on the Bantu-related ancestry, haplotype-based analyses identify two main clusters among Iron Age, historical, and present-day south central Bantu groups associated with different Bantu-related migrations. These results reveal a layered history in which at least two Bantu expansions radiated from the southern Congo Basin, with south central Africa acting both as a crossroads of these movements and as a staging area for the subsequent southward expansion toward southern Africa.

Mosaic evolution assembles organisms from ancestral and derived parts, and the same trait can mislead phylogenetic reconstruction while recording ecology. Crickets from mid-Cretaceous Myanmar amber embody this conflict, combining a cricket-like body with digging forelegs like those of mole crickets. We placed these fossils onto a molecular phylogeny of living crickets and removed the foreleg characters, using a living cricket with convergent digging legs as a control. This foreleg module was the main source of phylogenetic distortion: under parsimony criteria, the fossils remain close relatives of mole crickets without it, while the control species returns to its position within Gryllidae. The same module carries most ecological information: its removal reduces cross-validated habitat-prediction accuracy from 77.8% to as low as 16.7%, below the majority-class baseline of 44.4%. We show that partitioning convergent modules from the conserved body plan separates phylogenetic signal from ecological information in the same mosaic anatomy.

Diet has repeatedly shaped human genomes, yet adaptation of protein digestion remains poorly understood. Using 1,348 haplotype-resolved assemblies, we reconstructed the structural evolution of the human pepsinogen A (PGA) locus and found a west-to-east increase in copy-number across Eurasia that tracked regional reliance on plant-derived protein. Modern and ancient genomes further revealed a recent selective sweep in the East but signatures of balancing selection in the West. We traced this divergence primarily to expansion of PGA34A, the most proteolytically active paralog in vitro, and showed that recurrent nonallelic homologous recombination continually generated structural diversity in this locus. Independent PGA expansions were also enriched in plant-dominant mammals. These findings link paralog-specific dosage variation in protein digestion to dietary adaptation across human populations and diverse mammalian lineages.

The mammalian cerebral cortex is built from a conserved developmental program, yet exhibits profound species-specific complexity. To decode the regulatory changes driving human brain evolution, we reconstructed and aligned continuous single-cell differentiation trajectories across the developing human, macaque, mouse, and ferret cortices. This comparative framework revealed a fundamental principle of transcriptomic evolution during mammalian cortical development: while stable expression is the mammalian default, genes that diverge strictly shift their allocation to cell differentiation trajectories and developmental timing in tandem. By isolating these coupled regulatory shifts to the human lineage, we revealed that a canonical synaptic gene network uniquely redeployed into early human oligodendrocyte precursor cells (OPCs). Human, chimpanzee, and gorilla cortical organoids confirmed that this neuron-like OPC state is an exclusively human innovation. Spatial transcriptome analysis found that these specialized OPCs engage adjacent neural progenitors (outer radial glia) via synaptic-adhesion signaling during neurogenetic period. These findings demonstrate that this coupled spatiotemporal rewiring establishes novel developmental microenvironments, providing a discrete molecular engine for human cortical evolution.

The domestication of maize from teosinte involved dramatic remodeling of the ear, yet the cellular and genetic bases of this transformation remain unclear. Here, we generate a single-nucleus and spatial transcriptome atlas of developing maize and teosinte ears. Comparative analysis reveals divergence in cob-associated cell types, with enhanced cytokinin signaling and reduced growth-inhibitory signals collectively driving cob thickening and enlargement in maize. We further demonstrate that domestication expanded the spatial expression domain of key transcription factors in maize meristem cells, enhancing the potential for increasing kernel number. Additionally, we verified a major domestication gene, ZmSPD1, in which two nonsynonymous SNPs differentiate maize from teosinte and alter jasmonic acid (JA) levels in the ear, thereby suppressing spikelet abortion to effectively double kernel production. These findings provide a cell-resolved mechanistic framework for how cob architecture and kernel number were shaped during maize domestication, offering new insights into the formation of key agronomic traits.

Marine mammals - cetaceans, pinnipeds, sirenians, sea otters and polar bears - returned to the sea independently, yet whether their genomes converged on a shared adaptive programme or shifted in a common direction without a fixed toolkit has remained unclear. Here we separate marine specialization from general aquatic dependence across 302 mammals and 17,432 protein-coding genes and show that the dominant genomic signature of marine life is widespread evolutionary slowing, not acceleration: of 1,559 marine-associated genes, nearly 88% evolved more slowly, and this slow-direction bias persisted (98%) after removing cetaceans. Compact gene fingerprints that distinguish marine identity combine fast-rate remodeling of body-surface and sensory genes with slow-rate constraint on blood, metabolic and DNA-repair genes, but these fingerprints are sharpened by cetaceans and do not preserve a fixed functional toolkit across lineages. Species-level and ancestral-branch decompositions reveal that different marine mammals assembled marine-like genomic states through distinct gene combinations. Mammalian marine convergence is therefore directional rather than modular: a broad constraint landscape resolved into clade-weighted genomic fingerprints.

The United States is on the verge of losing measles elimination status, and the doses that could prevent it are already committed; what is still open is which schools get them first. Allocation theory answers that by ordering schools on marginal herd-immunity return rather than lowest coverage, and across 36,031 US schools the theorem's binding case is the common one: two thirds to three quarters of susceptible kindergarteners attend schools where each added dose buys increasing herd immunity. That ordering returns 1.92 times the indirect protection of lowest-coverage-first, or 1.16 times the total protection. But it assumes every school is equally likely to see a case. Pre-outbreak records from the 2025-26 Upstate South Carolina outbreak are inconsistent with that premise: exposed schools are over-represented 5.0-fold in the top decile of susceptible headcount (95% CI 3.0 to 7.3), while enrollment, a negative control carrying school size but not susceptibility, shows none. An independent outbreak in Clark County, Washington reproduces the scaling, but only two US jurisdictions publish records permitting this test, so how steeply risk scales is unidentified nationally. Under that uncertainty the theoretically optimal rule is the least robust of seven we evaluate, losing 86% of attainable benefit in its worst case, and that fragility holds however the uncertainty set is drawn. A light hedge on measured risk holds roughly 90% at the primary budget, computed from the two columns states already publish. Wherever targeting is optimized on a well-measured variable while exposure risk goes unmeasured, the point-estimate optimum is the fragile choice.

Eukaryotic genomes vary by several orders of magnitude, yet this vast variation bears little relation to the complexity of the organisms they encode. Thus, how genome evolution accompanies changes in organismal complexity remains unresolved. A central obstacle is that major differences in body plan usually occur among deeply divergent lineages, entangling body plan evolution with the genomic divergence accumulated over long independent histories. Duckweeds offer a rare system in which successive body plan reductions can be traced within a single plant family. Across this trajectory, body size declined by nearly an order of magnitude and roots were progressively lost, culminating in the extreme of angiosperm miniaturization. Yet genome size increased nearly sixfold. Here, using a new chromosome-scale genome of Wolffia globosa and comparative genomics across nested evolutionary scales, we show that genome size, gene number, and functional repertoire followed distinct trajectories during miniaturization. Genome expansion was driven largely by transposable element accumulation, whereas the number of protein-coding genes remained stable. Aquatic adaptation itself promotes functional simplification, but establishes only a baseline. Duckweeds pushed this streamlining much further through additional contraction of developmental, structural, and biotic defense functions, alongside selective expansion of functions associated with growth and abiotic adaptation. This remodeling accumulated across successive evolutionary transitions through continued contraction of the same gene families and, more commonly, contraction of different families affecting the same biological processes. Organismal complexity may therefore reflect not simply the size of a genome or its functional repertoire, but how that repertoire is selectively reconfigured through evolution.

Domestication often modifies multiple traits in concert, but whether fruit quality and reproductive mode share a genetic basis in perennial crops has not been tested at multi-omics resolution. In fig (Ficus carica), one of the earliest domesticated fruit trees and a crop with archaeobotanical evidence of cultivation over 11,000 years ago, domestication yielded both distinctive flavour and parthenocarpy, fruit development without pollination. We integrated whole-genome resequencing, transcriptomics, volatile and metabolite profiling, and taste sensor data across a diverse accession panel, using Bayesian GWAS/TWAS and multi-omics factor analysis. Flavour emerges as an integrated sensory system led by aroma, which modulates taste through cross-modal interactions, with sugar-acid balance as a secondary axis; these quality traits map to numerous independent loci. Parthenocarpy instead traces to a single perfectly concordant chromosome 04 haplotype (Eden) centred on FcMYB101-like, carrying a selective-sweep signature and a derived allele fixed in cultivated figs but rare across the genus. Flavour and reproductive mode thus evolved along separate genomic trajectories, allowing each to be improved independently.

Understanding the lineage relationships among individual cells is a key pursuit of modern biology, essential for unraveling the complexities of developmental processes and the adaptive mechanisms of disease progression, particularly in oncology. Retrospective single-cell clonal tracing has emerged as a transformative approach, offering a unique window into the evolutionary trajectories of cancer within clinical samples. While short-read single-cell transcriptomics (scRNA-seq) has revolutionized our ability to map cell states across human tumor atlases, it remains fundamentally limited in its capacity to link these states with high-resolution genomic alterations and the evolutionary trajectories inferred from these natural variants. Integrating somatic mutation discovery with transcriptomic profiles at single-cell resolution often requires separate, costly, and low-throughput genomic assays. Furthermore, existing methods frequently rely on exogenous genetic labeling or are restricted to short-read sequencing, which typically fails to resolve complex genomic rearrangements, large indels, or variations within highly repetitive regions,such as short tandem repeats (STRs), that could serve as potent endogenous clonal markers.

Deciphering the regulatory consequences of sequence divergence across human evolution is essential to understanding the molecular basis of human-specific traits and disease. Although millions of derived alleles distinguish humans from great apes, only a small fraction are likely to influence human-specific traits. Previous studies have focused on regions of elevated sequence divergence, assuming that rapid evolution reflects functional adaptation, yet individual high-impact regulatory mutations evade such scans. Here, we apply sequence-to-function deep learning to predict chromatin accessibility across modern human, archaic hominin, and great ape personalized genomes, identifying lineage-specific cis-regulatory elements (linCREs) across diverse cellular contexts. Compared to conserved elements, linCREs are shorter, less pleiotropic, less conserved, and enriched in neurodevelopmental pathways. Many linCREs occur in regions with limited sequence divergence that acceleration-based approaches would overlook. We validate lineage-specific enhancer activity through luciferase reporter assays and demonstrate that a single motif-generating derived allele nominated by model interpretability tools drives a hominin-specific neurodevelopmental enhancer.

A central question in immunity is how hosts arrest pathogen growth. Diverse plant pathogens create a water-soaked niche in host tissue essential for pathogenesis, yet how water shapes infection outcome is unknown. Using genetics and hyperspectral imaging, we show that extracellular water status is rate-limiting for both compatible and incompatible interactions. We find that the hypersensitive response of effector-triggered immunity (ETI) is, mechanistically, a desiccation event. Water loss imposes osmotic stress that arrests bacterial division while the pathogen remains alive and metabolically active, rather than killing it. Restoring apoplastic water reverses this stasis and licenses growth despite intact immune signaling and cell death. Water status, not immune signaling per se, gates pathogen growth. This reframes ETI as a controlled desiccation mechanism and identifies hydration as a decisive lever on disease outcome.

Root anatomical barriers, including the suberized and lignified walls of the endodermis and exodermis, and cortical aerenchyma, regulate water and nutrient transport, gas exchange, and rhizosphere interaction. Their adaptive function places them as an important target for breeding environmentally resilient plant species. Quantifying these structures at high resolution is a manual bottleneck that limits experimental scale. We present RADIX (Root Anatomy Deep- learning Image segmentation across species and platforms), a framework that adapts a large self-supervised vision-transformer foundation encoder (DINOv3), pre-trained on billions of natural images, to root anatomy by fine-tuning its encoder with a dense-prediction-transformer decoder. Transferring these general-purpose vision encoders to a specialized biological domain with a high-quality annotated dataset is what allows RADIX to generalize across species and imaging platforms. We train and evaluate it on the first expert-annotated benchmark of root anatomical structures at scale, comprising 1,695 high-quality fluorescence images spanning 17 monocot and dicot species, six anatomical structures, and three imaging platforms. RADIX segments all six structures at inter-annotator-level accuracy and generalizes to unseen species, genotypes, growth conditions, and an imaging platform from an independent laboratory. A single unified model surpasses monocot- and dicot-specialist models without sacrificing in-group accuracy. Predicted masks yield aerenchyma and suberin/lignin measurements matching expert annotation at [~]1.2 s per image with a single GPU, reducing weeks of manual analysis to minutes. Applying RADIX across genotypes, microbial treatments, and growth systems, we show that these cell type features form a coordinated, multidimensional, and context-dependent system shaped by genetic and environmental factors.

Cytokine receptor pairing rules, set by evolution, confine JAK-STAT signaling to a narrow region of a far larger combinatorial space. Of more than 1,200 pairings theoretically possible among the [~]36 JAK-associated human cytokine receptors, only [~]30-40 exist in nature. Using a double-orthogonal platform, we enforced pairings across the full all-by-all receptor matrix and resolved a fine-grained STAT atlas richer than the natural repertoire. Selected non-natural pairings generated emergent T cell states unpredictable from either parental receptor, with pairing orientation encoding signaling specificity. A synthetic IL-21R>IL-2R{beta} pairing, but not its reciprocal, drove a cytotoxic Tc17-like state, whereas natural IL-9R/{gamma}c drove a Tc1 fate despite similar STAT activation, showing that rebalancing quantitative STAT combinatorics can modulate T cell fate. Recombining IL-31R, not expressed in T cells, with STAT-biased receptor partners generated diverse states, several with superior antitumor efficacy. These findings define a non-natural pairing code for engineering synthetic T cell fates.

IS110 has emerged as a powerful genome-editing tool because it is the smallest RNA-guided system capable of diverse programmable insertions. Naturally existing elements are conventionally modeled as compact[~] 1.5-kb systems comprising a single transposase and a bridge RNA (bRNA). Using high-throughput junction mapping together with large-scale comparative genomics, we redefined the in vivo structural boundaries, growth, and mobilization of IS110 elements. We uncovered a previously unrecognized size continuum extending to[~] 100 kb, driven by progressive local expansion, with expanded loci being widespread across bacterial genomes. Experiments confirmed the activity of natural IS110s both well below and above the size range of previously characterized elements. These large systems preferentially accumulate adaptive cargo, including antimicrobial resistance determinants and heavy-metal detoxification systems, and are strongly enriched for plasmid-derived DNA. Boundary configurations at expanded loci and the range of partial excision intermediates they produce both indicate flexible sequence recognition by IS110, most commonly through half-matches between the bRNA and complementary DNA sequence. This sequence tolerance allows loci to expand with diverse cargo. Together, these findings redefine IS110 from a compact insertion sequence into a dynamic platform that disseminates adaptive cargo.

Bacteria of the genus Achromatium harbor hundreds of chromosomes that were previously suggested to be genetically diverse. By sequencing multiple regions from individual cells, we demonstrate that chromosomes within a single cell differ in nucleotide and amino acid sequence, reaching levels of divergence well below accepted bacterial species boundaries and below the range associated with homologous recombination. Sequencing of dividing cells further revealed that daughter cells inherit distinct chromosome populations, a mode of inheritance previously associated with sexual reproduction in eukaryotes. Combining subcellular sequencing with high-resolution microscopy, we reconstruct the three-dimensional cellular architecture of Achromatium and show that extensive intracellular heterogeneity arises from the spatial segregation of chromosome populations by the cells internal structure, which limits genome-wide recombination. Our findings establish cellular architecture as a determinant of genome evolution in giant polyploid bacteria and identify spatial genome segregation as a mechanism enabling the maintenance and inheritance of divergent chromosome populations in bacteria.

Protein-coding genes mapping to high-identity segmental duplications (SDs) have been difficult to annotate and characterize and are the source of most previously unknown protein-coding genes being discovered as part of the human pangenome. Here, we combine long-read assembled human genomes (298) and long-read transcriptome data (5.6 billion full-length cDNA from 83 tissues) to phylogenetically interrogate 493 gene families discovering 2713 potentially copy number polymorphic genes not present in the human reference genome. For reference SD gene families where paralog specificity can be assigned, we find that 60.0% are expressed and maintain open reading frames, with 45.7% showing high expression in brain, embryo, or testis. We revise 386 gene models, including 150 that absent or different from current T2T-CHM13 gene annotation and 236 (35.1%) pseudogenes as protein-coding where we find evidence of transcription, an open reading frame, and chromatin-accessible promoters. We find that 24.2% of SD genes show evidence of constraint for both copy number and amino acid mutation. The majority of these constraint genes are ancestral, whereas only 16.2% of derived duplicated genes that emerged recently in the human lineage show evidence of constraint. The pangenome provides unparalleled specificity to understand genetic variation in SD genes allowing us to distinguish functional genes from pseudogenes and highlighting potential gene innovations that arose most recently in human evolution.