Science

Historical crop remains preserved in everyday objects are an underused archive of agrobiodiversity change, yet their degraded DNA resists conventional analysis. We recovered cereal grains and straws used as upholstery padding in a Central European settee dated to about 1870 to 1900. We identified and characterized the specimen by genome skimming. Damage-aware sequencing confirmed authentic historical DNA of modest, late nineteenth-century age. The assembled plastome placed the specimen securely within rye, and a genome-wide SNP panel of rye landraces resolved it inside cultivated Secale cereale subsp. cereale, closest to a Hungarian bred rye and a Slovak upland landrace and remote from wild or eastern lineages. Screening 192 stress-associated loci recovered the structural machinery of resistance, abiotic stress and aluminum tolerance pathways, while heading-date genotyping showed the Weining earliness allele at Hd2R already present. Divergence across 36 domestication sweep regions concentrated at a few improvement loci. Integrating these genomic signals with genebank passport data and an 1891 newspaper record, we interpret the specimen as a tall Central European rye at the threshold between landrace and improved variety. Historical crop material, read this way, preserves both genomes and the traces of human agricultural practice.

Genomic surveillance has shown how SARS-CoV-2 lineage composition emerges in densely sequenced, high-income settings. Whether reconstruction is possible where sequencing is sparse and intermittent, as in most low- and middle-income countries like Bangladesh, remains untested. To address this, genomes were collected in Bangladesh between March 2020 and July 2025 against a globally distributed background to infer a time-calibrated phylogeny and delineate Bangladeshi transmission lineages. Source attribution was tested against two independent null models that hold background sampling constant. Substitutions enriched in Bangladeshi genomes, relative to a comparator matched on lineage and collection month, were classified as imported or locally arising according to whether they were present at the root of their host lineage. Lineage introduction events were inferred at 361, of which 51.8% left a single sampled genome with no detected onward transmission. India and the Gulf were jointly dominant as source regions, exceeding a rarefied null model by 10.8 and 8.1 percentage points, while East Asia, South-East Asia and Rest-of-World fell significantly below it. Eighteen enriched substitutions, clustered by shared carriers into eleven independent signals, generated 171 substitution-lineage occurrences, of which 53 arose after their host lineage had entered Bangladesh. Spike G446V arose locally in 17 of 19 host lineages and reached 267 of 291 genomes (91.8%) of an imported Delta lineage, indicating that a locally arising substitution could achieve clade expansion. Whether import dependence declined over time could not be evaluated, as the statistic is confounded with sequencing effort. Importation determined which lineages circulated in Bangladesh, while local evolution determined what happened within them. Local substitutions transmitted readily but rarely reached lineage-wide frequency because their host lineages remained under genomic observation for only a short interval.

Whole-genome duplications repeatedly expose ancestral gene lineages to the same broad evolutionary outcome-retention or loss of duplicated copies-but it remains unclear whether this history replays similarly across evolutionary scales. We placed duplicate retention in shared hierarchical orthologous-group coordinates and compared percentile ranks defined within each event-wide mapped universe. Three independent angiosperm whole-genome duplications showed reproducible replay (global rank effect T-replay = 0.210, bootstrap 95% confidence interval 0.172-0.248; permutation P = 1/100,001). A plant reference-panel score specified before target outcomes were examined predicted retention after the Apple/Pear duplication ({rho} = 0.169, n = 373). Deep transfer was heterogeneous: the teleost-genome-duplication estimate was positive but unresolved ({rho} = 0.107, n = 151, 95% confidence interval -0.050 to 0.260), whereas transfer to the ancient budding-yeast whole-genome duplication (yeast WGD) was supported ({rho} = 0.280, n = 186). Independently reconstructed animal outcomes also replayed between teleost and Stylommatophora duplications (r = 0.226, n = 146, P = 0.00326), although the effect remained below a prespecified strong-effect threshold. A strict plant-animal comparison was limited to 25 deeply one-to-one lineages and was unresolved (r = 0.033, 95% confidence interval -0.303 to 0.340). Thus, ancestral gene-lineage identity contributes reproducibly to duplicate retention after independent whole-genome duplications, but replay is structured by evolutionary lineage and modified by event-specific history rather than governed by one universal gene-fate ranking.

Alphaviruses are arthropod-borne viruses that recognize cellular receptors in both vertebrate hosts and mosquito vectors to complete their transmission cycle, yet how they maintain recognition of receptors across evolutionarily divergent host species remains unresolved. Among alphaviruses, chikungunya virus (CHIKV), which is primarily vectored in urban settings by Aedes species mosquitoes, is the most widespread, and causes explosive outbreaks that can involve hundreds of thousands to millions of cases annually. The cell adhesion protein Lachesin is a mosquito-specific cellular receptor for CHIKV and multiple other arthritogenic alphaviruses. The envelope E2-E1 glycoproteins of these alphaviruses broadly recognize Lachesin orthologs from diverse mosquito species, but not other insects or arachnids. Lachesin genetic manipulation to prevent mosquito virus infection without interfering with endogenous receptor function could have a major impact for CHIKV control. Here, we determined high-resolution cryo-electron microscopy (cryo-EM) structures of alphaviruses bound to Aedes albopictus Lachesin. Comparative analysis of Lachesin-bound CHIKV, Semliki Forest virus (SFV), and Middelburg virus (MIDV) revealed that these three genetically divergent viruses use a similar surface to recognize Lachesin domain 1, but with reorganized E2-E1 glycoprotein contact residues. We show that a soluble Ae. albopictus Lachesin receptor decoy protein blocks the E2-E1-mediated entry of CHIKV and other arthritogenic alphaviruses into mammalian cells with greater breadth than a vertebrate receptor MXRA8 decoy and protects against lethal SFV challenge and CHIKV pathogenesis in murine models. Additionally, we identified a naturally occurring single residue Lachesin polymorphism that is found in some Anopheles (malaria vector) mosquitoes, and fully ablates CHIKV E2-E1 recognition, informing strategies for mosquito-targeted genetic interventions that could prevent mosquito vector infection and virus transmission. These findings define distinct determinants of receptor binding in mosquitoes and humans for arthritogenic alphaviruses, with implications for countermeasure development and outbreak preparedness.

Despite recent climate change, many plants and animals are not yet tracking climate as predicted. We reconstruct realized climatic niches for 16 plants and 45 mammals across North America from the end of the last deglaciation to the present, calculating climate fidelity to measure temporal niche stability. Plants consistently exhibit higher climate fidelity than mammals, despite limited dispersal. During the deglaciation, which had lower human impact, some large mammals tracked warming climates as effectively as plants. Following European colonization, mammalian niches shifted markedly. Large mammals were displaced from warm, humid regions toward colder, drier areas, while some small mammals expanded into human-modified landscapes. In contrast, plant niches remained largely structured by climate, highlighting stronger anthropogenic constraints on mammalian responses to climate change thus far.

The human heart depends on coordinated muscular, electrical, vascular, lymphatic, and neural systems, but their three-dimensional relationships remain unresolved at microscopic resolution across an intact adult organ. Using hierarchical phase-contrast tomography, we generated a continuous three-dimensional structural reference of a whole adult human heart at 8.01 micrometer isotropic voxel size, without sectioning or staining. Organ-wide imaging revealed hierarchical myocardial architecture, and quantitative orientation analysis identified regional differences in myocardial cell aggregate organization. The atrioventricular conduction axis was traced into a distinct subendocardial Purkinje network interfacing with working myocardium. Integrated segmentation showed that coronary vessels, lymphatic collectors, and autonomic nerves occupy shared epicardial corridors. This publicly accessible dataset integrates cardiac systems within a common spatial framework for anatomy, computational modeling, and future molecular atlases.

Under climate change, will forests grow more or less? The answer differs from place to place, obscuring the overall direction. Here we trace it by learning nonlinear climate--tree-growth relationships from 4110 Northern Hemisphere tree-ring chronologies recorded since 1902, spanning more than 12 million ring-width measurements, and projecting them through the twenty-first century under CMIP6 scenarios. Projected growth declines, and gains and losses are temporally asymmetric: once losses emerge, they are rarely reversed (90% retained), whereas gains fade (56% retained). This asymmetry holds in every well-sampled region and strengthens under higher forcing. The decline itself is driven by warming and rising atmospheric water demand, whose broadly negative contribution outweighs precipitation-driven gains. Across the Northern Hemisphere, growth does not just move between gains and losses; it is drawn steadily downward.

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.

Reactive nitrogen (N) inputs underpin global food production, but increasing protein provision while limiting agricultural N pressure remains a major sustainability challenge. Here, we analyzed changes in N use, cropland N surplus and protein supply across 130 countries from 1992 to 2022 to assess whether recurrent N-transition patterns emerge during agricultural and economic development. Countries followed divergent trajectories rather than converging toward a common N transition. Absolute decoupling, with increasing protein supply and declining cropland N surplus, occurred in 35.4% of countries, while others showed relative improvements or increasing N pressure. Cropland N surplus rose more steeply as agricultural N inputs intensified. Long-term trajectories revealed contrasting forms of N-system reorganization, from persistently lower-pressure systems to intensifying systems. Absolute decoupling occurred across diverse economic contexts and was not systematically associated with development level. Higher-development countries that decoupled generally reduced N surplus from higher starting levels but still ended with higher surpluses. Thus, increasing protein provision while reducing N surplus is achievable, but improvement does not necessarily imply convergence toward low N pressure.

Resistance to one drug often raises susceptibility to another; such collateral sensitivity is expected to constrain multidrug resistance. This is hard to test: failure to reach a state is indistinguishable from never having been driven toward it. We therefore recorded the change we imposed: a closed-loop system updated each lineage's drug environment daily based on its measured distance to a target. Steered toward triple chloramphenicol-norfloxacin-kanamycin resistance for 70 days, 52 Escherichia coli lineages gained substantial resistance without converging on the target. The mismatch between imposed and observed movement mapped accessibility, locating a region immediately before the target where progress was reproducibly slowed. Crossing it was associated not with broad resistance mutations shared by most lineages, but with recurrent mutations upstream of the efflux pump gene cmr, which raised chloramphenicol resistance threefold without detectable cost. Progression toward multidrug resistance was therefore constrained without being prevented, at a location consistent with a known physiological trade-off; recording the imposed change makes accessibility measurable during evolution.

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.

How a flexible mammalian embryo gives rise to a reproducible body plan remains unclear, partly because cell lineages cannot be followed continuously in vivo. We combined DNA Typewriter lineage recording with tetraploid complementation to reconstruct high-resolution single-cell genealogies across mouse development and built FateVec, an analysis framework that infers fate-bias dynamics and lineage-associated transcriptional programs from reconstructed phylogenies. Loss of developmental potential proved progressive and asynchronous, with multiple lineages acquiring detectable fate bias before morphological diversification at gastrulation. Within the neural crest, most cells remained multipotent over an extended window, while independent founder clades differed markedly in restriction timing. Extending lineage recording to a stem-cell-derived embryo model revealed that cells with shared transcriptional identities can arise from distinct lineage relationships. We further found embryonic-lineage contributions to extraembryonic-like states, exposing an unexplored lineage plasticity. This lineage-resolved view of embryogenesis reveals that cell identity alone predicts neither developmental ancestry nor the timing of fate restriction.

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.

A critical first step in human evolutionary divergence from chimpanzees and other primates is the production of greatly increased numbers of cortical pyramidal neurons during development and over evolutionary time. This expansion underpins the enlarged human cerebral cortex and, consequently, higher-order cognition and consciousness. However, the cellular and molecular mechanisms driving this progressive increase in cortical neuron number remain incompletely understood. Here we show that elevated ERK signaling in human cortical radial glia (RGs), relative to mouse RGs, arises from evolutionary changes in the developmental expression of existing shared genes. Using the Emx1-Cre line to overexpress MEK1DD, a constitutively active mutant of rat MAP2K1, we found that enhanced ERK signaling in mouse cortical RGs upregulates cAMP-PKA signaling, along with promoting self-renewal, expanding the RG pool, and accelerating cell cycle progression. Conversely, overexpression of PKA signaling in mouse cortical RGs via in utero electroporation of constitutively active PRKACA mutants (L206R or W196G) reduces ERK activity, prolongs the cell cycle, suppresses SHH-SMO and YAP/TAZ pathway activity, and blocks ependymal gliogenesis. Together, our results demonstrate that ERK and PKA signaling in cortical RGs engage a dynamic balance of synergistic and antagonistic interactions. This interplay couples evolutionarily enhanced ERK and PKA activities to increased cortical RG numbers, prolonged cell cycle progression, and an extended neurogenic period, which collectively culminate in a marked increase in neuronal production. We conclude that heightened ERK pathway activity in cortical RGs serves as a central driver of progressive neocortical expansion across mammalian evolution. Significance StatementThe human brains extraordinary cognitive abilities stem from a dramatic increase in cortical neuron numbers during evolution. This study reveals that enhanced ERK signaling in human cortical radial glia neural stem cells, relative to other primates, is a key driver of this expansion. By manipulating this pathway in mice, we demonstrate that ERK coordinates multiple mechanisms--including self-renewal, cell cycle acceleration, and a dynamic interplay with PKA signaling--to boost neuronal output. These findings identify a core molecular axis underlying mammalian cortical evolution and provide a framework for understanding how the human cortex acquired its unique size and, consequently, its remarkable complexity.

The heartbeat originates in the sinoatrial (SA) node, where spontaneously firing pacemaker myocytes interact to generate a coherent rhythm. The classical entrainment account is deterministic: the fastest cells entrain the rest, and variability is an error term that coupling suppresses. We proposed previously that the node instead exploits its own noise through stochastic resonance, with rhythm quality peaking at intermediate fluctuation amplitude, and since mapped a metabolic gradient capable of supplying it. Two-photon imaging of the voltage sensor ASAP5 in the intact mouse node resolved the subthreshold regime that tissue-scale mapping averages away. Diastolic coherence followed an inverted-U against endogenous noise amplitude in both poles, with optima 3.5-fold apart, and each pole operated near its own. {beta}-adrenergic stimulation raised noise in both poles to a common level. The inferior pole, which began below its optimum, gained coherence, while the superior pole, already at its optimum, lost interval regularity. Blocking HCN-mediated If with ivabradine lowered superior coherence without changing superior noise, and lowered inferior noise without lowering inferior coherence, dissociating the two coordinates. Thus, coherence is a surface defined by noise and coupled-clock drive. Phosphoinositide 4,5-bisphosphate (PIP2), an ATP-dependent lipid cofactor for HCN channels, increased firing rate and noise in both poles but improved coherence only in the energy-poor inferior node. Prior If block abolished that rescue. Pacemaking is therefore graded by a bioenergetic supply chain that sets the noise, not by entrainment alone. Noise, long treated as a nuisance to be averaged away, is an active ingredient of the pacemaker.

Adaptive control of breathing is essential for life, yet the neural circuits that couple respiration to locomotion and internal physiological state remain poorly understood. Insects regulate gas exchange through spiracles: valve-like openings in the cuticle that allow oxygen uptake while minimizing water loss. We find that spiracle opening in Drosophila is dynamically matched to flight power and reduced by dehydration. We identify the motor neurons that innervate the spiracle muscles and show that their optogenetic activation closes all eighteen spiracles and rapidly limits flight power. Inhibitory interneurons transmit descending flight commands to the spiracle motor neurons, opening spiracles in proportion to metabolic demand. A parallel interoceptive pathway converges on the same interneurons to close the spiracles and suppress flight. Feedforward descending commands thus couple flight power to spiracle opening, while interoceptive feedback pathways close spiracles to balance oxygen supply against water loss. This compact circuit architecture may reflect a general solution for matching respiration to the competing demands of locomotion and water conservation.

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.