Nature Ecology & Evolution

Emerging infectious diseases threaten public health and biodiversity across the globe1,2. Disease outcomes are frequently dependent on local environmental conditions3-5, but how these factors shape host adaptation and long-term recovery are often unknown6. Here we combine two decades of population, disease, and environmental data with a common garden experiment to investigate the drivers of variable declines and recovery for remnant bat populations following the emergence of the fungal disease, white-nose syndrome. We find that initial declines were greater and faster in warmer sites (88.3% vs. 74.2% in cold sites), but these populations recovered more quickly and hosts developed higher resistance (1.5x reduction of fungal loads) than populations from colder sites that were buffered from initial impacts. Our experimental data suggest that warm sites served as hotspots of host adaptation where selective pressures were stronger because thermal conditions approached optimal growth for the pathogen, which eventually favored the development of high pathogen resistance. Populations in colder sites experienced weaker selective pressure and thus remain more susceptible, although bats from larger colonies were more likely to survive, suggesting that adaptive traits exist in these populations, but at much lower frequency. These findings show that the environmental conditions that initially buffer populations from collapse can simultaneously constrain their evolutionary response to emerging threats, and ultimately determine differential recovery following disease-induced declines.

Tumour prevalence varies dramatically throughout the animal kingdom despite broadly conserved cellular and developmental processes, raising the question of how evolution has shaped susceptibility 1,2. Here, we link macroevolutionary variation in tumour prevalence to gene-level selection by integrating comparative genomics data from 109 species of birds and mammals using a Bayesian phylogenetic framework to estimate pangenome-wide rates of genetic evolution across >150 million years of evolutionary change. We identify 3,206 genes in which natural selection is associated with shifts in tumour prevalence, with more than 80% of which are linked to reduced prevalence, suggesting pervasive selection for cancer suppression. Using causal phylogenetic inference, we show that genes associated with reduced tumour prevalence act predominantly through indirect effects on body size, revealing growth as a key mediator of cancer risk across species. In contrast, genes associated with increased tumour prevalence exert direct effects independent of body size. Finally, at the species-level, we demonstrate that exceptionally low rates of benign tumours do not necessarily coincide with reduced malignancy, revealing that benign and malignant tumour processes are evolutionarily decoupled. Together, these results reveal how natural selection has fine-tuned the link between genotype, phenotype, and cancer risk across species.

Climate warming is altering the timing of seasonal events across ecosystems, impacting the temporal synchrony of interactions among species1,2. For trophic interactions, the match-mismatch hypothesis predicts that when consumers become phenologically asynchronous with key ephemeral resources their fitness will decline3-5. Most studies of mismatch focus on single resource-consumer species pairs, and implicitly assume trophic specialisation. However, many consumers exploit more than one resource species, giving rise to several mechanisms whereby the negative impacts of mismatch on individuals and populations could be buffered6. Here we experimentally manipulate phenological asynchrony across 48 plant-caterpillar interactions in a spring woodland food-web system and assay caterpillar performance. As asynchrony increases, we find strong evidence for a decline in survival that generalises across host-caterpillar interactions, whereas caterpillar growth and development are largely unaffected. We also show that focus in the literature on a single model interaction (Oak-Winter Moth)7,8 has likely overestimated the general impact asynchrony in this system. The strength of the effect of mismatch varies markedly among host-plants, caterpillars, and their interactions--with a small number of interactions showing little or no decline in consumer performance despite substantial asynchrony. Our results demonstrate that the fitness consequences of phenological mismatch are widespread but interaction-specific, revealing substantial heterogeneity in how trophic interactions are expected to respond to climate-driven shifts in seasonal timing. This variation in response could allow resource diversity and resource switching to buffer consumer guilds against the phenological impacts of ongoing climate change, stabilising the abundance of caterpillars for higher trophic levels.

Algal blooms are frequently dominated by motile species1,2 whose vertical migration enhances resource acquisition and bloom development3,4. Yet bloom conditions present a paradox: high cell densities intensify nutrient depletion5 and self-shading6, making individual swimming increasingly costly under severe resource limitation. How motile blooms persist and remain resilient under such stress remains unresolved7, particularly as climate-driven warming strengthens stratification and resource scarcity8,9. Here we show that the red-tide-forming phytoplankton Heterosigma akashiwo overcomes bloom-induced constraints through bioconvection, a self-generated active flow that emerges above a critical cell density (>1.5x105 cells/ml). Using a custom ocean-on-chip platform that recapitulates bloom-relevant constraints, we identify an optimal synergy of cell concentration, swimming speed and gravitactic stability that promotes the formation of persistent bioconvective plumes. At constant cell density, plume onset is governed by two phenotypic traits-- vertical swimming velocity and reorientation time--demonstrating that collective transport is governed by the biophysical traits of single cells. We show that bioconvection drives ecologically relevant multiscale transport, enhancing exchange of molecules and micro-cargo across stratified interfaces, mimicking transport of nutrients, extracellular vesicles10 and co-existing species in a bloom environment11. By enabling cells to hitch a hike on self-generated flows when active propulsion becomes energetically prohibitive, bioconvection-mediated transport improves nutrient delivery, restores photosynthetic performance, reverses lipid accumulation associated with nutrient-stress, and facilitates recovery of cellular motility to ultimately mitigate resource limitations. Our findings identify bioconvection as a population-level adaptive mechanism that sustains algal blooms, and reveal a previously unrecognised role of collective microbial motion in bloom persistence under ecological stresses. One sentence summarySelf-organised bioconvection drives multiscale transport and resilience in algal blooms.

The impact of projected extinctions on global animal colour diversity remains unknown. Combining citizen science with self-supervised deep learning, we built novel representations of bird plumage colour patterning based on >125,000 museum specimen images covering 9,143 species. We demonstrate that losing currently threatened bird species will drive a disproportionate reduction in avian plumage diversity, with the most severe losses occurring in tropical and subtropical regions. Furthermore, while humans generally find non-typical plumage phenotypes more aesthetically attractive, threatened species are unexpectedly deemed less visually appealing despite their comparatively unusual plumages. Overall, our results highlight severe, imminent threats to the existing avian colourscape and raise critical questions about the future of animal colour diversity in a changing world.

Climate is a strong predictor of global species richness, but the effects of climatic conditions are difficult to separate from the geography of the climates themselves. Recent work in climate space has shown that the area and isolation of discrete climatic conditions explain broad-scale richness gradients, yet the internal spatial cohesion of those climates remains poorly characterized. Here, we introduce climate percolation as a complementary descriptor of climate geography, measuring the degree to which the total area of a climate bin is concentrated within effectively connected fragments. Using global range maps for amphibians, birds, mammals and reptiles, we quantified species richness across a two-dimensional climate space defined from 12 climatic variables and evaluated the independent and joint effects of climate area, climate isolation and climate percolation across multiple climate-space resolutions. Climate isolation and percolation were strongly coupled: their first joint axis explained, on average, more than 95% of their shared variation, revealing a dominant gradient of climate fragmentation along which geographically isolated climates are also internally subdivided. Despite this collinearity, percolation consistently outperformed isolation in cross-validation across all four vertebrate groups, with particularly strong predictive gains for birds and mammals. The largest improvements, however, came from the shared isolation-percolation axis, indicating that vertebrate richness in climate space is more strongly associated with the integrated geographical structure of climates than with either inter-fragment distance or internal cohesion alone. These results suggest that climate fragmentation is a multidimensional property of environmental space, combining both the distance among climate fragments and the dominance structure of connected areas. By extending climate-space approaches from area and isolation to percolation, our framework provides a more complete description of how the geography of climate may shape global richness gradients and offers a structural basis for anticipating how future changes in climate connectivity could alter biodiversity patterns.

Why independent origins of the same complex physiological trait repeatedly produce similar body forms and physiological changes remains central in evolutionary biology. Endothermy, the internal production and retention of metabolic heat, evolved at least four times in ray-finned fishes, providing natural replicates for convergent genomic signatures. We present a chromosome-scale analysis of three transitions (opah, tunas, and swordfish), including a new chromosome-level genome of the rare, charismatic Pacific oarfish, analyzed with 31 other teleost genomes. The strongest signal is regulatory: of 253,680 conserved noncoding elements, 577 are rate-accelerated in endothermic lineages, with 67 accelerated in all three, exceeding matched ectothermic controls and enriched near developmental transcription factors and Wnt-signaling genes (e.g., irx1a, irx5a, her9, and lmo1). These elements overlap zebrafish developmental enhancers more than expected by chance but are not tied to genes emphasized by expression or coding-selection studies of endothermic lineages, marking a regulatory layer distinct from that metabolic layer. This convergence is part of a broader mosaic: endothermic lineages also share transition-biased substitution and convergent duplication signatures, including excess tandem duplications and lineage-specific gene-family expansion, whereas chromosome organization and protein-coding sequence change little. Endothermic convergence therefore leaves its clearest signal in regulatory remodeling, alongside shifts in substitution bias and gene-family evolution.

Genetic interventions to modify wild population densities are typically framed around pest suppression, with parallel approaches for boosting beneficial or endangered populations remaining largely undeveloped. Imposing a sustained but non-eliminative genetic load could in principle address both objectives, but existing designs rely on genes with intermediate fitness effects whose loads are difficult to predict under field conditions. Here we describe engineered balanced lethal systems, in which CRISPR-based gene drive establishes two complementing recessive-lethal alleles at a single locus, producing a sustained 50% load through Mendelian segregation. Modelling shows these systems spread from small releases, and that the resulting population-level consequences depend on density regulation and on the timing of lethality: the same 50% load can suppress pests, boost populations of beneficial or endangered species, dampen boom-bust cycles, or raise effective population size. Additional systems at independent loci scale the effect in stepwise increments, and a split-drive variant localises it geographically. These results demonstrate that gene drives imposing genetic load can be expanded beyond elimination, to support and preserve beneficial and endangered populations.

Urbanization creates mosaics of microhabitats that sustain diverse plant communities, and offer untapped opportunities to understand contemporary ecological and evolutionary processes. Using a city-wide colonization experiment in Cologne (Germany), we identified the environmental factors limiting establishment and persistence of the ruderal species Arabidopsis thaliana and the genetic variants enabling adaptation. We show that standing genetic variation is essential for realizing the species urban niche, enabling rapid adaptation to fine-scale gradients in disturbance, vegetation, and soil conditions. Despite originating from only two parental genotypes, populations evolved substantial adaptive differentiation within three generations, revealing a highly polygenic basis of local adaptation. More broadly, our approach establishes cities as powerful open-air laboratories for uncovering and fostering ecological and evolutionary processes that generate and sustain biodiversity in human-dominated landscapes.

Structural variants (SVs) contribute substantially to genetic variation and play vital roles in adaptation and disease1,2. Nonetheless, SVs are poorly captured by short reads and thus remain understudied, especially in non-model organisms3,4. Here, using haplotype-resolved genome assemblies from >600 vertebrate species, we comprehensively survey the landscape of SVs across >500 million years of evolution. We identify 35.3 million SVs and 3.12 billion single nucleotide variants (SNVs) segregating between two representative haplotypes across species, with SVs impacting [~]12-fold more base pairs. SV and SNV heterozygosity are correlated across species, with endangered and threatened species exhibiting reduced genetic diversity. However, the contribution of SVs relative to SNVs fundamentally differs across major vertebrate clades: given the same number of SNVs, fishes, amphibians, and reptiles have 4.3-to-9.1 times the number of SVs than birds, and 1.7-to-3.6 times more than mammals. This reduction in the relative contribution of SVs in mammals and birds is linked to fewer non-repeat-associated SVs as well as lower transposable element (TE) abundance and diversity. We identify features underlying genomic instability across vertebrates, finding that SVs frequently occur in repetitive and SNV-rich regions and are mediated by both homology and non-canonical DNA structures. Notably, G-quadruplex structures are enriched 11.5-fold around SV breakpoints in birds, while Z-DNA structures are enriched 2.2-fold in cartilaginous fishes. TEs uniquely contribute to SVs both directly through transposition and indirectly by mediating ectopic recombination, with the proportion of TE-mediated SVs influenced by both genomic TE density and diversity. We identify >10,000 instances of recent TE turnover including extinction of LINE-2 in therian mammals and slowing of CR1 activity in passerine birds. Finally, we show that SVs have an outsized role in functional genetic variation and are >70 times more likely to strongly impact protein-coding sequences than SNVs. While SVs are on average deleterious, we identify extensive recurrent structural variation across multiple taxa in genes involved in sensory, immune, and metabolic systems. Together, this study highlights extraordinary variation in the abundance, composition, mechanism, and functional impact of SVs across vertebrates.

Adaptation of organisms to extreme environments requires dramatic phenotypic changes. Studying these changes can elucidate mechanisms underlying phenotypic differences in the context of both evolution and human disease. The Mexican tetra, Astyanax mexicanus, is a powerful model of extreme adaptation over a short evolutionary time scale. This fish species includes surface- and cave-dwelling ecotypes, with cavefish displaying many adaptations to subterranean life, including behavioral changes such as sleep loss, increased appetite, and reduced aggression. Unraveling the mechanisms underlying these changes has been challenging, presumably because they are complex traits that required coordinated changes across multiple cell types to evolve. Here, we present a spatially integrated comparative cell atlas of whole adult brains of surface and cavefish. After establishing the molecular signatures of 35 cell types, we show that cave colonization drove canalized regulatory changes to gene expression across diverse cell types. Cavefish brains show shifts in cell-type composition compared to their surface counterparts, as well as complex regulatory changes to pathways governing hypoxia response and circadian rhythm. Microglia in the cavefish brain underwent extensive transcriptional remodelling, including changes in senescence and AMPK pathways. Further, cell-cell communication analysis identified a cave-enriched ligand-receptor communication pattern centered on signals sent from glial cells to diverse populations of neurons. This atlas identifies genetic changes associated with neural and behavioral evolution and provides a resource for mechanistic studies examining brain evolution.

Free-living nematodes are among the most abundant animals on Earth and play critical ecological roles in soil ecosystems. However, the global population structure and evolutionary history of most species remain poorly understood. Here, we analyzed genome-wide variation in Oscheius tipulae using whole-genome sequence data from 31 isolates, including 28 publicly available genomes and three newly collected strains from Korea. Population structure analyses, phylogenomic inference, and ancestry estimation consistently identified three deeply divergent lineages. These analyses did not detect admixture among lineages and collectively supported a predominantly tree-like evolutionary history. Notably, the lineages were structured by latitude rather than geographic proximity. Isolates from similar latitudinal zones clustered together regardless of continental origin, forming three major groups: northern mid-latitude (NML), low-latitude (LL), and southern mid-latitude (SML). This pattern indicates that the lineages have maintained largely independent evolutionary trajectories over extended timescales despite the potential for long-distance dispersal. Furthermore, environmentally associated variants showed significant differentiation among lineages, indicating that environmental selection may contribute to the maintenance of this latitudinally structured diversity. Our results reveal unexpectedly deep global divergence within O. tipulae, and highlight the importance of ecological divergence and long-term lineage retention in shaping the global diversity of this group.

The evolutionary origins of asexuality remain poorly understood, despite extensive research on its ecological and evolutionary consequences. Asexuality often arises through hybridization between species with intermediate genomic divergence, implying that hybrid-induced asexuality may be partly repeatable. The Amazon molly (Poecilia formosa), the first asexual vertebrate known to science, challenges this view: repeated experimental crosses between its extant parental species have failed to recreate a stable Amazon molly-like lineage. This apparent paradox gave rise to the Rare Formation Hypothesis, which proposes that stable asexuality requires an exceptionally specific genomic combination. Here, we combine experimental crosses, molecular cytogenetics, and population genomics to test whether ancestral introgression before the hybrid speciation event set the stage for the singular origin of the Amazon molly. We show that most experimental hybrids are viable but sexual, but that a subset of F1 hybrids produce unreduced eggs through a mechanism distinct from that of the Amazon molly. Population genomic analyses reveal that introgression between parental species likely predated the formation of the Amazon molly, and shared homozygous tracts across Amazon molly genomes support inheritance from admixed progenitors. Together, our findings reconcile the repeatable and contingent views of the origin of asexuality, suggesting that ancestral introgression may be the missing mechanism assembling the rare genomic combinations required for seemingly unrepeatable evolutionary innovations, including the emergence of asexual species.

Ancient whole-genome duplications (WGDs) are thought to have played a major role in plant evolution, but robust inference of the patterns and drivers of polyploid establishment through deep time remains challenging. We re-evaluate the recent large-scale study by Chen et al. (2026), which linked polyploid establishment throughout angiosperm evolution to periods of climatic instability and low species richness. We identify five conceptual and methodological issues that substantially affect these conclusions and collectively undermine the proposed temporal and ecological associations. We hope that clarifying these issues will support future efforts to understand the evolutionary role of polyploidy in plant evolution.

How gene regulatory networks are rewired to generate phenotypic and functional innovation remains a central question in evolutionary biology. Parasitoid wasp venoms provide a powerful system for addressing this question, as their repertoires evolve rapidly through extensive lineage-specific turnover, yet the regulatory principles underlying such flexibility are largely unknown. Here we integrate tissue-resolved transcriptomic, chromatin-accessibility and histone-modification profiling to reconstruct the venom regulatory network of the parasitoid wasp Pteromalus puparum. We show that venom expression is embedded in distinct chromatin states and shaped by regulatory elements associated with venom-gland transcription. Comparative and functional analyses support a general model in which regulators related to the endoplasmic reticulum stress and unfolded protein response pathways have been repeatedly recruited to venom regulation across venomous lineages. Unexpectedly, we identify the recently co-opted homeobox gene Lbx as a lineage-specific hub that regulates more than half of venom genes and is linked to enhancer evolution. These results reveal a nested model of venom regulatory evolution, in which an ancestral secretory programme provides a reusable regulatory backbone, while newly co-opted homeobox gene specify a lineage-specific venom expression. Our study highlights regulatory co-option as a mechanism by which conserved developmental genes can acquire new physiological functions during adaptive evolution.

Photosynthetic organelles (plastids), which originated via primary endosymbiosis between an Archaeplastida ancestor and cyanobacteria, have shaped the Earth's oxygen-rich atmosphere and spread across the eukaryotic tree of life through multiple secondary and higher order endosymbioses. Yet, the mechanisms driving the transition from endosymbiont to organelle remain poorly understood, highlighting the need for novel systems to elucidate the stages of endosymbiont integration and test the generality of plastid evolution models. Here, we employ single-cell genomics and catalyzed reporter deposition fluorescence in-situ hybridization (CARD-FISH) to investigate the dictyochophyte plastids of the poorly known marine centrohelid Meringosphaera across diverse geographic locations. Our analyses detected novel microdiversity of cells both containing and lacking plastids. Using phylogenomics we show that host and plastid data are perfectly congruent across a large plastid-containing clade (named MER-2), strongly indicating co-evolution. Extensive environmental screening using double CARD-FISH simultaneously targeting host and plastid further confirms that MER-2 cells almost always harbor plastids, supporting the hypothesis of permanent plastid integration and vertical transmission. Additionally, we find that both MER-2 hosts and other Meringosphaera lineages encode multiple plastid-associated genes from diverse phylogenetic origins, with many of their products predicted to be plastid-targeted. Collectively, our findings represent the first report of algae in centrohelids, a large eukaryotic group of otherwise heterotrophic predators. The discovery of new plastids is rare and underscores the importance of exploring uncultured algae to provide new insights into plastid origin and evolution.

Chromosomal variation underlies species evolution, but reconstructing its large-scale dynamics remains challenging, obscuring its adaptive significance. Here, we introduce GouMang, a framework that mines conserved genic section compositions across diverse species to trace karyotype evolution. In grasses, applied to 818 highly varied chromosomes spanning eight subfamilies, GouMang resolved a shared karyotype evolution path of 9-to-18 ({rho} whole genome duplication, {rho}WGD)-to-12 chromosomes, followed by lineage specific rearrangements or WGDs. Genes retained from the early {rho}WGD are linked to cold/light adaptation, supporting a key biomass expansion event that impacted subsequent global ecological pattern and human agricultural civilization, in which K-Pg global cooling and subsequent forest degradation drove early understory grasses to sun plants. Parallel analysis in Brassicaceae reconstructed karyotype evolution as well as {beta}WGD which unlinked to cold/light adaptation, reflecting a divergent biogeographic history compared to grasses. Together, GouMang depicts a widespread plant evolutionary pattern where karyotype constantly diversified with WGDs recurrently fueling adaptation.

Novel antagonistic interactions between species are expected to drive especially rapid coevolution. However, little is known about the genomic basis of such coevolution in nature because novel inter-specific interactions are rarely observed. Here, we study two species that recently came into first contact in Hawaii, the parasitoid fly Ormia ochracea and its cricket host Teleogryllus oceanicus. The fly locates crickets acoustically using their song, and parasitism usually results in host death. In response, protective male-silencing mutations have rapidly spread through cricket populations over the last ~25 years, imposing novel selective pressure on flies. By integrating population genomic analyses of 358 re-sequenced flies with field surveys of selection imposed by host adaptations, we discover genomic signatures of recent selective sweeps driven by host adaptations, indicative of escalating arms-race dynamics. This evolutionary response is occurring despite severely depleted genetic variation after bottlenecks in Hawaiian fly populations. Comparative analyses suggest that the genomic substrate of modern-day, rapid counter-adaptation in O. ochracea has been under positive selection on intermediate and long-term timescales across parasitoid flies. Our findings thus support predictions of influential arms race coevolution models and illustrate the current and ancient genomic bases of counteradaptation in nature.

The vertebrate pallium harbors independently evolved structures that, nevertheless, support strikingly similar sensory and cognitive circuit architectures. The mechanisms and evolutionary timing driving the emergence of these parallel pallial circuits remain unelucidated. Here, we integrated spatial transcriptomic and single-nucleus RNA-seq datasets from eight representative vertebrate species spanning approximately 500 million years of evolution to reconstruct the evolutionary assembly of the primary sensory-allocortical (Pr-Al) molecular axis, a conserved cortical hierarchical axis defined in our prior work. We uncovered that Pr- and Al-like neuronal identities are deeply conserved across sarcopterygians, encompassing all tetrapods and lobe-finned fishes. Intriguingly, this ancestral neuronal homology is uncoupled from spatially partitioned patterning: only tetrapods further compartmentalized these Pr- and Al- neurons into distinct pallium regions. Functional enrichment of Pr- and Al- gene programs uncovered a conserved tetrapod genetic core suite including MAPK signaling and axon guidance pathways. This core toolkit underwent sequential functional refinement from amphibians through mammals. Notably, mammals and birds convergently evolved association-cortical molecular profiles enriched for synaptic regulatory genes to support advanced cognitive functions. Collectively, this work delineates a stepwise vertebrate pallium evolutionary paradigm that explains how conserved molecular modules shape spatially organized brain circuitry across deep evolutionary time.

Limb loss in vertebrate animals is surprisingly common despite imposing strong functional constraints. These pressures funnel species towards regions of limited ecological and phenotypic space. To date, snakes have been considered unique in having escaped this pattern. Using a new species-level phylogeny and comparative morphological and dietary datasets, we show that pygopods, a group of limbless Australo-Papuan geckos, have undergone a similar evolutionary trajectory to snakes. Our analyses provide evidence of exceptional morphological and diet evolution. This is exemplified by strong niche partitioning among genera through dietary specialization and greater than expected dietary disparity. Diversification in pygopods has also been driven by extreme phenotypic evolution, with pygopods encompassing much of the morphological space covered by all other limb-reduced lizards. Interestingly, the diversification of pygopods has resulted in only a modest number of species, emphasizing the decoupling of diversity and richness possible in adaptive radiations.