Nectar is a hub for plant-pollinator interactions, yet gene-level causal links between plant genetic variation, pollinator foraging, and nectar microbial assembly remain poorly resolved. Using near-isogenic lines, innovative field time-lapse monitoring of pollinator visits, and long-read amplicon sequencing of nectar microbiota, we show that a natural single-nucleotide variant at a cell-wall invertase gene (HaCWINV2) controls sunflower nectar chemistry and influences both pollinators and microbes. Plants homozygous for a loss-of-function HaCWINV2 allele produce sucrose-rich nectar, resulting in fewer bee visits under field conditions. In pollinator-excluded flowers, invertase-deficient plants harbored greater fungal diversity and compositionally distinct communities, indicating that nectar sugar profiles act as ecological filters shaping the nectar microbiome. This loss-of-function allele is rare in wild sunflowers, but fixed in 35% of cultivated lines, indicating positive selection during domestication. Our findings establish a causal link between a single gene and nectar chemistry, with cascading ecological effects in a plant-pollinator system, thus illustrating how subtle genetic changes scale up to alter nectar traits, microbial assembly, and pollinator foraging behavior.
Root hairs (RHs) are critical for nutrient acquisition, yet the mechanisms by which their elongation is calibrated to environmental cues remain poorly understood. While the lateral root cap (LRC) physically encases the root tip, its potential regulatory role in determining the fate of the neighboring epidermis has been largely overlooked. In this study, we demonstrate that the persistence of LRC is required for a transient signaling hub that remotely controls RH elongation in Arabidopsis. The LRC-localized NAC transcription factor SOMBRERO acts as the integrative hub of an auxin-driven communication pathway between the LRC and epidermis. Specifically, ANAC033/SOMBRERO (SMB) coordinates auxin transport and biosynthesis by regulating the expression of AUX1 and the indole-3-butyric acid (IBA)-to-IAA conversion gene ECH2, which cooperatively create auxin maxima in the epidermis to drive RH elongation. Furthermore, we showed that SOMBRERO is required for maintaining basal expression levels of genes associated with RH development and acquisition of nitrogen and phosphorus, thereby regulating the RH responses to external nutrient conditions. Our findings uncover a non-cell-autonomous mechanism within the LRC through which SMB activates a precise transcriptional circuit that is coordinated with the LRC developmental program to optimize RH foraging strategies under fluctuating environments.
The extinct “American cheetah” (Miracinonyx trumani) has long been considered a North American ecological analog of the African cheetah1,2 (Acinonyx jubatus) based on convergent cursorial morphology, yet this paradigm rests on limited data3 and untested assumptions about its evolutionary relationships and ecology.2,4 Here, we generate nuclear paleogenomes from M. trumani specimens from Wyoming (∼23 kya; thousand years ago) and Yukon (∼31 kya), definitively placing this enigmatic felid within the evolutionary tree of cats. Phylogenomic analyses confirm M. trumani as sister to pumas (Puma concolor), not cheetahs, with a divergence of ∼2.6 million years ago (mya) during rapid Pliocene-Pleistocene climate oscillations. The Yukon specimens extend the species’ known range2 by over 20° latitude into the Arctic, and stable isotope analyses reveal striking ecological differentiation, with the Yukon population occupying an elevated trophic position consistent with exploitation of anadromous fish, while the Wyoming population functioned as a generalist terrestrial predator. This evidence suggests that M. trumani exhibited remarkable ecological versatility, while loss-of-function mutations in circadian genes may reflect relaxed constraints on circadian regulation. Together, these findings underscore how morphological convergence can obscure the true diversity and complexity of extinct megafaunal ecosystems.
The nucleus accumbens (NAc) orchestrates a range of critical physiological functions, including reward and motivation, yet single-neuron-level connectivity of its inputs and outputs remains less comprehensively characterized. Here, we examined the organizing principle of input and projection of medium spiny neurons (MSNs) across NAc in adult male mice at single-cell resolution. Our results revealed topographic distribution principles of these neurons and their terminals in the substantia innominata (SI) subdivision. Rabies virus tracing uncovered different monosynaptic inputs to Tac2+ (D1 subtype) versus Calcr+ (D2 subtype) MSNs across NAc subregions. Furthermore, cortical neurons projecting to NAc core or shell showed distinct cortical origins and collateralization. Hippocampal neurons projecting to the NAc preferentially innervate the core and medial shell with longitudinal topography and the strongest co-projection to the hypothalamus. Together, these data delineated the neuronal connectivity patterns of different neuronal subtypes in NAc, providing an anatomical basis for further understanding the neural circuit mechanisms underlying the functional role of NAc.
Rett syndrome (RTT) is a neurodevelopmental disorder caused by mutations in MECP2. Disordered breathing is a hallmark feature of RTT that negatively impacts quality of life and can be life-threatening. Despite this, the mechanisms underlying disordered breathing in RTT are poorly understood. Although RTT is primarily considered a central nervous system disorder, we found that increased drive from peripheral respiratory chemoreceptors may contribute to unstable breathing in MeCP2-deficient mice. Consistent with this, breathing pure oxygen to limit the output of peripheral chemoreceptors stabilized breathing in MeCP2-deficient mice. Also, knockdown of MeCP2 within the carotid body recapitulates RTT-like unstable breathing. We also found that MeCP2 deficiency alters the carotid body transcriptome, including the disruption of genes involved in dopaminergic signaling, and treatment with a dopamine receptor agonist stabilized breathing in MeCP2-deficient mice. These results identify the peripheral chemoreceptors as high-priority therapeutic targets for disordered breathing in RTT.
Snake embryos are often tightly coiled, but the biological basis for this developmental trait remains a puzzle. To understand how and why they coil, we first investigated directions of coiling within and across 39 snake and other limbless squamate species. In early developmental stages, coiling orientation appears to be nearly fixed right-handed across multiple species. We present evidence that accelerated somitogenesis outpaces gastrointestinal extension at these stages, causing the axial column and somitic series to coil around the delayed visceral tissues. To allow this, the body axis and the gut are physically separate, where the latter forms a pillar-like structure from the stomach to the cloaca. The initial dextral directional bias in these early embryos is likely passively determined by the left-sided yolk mass. Coiling becomes looser and more inconsistent later in development when the embryos acquire mobility through maturation of axial musculoskeletal tissues and with a sufficiently extended gut. These consilient lines of observations reveal, in embryonic coiling, a series of responses of the growing tissues to spatial limitations during snake embryogenesis. As these parameters conflict at some developmental stages (e.g., the offset growth curves between the gut and the body axis), snakes apparently solve some of the many challenges to patterning their startlingly elongate bodies by coiling, which takes advantage of what could otherwise be discordant features of embryonic growth.
Animals exhibit sex-specific behaviors that are governed by sexually dimorphic circuits. One such behavior in male Drosophila melanogaster, courtship, is regulated by various sensory modalities, including olfaction. Here, we reveal how sexually dimorphic olfactory pathways in male flies converge onto lateral horn output neurons, third-order neurons in the olfactory circuit, to regulate courtship. To achieve this, we developed ds-Tango, a modified version of the monosynaptic tracing and manipulation tool trans-Tango. In ds-Tango, two distinct configurations of trans-Tango are positioned in series, thus providing selective genetic access not only to the monosynaptic partners of starter neurons but also to their disynaptic connections. Using ds-Tango, we identified a node of convergence for three sexually dimorphic olfactory pathways. Males in which this node is silenced aberrantly court other males, unless a female is present. Thus, our results identify lateral horn output neurons important for proper courtship behavior and establish ds-Tango as a tool for disynaptic circuit tracing.
Deep neural networks (DNNs) excel at predicting neural responses across the visual hierarchy,1,2,3,4,5 a success widely interpreted as evidence of shared object recognition computations.6,7 Yet improving DNN object recognition accuracy does not reliably increase neural predictivity,8,9 and even untrained networks predict brain responses above chance.9,10,11 This disconnect suggests that object recognition may not drive DNN-brain alignment. Texture-like statistics are represented in both DNNs and mid-level visual cortex (A.V. Jagadeesh and M. Livingstone, 2024, ICLR, presentation).12,13,1416 In natural images, these statistics are carried by objects and backgrounds, shaping representations and recognition in both systems.16,17,18,19 Does DNN-brain alignment reflect a shared sensitivity to object-related information or texture-like statistics? To dissociate these factors, we recorded electroencephalograms (EEGs) from 57 participants viewing natural scenes, texture-synthesized images preserving local statistics while disrupting global form, and object-only images with backgrounds removed. If alignment reflects texture-like statistics, then it should peak for texture-synthesized images. If it reflects object-related processing, then alignment should be strongest for natural and object-only conditions, which preserve object information. We compared EEG responses with DNN activations via weighted representational similarity analysis.20,21 Texture-synthesized images yielded the strongest DNN-EEG alignment, peaking in early responses (<200 ms) and explaining up to ∼85% of noise-ceiling-normalized explainable variance versus ∼44% for natural and ∼55% for isolated objects. Crucially, object categories were more decodable for natural and object-only images than texture-synthesized images, yet these object-rich conditions showed weaker alignment. This dissociation reveals that DNNs capture the texture-statistical component of early visual responses while failing to explain later, object-related variance.
Plant pathogen evolution is driven by complex biological and ecological processes with major consequences for food security. Understanding how genetic diversity arises and is maintained is critical for predicting disease emergence. The wheat stripe rust fungus Puccinia striiformis f. sp. tritici is among the world's most destructive crop pathogens. As a dikaryotic fungus harboring two distinct haploid nuclei, Puccinia striiformis f. sp. tritici offers an excellent model to investigate nuclear-level evolution. Here, using population genomics of 507 global isolates and haplotype-phased genomes, we reconstruct the evolutionary history of Puccinia striiformis f. sp. tritici and its two nuclei. We show that two ancient nuclear lineages, nuclA and nuclB, originated from a common ancestor and diverged approximately 10,000 years ago, predating modern agriculture. Their differentiation was reinforced during wheat domestication and early agricultural expansion, which imposed new ecological and selective pressures. Subsequent wheat dispersal and regional adaptation promoted the emergence of two allopatric homozygous populations: nuclA-nuclA, which is predominant in south Asia/east Africa, while nuclB-nuclB is predominant in China, with both undergoing sexual recombination. In contrast, later agricultural intensification favored clonal propagation and facilitated recurrent somatic nuclear exchange, giving rise to a globally dominant heterokaryotic population (nuclA-nuclB) with high heterozygosity and broad adaptability. Notably, similar virulence traits can arise independently in clonal populations and sexual populations, resulting in convergent evolutionary outcomes. Together, our results establish a unified evolutionary framework in which host domestication, reproductive strategy, and nuclear-lineage dynamics jointly shape the origin, diversification, and global success of a major crop pathogen.
Hydra vulgaris is one of the few cnidarian species that live in freshwater environments. To understand this adaptation, we studied Hydra's mechanisms of osmoregulation. Behavioral imaging showed that Hydra accumulates water in its gastric cavity over time and periodically excretes it through the mouth. Comparative genetic analysis revealed unique aquaporin water-channel expression in Hydra's endodermal epithelium, where ultrastructural data demonstrated small clear vesicles near the gastric cavity, suggesting a potential water-release pathway. We further found that endodermal rhythmic potential 2 (RP2) neurons increase their activity before water excretion, until a threshold activity level is reached, when the mouth opens, and their activity abruptly declines. The ramping of RP2 activity, well modeled by spike-count and leaky-integration algorithms with a 30 s integration time window, leads to the specific activation of epithelial muscle cells near the mouth region before mouth opening. Confirming a causal role of RP2 in the behavior, two-photon activation of RP2 neurons induces water excretion, while ablating RP2 neurons alters it. Consistent with this, GLWamide peptides, synthesized by RP2 neurons, induce water excretion. We conclude that activation of RP2 neurons and subsequent release of GLWamide-family peptides promote water excretion and propose a circuit model for the temporal integration and sequential unfolding of this osmoregulatory cycle. Our work demonstrates that neural integration algorithms and peptide-based signaling can be used by simple nervous systems to coordinate a behavioral and physiological program.
To survive, animals must select contextually appropriate behavioral responses to threatening sensory stimuli. However, how the circuits that process specific sensory stimuli might disseminate information to, and be affected by, other brain regions whose activities reflect these states is incompletely understood. We examined the response of fruit flies to a looming visual object, a well-studied model of visual threat. Prior work has characterized how such stimuli can activate specific neural circuits to evoke distinct behavioral responses. However, how looming stimuli might alter neural activity in other parts of the brain is incompletely understood. We examined loom-evoked changes in brain-wide neural activity using volumetric two-photon imaging in behaving flies. These studies revealed that the looming stimulus evokes a broad increase in neural activity spanning many brain regions, both visual and motor areas as well as sensory areas that process non-visual cues. Across many stimulus presentations, we identified distinct locomotor responses. By comparing neural signals across these behavioral categories, we discovered temporally unique patterns of neural activity in distinct anatomical regions. Moreover, we observed a quiescent state in which the animal displays a significant stimulus-evoked neural response that fails to elicit a change in behavior, thereby decoupling perception from action. Finally, we show that the neural state before the stimulus can accurately predict subsequent behavioral responses and that this accuracy depends on signals from a small set of central brain regions. Taken together, these data argue that action selection is telegraphed by differences in the initial neural state expressed in specific brain regions.
Nod factors (NFs) are microbial signals originally identified for their key role in the nitrogen-fixing root nodule symbiosis in legumes. Beyond symbiosis, NFs also possess a conserved capacity to induce lateral-root formation across diverse plant species, including non-legumes. It is now well established that the nodule organogenesis program has co-opted several molecular mechanisms involved in root development, which raises the question of the developmental pathway controlled by NFs to trigger lateral-root formation and how it overlaps with nodule organogenesis in legumes. In Medicago truncatula, NF stimulation of lateral-root formation is independent of the cytokinin receptor CYTOKININ RESPONSE 1 (CRE1), a negative regulator of lateral-root formation. Here, we show that this stimulation is also independent of the NODULE INCEPTION (NIN) transcription factor, a major regulator of nodule organogenesis acting downstream of cytokinin perception. Instead, NFs stimulate lateral-root formation by influencing auxin biosynthesis and modulating auxin signaling, notably through Auxin/INDOLE-3-ACETIC ACID 7 (Aux/IAA7) in M. truncatula. Using reverse genetics and cross-species complementation, we show that orthologs of MtIAA7, AtIAA29 in Arabidopsis thaliana and SlIAA29 in tomato share a conserved role in lateral-root formation. MtIAA7 also interacts with AUXIN RESPONSE FACTOR (ARF) orthologs of AtARF7 and AtARF19, which are known to control lateral-root formation in Arabidopsis. Altogether, our findings show that NFs control a true lateral-root formation pathway, independent of the nodule organogenesis pathway in M. truncatula, by acting through a conserved auxin signaling module.
Like other rorqual whale species, blue whales (Balaenoptera musculus) evolved to specialize in consuming large numbers of small-bodied prey through engulfment filter feeding.1,2 Blue whales in the eastern North Pacific feed almost exclusively on ephemeral swarms of krill.3,4,5 The densest and most energetically profitable krill aggregations are often associated with bathymetric features5,6,7,8 and circulation phenomena,8,9,10,11,12 but how the whales find patchy krill swarms in a vast dynamic habitat remains largely unknown. Integrating animal- and satellite-borne sensing in the eastern North Pacific, we show that blue whales can precisely localize feeding in a favorable foraging habitat by sensing horizontal thermal gradients near the ocean surface. While tracking a dynamic upwelling plume front over hundreds of kilometers, blue whales repeatedly: (1) responded to frontal encounters by sharply changing course and conducting deep exploratory dives; (2) systematically transected across and along the variable local orientation of frontal gradients—particularly during nighttime search periods that preceded intensive daytime feeding; and (3) localized temperature minima before moving toward the warm side of the front while feeding. Such persistent orientation of movement relative to thermal gradients during day and night, with or without the result of feeding, is consistent with thermal sensory perception and memory serving as the primary search modality. This case study, enabled by a rarely achievable integration of high-resolution sensing, motivates a broader examination of how highly mobile marine species track resources relative to the dynamic physical gradients that structure marine ecosystems.
The banana family (Musaceae) exhibits remarkable diversity in karyotype structure and bract coloration, yet the evolutionary dynamics of chromosome rearrangements and the regulatory basis underlying color diversification remain poorly understood. Here, we present a telomere-to-telomere (T2T), gap-free genome assembly of Musa exotica, an ornamental species with brightly colored bracts, representing an early-branching lineage within sect. Callimusa (Musa L.). By integrating this high-quality genome with available Musaceae genomes, we reconstruct the ancestral Musaceae karyotype (AMK) with a haploid chromosome number of n = 17. Comparative genomic analyses reveal recurrent, lineage-specific inter-chromosomal rearrangements across extant Musaceae lineages, resulting in stepwise chromosome number reductions to n = 11, 10, and 9. This karyotype trajectory is consistent with DNA-based phylogenetic relationships and suggests that chromosomal reorganization contributed to early lineage diversification within the family. Notably, rearrangement-associated regions are enriched for functionally important genes, particularly structural genes (chalcone synthase [CHS] and flavanone 3-hydroxylase [F3H]) and regulatory transcription factors (MYB and basic-helix-loop-helix [bHLH]) involved in anthocyanin biosynthesis. Integrative transcriptomic and regulatory analyses demonstrate coordinated activation of anthocyanin biosynthetic genes (CHS, CHI, F3'5'H, and ANS) in brightly colored bracts, with expression divergence largely decoupled from gene dosage and predominantly driven by transcriptional regulation. Co-expression analyses reveal extensive MYB- and bHLH-enzyme interactions, underscoring their central role in modulating pathway activity and color diversification. Collectively, our results provide a comprehensive evolutionary framework for Musaceae genomic evolution and lineage divergence and link chromosome structural evolution to regulatory rewiring and phenotypic diversification.
Multivesicular bodies (MVBs) contain intraluminal vesicles (ILVs) designated for degradation in lysosomes or release as exosomes for cell-to-cell communication. The mechanisms governing ILV/exosome formation are not fully understood. Here, we show that the integral endoplasmic reticulum (ER) membrane protein bridge-like lipid transfer protein 2 (BLTP2; KIAA0100) is indispensable for ILV/exosome formation and that secretory carrier membrane protein 3 (SCAMP3) recruits BLTP2 to ER-MVB membrane contact sites (MCSs) in a Rab5-dependent manner. Our results indicate that this recruitment is hindered by NEDD4-mediated ubiquitination of SCAMP3. Depletion of BLTP2 was found to impede ILV/exosome formation and selectively reduce the levels of cone-shaped phospholipids, including bis(monoacylglycero)phosphate (BMP), and of the BMP precursor phosphatidylglycerol (PG) within endosomes. BLTP2 knockout also hampered cell proliferation and tumorigenicity, which could be restored by supplementation with exosomes from wild-type cells. Our findings suggest that BLTP2 transfers the BMP/lysobisphosphatidic acid (LBPA) precursor PG to MVBs for BMP/LBPA synthesis and promotes ILV/exosome formation at SCAMP3-dependent ER-MVB MCSs.
Rapid adaptation to novel environments is often shaped not only by newly acquired mutations but also by historical genetic backgrounds established through prior evolutionary events. However, the extent to which such historical contingency contributes to the rapid evolution of insecticide resistance remains poorly understood. Here, we investigated the emergence of resistance to flonicamid, a recently deployed insecticide, in the green peach aphid, Myzus persicae. We show that constitutive overexpression of the P450 enzymes CYP6CY3 and CYP6CY4, already widespread in populations of M. persicae before flonicamid deployment, confers a previously cryptic tolerance phenotype to flonicamid. However, biochemical and transgenic analyses demonstrated that these metabolic adaptations provide only weak protection against flonicamid. Following flonicamid deployment, however, a novel target-site mutation, NaamV251I, in the recently identified molecular target of 4-trifluoromethylnicotinamide (TFNA-AM), emerged in M. persicae on a genetic background of CYP6CY3 or CYP6CY4 overexpression. Structural modeling, enzymatic assays, and CRISPR-Cas9 genome editing demonstrated that this mutation reduces target sensitivity and independently confers moderate resistance. Strikingly, combining the nicotinamidase (Naam) mutation with pre-existing CYP6CY3 or CYP6CY4 overexpression produced substantially elevated resistance phenotypes that far exceeded the effects of either mechanism alone. Our results demonstrate that the pre-existing metabolic background did not itself evolve further following flonicamid deployment but fundamentally altered the phenotypic consequences of a subsequently acquired target-site mutation. These findings provide direct evidence that historical adaptive variation can potentiate rapid resistance evolution to newly introduced insecticides and reveal how interactions between past and contemporary adaptations shape evolutionary responses to novel environmental challenges.
Fungi transition between cell morphologies to adapt to and colonize environments. For Candida albicans, commensal colonization of humans and virulence depend on a reversible switch between invasive hyphae and disseminating yeast cells. The yeast-to-hyphae transition is well understood, but comparatively little is known about the reverse transition from hyphae back to yeast. By developing an imaging assay to visualize and quantify the hyphae-to-yeast transition, we show that the bacterial natural product gladiolin accelerates the transition. Gladiolin reprograms C. albicans metabolism, causing faster glucose consumption and increased cellular ergosterol content. In turn, faster glucose depletion accelerates the hyphae-to-yeast transition by decreasing glucose metabolism and signaling via Ras-cyclic AMP (cAMP). Transcriptional activators of glycolysis, Tye7 and Gal4, regulate the timing of the hyphae-to-yeast transition and contribute to its acceleration by gladiolin, while the ergosterol biosynthesis activator Upc2 represses the transition by maintaining hyphal elongation. Our findings shed light on the metabolic and regulatory programs that control the hyphae-to-yeast transition, revealing how changing nutrient levels and bacterial metabolites create conditions that may promote fungal dissemination.
Viviparity (live-bearing) is a major evolutionary transition repeatedly linked with ecological and evolutionary diversification throughout vertebrates. Live-bearing reproduction entails a novel suite of phenotypes and life history traits, but the genetic processes by which such a reproductive innovation evolves are unknown. Remarkable among amniotes, the common lizard (Zootoca vivipara) has extant oviparous (egg-laying) and viviparous lineages and a to-date unresolved history of parity mode emergence. This species represents an ideal model to reconstruct the evolutionary and genetic mechanisms of how viviparity arises. By analyzing whole genomes of individuals from across the species’ distribution, we robustly show that viviparity evolved once. However, gene flow from oviparous to viviparous populations is found to be long-term and extensive, causing pronounced gene tree discordance. We inferred signals of selection for viviparity in many independent regions across the genome, and these were recruited over considerable time. Genomic barriers to gene flow between oviparity and viviparity were found genome wide. These are enriched for regions under selection for parity mode and for genes known to be involved in pregnancy and parturition in squamates and mammals. Further implicating their functional role in viviparity, we show that genes in genomic regions under selection and resisting gene flow are more highly expressed in the uterus of viviparous lizards during pregnancy. Our study demonstrates that viviparity in an amniote evolved by selection in the face of gene flow and primarily by the genome-wide accumulation of functional regulatory variants. These results reveal how complex adaptive innovations can arise and be maintained.
The hippocampus is known for spatial mapping through place cells, but much less is understood about the cognitive map that integrates task and reward information. Recent work has identified elements of this map as “reward” cells that encode distance relative to rewards. However, their detailed characteristics, regulatory mechanisms, and importance for goal-oriented behavior remain unknown. Using a virtual reality task with multiple shifts of a hidden reward zone and two-photon calcium imaging in mice, we characterized the coding properties of pyramidal neurons, identifying place cells and reward cells that were active at consistent distances from rewards. The lifetime of both reward and place cells was short, lasting a few reward translocations, but reward cells persisted longer than place cells within and across days. Reward and place cell populations remained largely segregated across reward shifts, suggesting reward-cell-specific regulation mechanisms. Indeed, we identified vasoactive intestinal peptide (VIP+) interneuron activity as a critical regulator of reward cell formation and task performance. Optogenetic inhibition of VIP+ neurons reduced reward cell numbers, decreased goal representation, and impaired task performance. Activation produced the opposite with increased reward cells, stronger goal representation, and enhanced performance. Surprisingly, this circuit regulation was largely specific to reward cells since the spatial map was unchanged by VIP+ activity manipulation, with no alteration in place cell number or position decoding. Our findings reveal that reward cell activity is necessary for flexible, goal-directed learning, and VIP+ neuronal activity plays a specific role in controlling the formation and coding of this cognitive map.
