PLOS Biology

Accurate localization of anatomical landmarks is a foundational skill in anatomy and imaging that is often taught informally through expert mentorship, requiring access to data and desktop software. There is no openly accessible, interactive resource that teaches neuroanatomy with quantitative feedback. We present the AFIDs-Validator (validator.afids.io), an open-access, browser-based platform that pairs guided instruction with quantitative assessment. The platform combines (1) a learning mode in which a language-model neuroanatomy tutor operates inside an MRI viewer, giving anatomy-first instruction that responds to the learner's current image slice, orientation, and cursor position; and (2) a validation engine that accepts a learner's landmark file and returns per-landmark Euclidean error against expert-annotated references spanning 21 brain templates. To make the feedback interpretable, we analyzed 15,000 landmark annotations across 132 human subjects and found that landmark difficulty varies fourfold (median error ranged from 0.37 mm at the anterior commissure to 1.50 mm at the temporal horns) with heavy-tailed distributions at every landmark. These distributions are compiled into per-landmark reliability priors, so learners are scored against the empirical spread of trained raters rather than an arbitrary threshold, and difficult landmarks are not mistaken for poor performance. The AFIDs-Validator requires no installation, licensed software, or local data, and all code, reference data, and tutor design are openly released.

Research on butterflies has uncovered a conserved "toolkit" of genes for color pattern development and evolution. One of these genes is optix, a homeobox transcription factor that regulates ommochrome and melanin pigmentation, as well as structural coloration, in nymphalid butterflies. It remains unclear, however, whether optix plays any roles in color patterning outside of the Nymphalidae. We used CRISPR-Cas9 to disrupt optix in the tobacco hornwormmoth Manduca sexta and observed a dramatic abdominal pigmentation phenotype, where orange pigmentation was replaced by black eumelanin. Chemical assays suggest that the orange pigment is not an ommochrome, indicating that optix modulates an alternative, uncharacterized pigment pathway in M. sexta. RNA-seq and chemical analyses of orange and black abdominal scales lead us to speculate that the orange pigment may be a type of melanin, perhaps N-{beta}-alanyldopamine (NBAD) sclerotin. Our results suggest that optix plays a deeply ancestral role in pigment regulation in Lepidoptera, and demonstrates evolutionary flexibility in how it interfaces with pigment chemistry across moths and butterflies.

Collateral sensitivity (CS) - resistance to one antibiotic inducing hypersensitivity to another - offers an evolutionary trap for multidrug-resistant pathogens. A strongly connected component (SCC) in the directed CS graph is a closed cycle in which every drug is reachable from every other. Prior evidence for CS SCCs is exclusively in vitro. We mined 104,337 susceptibility records from BV-BRC spanning four WHO critical-priority pathogens (Klebsiella pneumoniae, Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa; 18,821 isolates), using Fisher's exact tests with Benjamini-Hochberg FDR correction, Tarjan's algorithm, and permutation testing (n = 1,000). Two species yielded qualifying SCCs. In K. pneumoniae (4,286 isolates), a 3-node SCC - imipenem, meropenem, tetracycline - was detected (empirical p = 0.001); both carbapenem-tetracycline edges are bidirectional (OR = 1.81-1.82, q < 0.002, n > 850 per edge). In E. coli (6,720 isolates), a bidirectional 2-node SCC links colistin and cefotaxime (OR = 10.13, 95% CI 2.82-46.12, q = 0.042, n = 87; permutation p = 0.008); with a fragility index of 1, we report it as a hypothesis, not an established effect size. The carbapenem signal is tetracycline-specific: tigecycline shows co-resistance (OR < 0.35), as its distinct RamA/AcrAB-TolC mechanism predicts. ORs of 2.2-2.7 persisted across independent year bands (2009-2014). S. aureus returned no qualifying SCC, but that null is power-limited: only 8% of testable pairs could detect the K. pneumoniae effect size. Prior clinical analyses characterised pairwise and three-way collateral effects; to our knowledge these are the first closed CS cycles identified in clinical surveillance data, motivating experimental follow-up.

Gene loss is a widespread phenomenon that shapes genome evolution, yet the factors determining why certain genes are repeatedly lost while other functionally related genes are retained remain poorly understood. We addressed this question using the peptide-processing metallocarboxypeptidases carboxypeptidase E (CPE) and carboxypeptidase D (CPD), conserved paralogues that are essential for neuropeptide maturation but strikingly differ in their evolutionary fate: the cpe gene has been independently lost in two major insect lineages, whereas cpd/svr has been universally retained. Combining gene phylogenetic analyses and functional genetics in the beetle Tribolium castaneum, and cross-species rescue experiments in the fly Drosophila melanogaster, we show that CPE and CPD retained partially interchangeable enzymatic functions despite considerable differences in structure, organismal importance and expression. Contrary to expectations, cpe proved more critical than cpd/svr for survival and developmental robustness in Tribolium, while simultaneous RNAi-mediated downregulation of both genes caused complete larval lethality, demonstrating only partial functional redundancy. Moreover, beetle CPE partially rescued the lethal loss of Drosophila CPD, establishing conserved molecular interchangeability across [~]300 million years of insect evolution. Gene phylogenetic analyses further indicate that bilaterian CPE originated through duplication of the second catalytic domain of an ancestral CPD. Together, our results demonstrate that repeated loss of insect cpe cannot be explained by reduced functional importance. Instead, we propose that the structural versatility, broader tissue distribution and multifunctionality of CPD, including its multidomain architecture and splice isoforms, enabled compensation for CPE after gene loss, thereby shaping long-term patterns of gene retention and loss during insect evolution.

Major transitions in evolution are associated with the loss of independent reproduction by formerly autonomous units. Termites provide a powerful system for studying this process because they exhibit diverse social systems in which worker developmental and reproductive potential declines with increasing colony-level organismality. However, the evolutionary sequence and developmental genetic basis of these transitions remain unresolved. Here, using comparative developmental transcriptomics across seven termite species that differ in workers' reproductive potential, we reconstructed the evolutionary history of termite social systems. We found that linear caste development, in which workers retain full reproductive potential, represents the ancestral state of termites. Bifurcated caste development, in which workers partially lose reproductive potential early in development, evolved independently multiple times, with two origins subsequently giving rise to superorganisms with unipotent, sterile workers. Ancestral gene regulatory network (GRN) reconstruction revealed that linear caste development evolved through retention of a juvenile-like worker state and co-option of a conserved developmental GRN characterizing hemimetabolous insect nymphal development, in which juvenile hormone, ecdysone and TGF-{beta} signaling pathways play central roles. The convergent evolution of bifurcated caste development repeatedly co-opted the GRN underlying linear caste development, heterochronically shifting its activity to earlier developmental stages. Finally, we found that the evolution of termite superorganisms involved somatization of the worker caste and co-option of a conserved endocrine GRN for terminal differentiation. Together, these findings uncovered repeated routes to reduced workers' reproductive potential through GRN co-option and highlight striking parallels between superorganism evolution in social insects and organismal evolution in metazoans.

Longitudinal animal experiments generate behavior that is individual, history-dependent, and sometimes affected by ordinary procedural irregularities, yet analyses commonly reduce such records to pooled averages or synchronous trial-level explanations. We introduce history-structured forecasting as an auditable framework for determining whether an animals own preceding behavior carries predictive information beyond current-trial context. We applied the framework to 213,990 events from rats performing an auditory duration-discrimination task, using leakage-safe chronological forward-chaining, explicit trivial baselines, and controls that reset, exchange, or disrupt behavioral history. A transparent gradient-boosted model achieved 51.7% four-class accuracy, exceeding last-action persistence (40.9%) and prefix-derived subject-modal prediction (37.2%); decline-class AUPRC was 0.525 against a prevalence baseline of 0.303. Validation showed that the predictive advantage depended predominantly on each animals short-range sequential action history rather than group-level history, subject identity alone, or reward/correctness features, and strengthened on genuine choice trials. Forecasting remained informative across all 23 labeled animals, including six with recoverable records affected by incorrect training programming. These results revise the interpretation of rewarded give-up behavior while demonstrating how recoverable irregular records can be retained in transparent robustness analyses. History-structured forecasting offers a reusable open-science strategy for extracting reproducible evidence from imperfect longitudinal animal records without creating an artificially clean cohort.

The timing of the origins of the crown-group placental mammals has provided one of the classic battlefields in the long-running debate over when clades arise. Undoubted fossil crown-group placentals appear only in the Paleogene, but even so most molecular analyses, and many palaeontologists, have suggested their true origin is somewhere between 70-100 Ma. However, apart from the fact of the fossil record itself, there are several reasons to believe that the true origin is indeed post-Cretaceous, including consideration of the dynamics of stem and crown groups, which strongly favour crown-group origins to lie just after, and not just before, mass extinctions. Here we consider this "hard explosive" model in the light of the newly-developed "Covariant Evolutionary Tempo (CET)" model which allows diversification and molecular evolution rates to covary. It predicts "early bursts" in both lineage creation and molecular evolution at the base of major radiations which lead to highly unequally-sized clades; and an inheritance of rapid rates from this initial event by extant rapidly-evolving clades. We show that when the placentals are constrained to emerge after the K-Pg boundary, they indeed show elevated rates of both diversification and molecular evolution, which rapidly decline. Nevertheless, although elevated, these rates are comparable to the fastest rates seen in extant clades such as the rodents. In addition, the contiguous lineages leading from the origin to the rodents and other fast evolving clades also show elevated rates. These patterns suggest that not only is a Paleogene origin for the placental crown-group plausible, as fossil evidence suggests, but they also provide support for the CET model, which should be considered in other cases of pronounced fossil record/molecular clock mismatch.

Long considered a structure dedicated primarily to motor control, the cerebellum is now known to contain regions that respond selectively to language. However, how cerebellar language specialization emerges during development remains unknown. The prevailing proposal is that cerebellar functional specialization critically depends on inputs from the contralateral neocortex, received through well-established reciprocal cortico-cerebellar connections. Here, we test this hypothesis in a right-handed woman (EG) who lacks most of her left temporal lobe (presumably, from birth) and whose neocortical language network resides in her right hemisphere. Using precision functional MRI in EG and a cohort of 74 typically developing adults, we find that EG's cerebellar language network shows a strong left-hemispheric bias, mirroring the atypical lateralization of language in her cerebral cortex, while preserving canonical topography and response profiles of the language-dominant cerebellar regions. Critically, however, EG's right cerebellar hemisphere also responds to language and even contains a language-selective region despite the absence of language regions in the neocortical left hemisphere. These findings challenge the view that cerebellar specialization critically requires contralateral neocortical inputs, and point instead to some degree of intrinsic neocortex-independent cerebellar organization.

Viral population dynamics are shaped by production and loss. For viruses of microbes, high standing levels of viral abundances are interpreted as evidence of high rates of viral-induced cellular loss and viral production, followed by rapid extracellular viral decay. Here we reassess assumptions of rapid extracellular decay in 17 curated datasets, finding that biphasic decay either fits better or is statistically indistinguishable from exponential decay in approximately half the datasets. In addition to intrinsic heterogeneity in decay rates, biphasic decay at population scales can arise generically through aggregation mechanisms, where single virions decay and viral aggregates are protected. Integrating aggregation-induced biphasic decay into a virus-host model reveals that accounting for aggregation can recapitulate joint observations of high virion abundances and low infection prevalence, without assuming significant levels of uniformly inefficient infection. Together, our results suggest that durable extracellular virion persistence is environmentally relevant in shaping virus-microbe population dynamics.

Active sensing systems are known to adapt the structure of sensory signals. Whether they can improve perception by controlling when sensory information is acquired remains unclear. We show that echolocating fruit bats exposed to rhythmic noise preferentially emit calls during recurring low-noise periods, a behaviour we term "dip echolocation". Dip echolocation occurred in laboratory and wild bats and represents an active-sensing analogue of dip listening in humans. A normative model showed that temporal positioning of calls emerges from a trade-off between sensory information and energetic cost, alongside concurrent adaptations of call structure. Pharmacological inactivation of the frontal auditory field disrupted precise temporal control, implicating a role for frontal cortical circuits in adaptive vocal timing. These findings identify adaptive vocal timing as an active-sensing strategy for overcoming acoustic interference.

During the lifetime of many animals, the microbiota fulfills multiple functions. After death of their hosts, these microbes contribute to cadaver decomposition, with implications for forensics, fossilization and soil nutrient and microbial community dynamics. Here, we draw attention to the possibility that host microbiota can also influence the evolution of pathogen lifestyles. We hypothesized that competition between microbiota and pathogens after host death can reduce benefits to pathogens of killing and decomposing their host. To test this hypothesis, we conducted infection experiments in which we injected the entomopathogenic bacteria Pseudomonas entomophila into Tenebrio molitor larvae. Our results show that bacterial proliferation after pathogen-induced host death occurs in larvae with strongly reduced microbiota, but not in larvae with intact gut microbiota. Strikingly, we found that gut microbiota can suppress the proliferation of an about 100 times larger pathogen population. In addition, we identified a microbiota member that might have mediated competitive suppression of pathogen proliferation after host death. Taken together, our results support our hypothesis that decomposing host microbiota can effectively compete with pathogens, thereby reducing the fitness of pathogens that kill and then exploit dead hosts. Based on a reanalysis of an existing theoretical model, we conclude that the host microbiota can facilitate the evolution of more benign pathogens that are less likely to kill their host for cadaver exploitation. Thus, our findings highlight the potentially important but so far unexplored possibility that pathogen-microbiota interactions in dead hosts can affect living hosts by influencing the evolution of pathogens lifestyles.

Interoceptive sensations, arising from the body's visceral organs such as the heart, are known to impact exteroceptive sensory perception. The classical explanation for heart-to-brain influence, the Baroreceptor Hypothesis, posits that baroreceptors firing during the systolic blood pressure peaks that follow each heartbeat suppress the magnitude of neural responses to exteroceptive sensations. More recent work, however, has demonstrated qualitative (rather than merely magnitude) differences in perception as a function of the cardiac cycle; since it is not obvious how the Baroreceptor Hypothesis could explain these findings, even in principle, they have often been characterized as incompatible. We propose baroreceptor-related suppression of early sensorineural responses need not manifest simply as suppression of corresponding conscious percepts. In a validated computational model of auditory cortex that segregates an ambiguous tone sequence into either one or two auditory objects or "streams," we found suppression of the neural response to one tone type increases the likelihood that tone is parsed into a distinct stream. We subsequently verified this prediction empirically: when presenting such ambiguous sequences to human participants in a manner such that one tone type only occurs during cardiac systole, the initial neural response to that tone -- indexed by the electroencephalographic (EEG) frequency-following response (FFR) -- is indeed suppressed, while participants report hearing the sequence as two separate sounds streams more frequently. Thus, suppression of early sensorineural responses can be sufficient to explain qualitative, not just magnitude, differences in perception when considered in the context of larger neural circuits.

The K-Pg extinction ended the world of non-avian dinosaurs 66 Mya and ushered in the Age of Mammals. During the [~]10 My of recovery, Schizophora, an immensely successful group of flies, appeared, flourished and diversified. This large radiation produced over half of all dipteran families ([~]78/150), including the family for Drosophila, the model genetic powerhouse. In the context of this evolutionary radiation, we investigate the loss of two of three highly conserved, neurosensory transmembrane channel (TMC) genes. Here, we show that these genes were separately lost across multiple diverging schizophoran lineages of the early Paleogene, suggesting a powerful environmental driver was involved. We also show that unlinked genes encoding the calcium- and integrin-binding (CIB) subunits of the missing TMC complexes were lost during the same time frame. Because the lost genes encode complexes involved in thermal nociception, we propose the external driver was likely the Paleocene- Eocene thermal maximum (PETM), a 200 ky interval of elevated global temperatures occurring 56 Mya, slightly before the earliest schizophoran fossil from 53 Mya. These results suggest that gene loss may have been adaptive for most schizophoran lineages to emerge past the hothouse Earth of the PETM.

The temporal structure of speech has traditionally been characterized by the rhythmicity of its canonical linguistic units (phonemes, syllables, words), each summarized by a mean occurrence rate. While valid, this view overlooks whether speech carries a finer, context-dependent and probabilistic temporal structure that could support temporal predictive coding during listening. Using large French and English speech corpora, we trained models of increasing complexity to predict the onsets of linguistic units. Recurrent neural networks (RNNs) outperform mean-rate and hazard-rate models, showing that the variability around these rates is not noise but a temporal structure shaped by local context, statistically predictable across phonemes, syllables and words. Recording from 7,698 intracerebral electrodes in 53 neurosurgical patients listening to natural speech, we next show that the models' output), the continuous probability of an upcoming onset (when), explains neural activity beyond acoustic and linguistic content (what) features, with markedly stronger effects for RNNs than for mean- or hazard-rate models. This dynamic neural prediction of when an onset will occur is dissociable from the encoding of linguistic content, relying on largely distinct channel populations. Temporal predictions engage a distributed cortical network extending from bilateral temporal cortex into left frontal and sensorimotor regions. Together, these results establish temporal prediction in speech as a dynamic, context-dependent and probabilistic process in its own right.

How does the auditory system implement spatial selection without a dedicated cortical map for space? One hypothesis holds that auditory spatial attention draws on a supra-modal network including the parietal-occipital cortex; an alternative implicates subcortical structures (e.g., superior colliculus) with no direct recruitment of visual cortex. To adjudicate between these accounts, we used a dichotic listening paradigm and tested whether sustained auditory spatial attention produces the behavioral and neural signatures of visual spatial attention, which would only be expected if auditory attention engages the same cortical mechanisms. Participants listened to two digit streams, spoken by male and female voices, played from left and right speakers. They were instructed to attend to either the left stream, the right stream, or a specific voice gender. A behavioral experiment (N=24) showed higher discrimination accuracy for visual stimuli appearing intermittently at the auditorily attended relative to unattended location. Furthermore, participants gaze was reliably biased towards the attended location. In a second experiment (N=14), we used electrophysiological recordings of frequency-tagged visual evoked potentials to more directly assess early visual processing, and found enhanced visual-cortical responses for stimuli matching the location of the attended auditory stream. In addition, occipital alpha power (8-11 Hz) was reduced over the hemisphere contralateral to the attended sound stream. Together, these effects mirror the hallmarks of visual-spatial attention, suggesting that auditory spatial attention co-opts the architecture of the visual cortex to implement spatial selection, thereby directly enhancing visual processing. Significance statementHuman can effortlessly direct spatial attention to a sounds location in the external world. Yet the auditory system has no dedicated spatial map in the brain, raising a fundamental question: how does auditory spatial attention arise? We show that sustained attention to a sound based on its location produces well-known signatures of visual spatial attention: enhanced visual-perceptual sensitivity, larger early visual-cortical responses, and modulation of occipital alpha-band activity and oculomotor behavior. This converging behavioral and neural evidence demonstrates that auditory spatial attention actively engages and reshapes early visual processing, pointing to a supra-modal attention system shared across the senses.

How conserved neural circuits are modified during mammalian evolution remains poorly understood. Here we combine cross-species single-cell transcriptomics, in situ validation, retinal physiology, and conditional genetics to identify a superorder-associated adrenergic module in the mammalian retina. We find that ADRB1, which encodes the {beta}1-adrenergic receptor, is uniquely expressed in rod bipolar cells of sampled Euarchontoglires, but is absent from homologous cells in sampled Laurasiatheria and Marsupialia. In mice, {beta}1-adrenergic receptor localizes to rod bipolar cell terminals and boosts transmission to AII amacrine cells through Gs-adenylyl cyclase-cAMP-PKA signaling pathway. This modulation enhances synchronous release, accelerates downstream ganglion cell output, and increases scotopic electroretinographic responses, while rod-bipolar-cell-specific Adrb1 deletion abolishes norepinephrine-induced enhancement without disrupting baseline vision. In the diurnal tree shrew, a Euarchontoglires species with a cone-dominated retina, ADRB1 is instead redeployed from rod bipolar cells to cone photoreceptors. These findings reveal an evolutionarily mobile neuromodulatory module that tunes retinal computation according to visual ecology.

Prediction errors (PEs) are commonly described as cortical signals generated within sensory hierarchies, but whether the thalamus participates in their encoding and transmission remains unclear. We recorded Local Field Potentials (LFP) from the medial and lateral geniculate nuclei and electrocorticography (ECoG) from multiple cortical regions in three awake cats during two auditory prediction tasks. Mutual information (MI) analyses revealed PE encoding in both thalamic and cortical signals. Co-information (co-I) analyses showed off-diagonal temporal synergy between early and later thalamic response components, consistent with an early response inducing a neural state change that shaped the informational content of subsequent activity. Multivariate co-information (MVCo-I) further revealed that thalamic and cortical population activity carried complementary PE information unavailable from either thalamic or cortical areas alone. These synergistic interactions were reliable across animals for violations of structured auditory sequences and weaker for repetition-based deviants. These findings show that auditory PEs are not simply relayed or duplicated across the thalamocortical hierarchy. Instead, they emerge through state-dependent transformations within the thalamus and complementary interactions between thalamic and cortical populations, identifying the thalamus as an active node of context-dependent PE processing.

Despite antigenic evolution at the global scale, positive selection of influenza virus antigenic variants is not readily observed within hosts. Here, we tested the extent to which fitness tradeoffs, the timing of immune pressure, and stochastic effects impede antigenic selection within pre-immune hosts. We used genetically barcoded influenza A/Texas/50/2012 (H3N2) viruses (Tx/12) in a guinea pig model to probe these dynamics. Positive selection of an antigenic variant was reliant on a high strength of immune pressure acting early in infection. However, when fitness tradeoffs of the antigenic change were lessened, a lower strength and later introduction of immune pressure favored the antigenic variant. In all conditions, barcode dynamics revealed moderate stochastic effects. Our results suggest that stochastic evolution does not impede selection during acute influenza virus infection. The rarity of antigenic escape may instead stem from low mutational supply, fitness tradeoffs, and the intrinsic delay between infection and antibody recall.

Webers law is a rare quantitative regularity in psychology, yet its origins remain debated. Here we provide causal evidence that it arises from the more fundamental principle of efficient coding. This principle posits that representational resources are allocated according to stimulus frequencies: distributions skewed toward smaller stimuli thus result in discriminability decreasing with magnitude, as in Webers law. Skewing frequencies in the other direction--making large magnitudes more frequent than small ones--enabled us to invert this pattern, and to break Webers law. In discrimination tasks with three different sensory modalities, human subjects discriminability across stimuli was sensitive to the stimulus distribution, and this adaptation improved task performance. These findings establish efficient coding as a dynamic, organizing principle, explaining when and why Webers law holds.

Heart rate continuously adjusts to accommodate perception and action, and these shifts are frequently explained through predictive processes. Yet direct evidence that interbeat intervals exhibit graded scaling with prediction remains limited. Here we investigate millisecond-resolved physiological signatures of prediction processing using a mechanistically constrained analysis of beat-to-beat cardiac dynamics. We analysed trial-by-trial electrocardiogram and electroencephalogram recordings from 34 participants performing a probabilistic learning task. We quantified stimulus-locked cardiac responses as changes between consecutive interbeat intervals and accounted for cardiac phase at feedback. This single-beat approach separated anticipatory slowing, stimulus-locked parasympathetic brake, and subsequent acceleration. Anticipatory deceleration and rebound acceleration scaled with model-derived expectations, whereas the second heartbeat after feedback tracked signed prediction errors and outcome valence, particularly when feedback occurred early in the cardiac cycle. Peak stimulus-locked cardiac deceleration covaried with parietal P3b rather than prediction features. Thus, individual cardiac cycles carry separable signatures of anticipation, orienting, and feedback-based updating. These findings demonstrate how predictive processing propagates into human autonomic physiology on a beat-to-beat timescale and provide an interpretable, mechanistically grounded framework for quantifying brain-body co-modulation during adaptive behaviour.