title: Reward-specific satiety affects subjective value signals in orbitofrontal cortex during multi-component economic choice


title: The Internal Structure of Metacommunities

abstract: Current analyses of metacommunity data largely focus on global attributes across the entire metacommunity, such as mean alpha, beta, and gamma diversity, as well as the partitioning of compositional variation into single estimates of contributions of space and environmental effects and, more recently, possible contributions of species interactions. However, this view neglects the fact that different species and sites in the landscape can vary widely in how they contribute to these metacommunity-wide attributes. We argue for a new conceptual framework with matched analytics with the goals of studying the complex and interactive relations between process and pattern in metacommunities that is focused on the variation among species and among sites which we call the  internal structure of the metacommunity. To demonstrate how the internal structure could be studied, we create synthetic data using a process-based colonization-extinction metacommunity model. We then use Joint Species Distribution Models to estimate how the contributions of space, environment and biotic interactions driving metacommunity assembly differ among species and sites. We find that this approach to the internal structure of metacommunities provides useful information about the distinct ways that different species and different sites contribute to metacommunity structure. Although it has limitations, our work points at a more general approach to understand how other possible complexities might affect internal structure and might thus be incorporated into a more cohesive metacommunity theory.

category: ecology


title: Harnessing the central dogma for stringent multi-level control of gene expression

abstract: Strictly controlled inducible gene expression is crucial when engineering biological systems where even tiny amounts of a protein have a large impact on function or host cell viability. In these cases, leaky protein production must be avoided at all costs, but ideally without affecting the achievable range of expression. Here, we demonstrate how the central dogma offers a simple way to effectively address this challenge. By simultaneously regulating both transcription and translation, we show how relative basal expression of an inducible system can be greatly reduced, with minimal impact on the maximum induced expression rate. Using this approach, we create several stringent expression systems displaying >1000-fold change in their output after induction in vivo and up to a 350-fold change when used in a cell-free expression system. Furthermore, we find that multi-level regulation is able to suppress transcriptional noise and creates a digital-like switch when transitioning between  on and  off states. This work provides foundational knowledge and a genetic toolkit of parts to create multi-level gene expression controllers for those working with toxic genes or requiring precise regulation and propagation of cellular signals. It also demonstrates the value of exploring more complex and diverse regulatory designs for synthetic biology.

category: synthetic biology


title: Dynamic transitions between neural states are associated with flexible task-switching during a memory task

abstract:
Flexible behavior requires switching between different task conditions. It is known that such task- switching is associated with costs in terms of slowed reaction time, reduced accuracy, or both. The neural correlates of task-switching have usually been studied by requiring participants to switch between distinct task demands that recruit different brain networks. Here, we investigated the transition of neural states underlying switching between two opposite memory-related processes (i.e., memory retrieval and memory suppression) in a memory task. We investigated 26 healthy participants who performed a Think/No-Think task while being in the fMRI scanner. Behaviorally, we show that it was more difficult for participants to suppress unwanted memories when a No-Think was preceded by a Think trial instead of another No- Think trial. Neurally, we demonstrate that Think-to-No-Think switches were associated with an increase in control-related and a decrease in memory-related brain activity. Neural representations of task demand, assessed by decoding accuracy, were lower immediately after task switching compared to the non-switch transitions, suggesting a switch-induced delay in the neural transition towards the required task condition. This suggestion is corroborated by an association between condition-specific representational strength and condition-specific performance in switch trials. Taken together, we provided neural evidence from the time-resolved decoding approach to support the notion that carry-over of the previous task-set activation is associated with the switching cost leading to less successful memory suppression.

Significance statementOur brain can switch between multiple tasks but at the cost of less optimal performance during transition. One possible neuroscientific explanation is that the representation of the task condition is not easy to be updated immediately after switching. Thus, weak representations for the task at hand explain performance costs. To test this, we applied brain decoding approaches to human fMRI data when participants switched between successive trials of memory retrieval and suppression. We found that switching leads to a weaker representation of the current task. The remaining representation of the previous, opposite task is associated with inferior performance in the current task. Therefore, timely updating of task representations is critical for task switching in the service of flexible behaviors.

category: neuroscience


title: No evidence for long-range male sex pheromones in two malaria mosquitoes

abstract: AO_SCPLOWBSTRACTC_SCPLOWCues involved in mate seeking and recognition prevent hybridization and can be involved in speciation processes. In malaria mosquitoes, females of the two sibling species Anopheles gambiae s.s. and An. coluzzii mate in monospecific male swarms and hybrids are rare. Long-range sex pheromones driving this behavior have been debated in literature but to date, no study has proven their existence or their absence. Here, we attempted to bring to light their existence. To put all the odds in our favor, we used different chemical ecology methods such as behavioral and electrophysiological assays as well chemical analyses, and we worked with mosquitoes at their optimal physiological mating state i.e. with swarming males during their natural swarming windows. Despite all our efforts, our results support the absence of long-range sex pheromones involved in swarm detection and recognition by females. We briefly discuss the implications of this finding in ecology, evolution and for control strategies.


title: The ER membrane chaperone Shr3 acts in a progressive manner to assist the folding of related plasma membrane transport proteins

abstract: Proteins with multiple membrane-spanning segments (MS) co-translationally insert into the endoplasmic reticulum (ER) membrane of eukaryotic cells. In Saccharomyces cerevisiae, Shr3 is an ER membrane-localized chaperone that is specifically required for the functional expression of amino acid permeases (AAP), a family of eighteen transporters comprised of 12 MS. Here, comprehensive scanning mutagenesis and deletion analysis of Shr3, combined with a modified split-ubiquitin approach, were used to probe chaperone-substrate interactions with seven different AAP in vivo. Our findings indicate that Shr3 specifically recognizes AAP substrates, largely independent of sequence-specific interactions involving membrane and luminally oriented domains. Shr3 selectively and robustly interacts with nested C-terminal AAP truncations in marked contrast to similar truncations of non-Shr3 substrate polytopic sugar transporters. Strikingly, Shr3-AAP interactions initiate with the first 4 MS of AAP and successively strengthen, but abruptly weaken when all 12 MS are present. The data are consistent with Shr3 acting in a temporal manner as a scaffold preventing AAP translation intermediates from engaging in non-productive interactions.

category: cell biology


title: Crash landing of Vibrio cholerae by MSHA pili-assisted braking and anchoring in a viscoelastic environment

abstract: Mannose-sensitive hemagglutinin (MSHA) pili and flagellum are critical for the surface attachment of Vibrio cholerae, the first step of V. cholerae colonization on host surfaces. However, the cell landing mechanism remains largely unknown, particularly in viscoelastic environments such as the mucus layers of intestines. Here, combining the cysteine-substitution-based labelling method with single-cell tracking techniques, we quantitatively characterized the landing of V. cholerae by directly observing both pili and flagellum of cells in a viscoelastic non-Newtonian solution consisting of 2% Luria-Bertani and 1% methylcellulose (LB+MC). The results show that MSHA pili are evenly distributed along the cell length and can stick to surfaces at any point along the filament. With such properties, MSHA pili are observed to act as a brake and anchor during cell landing which include three phases: running, lingering, and attaching. Importantly, loss of MSHA pili results in a more dramatic increase in mean path length in LB+MC than in 2% LB only or in 20% Ficoll solutions, indicating that the role of MSHA pili during cell landing is more apparent in viscoelastic non-Newtonian fluids than viscous Newtonian ones. Our work provides a detailed picture of the landing dynamics of V. cholerae under viscoelastic conditions, which can provide insights into ways to better control V. cholerae infections in real mucus-like environment.

category: microbiology


title: Understanding the Unique Advantage of Adolescents in Stochastic, Volatile Environments: Combining Reinforcement Learning and Bayesian Inference

abstract: During adolescence, youth venture out, explore the wider world, and are challenged to learn how to navigate novel and uncertain environments. We investigated whether adolescents are uniquely adapted to this transition, compared to younger children and adults. In a stochastic, volatile reversal-learning task with a sample of 291 participants aged 8-30, we found that adolescents outperformed both younger and older participants. We developed two independent cognitive models, based on Reinforcement learning (RL) and Bayesian inference (BI). The RL parameter for learning from negative outcomes and the BI parameters specifying participants mental models peaked closest to optimal in adolescents, suggesting a central role in adolescent cognitive processing. By contrast, persistence and noise parameters improved monotonously with age. We distilled the insights of RL and BI using principal component analysis and found that three shared components interacted to form the adolescent performance peak: adult-like behavioral quality, child-like time scales, and developmentally-unique processing of positive feedback. This research highlights adolescence as a neurodevelopmental window that may be specifically adapted for volatile and uncertain environments. It also shows how detailed insights can be gleaned by using cognitive models in new ways.


title: Reinforcement Learning and Bayesian Inference Provide Complementary Models for the Unique Advantage of Adolescents in Stochastic Reversal


title: Distinct mechanisms underlie the subsynaptic mobility of presynaptic metabotropic glutamate receptor types to tune receptor activation

abstract: Presynaptic metabotropic glutamate receptors (mGluRs) are essential for activity-dependent modulation of synaptic transmission. However, the mechanisms that control the subsynaptic dynamics of these receptors and their contribution to synaptic signaling are poorly understood. Here, using complementary super-resolution microscopy and single-molecule tracking techniques, we provide novel insights into the molecular mechanisms that control the nanoscale distribution and mobility of presynaptic mGluRs in hippocampal neurons. We demonstrate that the group II receptor mGluR2 localizes diffusely along the axon and boutons, and is highly mobile, while the group III receptor mGluR7 is stably anchored at the active zone, indicating that distinct mechanisms underlie the dynamic distribution of these receptor types. Surprisingly, using domain swapping experiments we found that intracellular interactions modulate surface diffusion of mGluR2, but not mGluR7. Instead, we found that immobilization of mGluR7 at the active zone relies on its extracellular domain. Importantly, receptor activation or increase in synaptic activity did not alter the surface mobility of presynaptic mGluRs. Finally, computational modeling of presynaptic mGluR activity revealed that the precise subsynaptic distribution of mGluRs controls their activation probability and thus directly impacts their ability to modulate neurotransmitter release. Altogether, this study demonstrates that distinct mechanisms control surface mobility of presynaptic mGluRs to differentially contribute to the regulation of glutamatergic synaptic transmission.


title: Highly efficient CRISPR-mediated homologous recombination via NHEJ deficiency rather than HDR factors overexpression in Populus

abstract: CRISPR-mediated genome editing has become a powerful tool for genetic modification of biological traits. However, developing an efficient, site-specific, gene knock-in system based on homology-directed DNA repair (HDR) remains a significant challenge in plants, especially in woody species like poplar. Here, we show that simultaneous inhibition of non-homologous end joining (NHEJ) recombination cofactor XRCC4 and overexpression of HDR enhancer factors CtIP and MRE11 can improve the HDR efficiency for gene knock-in. Using this approach, the BleoR gene was integrated onto the 3' end of the MKK2 MAP Kinase gene to generate a BleoR-MKK2 fusion protein. Based on exogenous BleoR expression, the HDR-mediated knock-in efficiency was up to [~]40-fold greater when using a XRCC4 silencing incorporated with a combination of CtIP and MRE11 overexpression compared to no HDR enhancement or NHEJ silencing. Furthermore, this corporation of HDR enhancer overexpression and NHEJ repression also resulted in 7-fold fewer CRISPR-induced Insertions and Deletions (InDels), resulting in no functional effects on MKK2-based salt stress responses in poplar. Therefore, this approach may be useful not only in poplar and plants or crops but also in mammalians for improving CRISPR-mediated gene knock-in efficiency.

category: plant biology


title: Enhancement of CRISPR-mediated homologous recombination-based gene knock-in efficiency by simultaneous HDR overexpression and NHEJ suppression in poplar


title: Precise exogenous insertion and sequence replacements in poplar by simultaneous HDR overexpression and NHEJ suppression using CRISPR-Cas9


title: Tracking age differences in neural distinctiveness across representational levels

abstract:
The distinctiveness of neural information representation is crucial for successful memory performance but declines with advancing age. Computational models implicate age-related neural dedifferentiation on the level of item representations, but previous studies mostly focused on age differences of categorical information representation in higher-order visual regions. In an age-comparative fMRI study, we combined univariate analyses and whole-brain searchlight pattern similarity analyses to elucidate age differences in neural distinctiveness at both category and item levels and their relation to memory. Thirty-five younger (18-27 years old) and 32 older (67-75 years old) women and men incidentally encoded images of faces and houses, followed by an old/new recognition memory task. During encoding, age-related neural dedifferentiation was shown as reduced category-selective processing in ventral visual cortex and impoverished item specificity in occipital regions. Importantly, successful subsequent memory performance built upon high item stability, that is, high representational similarity between initial and repeated presentation of an item, which was greater in younger than older adults. Overall, we found that differences in representational distinctiveness coexist across representational levels and contribute to interindividual and intraindividual variability in memory success, with item specificity being the strongest contributor. Our results close an important gap in the literature, showing that older adults' neural representation of item-specific information in addition to categorical information is reduced compared to younger adults.

Significance StatementA long-standing hypothesis links age-related cognitive decline to a loss of neural specificity. While previous evidence supports the notion of age-related neural dedifferentiation of category-level information in ventral visual cortex, whether or not age differences exist at the item level was a matter of debate. Here, we observed age group differences at both levels as well as associations between both categorical distinctiveness and item specificity to memory performance, with item specificity being the strongest contributor. Importantly, age differences in occipital item specificity were largely due to reduced item stability across repetitions in older adults. Our results suggest that age differences in neural representations can be observed across the entire cortical hierarchy and are not limited to category-level information.


title: Sexually divergent development of depression-related brain networks during healthy human adolescence

abstract: We hypothesized that there are sexual differences in human brain network development underlying the female > male divergence in adolescent depression. We tested for sex differences in parameters of brain network development (accelerated longitudinal fMRI, N=298 healthy adolescents, each scanned 1 to 3 times). Sexually divergent development of functional connectivity was located in default mode network (DMN), limbic cortex, and subcortical nuclei. Females had a more "disruptive" pattern of development, where weak functional connectivity at age 14 became stronger during adolescence. This fMRI-derived map of divergent adolescent development was co-located with (i) a map of functional dysconnectivity associated with adult major depressive disorder (MDD); and (ii) an adult brain gene expression pattern enriched for genes on the X chromosome, neurodevelopmental genes, and risk genes for MDD. Sexual divergence in disruptive development of DMN, limbic and subcortical functional networks is potentially relevant to the increased risk of depression in adolescent females.


title: Enabling in vivo Analysis Via Nanoparticle-mediated Intracellular Assay Probe Delivery: Using RAS as the Prototype

abstract: Many experimental protocols must be executed in vitro due to a lack of cell-permeable analysis probes. For instance, the cellular signaling moderator RAS proteins alternate between the active GTP-binding and the inactive GDP-binding states. Though many GTP analogs can serve as probes for RAS activity analysis, their cell impermeability renders in vivo analysis impossible. On the other hand, the lipid/calcium/phosphate (LCP) nanoparticle has enabled efficient intracellular delivery of a nucleotide analog as a chemotherapy agent. Thus, using RAS analysis and LCP nanoparticle as the prototype, we tackled the cell-impermeability issue via nanoparticle-mediated intracellular delivery of the analysis probe. Briefly, BODIPY-FT-GTP-{gamma}-S, a GTP analog that becomes fluorescent only upon protein binding, was chosen as the analysis probe, so that GTP binding can be quantified by fluorescent activity. BODIPY-FT-GTP-{gamma}-S-loaded LCP-nanoparticle was synthesized for efficient intracellular BODIPY-FT-GTP-{gamma}-S delivery. Binding of the delivered BODIPY-FT-GTP-{gamma}-S to the RAS proteins were consistent with previously reported observations; the RAS GTP binding activity was reduced in serum-starved cells; and a transient activation peak of the binding activity was observed upon subsequent serum reactivation of the cells. In a word, nanoparticle-mediated probe delivery enabled an in vivo RAS analysis method. The approach should be applicable to a wide variety of analysis protocols.

category: biochemistry


title: Dual mechanism estrogen receptor inhibitors

abstract:
Efforts to improve estrogen receptor-a (ER)-targeted therapies in breast cancer have relied upon a single mechanism, with ligands having a single side chain on the ligand core that extends outward to determine antagonism of breast cancer growth. Here, we describe inhibitors with two ER-targeting moieties, one of which uses an alternate structural mechanism to generate full antagonism, freeing the side chain to independently determine other critical properties of the ligands. By combining two molecular targeting approaches into a single ER ligand, we have generated antiestrogens that function through new mechanisms and structural paradigms to achieve antagonism. These dual-mechanism ER inhibitors (DMERIs) cause alternate, non-canonical structural perturbations of the receptor ligand-binding domain (LBD) to drive antagonism of proliferation in ER-positive breast cancer cells and in allele-specific resistance models. Solution structural and coregulator peptide binding analyses with DMERIs highlight marked differences from current standard-of-care, single-mechanism antiestrogens. These findings uncover an enhanced flexibility of the ER LBD through which it can access non-consensus conformational modes in response to DMERI binding, broadly and effectively suppressing ER activity.

Significance StatementTo address the unmet clinical need for effectively suppressing estrogen receptor (ER) activity with both de novo resistance and in advanced ER-positive breast cancers that are resistant to standard-of-care antiestrogens, we have developed dual-mechanism ER inhibitors (DMERIs) that employ two distinct ER targeting moieties. These DMERI elicited non-canonical structural perturbations of the receptor ligand-binding domain and stabilized multiple antagonist sub-states within the dimer to generate highly efficacious antagonism of proliferation in ER-positive breast cancer cells and in allele-specific resistance models. This work reveals new conformational modes by which the activity of ER can be effectively suppressed to block breast cancer proliferation.

category: cancer biology


title: Neutrophil extracellular traps impair regeneration

abstract: Fibrosis is a major health burden across diseases and organs. To remedy this, we study wound induced hair follicle regeneration (WIHN) as a model of non-fibrotic healing that recapitulates embryogenesis for de novo hair follicle morphogenesis after wounding. We have previously demonstrated that TLR3 promotes WIHN through binding dsRNA, but the source of which is still unclear. Here, we demonstrate that multiple distinct contexts of high WIHN all show a strong neutrophil signature, and given the likelihood of nuclear dsRNA release during the production of neutrophil extracellular trap (NETs), we hypothesized that mature neutrophils and NETs might promote WIHN. Consistent with this, in addition to the presence of mature neutrophils shortly after wounding, neutrophils remain within the wound after the barrier is reestablished, where they produce extracellular traps (NETs) that likely release spliceosomal U1 dsRNA. Contrary to our hypothesis, genetic models of neutrophil depletion show enhanced WIHN. Pad4 null mice that are defective in NET production also augment WIHN. Finally, using single-cell RNA sequencing, we identified a dramatic increase in mature neutrophils in the wound beds of low regenerating Tlr3-/- mice. Taken together, these results demonstrate that although mature neutrophils are stimulated by a common pro-regenerative cue, their presence and NETs hinder WIHN.

category: developmental biology


title: Beta Turn Propensity and a Model Polymer Scaling Exponent Identify Disordered Proteins that Phase Separate

abstract: The complex cellular milieu can spontaneously de-mix in a process controlled in part by proteins that are intrinsically disordered (ID). A proteins propensity to de-mix is thought to be driven by the preference for protein-protein rather than protein-solvent interactions. The hydrodynamic size of monomeric proteins, as quantified by the polymer scaling exponent (v), is driven by a similar balance. We hypothesize that mean v, as predicted by the protein sequence, will be smaller for proteins with a strong propensity to de-mix. To test this hypothesis, we analyzed protein databases containing subsets that are either folded, disordered, or disordered and known to spontaneously phase separate. We find that the phase separating disordered proteins, on average, have lower calculated values of v compared to their non-phase separating counterparts. Moreover, these proteins have a higher sequence-predicted propensity for {beta}-turns. Using a simple, surface areabased model, we propose a physical mechanism for this difference: transient {beta}-turn structures reduce the desolvation penalty of forming a protein-rich phase and increase exposure of atoms involved in {pi}/sp2 electronic interactions. By this mechanism, {beta}-turns act as energetically favored nucleation points, which may explain the increased propensity for turns in ID regions (IDRs) that are utilized biologically for phase separation. Phase separating IDRs, non-phase separating IDRs, and folded regions could be distinguished by combining v and {beta}-turn propensity, and we propose a new algorithm, ParSe (partition sequence), for predicting phase separating protein regions. ParSe is able to accurately identify folded, disordered, and phase-separating protein regions from the primary sequence.

category: biophysics


title: Quantitative profiling of native RNA modifications and their dynamics using nanopore sequencing

abstract: A broad diversity of modifications decorate RNA molecules. Originally conceived as static components, evidence is accumulating that some RNA modifications may be dynamic, contributing to cellular responses to external signals and environmental circumstances. A major difficulty in studying these modifications, however, is the need of tailored protocols to map each modification type individually. Here, we present a new approach that uses direct RNA nanopore sequencing to identify and quantify RNA modifications present in native RNA molecules. First, we show that each RNA modification type results in a distinct and characteristic base-calling  error signature, which we validate using a battery of genetic strains lacking either pseudouridine (Y) or 2-O-methylation (Nm) modifications. We then demonstrate the value of these signatures for de novo prediction of Y modifications transcriptome-wide, confirming known Y-modified sites as well as uncovering novel Y sites in mRNAs, ncRNAs and rRNAs, including a previously unreported Pus4-dependent Y modification in yeast mitochondrial rRNA, which we validate using orthogonal methods. To explore the dynamics of pseudouridylation across environmental stresses, we treat the cells with oxidative, cold and heat stresses, finding that yeast ribosomal rRNA modifications do not change upon environmental exposures, contrary to the general belief. By contrast, our method reveals many novel heat-sensitive Y-modified sites in snRNAs, snoRNAs and mRNAs, in addition to recovering previously reported sites. Finally, we develop a novel software, nanoRMS, which we show can estimate per-site modification stoichiometries from individual RNA molecules by identifying the reads with altered current intensity and trace profiles, and quantify the RNA modification stoichiometry changes between two conditions. Our work demonstrates that Y RNA modifications can be predicted de novo and in a quantitative manner using native RNA nanopore sequencing.

category: molecular biology


title: Conserved heterodimeric GTPase Rbg1/Tma46 promotes efficient translation in eukaryotic cells

abstract: Conserved developmentally-regulated GTP-binding (Drg) proteins and their binding partner Dfrp proteins are known to be important for embryonic development, cellular growth control, differentiation and proliferation. Here, we report that the yeast Drg1/Dfrp1 ortholog, Rbg1/Tma46, facilitates translational initiation, elongation and termination via suppressing prolonged ribosome pausing. Consistent with the genome-wide observations, Rbg1 reverses the growth defect resulting from translation stalling and stabilizes mRNAs against no-go decay. Furthermore, we provide a cryoEM structure of the 80S ribosome bound with Rbg1/Tma46 that reveals the molecular interactions responsible for Rbg1/Tma46 function. The Rbg1 subunit binds to the GTPase association center of the ribosome and the A-tRNA, and the N-terminal zinc finger domain of Tma46 subunit binds to the 40S, establishing an interaction critical for the complex ribosomal association. Our results answer the fundamental question on how a paused ribosome resumes translation and show that Drg1/Dfrp1 proteins play a critical role in ensuring orderly translation.


title: Wide-Field Calcium Imaging of Dynamic Cortical Networks During Locomotion

abstract: Motor behavior results in widespread activation of the cerebral cortex. Therefore, fully understanding the cerebral cortexs role in motor behavior requires a mesoscopic level description of the engaged cortical regions and their functional interactions. Mesoscopic imaging of Ca2+ fluorescence through transparent polymer skulls implanted on transgenic Thy1-GCaMP6f mice reveals widespread activation of the cerebral cortex during locomotion, including not only in primary motor and somatosensory regions but also in secondary motor, retrosplenial, and visual cortices. Using the time series of Ca2+ fluorescence from 28 regions (nodes) we found to be consistent across mice, we examined the changes in functional connectivity from rest to locomotion. At the initiation of locomotion, the most anterior nodes of the secondary motor cortex increase in correlation with other nodes, while other nodes decrease in correlation. Eigenvector centrality confirms these changes in functional connectivity. Directed Granger causality analysis reveals an increase in causal influence of anterior regions of secondary motor cortex on other dorsal cortical regions at the onset of locomotion. These results highlight the global changes in correlation, centrality, and causality occurring throughout the cerebral cortex between rest and locomotion and suggest that the premotor areas play an important role in organizing these changes.


title: Ghat: An R package for identifying adaptive polygenic traits

abstract: Identifying selection on polygenic complex traits in crops and livestock is important for understanding evolution and helps prioritize important characteristics for breeding. The QTL that contribute to polygenic trait variation often exhibit small or infinitesimal effects. This hinders the ability to detect QTL controlling polygenic traits because enormously high statistical power is needed for their detection. Recently, we circumvented this challenge by introducing a method to identify selection on complex traits by evaluating the relationship between genome-wide changes in allele frequency and estimates of effect-size. The approach involves calculating a composite-statistic across all markers that captures this relationship, followed by implementing a linkage disequilibrium-aware permutation test to evaluate if the observed pattern differs from that expected due to drift during evolution and population stratification. In this manuscript, we describe "Ghat", an R package developed to implement this method to test for selection on polygenic traits. We demonstrate the package by applying it to test for polygenic selection on 15 published European wheat traits including yield, biomass, quality, morphological characteristics, and disease resistance traits. Moreover, we applied Ghat to different simulated populations with different breeding history and genetic architecture. The results highlight the power of Ghat to identify selection on complex traits. The Ghat package is accessible on CRAN, the Comprehensive R Archival Network, and on GitHub.

category: genomics


title: Universal rules of life: metabolic rates, biological times and the equal fitness paradigm

abstract: Here we review and extend the equal fitness paradigm (EFP) as an important step in developing and testing a synthetic theory of ecology and evolution based on energy and metabolism. The EFP states that all organisms are equally fit at steady state, because they allocate the same quantity of energy, ~22.4 kJ/g/generation to production of offspring. On the one hand, the EFP may seem tautological, because equal fitness is necessary for the origin and persistence of biodiversity. On the other hand, the EFP reflects universal laws of life: how biological metabolism - the uptake, transformation and allocation of energy - links ecological and evolutionary patterns and processes across levels of organization from: i) structure and function of individual organisms, ii) life history and dynamics of populations, iii) interactions and coevolution of species in ecosystems. The physics and biology of metabolism have facilitated the evolution of millions of species with idiosyncratic anatomy, physiology, behavior and ecology but also with many shared traits and tradeoffs that reflect the single origin and universal rules of life.


title: Studying models of balancing selection usingphase-type theory

abstract: Balancing selection (BLS) is the evolutionary force that maintains high levels of genetic variability in many important genes. To further our understanding of its evolutionary significance, we analyse models with BLS acting on a biallelic locus: an equilibrium model with long-term BLS, a model with long-term BLS and recent changes in population size, and a model of recent BLS. Using phase-type theory, a mathematical tool for analysing continuous time Markov chains with an absorbing state, we examine how BLS affects polymorphism patterns in linked neutral regions, as summarised by nucleotide diversity, the expected number of segregating sites, the site frequency spectrum, and the level of linkage disequilibrium (LD). Long-term BLS affects polymorphism patterns in a relatively small genomic neighbourhood, and such selection targets are easier to detect when the equilibrium frequencies of the selected variants are close to 50%, or when there has been a population size reduction. For a new mutation subject to BLS, its initial increase in frequency in the population causes linked neutral regions to have reduced diversity, an excess of both high and low frequency derived variants, and elevated LD with the selected locus. These patterns are similar to those produced by selective sweeps, but the effects of recent BLS are weaker. Nonetheless, compared to selective sweeps, non-equilibrium polymorphism and LD patterns persist for a much longer period under recent BLS, which may increase the chance of detecting such selection targets. An R package for analysing these models, among others (e.g., isolation with migration), is available.

category: evolutionary biology


title: Type I photosynthetic reaction center in an anoxygenic phototrophic member of the Chloroflexota

abstract: Phototrophic members of the Chloroflexota phylum are enigmas in the evolution of phototrophy. Although all previously characterized phototrophic Chloroflexota members use a Type II reaction center (RCII) to perform light energy conversion1,2, many members host chlorosomes, a light-harvesting apparatus only otherwise reported among Type I reaction center (RCI)-containing phototrophs3. Here we report the discovery and cultivation of "Candidatus Chlorohelix allophototropha", the first known member of the Chloroflexota to use RCI, rather than RCII, for phototrophy. Cultivated from an iron-rich Boreal Shield lake, "Ca. Chx. allophototropha" cells contain chlorosomes and encode a novel fifth clade of RCI protein. Phylogenomic data demonstrate that "Ca. Chx. allophototropha" shares closest ancestry to RCII-utilizing relatives for multiple photosynthesis accessory genes, including chlorosomes. Thus, we propose that the enigmatic distribution of chlorosomes in the Chloroflexota phylum resulted from genetic interaction of RCI- and RCII-utilizing Chloroflexota members. Although undetected previously, metatranscriptome data demonstrate that RCI-utilizing Chloroflexota members can be among the most active populations in illuminated anoxic waters of Boreal Shield lakes, which number in the millions globally4. Our results establish the Chloroflexota as the only bacterial phylum containing RCI- and RCII-utilizing anoxygenic phototrophs, providing new context for understanding the origins of phototrophic life on Earth.


title: Multiple dimensions of social motivation in adult female degus

abstract: Many animals become more motivated to interact after a period of isolation. This phenomenon may involve general drives, e.g. for social touch or companionship, as well as drives that are specific to particular peers, and which ultimately serve to reestablish relationships between the individuals. Female degus are known to be affiliative with multiple other individuals, including unrelated and unfamiliar conspecifics, offering an opportunity to study social motivation independent from exclusive pair-bonds or overt, same-sex competition. We attempted to disentangle factors driving peer interaction by examining reunion behavior across several social isolation and separation manipulations. High levels of interaction were observed between adult females who had been separated even without isolation, revealing a drive to re-establish relationships with specific peers. The content of separation-only reunions differed from isolation, with the latter involving more early-session interaction, higher levels of allogrooming before rear-sniffing, and a higher ratio of chitter vocalizations. To assess whether post-isolation behavior was related to stress, we examined reunions following a non-social (footshock) stressor. Like isolation, footshock increased early-session interactions, but did not increase allogrooming before rear-sniffing or chittering, as compared with controls. To test whether separation-only reunion behavior shared qualities with relationship formation, we also examined reunions of new (stranger) dyads. Strangers exhibited higher levels of interaction than cagemates, with particularly high levels of late-session rear-sniffing. Like separation-only reunions, strangers showed more non-chitter vocalizations and lower levels of allogrooming before rear-sniffing. Across experiments, an exploratory clustering method was used to identify vocalizations that differed between conditions. This yielded promising leads for future investigation, including a chaff-type syllable that may have been more common during relationship renewal. Overall, results are consistent with the hypothesis that female degu reunions are supported by both general and peer-stimulus specific drives, expressed through the structure of physical and vocal interactions over time.

category: animal behavior and cognition


title: Insights into the genomic evolution of insects from cricket genomes

abstract: Most of our knowledge of insect genomes comes from Holometabolous species, which undergo the complete metamorphosis and have genomes under 2Gb with little signs of DNA methylation. In contrast, Hemiemetabolous insects undergo the ancestral incomplete metamorphosis and have larger genomes with high levels of DNA methylation. Hemimetabolous species from the Orthopteran order (grasshoppers and crickets) have some of the largest insect genomes. What drives the evolution of these unusual insect genome sizes, remains unknown. Here we report the sequencing, assembly and annotation of the 1.66-Gb genome of the Mediterranean field cricket Gryllus bimaculatus, and the annotation of the 1.60-Gb genome of the Hawaiian cricket Laupala kohalensis. We compare these two cricket genomes with those of 14 additional insects, and find evidence that hemimetabolous genomes expanded due to transposable element activity. Based on the ratio of observed to expected CpG sites, we find higher conservation and stronger purifying selection of methylated genes than non-methylated genes. Finally, our analysis suggests an expansion of the pickpocket class V gene family in crickets, which we speculate might play a role in the evolution of cricket courtship, including their characteristic chirping.


title: The evolutionary history of ACE2 usage within the coronavirus subgenus Sarbecovirus

abstract: SARS-CoV-1 and SARS-CoV-2 are not phylogenetically closely related; however, both use the ACE2 receptor in humans for cell entry. This is not a universal sarbecovirus trait; for example, many known sarbecoviruses related to SARS-CoV-1 have two deletions in the receptor binding domain of the spike protein that render them incapable of using human ACE2. Here, we report three sequences of a novel sarbecovirus from Rwanda and Uganda which are phylogenetically intermediate to SARS-CoV-1 and SARS-CoV-2 and demonstrate via in vitro studies that they are also unable to utilize human ACE2. Furthermore, we show that the observed pattern of ACE2 usage among sarbecoviruses is best explained by recombination not of SARS-CoV-2, but of SARS-CoV-1 and its relatives. We show that the lineage that includes SARS-CoV-2 is most likely the ancestral ACE2-using lineage, and that recombination with at least one virus from this group conferred ACE2 usage to the lineage including SARS-CoV-1 at some time in the past. We argue that alternative scenarios such as convergent evolution are much less parsimonious; we show that biogeography and patterns of host tropism support the plausibility of a recombination scenario; and we propose a competitive release hypothesis to explain how this recombination event could have occurred and why it is evolutionarily advantageous. The findings provide important insights into the natural history of ACE2 usage for both SARS-CoV-1 and SARS-CoV-2, and a greater understanding of the evolutionary mechanisms that shape zoonotic potential of coronaviruses. This study also underscores the need for increased surveillance for sarbecoviruses in southwestern China, where most ACE2-using viruses have been found to date, as well as other regions such as Africa, where these viruses have only recently been discovered.


title: Repeated loss of variation in insect ovary morphology highlights the role of developmental constraint in life-history evolution

abstract: The number of offspring an organism can produce is a key component of its evolutionary fitness and life-history. Here we perform a test of the hypothesized trade off between the number and size of offspring using thousands of descriptions of the number of egg-producing compartments in the insect ovary (ovarioles), a common proxy for potential offspring number in insects. We find evidence of a negative relationship between egg size and ovariole number when accounting for adult body size. However in contrast to prior claims, we note that this relationship is not generalizable across all insect clades, and we highlight several factors that may have contributed to this size-number trade off being stated as a general rule in previous studies. We reconstruct the evolutionary history of the nurse cell arrangement within the ovariole, and show that the diversification of ovariole number and egg size have both been largely independent of nurse cell presence or position within the ovariole. Instead we show that ovariole number evolution has been shaped by a series of transitions between variable and invariant states, with multiple independent lineages evolving to have almost no variation in ovariole number. We highlight the implications of these invariant lineages on our understanding of the specification of ovariole number during development, as well as the importance of considering developmental processes in theories of life-history evolution.


title: Enhancer-associated H3K4 methylation safeguards in vitro germlinecompetence

abstract: Germline specification in mammals occurs through an inductive process whereby competent cells in the post-implantation epiblast differentiate into primordial germ cells (PGC). The intrinsic factors that endow epiblast cells with the competence to respond to germline inductive signals remain unknown. Single-cell RNA sequencing across multiple stages of an in vitro PGC-like cells (PGCLC) differentiation system shows that PGCLC genes initially expressed in the naive pluripotent stage become homogeneously dismantled in germline competent epiblast like-cells (EpiLC). In contrast, the decommissioning of enhancers associated with these germline genes is incomplete. Namely, a subset of these enhancers partly retain H3K4me1, accumulate less heterochromatic marks and remain accessible and responsive to transcriptional activators. Subsequently, as in vitro germline competence is lost, these enhancers get further decommissioned and lose their responsiveness to transcriptional activators. Importantly, using H3K4me1 deficient cells, we show that the loss of this histone modification reduces the germline competence of EpiLC and decreases PGCLC differentiation efficiency. Our work suggests that, although H3K4me1 might not be essential for enhancer function, it can facilitate the (re)activation of enhancers and the establishment of gene expression programs during specific developmental transitions.


title: Listeners with congenital amusia are sensitive to context uncertainty in melodic sequences

abstract: In typical listeners, the perceptual salience of a surprising auditory event depends on the uncertainty of its context. For example, in melodies, pitch deviants are more easily detected and generate larger neural responses when the context is highly predictable than when it is less so. However, it is not known whether amusic listeners with abnormal pitch processing are sensitive to the degree of uncertainty of pitch sequences and, if so, whether they are to a different extent than typical non-musician listeners. To answer this question, we manipulated the uncertainty of short melodies while participants with and without congenital amusia underwent EEG recordings in a passive listening task. Uncertainty was manipulated by presenting melodies with different levels of complexity and familiarity, under the assumption that simpler and more familiar patterns would enhance pitch predictability. We recorded mismatch negativity (MMN) responses to pitch, intensity, timbre, location, and rhythm deviants as a measure of auditory surprise. In both participant groups, we observed reduced MMN amplitudes and longer peak latencies for all sound features with increasing levels of complexity, and putative familiarity effects only for intensity deviants. No significant group-by-complexity or group-by-familiarity interactions were detected. However, in contrast to previous studies, pitch MMN responses in amusics were disrupted in high complexity and unfamiliar melodies. The present results thus indicate that amusics are sensitive to the uncertainty of melodic sequences and that preattentive auditory change detection is greatly spared in this population across sound features and levels of predictability. However, our findings also hint at pitch-specific impairments in this population when uncertainty is high, thus suggesting that pitch processing under high uncertainty conditions requires an intact frontotemporal loop.


title: Sex-biased genes expressed in the cricket brain evolve rapidly

abstract: Sex-biased gene expression, particularly sex-biased expression in the gonad, has been linked to rates of protein sequence evolution (nonsynonymous to synonymous substitutions, dN/dS) in animals. However, in insects, sex-biased expression studies remain centered on a few holometabolous species, and moreover, other major tissue types such as the brain remain underexplored. Here, we studied sex-biased gene expression and protein evolution in a hemimetabolous insect, the cricket Gryllus bimaculatus. We generated novel male and female RNA-seq data for two sexual tissue types, the gonad and somatic reproductive system, and for two core components of the nervous system, the brain and ventral nerve cord. From a genome-wide analysis, we report several core findings. Firstly, testis-biased genes had accelerated evolution, as compared to ovary-biased and unbiased genes, which was associated with positive selection events. Secondly, while sex-biased brain genes were much less common than for the gonad, they exhibited a striking tendency for rapid protein evolution, an effect that was stronger for the female than male brain. Further, some sex-biased brain genes were linked to sexual functions and mating behaviors, which we suggest may have accelerated their evolution via sexual selection. Thirdly, a tendency for narrow cross-tissue expression breadth, suggesting low pleiotropy, was observed for sex-biased brain genes, suggesting relaxed purifying selection, which we speculate may allow enhanced freedom to evolve adaptive protein functional changes. The findings of rapid evolution of testis-biased genes and male and female-biased brain genes are discussed with respect to pleiotropy, positive selection, and the mating biology of this cricket.


title: Evolutionary dynamics of sex-biased genes expressed in cricket brains and gonads


title: Active Strategies for Multisensory Conflict Suppression in the Virtual Hand Illusion

abstract: The perception of our body in space is flexible and manipulable. The predictive brain hypothesis explains this malleability as a consequence of the interplay between incoming sensory information and our body expectations. However, given the interaction between perception and action, we might also expect that actions would arise due to prediction errors, especially in conflicting situations. Here we describe a computational model, based on the free-energy principle, that forecasts involuntary movements in sensorimotor conflicts. We experimentally confirm those predictions in humans using a virtual reality rubber-hand illusion. Participants generated movements (forces) towards the virtual hand, regardless of its location with respect to the real arm, with little to no forces produced when the virtual hand overlaid their physical hand. The congruency of our model predictions and human observations indicates that the brain-body is generating actions to reduce the prediction error between the expected arm location and the new visual arm. This observed unconscious mechanism is an empirical validation of the perception-action duality in body adaptation to uncertain situations and evidence of the active component of predictive processing.


title: Intramolecular quality control: HIV-1 Envelope gp160 signal-peptide cleavage as a functional folding checkpoint

abstract: Removal of the membrane-tethering signal peptides that target secretory proteins to the endoplasmic reticulum is a prerequisite for proper folding. While generally thought to be removed well before translation termination, we here report two novel post-targeting functions for the HIV-1 gp120 signal peptide, which remains attached until gp120 folding triggers its removal. First, the signal peptide improves fidelity of folding by enhancing conformational plasticity of gp120 by driving disulfide isomerization through a redox-active cysteine, at the same time delaying folding by tethering the N-terminus to the membrane, which needs assembly with the C-terminus. Second, its carefully timed cleavage represents intramolecular quality control and ensures release and stabilization of (only) natively folded gp120. Postponed cleavage and the redox-active cysteine both are highly conserved and important for viral fitness. Considering the [~]15% secretory proteins in our genome and the frequency of N-to-C contacts in protein structures, these regulatory roles of the signal peptide are bound to be more common in secretory-protein biosynthesis.


title: Antagonistic Co-contraction Can Minimize Muscular Effort in Systems with Uncertainty

abstract: Muscular co-contraction of antagonistic muscle pairs is often observed in human movement, but it is considered inefficient and it can currently not be predicted in simulations where muscular effort or metabolic energy is minimized. Here, we investigated the relationship between minimizing effort and muscular co-contraction in systems with random uncertainty to see if muscular co-contraction can minimize effort in such system. We also investigated the effect of time delay in the muscle, by varying the time delay in the neural control as well as the activation time constant. We solved optimal control problems for a one-degree-of-freedom pendulum actuated by two identical antagonistic muscles, using forward shooting, to find controller parameters that minimized muscular effort while the pendulum remained upright in the presence of noise added to the moment at the base of the pendulum. We compared a controller with and without feedforward control. Task precision was defined by bounding the root mean square deviation from the upright position, while different perturbation levels defined task difficulty. We found that effort was minimized when the feedforward control was nonzero, even when feedforward control was not necessary to perform the task, which indicates that co-contraction can minimize effort in systems with uncertainty. We also found that the optimal level of co-contraction increased with time delay, both when the activation time constant was increased and when neural time delay was added. Furthermore, we found that for controllers with a neural time delay, a different trajectory was optimal for a controller with feedforward control than for one without, which indicates that simulation trajectories are dependent on the controller architecture. Future movement predictions should therefore account for uncertainty in dynamics and control, and carefully choose the controller architecture. The ability of models to predict co-contraction from effort or energy minimization has important clinical and sports applications. If co-contraction is undesirable, one should aim to remove the cause of co-contraction rather than the co-contraction itself.

category: bioengineering


title: Calponin-Homology Domain mediated bending of membrane associated actin filaments

abstract: Actin filaments are central to numerous biological processes in all domains of life. Driven by the interplay with molecular motors, actin binding and actin modulating proteins, the actin cytoskeleton exhibits a variety of geometries. This includes structures with a curved geometry such as axon-stabilizing actin rings, actin cages around mitochondria and the cytokinetic actomyosin ring, which are generally assumed to be formed by short linear filaments held together by actin cross-linkers. However, whether individual actin filaments in these structures could be curved and how they may assume a curved geometry remains unknown. Here, we show that "curly", a region from the IQGAP family of proteins from three different organisms, comprising the actin-binding calponin-homology domain and a C-terminal unstructured domain, stabilizes individual actin filaments in a curved geometry when anchored to lipid membranes. Whereas F-actin is semi-flexible with a persistence length of ~10 m, binding of mobile curly within lipid membranes generates actin filament arcs and full rings of high curvature with radii below 1 m. Higher rates of fully formed actin rings are observed in the presence of the actin-binding coiled-coil protein tropomyosin and also when actin is directly polymerized on lipid membranes decorated with curly. Strikingly, curly induced actin filament rings contract upon the addition of muscle myosin II filaments and expression of curly in mammalian cells leads to highly curved actin structures in the cytoskeleton. Taken together, our work identifies a new mechanism to generate highly curved actin filaments, which opens a new range of possibilities to control actin filament geometries, that can be used, for example, in designing synthetic cytoskeletal structures.


title: Transcriptomically-inferred PI3K activity and stemness show a counterintuitive correlation with PIK3CA genotype in breast cancer

abstract: A PI3K-selective inhibitor has recently been approved for use in breast tumours harbouring mutations in PIK3CA, the gene encoding PI3K. Preclinical studies have suggested that the PI3K/AKT/mTORC1 signalling pathway influences stemness, a dedifferentiation-related cellular phenotype associated with aggressive cancer. No direct evidence for such a correlation has been demonstrated to date in human tumours. In two independent human breast cancer cohorts, encompassing nearly 3,000 tumour samples, transcriptional footprint-based analysis uncovered a positive linear association between transcriptionally-inferred PI3K signalling scores and stemness scores. Unexpectedly, stratification of tumours according to PIK3CA genotype revealed a "biphasic" relationship of mutant PIK3CA allele dosage with these scores. Relative to tumour samples without PIK3CA mutations, the presence of a single copy of a hotspot PIK3CA variant was associated with lower PI3K signalling and stemness scores, whereas tumours with multiple copies of PIK3CA hotspot mutations showed higher PI3K signalling and stemness scores. This observation was recapitulated in a human cell model of heterozygous and homozygous PIK3CAH1047R expression. Collectively, our analysis provides evidence for a signalling strength-dependent PI3K-stemness relationship in human breast cancer, which may aid future patient stratification for PI3K-targeted therapies.


title: Age Influences on the Molecular Presentation of Tumours

abstract: Cancer is often called a disease of aging. There are numerous ways in which cancer epidemiology and behaviour change with the age of the patient. The molecular bases for these relationships remain largely underexplored. To characterize them, we analyzed age-associations in the nuclear and mitochondrial somatic mutational landscape of 20,033 tumours across 35 tumour-types. Age influences both the number of mutations in a tumour and their evolutionary timing. Specific mutational signatures are associated with age, reflecting differences in exogenous and endogenous oncogenic processes such as a greater influence of tobacco use in the tumours of younger patients, but more activity of DNA damage repair signatures in those of older patients. We find that known cancer driver genes are mutated in age-associated frequencies, and these alter the transcriptome and predict for clinical outcomes. These effects are most striking in brain cancers where alterations like SUFU loss and ATRX mutation are age-dependent prognostic biomarkers. Using three cancer datasets, we show that age shapes the somatic mutational landscape of cancer, with clinical implications.


title: Modeling Reveals Cortical Dynein-Dependent Fluctuations in Bipolar Spindle Length

abstract:
Proper formation and maintenance of the mitotic spindle is required for faithful cell division. While much work has been done to understand the roles of the key molecular components of the mitotic spindle, identifying the consequences of force perturbations in the spindle remains a challenge. We develop a computational framework accounting for the minimal force requirements of mitotic progression. To reflect early spindle formation, we model microtubule dynamics and interactions with major force-generating motors, excluding chromosome interactions that dominate later in mitosis. We directly integrate our experimental data to define and validate the model. We then use simulations to analyze individual force components over time and their relationship to spindle dynamics, making it distinct from previously published models. We show through both model predictions and biological manipulation that rather than achieving and maintaining a constant bipolar spindle length, fluctuations in pole to pole distance occur that coincide with microtubule binding and force generation by cortical dynein. Our model further predicts that high dynein activity is required for spindle bipolarity when kinesin-14 (HSET) activity is also high. Together, our results provide novel insight into the role of cortical dynein in the regulation of spindle bipolarity.

SIGNIFICANCEThe mitotic spindle is a biophysical machine that is required for cell division. Here we have paired a modeling approach with experimental data to understand the maintenance and dynamics of a bipolar mitotic spindle in the absence of chromosome interactions. We present novel roles of cortical dynein in mitosis, and demonstrate its requirement for both dynamic changes in spindle length and in antagonizing HSET in bipolar spindle formation. Model outputs predict that cortical dynein activity would be limiting in contexts where HSET activity is high and may be of therapeutic relevance in cancer contexts where HSET is often over expressed.


title: Gradual Compaction of the Central Spindle Decreases its Dynamicity as Revealed in PRC1 and EB1 Gene-Edited Human Cells

abstract: During mitosis the spindle undergoes morphological and dynamic changes. It reorganizes at the onset of anaphase when the antiparallel bundler PRC1 accumulates and recruits central spindle proteins to the midzone. Little is known about how the dynamic properties of the central spindle change during its morphological changes in human cells. Using gene editing, we generated human cells that express from their endogenous locus fluorescent PRC1 and EB1 to quantify their native spindle distribution and binding/unbinding turnover. EB1 plus end tracking revealed a general slowdown of microtubule growth, while PRC1, similar to its yeast orthologue Ase1, binds increasingly strongly to compacting antiparallel microtubule overlaps. KIF4A and CLASP1 bind more dynamically to the central spindle, but also show slowing down turnover. These results show that the central spindle gradually becomes more stable during mitosis, in agreement with a recent  bundling, sliding and compaction model of antiparallel midzone bundle formation in the central spindle during late mitosis.


title: Widespread retention of ohnologs in key developmental gene families following whole genome duplication in arachnopulmonates

abstract: Whole genome duplications have occurred multiple times during animal evolution, including in lineages leading to vertebrates, teleosts, horseshoe crabs and arachnopulmonates. These dramatic events initially produce a wealth of new genetic material, generally followed by extensive gene loss. It appears, however, that developmental genes such as homeobox genes, signalling pathway components and microRNAs are frequently retained as duplicates (so called ohnologs) following whole-genome duplication. These not only provide the best evidence for whole-genome duplication, but an opportunity to study its evolutionary consequences. Although these genes are well studied in the context of vertebrate whole-genome duplication, similar comparisons across the extant arachnopulmonate orders are patchy. We sequenced embryonic transcriptomes from two spider species and two amblypygid species and surveyed three important gene families, Hox, Wnt and frizzled, across these and twelve existing transcriptomic and genomic resources for chelicerates. We report extensive retention of putative ohnologs, including amblypygids, further supporting the ancestral arachnopulmonate whole-genome duplication. We also find evidence of consistent evolutionary trajectories in Hox and Wnt gene repertoires across three of the five arachnopulmonate orders, with inter-order variation in the retention of specific paralogs. We identify variation between major clades in spiders and are better able to reconstruct the chronology of gene duplications and losses in spiders, amblypygids, and scorpions. These insights shed light on the evolution of the developmental toolkit in arachnopulmonates, highlight the importance of the comparative approach within lineages, and provide substantial new transcriptomic data for future study.


title: The Broken Window: An algorithm for quantifying and characterizing misleading trajectories in ecological processes

abstract:
A core issue in temporal ecology is the concept of trajectory--that is, when can ecologists have reasonable assurance that they know where a system is going? In this paper, we describe a non-random resampling method to directly address the temporal aspects of scaling ecological observations by leveraging existing data. Findings from long-term research sites have been hugely influential in ecology because of their unprecedented longitudinal perspective, yet short-term studies more consistent with typical grant cycles and graduate programs are still the norm. We use long-term insights to create  broken windows, that is, reanalyze long-term studies from short-term observational perspectives to examine discontinuities in trends at differing temporal scales.

The broken window algorithm connects our observations between the short-term and the long-term with an automated, systematic resampling approach: in short, we repeatedly  sample moving windows of data from existing long-term time series, and analyze these sampled data as if they represented the entire dataset. We then compile typical statistics used to describe the relationship in the sampled data, through repeated samplings, and then use these derived data to gain insights to the questions: 1) how often are the trends observed in short-term data misleading, and 2) can characteristics of these trends be used to predict our likelihood of being misled? We develop a systematic resampling approach, the  broken_window algorithm, and illustrate its utility with a case study of firefly observations produced at the Kellogg Biological Station Long-Term Ecological Research Site (KBS LTER). Through a variety of visualizations, summary statistics, and downstream analyses, we provide a standardized approach to evaluating the trajectory of a system, the amount of observation required to find a meaningful trajectory in similar systems, and a means of evaluating our confidence in our conclusions.

HighlightsTrends identified in short-term ecology studies can be misleading.

Non-random resampling can show how prone different systems are to misleading trends

The Broken Window algorithm is a new tool to help synthesize temporal data

This tool helps to understand how much data is needed for forecasting to be reliable It can also be used to quantify how likely it is that an observed trend is spurious.


title: Host-associated fungal communities are determined by host phylogeny and exhibit widespread associations with the bacterial microbiome

abstract:
Interactions between hosts and their resident microbial communities are a fundamental component of fitness for both agents. Though recent research has highlighted the importance of interactions between animals and their bacterial communities, comparative evidence for fungi is lacking, especially in natural populations. Using data from 49 species, we present novel evidence of strong covariation between fungal and bacterial communities across the host phylogeny, indicative of recruitment by hosts for specific suites of microbes. Using co-occurrence networks, we demonstrate that fungi form critical components of putative microbial interaction networks, where the strength and frequency of interactions varies with host taxonomy. Host phylogeny drives differences in overall richness of bacterial and fungal communities, but the effect of diet on richness was only evident in mammals and for the bacterial microbiome. Collectively these data indicate fungal microbiomes may play a key role in host fitness and suggest an urgent need to study multiple agents of the animal microbiome to accurately determine the strength and ecological significance of host-microbe interactions.

SIGNIFICANCE STATEMENTMicrobes perform vital metabolic functions that shape the physiology of their hosts. However, almost all research to date in wild animals has focused exclusively on the bacterial microbiota, to the exclusion of other microbial groups. Although likely to be critical components of the host microbiome, we have limited knowledge of the drivers of fungal composition across host species. Here we show that fungal community composition is determined by host species identity and phylogeny, and that fungi form extensive interaction networks with bacteria in the microbiome of a diverse range of animal species. This highlights the importance of microbial interactions as mediators of microbiome-health relationships in the wild.


title: New perspectives on the calculation of bioaccumulation metrics for active substances in living organisms

abstract: Today, only few ready-to-use and convenient decision-making tools are available in ecotoxicology concerning accumulation and effects of chemical substances on organisms, accounting for exposure situations that are known to be complex (routes of exposure, metabolism, mixtures, etc.). This paper presents new perspectives on the generic calculation of bioaccumulation metrics via the innovative web tool MOSAICbioacc (http://mosaic.univ-lyon1.fr/bioacc). MOSAICbioacc provides all kind of bioaccumulation metrics associated with their uncertainty whatever the species-compound combination. MOSAICbioacc expects accumulation-depuration data as inputs, even with complex exposure and clearance patterns, to quickly perform their relevant analysis. MOSAICbioacc intends to facilitate the daily work of regulators, or any ecotoxicologist, who will freely benefit from a user-friendly on-line interface that automatically fits toxicokinetic models without needs for users to invest in the technical aspects to get bioaccumulation metrics estimates. MOSAICbioacc also provides all results in a fully transparent way to ensure reproducibility.


title: Profiling the initial burst of beneficial genetic diversity in clonal cell populations to anticipate evolution

abstract: Clonal populations of cells continuously evolve new genetic diversity, but it takes a significant amount of time for the progeny of a single cell with a new beneficial mutation to outstrip both its ancestor and competitors to fully dominate a population. If these driver mutations can be discovered earlier--while they are still extremely rare--and profiled in large numbers, it may be possible to anticipate the future evolution of similar cell populations. For example, one could diagnose the likely course of incipient diseases, such as cancer and bacterial infections, and better judge which treatments will be effective, by tracking rare drug-resistant variants. To test this approach, we replayed the first 500 generations of a >70,000-generation Escherichia coli experiment and examined the trajectories of new mutations in eight genes known to be under positive selection in this environment in six populations. By employing a deep sequencing procedure using unique molecular identifiers and target enrichment we were able to track 301 beneficial mutations at frequencies as low as 0.01% and infer the fitness effects of 240 of these. Distinct molecular signatures of selection on protein structure and function were evident for the three genes in which beneficial mutations were most common (nadR, pykF, and topA). We detected mutations hundreds of generations before they became dominant and tracked beneficial alleles in genes that were not mutated in the long-term experiment until thousands of generations had passed. This type of targeted adaptome sequencing approach could function as an early warning system to inform interventions that aim to prevent undesirable evolution.


title: Large genetic diversity and strong positive selection in F-box and GPCR genes among the wild isolates of Caenorhabditis elegans

abstract:
The F-box and chemosensory GPCR (csGPCR) gene families are greatly expanded in nematodes, including the model organism Caenorhabditis elegans, compared to insects and vertebrates. However, the intraspecific evolution of these two gene families in nematodes remain unexamined. In this study, we analyzed the genomic sequences of 330 recently sequenced wild isolates of C. elegans using a range of population genetics approaches. We found that F-box and csGPCR genes, especially the Srw family csGPCRs, showed much more diversity than other gene families. Population structure analysis and phylogenetic analysis divided the wild strains into eight non-Hawaiian and three Hawaiian subpopulations. Some Hawaiian strains appeared to be more ancestral than all other strains. F-box and csGPCR genes maintained a great amount of the ancestral variants in the Hawaiian subpopulation and their divergence among the non-Hawaiian subpopulations contributed significantly to population structure. F-box genes are mostly located at the chromosomal arms and high recombination rate correlates with their large polymorphism. Moreover, using both neutrality tests and Extended Haplotype Homozygosity analysis, we identified signatures of strong positive selection in the F-box and csGPCR genes among the wild isolates, especially in the non-Hawaiian population. Accumulation of high-frequency derived alleles in these genes was found in non-Hawaiian population, leading to divergence from the ancestral genotype. In summary, we found that F-box and csGPCR genes harbour a large pool of natural variants, which may be subjected to positive selection. These variants are mostly mapped to the substrate-recognition domains of F-box proteins and the extracellular and intracellular regions of csGPCRs, possibly resulting in advantages during adaptation by affecting protein degradation and the sensing of environmental cues, respectively.

Significance statementThe small nematode Caenorhabditis elegans has emerged as an important organism in studying the genetic mechanisms of evolution. F-box and chemosensory GPCR proteins are two of the largest gene families in C. elegans. However, their intraspecific evolution within C. elegans was not studied before. In this work, using the nonsynonymous SNV (single nucleotide variant) data of 330 C. elegans wild isolates, we found that F-box and chemosensory GPCR genes showed larger polymorphisms and stronger positive selection than other genes. The large diversity is likely the result of rapid gene family expansion, high recombination rate, and gene flow. Analysis of subpopulation suggests that positive selection of these genes occurred most strongly in the non-Hawaiian population, which underwent a selective sweep possibly linked to human activities.


title: Multi-influential interactions alters behaviour and cognition through six main biological cascades in Down syndrome mouse models

abstract: Down syndrome (DS) is the most common genetic form of intellectual disability caused by the presence of an additional copy of human chromosome 21 (Hsa21). To provide novel insights into genotype-phenotype correlations, we used standardized behavioural tests, magnetic resonance imaging (MRI) and hippocampal gene expression to screen several DS mouse models for the mouse chromosome 16 region homologous to Hsa21. First, we unravelled several genetic interactions between different regions of chromosome 21 and how they contribute significantly to altering the outcome of the phenotypes in brain cognition, function and structure. Then, in-depth analysis of misregulated expressed genes involved in synaptic dysfunction highlighted 6 biological cascades centred around DYRK1A, GSK3{beta}, NPY, SNARE, RHOA and NPAS4. Finally, we provide a novel vision of the existing altered gene-gene crosstalk and molecular mechanisms targeting specific hubs in DS models that should become central to better understanding of DS and improving the development of therapies.

category: genetics


title: Denisovan introgression has shaped the immune system of present-day Papuans

abstract: Modern humans have substantially admixed with multiple archaic hominins. Papuans, in particular, owe up to 5% of their genome to Denisovans, a sister group to Neanderthals, whose remains have only been identified in Siberia and Tibet. Unfortunately, the biological and evolutionary significance of these introgression events remain poorly understood. Here we investigate the function of archaic alleles of both Denisovan and Neanderthal ancestry characterised within a previously published set of 56 genomes from individuals of Papuan genetic ancestry living in the island of New Guinea. By comparing the distribution of archaic and modern human variants, we are able to assess the consequences of archaic admixture across a multitude of different cell types and functional elements. We detect a consistent signal across Denisovan variants of strong involvement in immune-related processes throughout our analyses. Archaic alleles are often located within cis-regulatory elements and transcribed regions of the genome, suggesting that they are capable of contributing to a wide range of cellular regulatory processes. We identify 3,538 high-confidence Denisovan variants that fall within annotated cis-regulatory elements and have the potential to alter the affinity of multiple transcription factors to their cognate DNA motifs, highlighting a likely mechanism by which introgressed DNA can impact phenotypes in present-day humans. Lastly, we experimentally validate these predictions by testing the regulatory potential of five Denisovan variants segregating at high frequency within Papuan individuals, and find that two are associated with a significant reduction of transcriptional activities in plasmid reporter assays relative to modern human alleles. Together, these data provide support for the hypothesis that, despite their broadly deleterious nature, archaic alleles actively contribute to modern human phenotypic diversity to this day, and might have facilitated early adaptation to non-African environments.


title: A Convolution Based Computational Approach Towards DNA N6-methyladenine Site Identification and Motif Extraction in Rice Genome

abstract: DNA N6-methylation (6mA) in Adenine nucleotide is a post replication modification responsible for many biological functions. Automated and accurate computational methods can help to identify 6mA sites in long genomes saving significant time and money. Our study develops a convolutional neural network (CNN) based tool i6mA-CNN capable of identifying 6mA sites in the rice genome. Our model coordinates among multiple types of features such as PseAAC (Pseudo Amino Acid Composition) inspired customized feature vector, multiple one hot representations and dinucleotide physicochemical properties. It achieves auROC (area under Receiver Operating Characteristic curve) score of 0.98 with an overall accuracy of 93.97% using 5 fold cross validation on benchmark dataset. Finally, we evaluate our model on three other plant genome 6mA site identification test datasets. Results suggest that our proposed tool is able to generalize its ability of 6mA site identification on plant genomes irrespective of plant species. An algorithm for potential motif extraction and a feature importance analysis procedure are two by products of this research. Web tool for this research can be found at: https://cutt.ly/dgp3QTR.


title: SARS-CoV-2 induces human plasmacytoid pre-dendritic cell diversification via UNC93B and IRAK4

abstract: Several studies have analyzed antiviral immune pathways in late-stage severe COVID-19. However, the initial steps of SARS-CoV-2 antiviral immunity are poorly understood. Here, we have isolated primary SARS-CoV-2 viral strains, and studied their interaction with human plasmacytoid pre-dendritic cells (pDC), a key player in antiviral immunity. We show that pDC are not productively infected by SARS-CoV-2. However, they efficiently diversified into activated P1-, P2-, and P3-pDC effector subsets in response to viral stimulation. They expressed CD80, CD86, CCR7, and OX40 ligand at levels similar to influenza virus-induced activation. They rapidly produced high levels of interferon-, interferon-{lambda}1, IL-6, IP-10, and IL-8. All major aspects of SARS-CoV-2-induced pDC activation were inhibited by hydroxychloroquine. Mechanistically, SARS-CoV-2-induced pDC activation critically depended on IRAK4 and UNC93B1, as established using pDC from genetically deficient patients. Overall, our data indicate that human pDC are efficiently activated by SARS-CoV-2 particles and may thus contribute to type I IFN-dependent immunity against SARS-CoV-2 infection.

category: immunology


title: Endogenous piRNA-guided slicing triggers responder and trailer piRNA production from viral RNA in Aedes aegypti mosquitoes

abstract: In the germline of animals, PIWI interacting (pi)RNAs protect the genome against the detrimental effects of transposon mobilization. In Drosophila, piRNA-mediated cleavage of transposon RNA triggers the production of responder piRNAs via ping-pong amplification. Responder piRNA 3 end formation is coupled to the production of downstream trailer piRNAs mediated by the nuclease Zucchini, expanding the repertoire of transposon piRNA sequences. In Aedes aegypti mosquitoes, piRNAs are generated from viral RNA, yet, it is unknown how viral piRNA 3 ends are formed and whether viral RNA cleavage gives rise to trailer piRNA production. Here we report that in Ae. aegypti, virus- and transposon-derived piRNAs have sharp 3 ends, and are biased for downstream uridine residues, features reminiscent of Zucchini cleavage of precursor piRNAs in Drosophila. We designed a reporter system to study viral piRNA 3 end formation and found that targeting viral RNA by abundant endogenous piRNAs triggers the production of responder and trailer piRNAs. Using this reporter, we identified the Ae. aegypti orthologs of Zucchini and Nibbler, two nucleases involved in piRNA 3 end formation. Our results furthermore suggest that autonomous piRNA production from viral RNA can be triggered and expanded by an initial cleavage event guided by genome-encoded piRNAs.


title: Knockout of the serotonin transporter in the rat mildly modulates decisional anhedonia

abstract: Serotonin transporter gene variance has long been considered an essential factor contributing to depression. However, meta-analyses yielded inconsistent findings recently, asking for further understanding of the link between the gene and depression-related symptoms. One key feature of depression is anhedonia. While data exist on the effect of serotonin transporter gene knockout (5-HTT-/-) in rodents on consummatory and anticipatory anhedonia, with mixed outcomes, the effect on decisional anhedonia has not been investigated thus far. Here, we tested whether 5-HTT-/- contributes to decisional anhedonia. To this end, we established a novel touchscreen-based "go/go" task of visual decision-making. During the learning of stimulus discrimination, 5-HTT+/+ rats performed more optimal decision-making compared to 5-HTT-/- rats at the beginning, but this difference did not persist throughout the learning period. During stimulus generalization, the generalization curves were similar between both genotypes and did not alter as the learning progress. Interestingly, the response time in 5-HTT+/+ rats increased as the session increased in general, while 5-HTT-/- rats tended to decrease. The response time difference might indicate that 5-HTT-/- rats altered willingness to exert cognitive effort to the categorization of generalization stimuli. These results suggest that the effect of 5-HTT ablation on decisional anhedonia is mild and interacts with learning, explaining the discrepant findings on the link between 5-HTT gene and depression.


title: The organizational principles of de-differentiated topographic maps

abstract: Topographic maps are a fundamental feature of cortex architecture in the mammalian brain. One common theory is that the de-differentiation of topographic maps links to impairments in everyday behavior due to less precise functional map readouts. Here, we tested this theory by characterizing de-differentiated topographic maps in primary somatosensory cortex (SI) of younger and older adults by means of ultra-high resolution functional magnetic resonance imaging together with perceptual finger individuation and hand motor performance. Older adults SI maps showed similar amplitude and size to younger adults maps, but presented with less representational similarity between distant fingers. Larger population receptive field sizes in older adults maps did not correlate with behavior, whereas reduced cortical distances between D2 and D3 related to worse finger individuation but better motor performance. Our data uncover the drawbacks of a simple de-differentiation model of topographic map function, and motivate the introduction of feature-based models of cortical reorganization.


title: The organizational principles of de-differentiated topographic maps in somatosensory cortex


title: Bayesian inference of population prevalence

abstract: Within neuroscience, psychology and neuroimaging, the most frequently used statistical approach is null-hypothesis significance testing (NHST) of the population mean. An alternative approach is to perform NHST within individual participants and then infer, from the proportion of participants showing an effect, the prevalence of that effect in the population. We propose a novel Bayesian method to estimate such population prevalence that offers several advantages over population mean NHST. This method provides a population-level inference that is currently missing from study designs with small participant numbers, such as in traditional psychophysics and in precision imaging. Bayesian prevalence delivers a quantitative population estimate with associated uncertainty instead of reducing an experiment to a binary inference. Bayesian prevalence is widely applicable to a broad range of studies in neuroscience, psychology, and neuroimaging. Its emphasis on detecting effects within individual participants can also help address replicability issues in these fields.


title: Tomographic data of 'acanthodian' oral structures and a review of dental diversity in early chondrichthyans

abstract: The teeth of sharks famously form a series of transversely-organised files with conveyor-belt replacement that are borne directly on the jaw cartilages, in contrast to the dermal plate-borne dentition of bony fishes that undergoes site-specific replacement. A major obstacle in understanding how this system evolved is the poorly understood relationships of the earliest chondrichthyans and the profusion of morphologically and terminologically diverse bones, cartilages, splints and whorls that they possess. Here we use tomographic methods to investigate mandibular structures in several early branching  acanthodian-grade stem-chondrichthyans. We show that the dentigerous jaw bones of disparate genera of ischnacanthids are united by a common construction, being growing bones with non-shedding dentition. Mandibular splints, which support the ventro-lateral edge of the Meckels cartilage in some taxa, are formed from dermal bone and may be an acanthodid synapomorphy. We demonstrate that the teeth of Acanthodopsis are borne directly on the mandibular cartilage and that this taxon is deeply nested within an edentulous radiation, representing an unexpected independent origin of teeth. Many or even all of the range of unusual oral structures may be apomorphic, but they should nonetheless be considered when building hypotheses of tooth and jaw evolution, both in chondrichthyans and more broadly.

category: paleontology


title: Diverse stem-chondrichthyan oral structures and evidence for an independently acquired acanthodid dentition


title: The everyday acoustic environment and its association with human heart rate: evidence from real-world data logging with hearing aids and wearables

abstract:
We investigate the short-term association between multidimensional acoustic characteristics of everyday ambient sound and continuous mean heart rate. We used in-market data from hearing aid users who logged ambient acoustics via smartphone-connected hearing aids and continuous mean heart rate in five-minute intervals from their own wearables.

We find that acoustic characteristics explain approximately 4% of the fluctuation in mean heart rate throughout the day. Specifically, increases in ambient sound pressure intensity are significantly related to increases in mean heart rate, corroborating prior laboratory and short-term real-world data. In addition, increases in ambient sound quality - that is, more favourable signal to noise ratios - are associated with decreases in mean heart rate.

Our findings document a previously unrecognized mixed influence of everyday sounds on cardiovascular stress, and that the relationship is more complex than is seen from examination of sound intensity alone. Thus, our findings highlight the relevance of ambient environmental sound in models of human ecophysiology.

category: physiology


title: Rubisco proton production can drive the elevation of CO2 within condensates and carboxysomes

abstract: Membraneless organelles containing the enzyme Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) are a common feature of organisms utilizing CO2 concentrating mechanisms (CCMs) to enhance photosynthetic carbon acquisition. In cyanobacteria and proteobacteria, the Rubisco condensate is encapsulated in a proteinaceous shell, collectively termed a carboxysome, while some algae and hornworts have evolved Rubisco condensates known as pyrenoids. In both cases, CO2 fixation is enhanced compared with the free enzyme. Previous mathematical models have attributed the improved function of carboxysomes to the generation of elevated CO2 within the organelle via a co-localized carbonic anhydrase (CA), and inwardly diffusing HCO3-which has accumulated in the cytoplasm via dedicated transporters. Here we present a novel concept in which we consider the net of two protons produced in every Rubisco carboxylase reaction. We evaluate this in a reaction-diffusion, compartment model to investigate functional advantages these protons may provide Rubisco condensates and carboxysomes, prior to the evolution of HCO3-accumulation. Our model highlights that diffusional resistance to reaction species within a condensate allows Rubisco-derived protons to drive the conversion of HCO3-to CO2 via co-localized CA, enhancing both condensate [CO2] and Rubisco rate. Protonation of Rubisco substrate (RuBP) and product (PGA) plays an important role in modulating internal pH and CO2 generation. Application of the model to putative evolutionary ancestors, prior to contemporary cellular HCO3-accumulation, revealed photosynthetic enhancements along a logical sequence of advancements, via Rubisco condensation, to fully-formed carboxysomes. Our model suggests that evolution of Rubisco condensation could be favored under low CO2 and low light environments.


title: RefPlantNLR: a comprehensive collection of experimentally validated plant NLRs

abstract: Reference datasets are critical in computational biology. They help define canonical biological features and are essential for benchmarking studies. Here, we describe a comprehensive reference dataset of experimentally validated plant NLR immune receptors. RefPlantNLR consists of 442 NLRs from 31 genera belonging to 11 orders of flowering plants. This reference dataset has several applications. We used RefPlantNLR to determine the canonical features of functionally validated plant NLRs and to benchmark the five most popular NLR annotation tools. This revealed that although NLR annotation tools tend to retrieve the majority of NLRs, they frequently produce domain architectures that are inconsistent with the RefPlantNLR annotation. Guided by this analysis, we developed a new pipeline, NLRtracker, which extracts and annotates NLRs based on the core features found in the RefPlantNLR dataset. The RefPlantNLR dataset should also prove useful for guiding comparative analyses of NLRs across the wide spectrum of plant diversity and identifying under-studied taxa. We hope that the RefPlantNLR resource will contribute to moving the field beyond a uniform view of NLR structure and function.


title: GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing

abstract: GRIDSS2 is the first structural variant caller to explicitly report single breakends - breakpoints in which only one side can be unambiguously determined. By treating single breakends as a fundamental genomic rearrangement signal on par with breakpoints, GRIDSS2 can explain 47% of somatic centromeric copy number changes using single breakends to non-centromeric sequence, with chromosome 1 exhibiting a unique centromeric rearrangement signature. On a cohort of 3,782 deeply sequenced metastatic cancers, GRIDSS2 achieved an unprecedented 3.1% false negative rate and identified a novel 32-100bp duplication signature. Somatic structural variants are highly clustered with GRIDSS2 phasing 16% using just paired-end sequencing.

category: bioinformatics


title: Genomic Mutations and Changes in Protein Secondary Structure and Solvent Accessibility of SARS-CoV-2 (COVID-19 Virus)

abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly pathogenic virus that has caused the global COVID-19 pandemic. Tracing the evolution and transmission of the virus is crucial to respond to and control the pandemic through appropriate intervention strategies. This paper reports and analyses genomic mutations in the coding regions of SARS-CoV-2 and their probable protein secondary structure and solvent accessibility changes, which are predicted using deep learning models. Prediction results suggest that mutation D614G in the virus spike protein, which has attracted much attention from researchers, is unlikely to make changes in protein secondary structure and relative solvent accessibility. Based on 6,324 viral genome sequences, we create a spreadsheet dataset of point mutations that can facilitate the investigation of SARS-CoV-2 in many perspectives, especially in tracing the evolution and worldwide spread of the virus. Our analysis results also show that coding genes E, M, ORF6, ORF7a, ORF7b and ORF10 are most stable, potentially suitable to be targeted for vaccine and drug development.


title: Phage-delivered CRISPR-Cas9 for strain-specific depletion and genomic deletions in the gut microbiome

abstract: Mechanistic insights into the role of the human microbiome in the predisposition to and treatment of disease are limited by the lack of methods to precisely add or remove microbial strains or genes from complex communities. Here, we demonstrate that engineered bacteriophage M13 can be used to deliver DNA to Escherichia coli within the mouse gastrointestinal (GI) tract. Delivery of a programmable exogenous CRISPR-Cas9 system enabled the strain-specific depletion of fluorescently marked isogenic strains during competitive colonization and genomic deletions that encompass the target gene in mice colonized with a single strain. Multiple mechanisms enabled E. coli to escape targeting, including loss of the CRISPR array or even the entire CRISPR-Cas9 system. These results provide a robust and experimentally tractable platform for microbiome editing, a foundation for the refinement of this approach to increase targeting efficiency, and a proof-of-concept for the extension to other phage-bacterial pairs of interest.


title: The maintenance of polygenic sex determination depends on the dominance of fitness effects which are predictive of the role of sexual antagonism

abstract: In species with polygenic sex determination, multiple male- and female-determining loci on different proto-sex chromosomes segregate as polymorphisms within populations. The extent to which these polymorphisms are at stable equilibria is not yet resolved. Previous work demonstrated that polygenic sex determination is most likely to be maintained as a stable polymorphism when the proto-sex chromosomes have opposite (sexually antagonistic) fitness effects in males and females. However, these models usually consider polygenic sex determination systems with only two proto-sex chromosomes, or they do not broadly consider the dominance of the alleles under selection. To address these shortcomings, I used forward population genetic simulations to identify selection pressures that can maintain polygenic sex determination under different dominance scenarios in a system with more than two proto-sex chromosomes (modeled after the house fly). I found that overdominant fitness effects of male-determining proto-Y chromosomes are more likely to maintain polygenic sex determination than dominant, recessive, or additive fitness effects. The overdominant fitness effects that maintain polygenic sex determination tend to have proto-Y chromosomes with sexually antagonstic effects (male-beneficial and female-detrimental). In contrast, dominant fitness effects that maintain polygenic sex determination tend to have sexually antagonistic multi-chromosomal genotypes, but the individual proto-sex chromosomes do not have sexually antagonstic effects. These results demonstrate that sexual antagonism can be an emergent property of the multi-chromosome genotype without individual sexually antagonistic chromosomes. My results further illustrate how the dominance of fitness effects has consequences for both the likelihood that polygenic sex determination will be maintained as well as the role sexually antagonistic selection is expected to play in maintaining the polymorphism.