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Xenodens calminechari is a mosasaurid taxon named by Longrich et al. (2021) based on the holotype MHNM.KH.331, a left maxilla with several teeth. This holotype was obtained nonscientifically (without technical supervision) from an area in Morocco that yields many manipulated or forged specimens. Examination of Longrich et al. (2021) reveals four tooth crowns occupy what appear to be two alveoli in MHNM.KH.331, and there is potential adhesive connecting the tooth crowns to the maxilla on their lateral sides. We argue that the articulated tooth crowns of this taxon were artificially placed in the maxilla, rendering at least two apomorphies of this taxon the product of forgery. Longrich et al. (2021)'s claims of fused tooth 'roots' in MNHM.KH.331 are instead calcified periodontal ligament and alveolar bone that have ankylosed, resembling the typical mosasaurid condition. Differing tooth crown morphology does not preclude the referral of the teeth of this specimen to a younger ontogenetic stage of another mosasaur (possibly Carinodens) because many extant lizard species show drastic ontogenetic changes in the dentition. We argue that Xenodens calminechari represents a nomen dubium. This specimen constitutes a confluence of two persistent problems in vertebrate paleontology: material sourced from commercial excavations that has not been adequately tested for forgery, and taxa named from tooth-based holotypes that ignore the potential for intraspecific dental variation and interspecific convergence in dental characters, as are common in squamates. We suggest that Longrich et al. CT scan MHNM.KH.331, and we supply CT examples for identifying artificially added tooth crowns to Moroccan mosasaur jaws. Finally, we provide recommendations for the designation of mosasaurid holotypes., (© 2024 The Author(s). The Anatomical Record published by Wiley Periodicals LLC on behalf of American Association for Anatomy.)

Methane (CH 4 ) emissions are a factor in climate change; in addition, CH 4 production may affect reclamation of fluid fine tailings (FFT) in tailings ponds, and end-pit lakes (EPLs). In laboratory cultures, we investigated the effect of crystalline iron mineral (magnetite) on CH 4 production from the biodegradation of hydrocarbons added to FFT collected from methanogenically more and less active sites in a demonstration EPL. Magnetite enhanced CH 4 production from both sites, having a greater effect in more active FFT, where it increased the CH 4 production rate as much as 48% (from 6.67 μmol d -1 to 9.87 μmol d -1 ) compared to FFT without magnetite. Correspondingly, magnetite hastened biodegradation of hydrocarbons (monoaromatics, n-alkanes and iso-alkanes), with a pronounced effect on o-xylene, ethylbenzene, m/p-xylenes, n-octane, n-nonane, and 2-methyloctane, where biodegradation rates increased by 46, 117, 11, 45, 28 and 37%, respectively, compared to FFT without magnetite. Little Fe II was produced, suggesting that magnetite is not being used as an electron acceptor but rather functions as a conduit for electron transfer. Thus, magnetite may be a suitable amendment to enhance bioremediation of anaerobic environments contaminated with hydrocarbons. Importantly, our observations imply that magnetite may increase CH 4 emissions from terrestrial ecosystems, thus affecting carbon budget estimations., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Anthropogenic pollutants are near-ubiquitous in aquatic systems. Aquatic animals such as fishes are subject to physiological stress induced by pollution present in aquatic systems, which can translate to changes in behaviour. Key adaptive behaviours such as shoaling and schooling may be subject to change as a result of physiological or metabolic stress or neurosensory impacts of pollution. This can result in fitness and ecological impacts such as increased predation risk and reduced foraging success. Here, we conducted a systematic metanalysis of the existing literature, comprising 165 studies, on the effects of anthropogenic pollution on sociability and group cohesion in fish species. Both organic (number of studies = 92, posterior mean (PM) = -0.483, p < 0.01) and inorganic (n = 24, PM = -1.453, p < 0.001) chemical pollutants, as well as light exposure (n = 21, PM = -3.038, p < 0.01) were found to reduce sociability. These pollutants did not reduce group cohesion, indicating that effects may be masked in group settings, though fewer studies were carried out on group cohesion and this is a key area for future research. Mixtures of chemical pollutants (n = 16) were found to reduce cohesion (PM = -43.71, p < 0.01), but increase sociability (PM = 44.27, p < 0.01). Evidence was found that fish may behaviourally acclimate to two forms of pollutant, namely mixed chemical pollutants (PM = -0.668, p < 0.01) and noise exposure (n = 22, PM = -4.043, p < 0.01). While aquatic systems are often subject to pollution from multiple sources and of multiple types, very few studies investigated the effects of multiple stressors concurrently. This review identifies trends in the existing literature, and highlights areas where further research is required in order to understand the behavioural and ecological impacts of anthropogenic pollutants in aquatic systems., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Animals within social groups respond to costs and benefits of sociality by adjusting the proportion of time they spend in close proximity to other individuals in the group (cohesion). Variation in cohesion between individuals, in turn, shapes important group-level processes such as subgroup formation and fission-fusion dynamics. Although critical to animal sociality, a comprehensive understanding of the factors influencing cohesion remains a gap in our knowledge of cooperative behavior in animals. We tracked 574 individuals from six species within the genus Canis in 15 countries on four continents with GPS telemetry to estimate the time that pairs of individuals within social groups spent in close proximity and test hypotheses regarding drivers of cohesion. Pairs of social canids (Canis spp.) varied widely in the proportion of time they spent together (5%-100%) during seasonal monitoring periods relative to both intrinsic characteristics and environmental conditions. The majority of our data came from three species of wolves (gray wolves, eastern wolves, and red wolves) and coyotes. For these species, cohesion within social groups was greatest between breeding pairs and varied seasonally as the nature of cooperative activities changed relative to annual life history patterns. Across species, wolves were more cohesive than coyotes. For wolves, pairs were less cohesive in larger groups, and when suitable, small prey was present reflecting the constraints of food resources and intragroup competition on social associations. Pair cohesion in wolves declined with increased anthropogenic modification of the landscape and greater climatic variability, underscoring challenges for conserving social top predators in a changing world. We show that pairwise cohesion in social groups varies strongly both within and across Canis species, as individuals respond to changing ecological context defined by resources, competition, and anthropogenic disturbance. Our work highlights that cohesion is a highly plastic component of animal sociality that holds significant promise for elucidating ecological and evolutionary mechanisms underlying cooperative behavior., (© 2024 The Author(s). Ecology published by Wiley Periodicals LLC on behalf of The Ecological Society of America.)

Background and Objective : Nutrimetabolomics may reveal novel insights into early metabolic alterations and the role of dietary exposures on prostate cancer (PCa) risk. We aimed to prospectively investigate the associations between plasma metabolite concentrations and PCa risk, including clinically relevant tumor subtypes. Methods : We used a targeted and large-scale metabolomics approach to analyze plasma samples of 851 matched PCa case-control pairs from the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort. Associations between metabolite concentrations and PCa risk were estimated by multivariate conditional logistic regression analysis. False discovery rate (FDR) was used to control for multiple testing correction. Results : Thirty-one metabolites (predominately derivatives of food intake and microbial metabolism) were associated with overall PCa risk and its clinical subtypes ( p < 0.05), but none of the associations exceeded the FDR threshold. The strongest positive and negative associations were for dimethylglycine (OR = 2.13; 95% CI 1.16-3.91) with advanced PCa risk (n = 157) and indole-3-lactic acid (OR = 0.28; 95% CI 0.09-0.87) with fatal PCa risk (n = 57), respectively; however, these associations did not survive correction for multiple testing. Conclusions : The results from the current nutrimetabolomics study suggest that apart from early metabolic deregulations, some biomarkers of food intake might be related to PCa risk, especially advanced and fatal PCa. Further independent and larger studies are needed to validate our results.

Many species exhibit social living which offers ecological advantages such as increased foraging opportunities, more efficient locomotion and reduced predation risk. Additionally, exposure to multiple individuals of the same species can decrease an individual's stress and metabolic demand, termed social buffering. If disruption to an animal's social structure occurs and prevents social buffering, an elevated metabolic rate and thus ventilation frequency and gill permeability are likely. A potential consequence of this physiological response could be the increased accumulation of toxicants. The objective of this study was to investigate whether inducing social stress in marine threespine stickleback (Gasterosteus aculeatus) through social isolation during a sublethal water-borne copper (Cu) exposure would affect Cu uptake and whether that would translate to differences in behaviour and biochemical functioning. We hypothesized that isolating threespine stickleback during a Cu exposure would increase Cu uptake and sublethal toxicity compared to a grouped exposure. Wild-caught fish were exposed to control, low Cu or high Cu conditions (0 - 150 µg/L of Cu, nominally), either in isolation or groups of six for 96 h. Isolated stickleback travelled three times less distance, took six times longer to consume food and exhibited moderately increased gill sodium-potassium ATPase activity than group exposed fish, with no effect of Cu. Isolated stickleback also demonstrated significantly higher Cu levels in their gill and liver tissue compared to the group exposed fish. However, this Cu distribution was also present within the control fish, which had not been exposed to Cu, suggesting that the social context affects endogenous Cu distribution under stressful conditions. Our results illustrate the differences in physiology and behaviour that can arise when social contexts are manipulated and stress the importance of considering sociality when conducting toxicity tests with social organisms., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Diapause is a prevalent strategy employed by insects to survive adverse environmental conditions, by halting development and reducing metabolic activity. Although the suppression of DNA replication aligns logically with these reduced developmental and physiological activities, the role of DNA replication in regulating insect diapause remains largely unknown. In this study, we used the cabbage beetle, Colaphellus bowringi, to investigate the role of DNA replication pathway in regulating reproductive diapause. Transcriptome analysis identified DNA replication as a key pathway during diapause preparation in female adults. Fourteen DNA replication genes were isolated, encompassing essential stages of DNA replication, including DNA unwinding, primer synthesis, and DNA synthesis. These genes exhibited consistently reduced expression in diapause females compared to those in reproductive females. RNA interference knockdown of these genes in reproductive female adults resulted in 11 out of 14 gene depletions, manifesting typical diapause traits such as suppressed vitellogenesis, arrested ovary growth, and increased lipid accumulation. Furthermore, we demonstrated 20-hydroxyecdysone (20E), through canonical signaling pathway, regulates the differential expression of DNA replication genes between reproductive and diapause states. Our findings suggest 20E deficiency suppresses DNA replication to induce reproductive diapause, and highlighting the DNA replication process as a potential target for pest management., Competing Interests: Declaration of competing interest The authors declare that they do not possess any financial or commercial conflicts of interest., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Caring for newborn offspring hampers resource acquisition of mammalian females, curbing their ability to meet the high energy expenditure of early lactation. Newborns are particularly vulnerable, and, among the large herbivores, ungulates have evolved a continuum of neonatal antipredator tactics, ranging from immobile hider (such as roe deer fawns or impala calves) to highly mobile follower offspring (such as reindeer calves or chamois kids). How these tactics constrain female movements around parturition is unknown, particularly within the current context of increasing habitat fragmentation and earlier plant phenology caused by global warming. Here, using a comparative analysis across 54 populations of 23 species of large herbivores from 5 ungulate families (Bovidae, Cervidae, Equidae, Antilocapridae and Giraffidae), we show that mothers adjust their movements to variation in resource productivity and heterogeneity according to their offspring's neonatal tactic. Mothers with hider offspring are unable to exploit environments where the variability of resources occurs at a broad scale, which might alter resource allocation compared with mothers with follower offspring. Our findings reveal that the overlooked neonatal tactic plays a key role for predicting how species are coping with environmental variation., Competing Interests: Competing interests: The authors declare no competing interests., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)

The plant community has a strong track record of RNA sequencing technology deployment, which combined with the recent advent of spatial platforms (e.g. 10× genomics) has resulted in an explosion of single-cell and nuclei datasets that can be positioned in an in situ context within tissues (e.g. a cell atlas). In the genomics era, application of proteomics technologies in the plant sciences has always trailed behind that of RNA sequencing technologies, largely due in part to upfront cost, ease-of-use, and access to expertise. Conversely, the use of early analytical tools for characterizing small molecules (metabolites) from plant systems predates nucleic acid sequencing and proteomics analysis, as the search for plant-based natural products has played a significant role in improving human health throughout history. As the plant sciences field now aims to fully define cell states, cell-specific regulatory networks, metabolic asymmetry and phenotypes, the measurement of proteins and metabolites at the single-cell level will be paramount. As a result of these efforts, the plant community will unlock exciting opportunities to accelerate discovery and drive toward meaningful translational outcomes., (© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.)

Protein-O-mannosylation (POM) is a form of O-glycosylation that is ubiquitous and has been studied extensively throughout in fungi and animals. The key glycosyltransferase, protein O-mannosyltransferase (PMT), a member of family GT-39, is also found in over 3,800 bacterial genomes but has only been minimally examined from prokaryotes. In prokaryotes POM has only been investigated in terms of pathogenicity (in Mycobacterium tuberculosis) even though there are far more non-pathogenic bacteria that appear to carry out POM. To date, there is no consensus on what benefit POM imparts to the non-pathogenic bacteria that can perform it. Through the generation of a POM deficient mutant of Corynebacterium glutamicum - a widely utilized and known protein O-mannosylating actinobacteria - this work shows that even closely related actinobacterial GT-39 s (the enzymes responsible for the initiation of POM) can have different substrate specificities for targets of POM. Moreover, presented here is evidence that POM does not only occur in a SEC-dependent manner; POM also occurs with TAT and non-SEC secreted substrates in a specific and likely tightly regulated manner. Together these results highlight the need for further biochemical characterization of POM in these and other bacterial species to help elucidate the true nature of its biological functions., (© The Author(s) 2024. Published by Oxford University Press.)

The timing and amount of foraging in birds are shaped by many of the same extrinsic factors, including temperature and daylength, as well as intrinsic factors, such as sex and age. Here, we investigate co-variation between these traits. We observed a population of 143 individually marked black-capped chickadees ( Poecile atricapillus ) over a 90 day period during the winter. For each day, we recorded the time an individual began and ended feeder use relative to sunrise/sunset, and the total number of feeder visits. Within-individuals, both earlier first feeder visit and later last feeder visit were associated with higher total daily feeder visits but lower feeding rates. Individuals also differed consistently in the timing of first and last feeder visits, and individuals that consistently started feeder use earlier in the day ended feeder use later and had higher total daily feeder visits compared with those that started later, but had no difference in feeding rate. Our study demonstrates that variation in the timing of foraging can have important consequences for energy acquisition at both the within- and among-individual levels.

Female social insects represent a dramatic exception of the evolutionarily conserved physiological trade-off between reproduction and life span, where aging is positively correlated with reproduction. However, whether this facet of life history also pertains to male social insects, remains largely unknown. Male honey bees (drones) die in the act of copulation, placing them under opposing selective pressures. At the individual level, there is inter-male competition for a single successful mating attempt, leading to selective pressure that favors an increase in male fitness. Honey bee drones are haploid individuals and lack the allelic variation in their genome compared to diploid females. We hypothesized that this genetic limitation may result in trade-offs between pathological stress and fitness traits in honey bee males. In our study, we observed differences in size and fertility measures in old and young drones along with stressors of several endemic viruses and the transcriptional immune response. We found that infection does not appear to decrease fertility in old drones, despite evidence for a shift in immune expression away from established mechanisms. Contrary to our expectations, drones additionally do not appear to exhibit a physiological trade-off between size and fertility. These findings demonstrate that drones of different size are likely of different mating quality and that higher quality drones likely favor retaining reproductive output over immune function., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

The calcium-dependent protein kinase CPK28 regulates several stress pathways in multiple plant species. Here, we aimed to discover CPK28-associated proteins in Arabidopsis thaliana. We used affinity-based proteomics and identified several potential CPK28 binding partners, including the C7 Raf-like kinases MRK1, RAF26, and RAF39. We used biochemistry, genetics, and physiological assays to gain insight into their function. We define redundant roles for these kinases in stomatal opening, immune-triggered reactive oxygen species (ROS) production, and resistance to a bacterial pathogen. We report that CPK28 associates with and trans-phosphorylates RAF26 and RAF39, and that MRK1, RAF26, and RAF39 are active kinases that localize to endomembranes. Although Raf-like kinases share some features with mitogen-activated protein kinase kinase kinases (MKKKs), we found that MRK1, RAF26, and RAF39 are unable to trans-phosphorylate any of the 10 Arabidopsis mitogen-activated protein kinase kinases (MKKs). Overall, our study suggests that C7 Raf-like kinases associate with and are phosphorylated by CPK28, function redundantly in stomatal opening and immunity, and possess substrate specificities distinct from canonical MKKKs., (© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.)

Despite the growing concerns about the replicability of ecological and evolutionary studies, no results exist from a field-wide replication project. We conduct a large-scale in silico replication project, leveraging cutting-edge statistical methodologies. Replicability is 30%-40% for studies with marginal statistical significance in the absence of selective reporting, whereas the replicability of studies presenting 'strong' evidence against the null hypothesis H 0 is >70%. The former requires a sevenfold larger sample size to reach the latter's replicability. We call for a change in planning, conducting and publishing research towards a transparent, credible and replicable ecology and evolution., Competing Interests: Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Recent years have seen increasing scientific interest in whether neuron counts can act as correlates of diverse biological phenomena. Lately, Herculano-Houzel (2023) argued that fossil endocasts and comparative neurological data from extant sauropsids allow to reconstruct telencephalic neuron counts in Mesozoic dinosaurs and pterosaurs, which might act as proxies for behaviors and life history traits in these animals. According to this analysis, large theropods such as Tyrannosaurus rex were long-lived, exceptionally intelligent animals equipped with "macaque- or baboon-like cognition", whereas sauropods and most ornithischian dinosaurs would have displayed significantly smaller brains and an ectothermic physiology. Besides challenging established views on Mesozoic dinosaur biology, these claims raise questions on whether neuron count estimates could benefit research on fossil animals in general. Here, we address these findings by revisiting Herculano-Houzel's (2023) work, identifying several crucial shortcomings regarding analysis and interpretation. We present revised estimates of encephalization and telencephalic neuron counts in dinosaurs, which we derive from phylogenetically informed modeling and an amended dataset of endocranial measurements. For large-bodied theropods in particular, we recover significantly lower neuron counts than previously proposed. Furthermore, we review the suitability of neurological variables such as neuron numbers and relative brain size to predict cognitive complexity, metabolic rate and life history traits in dinosaurs, coming to the conclusion that they are flawed proxies for these biological phenomena. Instead of relying on such neurological estimates when reconstructing Mesozoic dinosaur biology, we argue that integrative studies are needed to approach this complex subject., (© 2024 The Authors. The Anatomical Record published by Wiley Periodicals LLC on behalf of American Association for Anatomy.)

Diapause is an adaptive developmental arrest commonly utilized by animals to cope with seasonal changes. Central to this process are hormonal events that bridge photoperiodic cues and physiological changes. In insect reproductive diapause, the absence of juvenile hormone (JH) serves as the primary endocrine event that governs key diapause traits, including ovarian developmental arrest and lipid accumulation. Conventionally, it is believed that the effects of JH are conveyed through the receptor Methoprene-tolerant (Met) and its transcriptional factor Krüppel homolog 1 (Kr-h1). However, our study with the bean bug Riptortus pedestris reveals that JH independently regulates lipid accumulation, bypassing Met and Kr-h1 pathways. R. pedestris enters reproduction under long-day (LD) conditions, while diapause occurs under short-day (SD) conditions. Treatment of SD females with the JH mimic methoprene stimulated reproductive activities, enhancing ovary development and reducing lipid accumulation. In contrast, silencing genes essential for JH biosynthesis in LD females led to pronounced diapause characteristics, including ovarian developmental arrest and substantial lipid accumulation. Interestingly, disruptions in the JH action genes, either Met or Kr-h1, solely affected ovary development, leaving lipid accumulation unchanged, indicating an independent pathway for regulating JH in lipid accumulation. This was further confirmed by RNA interference experiments in SD females, where knockdown of Met or Kr-h1 did not alter the effects of methoprene on lipid reduction. Collectively, these results suggest that JH controls ovary development through the established Met-Kr-h1 pathway, while it modulates lipid accumulation through an alternative, yet to be identified noncanonical pathway during reproductive diapause in R. pedestris., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Protein kinases are key components of multiple cell signaling pathways. Several receptor-like cytoplasmic kinases (RLCKs) have demonstrated roles in immune and developmental signaling across various plant species, making them of interest in the study of phosphorylation-based signal relay. Here, we present our investigation of a subgroup of RLCKs in Arabidopsis thaliana. Specifically, we focus on subgroup VIII RLCKs: MAZ and its paralog CARK6, as well as CARK7 and its paralog CARK9. We found that both MAZ and CARK7 associate with the calcium-dependent protein kinase CPK28 in planta, and furthermore that CPK28 phosphorylates both MAZ and CARK7 on multiple residues in areas that are known to be critical for protein kinase activation. Genetic analysis suggests redundant roles for MAZ and CARK6 as negative regulators of the immune-triggered oxidative burst. We find evidence that supports homo- and hetero-dimerization between CARK7 and MAZ, which may be a general feature of this subgroup. Multiple biochemical experiments suggest that neither MAZ nor CARK7 demonstrate catalytic protein kinase activity in vitro. Interestingly, we find that a mutant variant of MAZ incapable of protein kinase activity can complement maz-1 mutants, suggesting noncatalytic roles of MAZ in planta. Overall, our study identifies subgroup VIII RLCKs as new players in Arabidopsis immune signaling and highlights the importance of noncatalytic functions of protein kinases., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Society for Experimental Biology.)

Environmental filtering and dispersal history limit plant distributions and affect biogeographical patterns, but how their relative importance varies across evolutionary timescales is unresolved. Phylogenetic beta diversity quantifies dissimilarity in evolutionary relatedness among assemblages and might help resolve the ecological and biogeographical mechanisms structuring biodiversity. Here, we examined the effects of environmental dissimilarity and geographical distance on phylogenetic and taxonomic turnover for ~270,000 seed plant species globally and across evolutionary timescales. We calculated past and present dispersal barriers using palaeogeographical reconstructions and calculated geographical linear and least-cost distances, accounting for dispersal over water, mountains or areas with unsuitable climates. Environmental dissimilarity and geographical distance jointly explained most of the deviance in taxonomic (up to 86.4%) and phylogenetic turnover (65.6%). While environmental dissimilarity consistently showed strongly positive effects, the effect of geographical distance on phylogenetic turnover was less pronounced further back in evolutionary time. Past physiogeographical barriers explained a relatively low amount of the variation across all timescales, with a slight peak at intermediate timescales (20-50 Myr BP). Our results suggest that while old lineages have generally dispersed widely, the imprint of environmental filtering on range expansion persists, providing insights into biogeographical and evolutionary processes underlying global biodiversity patterns., Competing Interests: Competing interests: The authors declare no competing interests., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)

Ruminant livestock provide a rich source of products, such as meat, milk, and wool, and play a critical role in global food security and nutrition. Over the past few decades, genomic studies of ruminant livestock have provided valuable insights into their domestication and the genetic basis of economically important traits, facilitating the breeding of elite varieties. In this review, we summarize the main advancements for domestic ruminants in reference genome assemblies, population genomics, and the identification of functional genes or variants for phenotypic traits. These traits include meat and carcass quality, reproduction, milk production, feed efficiency, wool and cashmere yield, horn development, tail type, coat color, environmental adaptation, and disease resistance. Functional genomic research is entering a new era with the advancements of graphical pangenomics and telomere-to-telomere (T2T) gap-free genome assembly. These advancements promise to improve our understanding of domestication and the molecular mechanisms underlying economically important traits in ruminant livestock. Finally, we provide new perspectives and future directions for genomic research on ruminant genomes. We suggest how ever-increasing multiomics datasets will facilitate future studies and molecular breeding in livestock, including the potential to uncover novel genetic mechanisms underlying phenotypic traits, to enable more accurate genomic prediction models, and to accelerate genetic improvement programs., Competing Interests: Compliance and ethics. The author(s) declare that they have no conflict of interest., (© 2024. Science China Press.)

Understanding the origin of eukaryotic cells is one of the most difficult problems in all of biology. A key challenge relevant to the question of eukaryogenesis is reconstructing the gene repertoire of the last eukaryotic common ancestor (LECA). As data sets grow, sketching an accurate genomics-informed picture of early eukaryotic cellular complexity requires provision of analytical resources and a commitment to data sharing. Here, we summarise progress towards understanding the biology of LECA and outline a community approach to inferring its wider gene repertoire. Once assembled, a robust LECA gene set will be a useful tool for evaluating alternative hypotheses about the origin of eukaryotes and understanding the evolution of traits in all descendant lineages, with relevance in diverse fields such as cell biology, microbial ecology, biotechnology, agriculture, and medicine. In this Consensus View, we put forth the status quo and an agreed path forward to reconstruct LECA's gene content., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Richards et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

The Natural Products Magnetic Resonance Database (NP-MRD; https://np-mrd.org) is a comprehensive, freely accessible, web-based resource for the deposition, distribution, extraction, and retrieval of nuclear magnetic resonance (NMR) data on natural products (NPs). The NP-MRD was initially established to support compound de-replication and data dissemination for the NP community. However, that community has now grown to include many users from the metabolomics, microbiomics, foodomics, and nutrition science fields. Indeed, since its launch in 2022, the NP-MRD has expanded enormously in size, scope, and popularity. The current version of NP-MRD now contains nearly 7× more compounds (281 859 versus 40 908) and 7× more NMR spectra (5.5 million versus 817 278) than the first release. More specifically, an additional 4.6 million predicted spectra and another 11 000 spectra simulated from experimental chemical shifts were deposited into the database. Likewise, the number of NMR raw spectral data depositions has grown from 165 spectra per year to >10 000 per year. As a result of this expansion, the number of monthly webpage views has grown from 55 to 20 000 and the number of monthly visitors has increased from 7 to 2500. To address this growth and to better support the expanding needs of its diverse community of users, many additional improvements to the NP-MRD have been made. These include significant enhancements to the data submission process, notable updates to the database's spectral search utilities and useful additions to support better NMR spectral analysis/prediction. Significant efforts have also been undertaken to remediate and update many of NP-MRD's database entries. This manuscript describes these database improvements and expansion efforts, along with how they have been implemented and what future upgrades to the NP-MRD are planned., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Background/Objectives: Targeted metabolomics is often criticized for the limited metabolite coverage that it offers. Indeed, most targeted assays developed or used by researchers measure fewer than 200 metabolites. In an effort to both expand the coverage and improve the accuracy of metabolite quantification in targeted metabolomics, we decided to develop a comprehensive liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay that could quantitatively measure more than 700 metabolites in serum or plasma. Methods: The developed assay makes use of chemical derivatization followed by reverse phase LC-MS/MS and/or direct flow injection MS (DFI-MS) in both positive and negative ionization modes to separate metabolites. Multiple reaction monitoring (MRM), in combination with isotopic standards and multi-point calibration curves, is used to detect and absolutely quantify the targeted metabolites. The assay has been adapted to a 96-well plate format to enable automated, high-throughput sample analysis. Results: The assay (called MEGA) is able to detect and quantify 721 metabolites in serum/plasma, covering 20 metabolite classes and many commonly used clinical biomarkers. The limits of detection were determined to range from 1.4 nM to 10 mM, recovery rates were from 80% to 120%, and quantitative precision was within 20%. LC-MS/MS metabolite concentrations of the NIST ® SRM ® 1950 plasma standard were found to be within 15% of NMR quantified levels. The MEGA assay was further validated in a large dietary intervention study. Conclusions: The MEGA assay should make comprehensive quantitative metabolomics much more affordable, accessible, automatable, and applicable to large-scale clinical studies.

Metabolomics and lipidomics are pivotal in understanding phenotypic variations beyond genomics. However, quantification and comparability of mass spectrometry (MS)-derived data are challenging. Standardised assays can enhance data comparability, enabling applications in multi-center epidemiological and clinical studies. Here we evaluated the performance and reproducibility of the MxP ® Quant 500 kit across 14 laboratories. The kit allows quantification of 634 different metabolites from 26 compound classes using triple quadrupole MS. Each laboratory analysed twelve samples, including human plasma and serum, lipaemic plasma, NIST SRM 1950, and mouse and rat plasma, in triplicates. 505 out of the 634 metabolites were measurable above the limit of detection in all laboratories, while eight metabolites were undetectable in our study. Out of the 505 metabolites, 412 were observed in both human and rodent samples. Overall, the kit exhibited high reproducibility with a median coefficient of variation (CV) of 14.3 %. CVs in NIST SRM 1950 reference plasma were below 25 % and 10 % for 494 and 138 metabolites, respectively. To facilitate further inspection of reproducibility for any compound, we provide detailed results from the in-depth evaluation of reproducibility across concentration ranges using Deming regression. Interlaboratory reproducibility was similar across sample types, with some species-, matrix-, and phenotype-specific differences due to variations in concentration ranges. Comparisons with previous studies on the performance of MS-based kits (including the AbsoluteIDQ p180 and the Lipidyzer) revealed good concordance of reproducibility results and measured absolute concentrations in NIST SRM 1950 for most metabolites, making the MxP ® Quant 500 kit a relevant tool to apply metabolomics and lipidomics in multi-center studies., Competing Interests: DECLARATION OF INTERESTS G.K. is co-inventor (through Helmholtz Zentrum München) on patents regarding applications of metabolomics in diseases of the central nervous system and holds equity in Chymia LLC. A.L., T.H.P and T.K. were employed at biocrates life sciences ag at the time the experiment was conducted and/or at the time this manuscript was being written. K.C. is currently an AstraZeneca employee.

MarkerDB (https://markerdb.ca) has become a leading resource for comprehensive information on molecular biomarkers. Over the past 3 years, the database has evolved significantly, reflecting the dynamic landscape of biomarker research and increasing demands from its user community. This year's update, which is called MarkerDB 2.0, introduces key improvements to enhance the database's usability, consistency and the range of biomarkers covered. These improvements include (i) the addition of thousands of new biomarkers and associated health conditions, (ii) the inclusion of many new biomarker types and categories, (iii) upgraded searches and data filtering functionalities, (iv) new features for exploring and understanding biomarker panels and (v) significantly expanded and improved descriptions. These upgrades, along with numerous minor improvements in content, interface, layout and overall website performance, have greatly enhanced MarkerDB's usability and capacity to facilitate biomarker interpretation across various research domains. MarkerDB remains committed to providing a free, publicly accessible platform for consolidated information on a wide range of molecular (protein, genetic, chromosomal and chemical/small molecule) biomarkers, covering diagnostic, prognostic, risk, monitoring, safety and response-related biomarkers. We are confident that these upgrades and updates will improve MarkerDB's user friendliness, increase its utility and greatly expand its potential applications to many other areas of clinical medicine and biomedical research., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Symbiotic relationships between eukaryotes and prokaryotes played pivotal roles in the evolution of life and drove the emergence of specialized symbiotic structures in animals, plants and fungi. The host-evolved symbiotic structures of microbial eukaryotes - the vast majority of such hosts in nature - remain largely unstudied. Here we describe highly structured symbiosomes within three free-living anaerobic protists (Anaeramoeba spp.). We dissect this symbiosis using complete genome sequencing and transcriptomics of host and symbiont cells coupled with fluorescence in situ hybridization, and 3D reconstruction using focused-ion-beam scanning electron microscopy. The emergence of the symbiosome is underpinned by expansion of gene families encoding regulators of membrane trafficking and phagosomal maturation and extensive bacteria-to-eukaryote lateral transfer. The symbionts reside deep within a symbiosomal membrane network that enables metabolic syntrophy by precisely positioning sulfate-reducing bacteria alongside host hydrogenosomes. Importantly, the symbionts maintain connections to the Anaeramoeba plasma membrane, blurring traditional boundaries between ecto- and endosymbiosis., (© 2024. The Author(s).)

To cause infection, bacterial pathogens must overcome host immune factors and barriers to nutrient acquisition. Reproducing these aspects of host physiology in vitro has shown great promise for antibacterial drug discovery. When used as a bacterial growth medium, human serum replicates several aspects of the host environment, including innate immunity and iron limitation. We previously reported that a high-throughput chemical screen using serum as the growth medium enabled the discovery of novel growth inhibitors overlooked by conventional screens. Here, we report that a subset of compounds from this high-throughput serum screen display an unexpected growth enhancing phenotype and are enriched for synthetic siderophores. We selected 35 compounds of diverse chemical structure and quantified their ability to enhance bacterial growth in human serum. We show that many of these compounds chelate iron, suggesting they were acting as siderophores and providing iron to the bacteria. For two different pharmacophores represented among these synthetic siderophores, conjugation to the β-lactam antibiotic ampicillin imparted iron-dependent enhancement in antibacterial activity. Conjugation of the most potent growth-enhancing synthetic siderophore with the monobactam aztreonam produced MLEB-22043, a broad-spectrum antibiotic with significantly improved activity against Klebsiella pneumoniae , Escherichia coli , Acinetobacter baumannii , and Pseudomonas aeruginosa . This synthetic siderophore-monobactam conjugate uses multiple TonB-dependent transporters for uptake into P. aeruginosa . Like aztreonam, MLEB-22043 demonstrated activity against metallo-β-lactamase expressing bacteria, and, when combined with the β-lactamase inhibitor avibactam, was active against clinical strains coexpressing the NDM-1 metallo-β-lactamase and serine β-lactamases. Our work shows that human serum is an effective bacterial growth medium for the high-throughput discovery of synthetic siderophores, enabling the development of novel Trojan Horse antibiotics.

The pretectum of vertebrates contains neurons responsive to global visual motion. These signals are sent to the cerebellum, forming a subcortical pathway for processing optic flow. Global motion neurons exhibit selectivity for both direction and speed, but this is usually assessed by first determining direction preference at intermediate velocity (16-32 deg/sec), and then assessing speed tuning at the preferred direction. A consequence of this approach is that it is unknown if and how direction preference changes with speed. We measured directional selectivity in 114 pretectal neurons from 44 zebra finches ( Taeniopygia guttata ) across spatial and temporal frequencies, corresponding to a speed range of 0.062 to 1024°/s. Pretectal neurons were most responsive at 32-64°/s with lower activity as speed increased or decreased. At each speed, we determined if cells were directionally-selective, bidirectionally-selective, omnidirectionally responsive, or unmodulated. Notably, at 32°/s, 60% of the cells were directionally selective and 28% were omnidirectionally responsive. In contrast, at 1024°/s, 20% of the cells were directionally selective and nearly half of the population was omnidirectionally responsive. Only 15% of the cells were omnidirectionally excited across most speeds. The remaining 85% of the cells had direction tuning that changed with speed. Collectively, these results indicate a shift from a bias for directional tuning at intermediate speeds of global visual motion to a bias for omnidirectional responses at faster speeds. These results suggest a potential role for the pretectum during flight by detecting unexpected drift or potentials collisions, depending on the speed of the optic flow signal. Significance Statement During locomotion, images of edges and surfaces in the environment move across the retina, a signal of global visual motion called optic flow. Retinal recipient areas in the accessory optic system and the pretectum are the earliest sites to encode this signal, and the neurons are selective for direction and speed. Previous work suggested that directional selectivity may change across speeds but this has never been systematically studied. We measured direction preferences from 0.062 to 1024°/s in the avian pretectum. We found that pretectal global motion neurons are biased for temporal-to-nasal motion at intermediate speeds but biased for omnidirectional responses at faster speeds. These results suggest the pretectum could function to detect both unexpected drift and potential collisions during locomotion., (Copyright © 2024 Dash et al.)

In lichen research, metagenomes are increasingly being used for evaluating symbiont composition and metabolic potential, but the overall content and limitations of these metagenomes have not been assessed. We reassembled over 400 publicly available metagenomes, generated metagenome-assembled genomes (MAGs), constructed phylogenomic trees, and mapped MAG occurrence and frequency across the data set. Ninety-seven percent of the 1,000 recovered MAGs were bacterial or the fungal symbiont that provides most cellular mass. Our mapping of recovered MAGs provides the most detailed survey to date of bacteria in lichens and shows that 4 family-level lineages from 2 phyla accounted for as many bacterial occurrences in lichens as all other 71 families from 16 phyla combined. Annotation of highly complete bacterial, fungal, and algal MAGs reveals functional profiles that suggest interdigitated vitamin prototrophies and auxotrophies, with most lichen fungi auxotrophic for biotin, most bacteria auxotrophic for thiamine and the few annotated algae with partial or complete pathways for both, suggesting a novel dimension of microbial cross-feeding in lichen symbioses. Contrary to longstanding hypotheses, we found no annotations consistent with nitrogen fixation in bacteria other than known cyanobacterial symbionts. Core lichen symbionts such as algae were recovered as MAGs in only a fraction of the lichen symbioses in which they are known to occur. However, the presence of these and other microbes could be detected at high frequency using small subunit rRNA analysis, including in many lichens in which they are not otherwise recognized to occur. The rate of MAG recovery correlates with sequencing depth, but is almost certainly influenced by biological attributes of organisms that affect the likelihood of DNA extraction, sequencing and successful assembly, including cellular abundance, ploidy and strain co-occurrence. Our results suggest that, though metagenomes are a powerful tool for surveying microbial occurrence, they are of limited use in assessing absence, and their interpretation should be guided by an awareness of the interacting effects of microbial community complexity and sequencing depth., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Tagirdzhanova et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Introduction: Human metabolomics has made significant strides in understanding metabolic changes and their implications for human health, with promising applications in diagnostics and treatment, particularly regarding the gut microbiome. However, progress is hampered by issues with data comparability and reproducibility across studies, limiting the translation of these discoveries into practical applications., Objectives: This study aims to evaluate the fit-for-purpose of a suite of human stool samples as potential candidate reference materials (RMs) and assess the state of the field regarding harmonizing gut metabolomics measurements., Methods: An interlaboratory study was conducted with 18 participating institutions. The study allowed for the use of preferred analytical techniques, including liquid chromatography-mass spectrometry (LC-MS), gas chromatography-mass spectrometry (GC-MS), and nuclear magnetic resonance (NMR)., Results: Different laboratories used various methods and analytical platforms to identify the metabolites present in human stool RM samples. The study found a 40% to 70% recurrence in the reported top 20 most abundant metabolites across the four materials. In the full annotation list, the percentage of metabolites reported multiple times after nomenclature standardization was 36% (LC-MS), 58% (GC-MS) and 76% (NMR). Out of 9,300 unique metabolites, only 37 were reported across all three measurement techniques., Conclusion: This collaborative exercise emphasized the broad chemical survey possible with multi-technique approaches. Community engagement is essential for the evaluation and characterization of common materials designed to facilitate comparability and ensure data quality underscoring the value of determining current practices, challenges, and progress of a field through interlaboratory studies., (© 2024. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)

Social insects have the highest rates of meiotic recombination among Metazoa, but there is considerable variation within the Hymenoptera. We synthesize the literature to investigate several hypotheses for these elevated recombination rates. We reexamine the long-standing Red Queen hypothesis, considering how social aspects of immunity could lead to increases in recombination. We examine the possibility of positive feedback between gene duplication and recombination rate in the context of caste specialization. We introduce a novel hypothesis that recombination rate may be driven up by direct selection on recombination activity in response to increases in lifespan. Finally, we find that the role of population size in recombination rate evolution remains opaque, despite the long-standing popularity of this hypothesis. Moreover, our review emphasizes how the varied life histories of social insect species provide an effective framework for advancing a broader understanding of adaptively driven variation in recombination rates.

The complex nitrogen (N) cycle in groundwater systems is affected by both biological and environmental factors. The interactions between hydrogeological conditions and the microbial community assembly processes that impact N-cycling processes remain poorly understood. We explored the assembly patterns of N-cycling microbial communities along the groundwater flow path. The environmental heterogeneity in different hydrological phases increased along the flow path (mean Ed: 0.16-0.49), accompanied by different microbial community assembly patterns. The assembly patterns that engaged in dissimilatory nitrate reduction to ammonium (DNRA) and denitrification changed across the water-sediment phases. Nitrifying microorganisms in the discharge area were mainly influenced by heterogeneous selection (41-69 %), and were closely correlated with dissolved oxygen (DO) concentrations. Homogeneity along flow-through increased stochastic assemblies, such as downstream drift of anammox bacterial (AnAOB) communities. Thus, the N removal pathway changed from "nitrification-denitrification" in the recharge area to "partial nitrification-anammox" in the discharge area. The increasing environmental heterogeneity brought more deterministic assembly patterns of N-cycling communities, linked to higher community turnover along the groundwater flow path. This study indicated that groundwater flow regime determined microbial community assembly patterns, providing valuable insight into the response of N transitions to environmental variations in groundwater systems., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

We ask whether artificially induced testosterone pulses (T-pulses), administered to males in the wild at the territory boundary, adjust location preferences within the territory. Multiple transient T-pulses occurring after social interactions in males can alter behaviour and spatial preferences. We previously found that T-pulses administered at the nest induce male California mice, a biparental and territorial species, to spend more time at the nest likely through conditioned place preferences. We hypothesized that T's reinforcing effects would increase future time by the T-injected males at the boundary and promote territorial defence. Contrary to predictions, T-pulses induced a decrease in male time at the boundary, and instead appeared to promote male territorial/home range expansion, accompanied by shorter sustained vocalizations (SVs) and decreased proportion of three SV bouts. Shorter SVs are associated with aggression in the laboratory. Furthermore, in response to T-male behavioural changes, uninjected female partners decreased boundary time. Our results suggest new functions for socially induced T-pulses, such as extending territorial boundaries/home ranges. Location preferences induced through reinforcing/rewarding mechanisms may be more plastic and dependent on physical and social contexts than previously thought. Moreover, the results suggest that location preferences produced through rewarding/reinforcing mechanisms can be viewed from adaptive perspectives to influence future behaviour., Competing Interests: We declare we have no competing interests., (© 2024 The Author(s).)

Despite extensive efforts, extracting information on medication exposure from clinical records remains challenging. To complement this approach, we developed the tandem mass spectrometry (MS/MS) based GNPS Drug Library. This resource integrates MS/MS data for drugs and their metabolites/analogs with controlled vocabularies on exposure sources, pharmacologic classes, therapeutic indications, and mechanisms of action. It enables direct analysis of drug exposure and metabolism from untargeted metabolomics data independent of clinical records. Our library facilitates stratification of individuals in clinical studies based on the empirically detected medications, exemplified by drug-dependent microbiota-derived N -acyl lipid changes in a cohort with human immunodeficiency virus. The GNPS Drug Library holds potential for broader applications in drug discovery and precision medicine.

Macronutrients such as nitrogen (N), phosphorus (P), potassium (K) and sulphur (S) are critical for plant growth and development. Field-grown canola (Brassica napus L.) is supplemented with fertilizers to maximize plant productivity, while deficiency in these nutrients can cause significant yield loss. A holistic understanding of the interplay between these nutrient deficiency responses in a single study and canola cultivar is thus far lacking, hindering efforts to increase the nutrient use efficiency of this important oil seed crop. To address this, we performed a comparative quantitative proteomic analysis of both shoot and root tissue harvested from soil-grown canola plants experiencing either nitrogen, phosphorus, potassium or sulphur deficiency. Our data provide critically needed insights into the shared and distinct molecular responses to macronutrient deficiencies in canola. Importantly, we find more conserved responses to the four different nutrient deficiencies in canola roots, with more distinct proteome changes in aboveground tissue. Our results establish a foundation for a more comprehensive understanding of the shared and distinct nutrient deficiency response mechanisms of canola plants and pave the way for future breeding efforts., (© 2024 The Author(s). Plant, Cell & Environment published by John Wiley & Sons Ltd.)

Agricultural crop yield losses and food destruction due to infections by phytopathogenic bacteria such as Burkholderia gladioli , which causes devastating diseases in onion, mushroom, corn, and rice crops, pose major threats to worldwide food security and cause enormous damage to the global economy. Biocontrol using bacteriophages has emerged as a promising strategy against a number of phytopathogenic species but has never been attempted against B. gladioli due to a lack of quantitative infection models and a scarcity of phages targeting this specific pathogen. In this study, we present a novel, procedurally straightforward, and highly generalizable fully quantitative ex planta maceration model and an accompanying quantitative metric, the ex planta maceration index ( x PMI). In utilizing this model to test the ex planta virulence of a panel of 12 strains of B. gladioli in Allium cepa and Agaricus bisporus , we uncover substantial temperature-, host-, and strain-dependent diversity in the virulence of this fascinating pathogenic species. Crucially, we demonstrate that Burkholderia phages KS12 and AH2, respectively, prevent and reduce infection-associated onion tissue destruction, measured through significant ( P < 0.0001) reductions in x PMI, by phytopathogenic strains of B. gladioli , thereby demonstrating the potential of agricultural phage biocontrol targeting this problematic microorganism.IMPORTANCEAgricultural crop destruction is increasing due to infections caused by bacteria such as Burkholderia gladioli, which causes plant tissue diseases in onion, mushroom, corn, and rice crops. These bacteria pose a major threat to worldwide food production, which, in turn, damages the global economy. One potential solution being investigated to prevent bacterial infections of plants is "biocontrol" using bacteriophages (or phages), which are bacterial viruses that readily infect and destroy bacterial cells. In this article, we demonstrate that Burkholderia phages KS12 and AH2 prevent or reduce infection-associated plant tissue destruction caused by strains of B. gladioli , thereby demonstrating the inherent potential of agricultural phage biocontrol., Competing Interests: The authors declare no conflict of interest.

The major organelles of the endomembrane system were in place by the time of the last eukaryotic common ancestor (LECA) (~1.5 billion years ago). Their acquisitions were defining milestones during eukaryogenesis. Comparative cell biology and evolutionary analyses show multiple instances of homology in the protein machinery controlling distinct interorganelle trafficking routes. Resolving these homologous relationships allows us to explore processes underlying the emergence of additional, distinct cellular compartments, infer ancestral states predating LECA, and explore the process of eukaryogenesis itself. Here, we undertake a molecular evolutionary analysis (including providing a transcriptome of the jakobid flagellate Reclinomonas americana ), exploring the origins of the machinery responsible for the biogenesis of lysosome-related organelles (LROs), the Biogenesis of LRO Complexes (BLOCs 1,2, and 3). This pathway has been studied only in animals and is not considered a feature of the basic eukaryotic cell plan. We show that this machinery is present across the eukaryotic tree of life and was likely in place prior to LECA, making it an underappreciated facet of eukaryotic cellular organisation. Moreover, we resolve multiple points of ancient homology between all three BLOCs and other post-endosomal retrograde trafficking machinery (BORC, CCZ1 and MON1 proteins, and an unexpected relationship with the "homotypic fusion and vacuole protein sorting" (HOPS) and "Class C core vacuole/endosomal tethering" (CORVET) complexes), offering a mechanistic and evolutionary unification of these trafficking pathways. Overall, this study provides a comprehensive account of the rise of the LROs biogenesis machinery from before the LECA to current eukaryotic diversity, integrating it into the larger mechanistic framework describing endomembrane evolution., Competing Interests: Competing interests statement:The authors declare no competing interest.

Anthropogenic activities emit ~2,000 Mg y -1 of the toxic pollutant mercury (Hg) into the atmosphere, leading to long-range transport and deposition to remote ecosystems. Global anthropogenic emission inventories report increases in Northern Hemispheric (NH) Hg emissions during the last three decades, in contradiction with the observed decline in atmospheric Hg concentrations at NH measurement stations. Many factors can obscure the link between anthropogenic emissions and atmospheric Hg concentrations, including trends in the reemissions of previously released anthropogenic ("legacy") Hg, atmospheric sink variability, and spatial heterogeneity of monitoring data. Here, we assess the observed trends in gaseous elemental mercury (Hg 0 ) in the NH and apply biogeochemical box modeling and chemical transport modeling to understand the trend drivers. Using linear mixed effects modeling of observational data from 51 stations, we find negative Hg 0 trends in most NH regions, with an overall trend for 2005 to 2020 of -0.011 ± 0.006 ng m -3 y -1 (±2 SD). In contrast to existing emission inventories, our modeling analysis suggests that annual NH anthropogenic emissions must have declined by at least 140 Mg between the years 2005 and 2020 to be consistent with observed trends. Faster declines in 95th percentile Hg 0 values than median values in Europe, North America, and East Asian measurement stations corroborate that the likely cause is a decline in nearby anthropogenic emissions rather than background legacy reemissions. Our results are relevant for evaluating the effectiveness of the Minamata Convention on Mercury, demonstrating that existing emission inventories are incompatible with the observed Hg 0 declines., Competing Interests: Competing interests statement:The authors declare no competing interest.

The auxin signaling molecule regulates a range of plant growth and developmental processes. The core transcriptional machinery responsible for auxin-mediated responses is conserved across all land plants. Genetic, physiological and molecular exploration in bryophyte and angiosperm model species have shown both qualitative and quantitative differences in auxin responses. Given the highly divergent ontogeny of the dominant gametophyte (bryophytes) and sporophyte (angiosperms) generations, however, it is unclear whether such differences derive from distinct phylogeny or ontogeny. Here, we address this question by comparing a range of physiological, developmental and molecular responses to auxin in both generations of the model fern Ceratopteris richardii. We find that auxin response in Ceratopteris gametophytes closely resembles that of a thalloid bryophyte, whereas the sporophyte mimics auxin response in flowering plants. This resemblance manifests both at the phenotypic and transcriptional levels. Furthermore, we show that disrupting auxin transport can lead to ectopic sporophyte induction on the gametophyte, suggesting a role for auxin in the alternation of generations. Our study thus identifies developmental phase, rather than phylogeny, as a major determinant of auxin response properties in land plants., Competing Interests: Competing interests The authors declare no competing or financial interests., (© 2024. Published by The Company of Biologists Ltd.)

Oxidative weathering of sulfide minerals in sedimentary rocks releases carbon dioxide (CO 2 ) into the atmosphere. In permafrost zones, this could be a positive feedback on climate change if it increases with warming, yet sulfide oxidation rates and their temperature response remain unknown over large spatial and temporal scales. We analyze a 60-year sulfate concentration dataset from catchments across the Mackenzie River Basin. Sulfate fluxes increased by 45% in the mainstem with 2.3°C of warming, and the temperature sensitivity suggests that continental-scale CO 2 fluxes could double by 2100. The largest increases occur in catchments with geomorphic settings which act to rapidly expose rocks through physical weathering and thermokarst processes. Comparisons with a weathering model suggest that warming can increase reaction rates, and changes in the exposure of minerals with warming are also required. Future warming across vast Arctic landscapes could further increase sulfide oxidation rates and affect regional carbon cycle budgets.

Metagenome-assembled genomes (MAGs) were recovered from metagenomic assemblies from a nitrate-reducing benzene-degrading enrichment culture. Ten MAGs of high quality or functional interest to benzene degradation are reported, seven of which are single contig genomes., Competing Interests: The authors declare no conflict of interest.

We present a metagenome assembled genome (MAG) of an anaerobic bacterium from a nitrate-reducing, benzene-degrading enrichment culture (NRBC). The draft Thermincolales genome consists of 20 contigs with a total length of 4.09 Mbp and includes putative carboxylase genes likely involved in benzene activation., Competing Interests: The authors declare no conflict of interest.

Invasive alien plant species (IAPS) pose a serious threat to overall plant biodiversity across the globe. Nepal's national parks and protected areas are not devoid of the impact of IAPS. Unfortunately, there is a substantial gap in knowledge regarding the extent and impact of invasion in protected areas of Nepal. This study assessed the impact of invasive alien plant species on the resident plant species of the Koshi Tapu wildlife reserve. After a preliminary field observation, we selected five major IAPS in the area, Mesosphaerum suaveolens, Chromolaena odorata, Ipomoea carnea, Lantana camara , and Mikania micrantha for this study. Ten pairs of adjacent plots sized 4 m × 4 m were surveyed for each invasive species, comprising diverse vegetation types. Each pair consisted of one "invaded plot" where the invasive species was dominant with cover greater than 50%, and another "uninvaded plot" laid out in an adjacent area with similar site conditions but without the invasive species. We calculated the Sørensen Index of Similarity for each paired plot. Wilcoxon rank-sum test was employed to compare ecological parameters between invaded and uninvaded plots for various plant species. Similarly, the difference in impact between each of the five invasive species was assessed using the Kruskal-Wallis test. Species richness varied significantly between invaded and uninvaded plots for C. odorata and I. carnea . The most significant impact on species composition of invaded communities (39.6%) was observed for C. odorata . The cover of the other dominant species varied significantly between invaded and uninvaded plots for all five species studied. The Kruskal-Wallis test showed no significant difference in the impact caused by the five studied invasive species on Species richness, Shannon-Wiener diversity index, species evenness, and height of dominant species. However, a significant difference was observed between the impacts of five studied invasive species and the cover of other dominant species. The crown cover of dominant species decreased much more in the invaded plots of L. camara and M. micrantha than in other species. Specialized management efforts are required to control highly invasive species, such as C. odorata and I. carnea , alongside proactive measures to prevent further spread in ecologically sensitive areas., Competing Interests: None., (© 2024 The Author(s). Ecology and Evolution published by John Wiley & Sons Ltd.)

Spatial ecology tends to focus on average movement patterns within animal groups; however, recent studies highlight the value of considering movement decisions both within and among individuals. We used a marked population of black-capped chickadees ( Poecile atricapillus ), to assess the causes and consequences of within- and among-individual differences in chickadee space use. Individuals that used feeders in addition to their most-visited "core feeder" were defined as engaging in off-territory feeder use. We found that females were more likely than males to visit off-territory feeders as ambient temperatures decrease and energetic demands increase. This may be due to sex-related differences in dominance, where males which are the dominant sex in chickadees, have priority access to feeders, while females must increase their foraging areas to meet higher energetic demand. We also found that independent of temperature, adult males were less likely than juvenile males and both juvenile and adult females to forage off-territory. We suggest that this may be due to age-specific benefits of space use in males, where un-paired juvenile males may increase feeder exploration to gain information about potential mates. Finally, we found that chickadees that had a higher propensity to visit off-territory feeders were less likely to survive to the next fall. Overall, our results suggest that dominance hierarchies and individual energetics impact within- and among-individual variation in off-territory feeder use. We provide suggestions for future studies to further investigate fitness-related consequences of within- and among-individual variation in space use., (© The Author(s) 2024. Published by Oxford University Press on behalf of the International Society for Behavioral Ecology.)

The prothoracic gland (PG) is a major insect endocrine organ. It is the principal source of insect steroid hormones, and critical for key developmental events such as the molts, the establishment of critical weight (CW), pupation, and sexual maturation. However, little is known about the developmental processes that regulate PG morphology. In this study, we identified soul , which encodes a PG-specific basic helix-loop-helix (bHLH) transcription factor. We demonstrate that Tap, also a bHLH protein, dimerizes with Soul. Both are expressed in the developing PG. Interfering with either soul or tap function caused strikingly similar phenotypes, resulting in small and fragmented PGs, the abolishment of steroid hormone-producing gene expression, larval arrest, and a failure to undergo metamorphosis. Furthermore, both soul and tap showed expression peaks just prior to the CW checkpoint. Disrupting soul- or tap- function before, but not after, the CW checkpoint caused larval arrest, and perturbed highly similar gene cohorts, which were enriched for regulators and components of the steroid hormone biosynthesis pathway. Intriguingly, a chitin-based cuticle gene, Cpr49Ah , and a POU domain transcription factor gene, pdm3 , are direct target genes of the Soul/Tap complex, and disruption of either phenocopied key aspects of soul/tap loss-of-function phenotypes. Taken together, our findings demonstrate that the Soul/Tap heterodimer resides at the top of a complex gene hierarchy that drives PG development, CW establishment, and steroid hormone production., Competing Interests: Competing interests statement:The authors declare no competing interest.

Salmonella Typhi, the cause of typhoid fever, is a bacterial pathogen of substantial global importance. Typhoid toxin is a secreted AB-type toxin that is a key S. Typhi virulence factor encoded within a 5-gene genetic islet. Four genes in this islet have well-defined roles in typhoid toxin biology; however, the function of the fifth gene is unknown. Here, we investigate the function of this gene, which we name ttaP. We show that ttaP is cotranscribed with the typhoid toxin subunit cdtB, and we perform genomic analyses that indicate that TtaP is very highly conserved in typhoid toxin islets found in diverse salmonellae. We show that TtaP is a distant homolog of group XIV secreted phospholipase A2 (PLA2) enzymes, and experimentally demonstrate that TtaP is a bona fide PLA2. Sequence and structural analyses indicate that TtaP differs substantially from characterized PLA2s, and thus represents a novel class of PLA2. Secretion assays revealed that TtaP is neither cosecreted with typhoid toxin, nor is it required for toxin secretion. Although TtaP is a phospholipase that remains associated with the S. Typhi cell, assays that probed for altered cell envelope integrity failed to identify any differences between WT S. Typhi and a ttaP deletion strain. Collectively, this study identifies a biochemical activity for the lone uncharacterized typhoid toxin islet gene and lays the groundwork for exploring how this gene factors into S. Typhi pathogenesis. This study further identifies a novel class of PLA2, enzymes that have a wide range of industrial applications., Competing Interests: Conflict of interest The authors declare that they have no conflicts of interest with the contents of this article., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Most organisms are at risk of being consumed by a predator or getting infected by a parasite at some point in their life. Theoretical constructs such as the landscape of fear (perception of risk) and nonconsumptive effects (NCEs, costly responses sans predation or infection) have been proposed to describe and quantify antipredator and antiparasite responses. How prey/host species identify and respond to these risks determines their survival, reproductive success and, ultimately, fitness. Most studies to date have focused on either predator-prey or parasite-host interactions, yet habitats and ecosystems contain both parasitic and/or predatory species that represent a complex and heterogenous mosaic of risk factors. Here, we experimentally investigated the behavioral responses of a cactophilic fruit fly, Drosophila nigrospiracula, exposed to a range of species that include parasites (ectoparasitic mite), predators (jumping spiders), as well as harmless heterospecifics (nonparasitic mites, ants, and weevils). We demonstrate that D. nigrospiracula can differentiate between threat and non-threat species, increase erratic movements and decrease velocity in the presence of parasites, but decrease erratic movements and time spent grooming in the presence of predators. Of particular importance, flies could distinguish between parasitic female mites and nonparasitic male mites of the same species, and respond accordingly. We also show that the direction of these NCEs differs when exposed to parasitic mites (i.e., risk of infection) versus spiders (i.e., risk of predation). Given the opposing effects of predation versus infection risk on fly behavior, we discuss potential trade-offs between parasite and predator avoidance behaviors. Our findings illustrate the complexity of risk assessment in a landscape of fear and the fine-tuned NCEs that arise in response. Moreover, this study is the first to examine these behavioral NCEs in a terrestrial system., (© 2024 The Author(s). Ecology published by Wiley Periodicals LLC on behalf of The Ecological Society of America.)