Biology subjects

Berg, A.

Publications and source records attributed to Berg, A..

18 recordsLinked to original sources

bioRxiv2026

Contribution of the novel oxazolidinone TBD09 (MK-7762) to regimens with bedaquiline and pretomanid in a mouse model of tuberculosis

Linezolid is a key component of the bedaquiline, pretomanid, linezolid (BPaL) regimen for rifampin-resistant tuberculosis, but dose- and duration-dependent mitochondrial toxicity frequently limits its use. TBD09 (formerly MK-7762) is a novel oxazolidinone developed to maintain antitubercular potency comparable to linezolid while reducing related adverse events. We evaluated the contribution of TBD09 to the bactericidal and sterilizing activities of BPa-based regimens in a murine tuberculosis model. BALB/c mice were aerosol-infected with Mycobacterium tuberculosis H37Rv and treated starting 2 weeks post-infection. In Experiment 1, dose-ranging bactericidal activity of TBD09 (50, 100, 200 mg/kg) was assessed alone and in combination with BPa, with comparison to linezolid and sutezolid. In Experiment 2, the sterilizing activity of TBD09 (200 mg/kg) in combination with BPa and BPa plus moxifloxacin (M) was assessed by evaluating relapse after treatment durations of 4-22 weeks. TBD09 monotherapy was bacteriostatic, similar to linezolid over the first 4 weeks of treatment. The addition of TBD09 to BPa significantly enhanced bactericidal activity comparable to the addition of linezolid. In relapse assessments, BPa+TBD09 resulted in significantly fewer relapses compared to BPa alone after 14 weeks of treatment, and BPaM+TBD09 resulted in significantly fewer relapses compared to BPaM after 10 weeks. Model-based analysis estimated the treatment duration to 95% cure for BPa+TBD09 at 2.7 weeks, compared to 3.2 weeks for BPaL, although the time to 50% cure was similar. These results demonstrate that TBD09 provides bactericidal and sterilizing activity similar to linezolid in combination with BPa(M), supporting further clinical development of TBD09 for tuberculosis.

microbiology↗

bioRxiv2026

Convergent Roles of Growth Differentiation Factor-15 (GDF-15) in Mechanotransduction, Vascular Disorganization, and Immune Suppression in Melanoma

Melanoma, particularly in its advanced forms, remains one of the most lethal skin cancers, with limited effective treatments for both common cutaneous subtypes and rarer variants such as acral melanoma. The effects of the extracellular matrix (ECM) and other cancer-cell extrinsic processes on melanoma development remain underexplored. This study identifies Growth Differentiation Factor-15 (GDF-15) as a novel mechanosensing-regulated driver of melanoma pathogenesis across melanoma types. GDF-15 is shown here to be mechanically induced by ECM rigidity and compressive forces occurring during metastatic progression, leading to significantly elevated levels in both cutaneous and acral melanoma cells. In this study, ECM rigidity was recapitulated using cell-adhesive gelatin methacryloyl (GelMA) hydrogel microparticles (microgels) with tunable stiffness, providing a biomimetic platform to investigate how mechanical cues in the tumor microenvironment regulate GDF-15 expression in melanoma. A previously unrecognized synergy between GDF-15 and inflammatory factors commonly present in tumors was identified and found to promote a disorganized, hyperpermeable vasculature, thereby facilitating tumor nutrient access and impeding effective immune cell infiltration. GDF-15 knockdown reduced the intratumoral hemorrhage phenotype, indicating a causal role. GDF-15 also functions by directly suppressing natural killer (NK) cell-mediated cytotoxicity, revealing a second cooperating mechanism of immune evasion. These effects position GDF-15 as a key node linking mechanical stress, co-operation with inflammatory factors, abnormal vascular development, and immune dysfunction, thereby converging on a pathways and processes not previously described in melanomas. TEASERUncovering GDF-15 as a central mediator at the intersection of mechanical rigidity and external force, disorganized vascular hemorrhagic remodeling, co-operation with inflammatory factors, and immune evasion, revealing a previously unrecognized therapeutic vulnerability across both common and rare melanoma subtypes

cancer biology↗

bioRxiv2025

Characterisation of Two Plasmodium Virulence Factors Important for Lipid Metabolism and Disease Progression In Vivo

Malaria is caused by Plasmodium parasites and claims 610,000 deaths annually. Parasite invasion of red blood cells (RBCs) involves secretion of multiple proteins from specialised apical organelles (micronemes, rhoptries, and dense granules). These collectively facilitate host cell entry, establish a protective parasitophorous vacuole (PV), and directly and indirectly mediate interactions between the infected RBC (iRBC) and the endothelial wall. The cytoadherence of iRBCs results in sequestration within organs and plays a critical role in pathogenesis and virulence, but the function of many secreted parasite proteins remains poorly characterised. Here, we leverage spatial proteomics from Plasmodium falciparum to identify two novel Plasmodium berghei orthologue proteins containing hydrolase domains (MAP1, PBANKA_1425900, and RhoSH, PBANKA_1001500). Ultrastructure expansion microscopy reveals their localisation to the rhoptries in late schizogony, where co-immunoprecipitation assays show they interact with each other. In vivo studies demonstrate that these proteins help the parasite evade spleen-mediated clearance and contribute to disease progression. Deletion of both genes disrupts lipid metabolism and PV membrane morphology, suggesting a role in establishing or maintaining the protective PV membrane. Loss of map1 reduces sequestration of P. berghei iRBCs to adipose tissue, and conditional knockdown of the P. falciparum map1 orthologue results in reduced CD36-mediated cytoadhesion, suggesting a cross-species role in sequestration and cytoadherence. Our findings identify MAP1 and RhoSH as key mediators of Plasmodium virulence.

microbiology↗

bioRxiv2025

A modeling-based framework to evaluate forgiveness of TB drug combinations in a BALB/c relapsing mouse model.

Tuberculosis (TB) remains a leading cause of death due to an infectious agent. Adherence to long and complex TB treatments is supported by methods including directly observed therapy. The negative impact of missed drug doses on clinical outcomes is well-established, highlighting both the importance of adherence support and methods to quantify the ability of a regimen to continue exerting a biologic effect, during gaps in dosing known as "forgiveness" property. To explore the value of the BALB/c Relapsing Mouse Model of TB in evaluating treatment forgiveness, we assessed the impact of weekend dose holidays on the bactericidal, including RS ratio(R), and sterilizing efficacy of RHZE/RH and BPaMZ in perspective of each drug exposure. The cure/relapse data from this study plus multiple historical studies were used to identify a nonlinear mixed-effects Emax model that was used to estimate time to cure 50% and derive time to cure 90% mice (T90). Expected time-dependent bactericidal activity and reductions in RS ratio were observed for both treatments, with more rapid decreases for the BPaMZ groups. The weekend dosing holiday significantly decreased reductions in lung CFU and RS ratio earlier in RHZE/RH treatment, but no such effect was observed for BPaMZ. Similarly, the predicted T90 was significantly greater for RHZE/RH (but not BPaMZ), with weekend doses omitted. No major drug exposure difference was observed between the 2 dosing schedules. Our results suggest BPaMZ is more forgiving of missed doses than RHZE/RH and suggests utility of this methodology to support evaluation of TB treatment forgiveness.

pharmacology and toxicology↗

bioRxiv2025

A Stochastic Simulation-Based Approach to Inform Relapsing Mouse Model (RMM) Study Design for Non-Clinical Assessment of Tuberculosis

The development of new regimens to treat tuberculosis (TB), the disease caused by Mycobacterium tuberculosis (Mtb), is critical to improving patient outcomes and decreasing global infectious disease mortality. Early evaluation of candidate regimens in non-clinical models of TB, such as the relapsing mouse model (RMM), remains an important step in prioritizing the most efficacious regimens for further clinical evaluation. Although RMM studies may be informative, they are also animal-, labor-, and time-intensive to complete and represent significant investment in time and resources during non-clinical development. Given the strong pipeline of regimens in development, identification of "leaner" RMM studies may have a significant impact on resource utilization, and hence we compared alternative study designs with the goal of identifying study attributes that can be modified to improve resource use, particularly animal use. By simulating relapse outcomes from "virtual" studies (i.e., groups mice treated for selected durations with control and hypothetical anti-TB regimens) followed by model-based analysis of the simulated data, we were able to compare the "true" (input) values with model estimates of time to 95% cure probability (T95) and assess bias and precision of competing designs. Using this approach, we demonstrated that 28% fewer mice could be used in RMM studies while maintaining low bias and a precision for T95 estimation within +/- 1-2 weeks for most regimens. Therefore, it is expected that RMM studies based upon the alternative designs evaluated herein may be employed to promote improved animal stewardship while generating informative data for decision making.

pharmacology and toxicology↗

bioRxiv2025

High-efficiency Kemp eliminases by complete computational design

We present a fully computational workflow for de novo design of efficient enzymes using backbone fragments from natural proteins and without recourse to iterative experimental optimization. The best designed Kemp eliminase exhibits >140 mutations from any natural protein, high stability (>85 {degrees}C) and unprecedented catalytic efficiency (12,700 M-1s-1), surpassing previous computational designs by two orders of magnitude. We find that mutations both inside and outside the active site contribute synergistically to the high observed activity and stability. Mutation of an aromatic residue used in all prior Kemp eliminase designs increases efficiency to >105 M-1s-1. Our approach addresses critical limitations in design methodology, generating stable, high-efficiency, new-to-nature enzymes in complex folds and enables testing hypotheses on the fundamentals of biocatalysis through a limited experimental effort.

biochemistry↗

bioRxiv2024

Postglacial recolonization of the Southern Ocean by elephant seals occurred from multiple glacial refugia

The Southern Ocean is warming more rapidly than other parts of our planet. How this regions endemic biodiversity will respond to such changes can be illuminated by studying past events, through genetic analyses of time-series data sets including historic and fossil remains. Archaeological and subfossil remains show that the southern elephant seal (Mirounga leonina) was common along the coasts of Australia and New Zealand in the recent past. This species is now mostly confined to sub-Antarctic islands and the southern tip of South America. We analysed ancient seal samples from Australia (Tasmania), New Zealand, and the Antarctic mainland to examine how southern elephant seals have responded to a changing climate and anthropogenic pressures during the Holocene. Our analyses show that these seals formed part of a broader Australasian lineage, comprising seals from all sampled locations from the south Pacific sector of the Southern Ocean. Our study demonstrates that southern elephant seal populations have dynamically altered both range and population sizes under climatic and human pressures, over surprisingly short evolutionary timeframes for such a large, long-lived mammal. Significance StatementGenetic data, alongside historic, archaeological, and subfossil remains show that Australasian populations of the southern elephant seal have been shaped by range expansions and contractions following the Last Glacial Maximum, with subsequent contractions during the late Holocene. These expansion and contraction events are likely to have been a direct result of climate change-induced habitat expansion and contraction, along with Indigenous and European sealing. Prehistoric climate change and more recent human pressures have substantially altered the geographic distribution and population size of southern elephant seals over short evolutionary timescales.

ecology↗

bioRxiv2024

Redefining the Limits of Functional Continuity in the Early Evolution of P-Loop NTPases

At the heart of many nucleoside triphosphatases is a conserved sequence motif that binds phosphate. A current model of early enzyme evolution proposes that this 6-8 residue motif could have sparked the emergence of the very first nucleoside triphosphatases - a striking example of evolutionary continuity from simple beginnings, if true. To test whether this provocative evolutionary model holds for the ancient and ubiquitous P-Loop NTPases, the properties of seven disembodied Walker A-derived peptides were extensively characterized by Hamiltonian replica exchange molecular dynamics simulations. Although dynamic flickers of nest-like conformations were observed, significant structural similarity between the situated peptide and its disembodied counterpart was not detected - even in the presence of orthophosphate or a nucleotide. Simulations suggest that phosphate binding is non-specific, with a slight preference for GTP over orthophosphate. Control peptides with the same amino acid composition but different sequences and situated conformations behaved similarly to the Walker A peptides with respect to conformational dynamics and phosphate binding, revealing no indication that the Walker A sequence is privileged as a disembodied peptide. We conclude that the evolutionary history of the P-Loop NTPase family is unlikely to have started with a disembodied Walker A peptide in an aqueous environment. The limits of evolutionary continuity for this protein family, and the environmental context within which it emerged, must be reconsidered. Finally, we argue that motifs such as the Walker A motif may represent incomplete or fragmentary molecular fossils - the true nature of which have been eroded by time. Significance StatementThe first proteins were undoubtedly small, but when did those seeds emerge, and what did they look like? It is widely believed that the Walker A P-loop motif is a seed for the emergence of phosphate binding proteins, snugly binding phosphate in a structurally conserved nest. We probe this hypothesis through detailed computational characterization of disembodied Walker A and control peptides, showing that any nest formation is transient, and phosphate binding is weak and non-specific. Thus, we do not find structural continuity represented in the conserved Walker A motif, and current models of early P-loop evolution require revision. Further, care is required when interpreting highly conserved sequence fragments more broadly, as these may merely represent eroded molecular fossils.

biophysics↗

bioRxiv2024

Nematocida displodere Mechanosensitive Ion Channel of Small Conductance 2 assembles into a unique 6-channel super-structure in vitro

Mechanosensitive ion channels play an essential role in reacting to environmental signals and sustaining cell integrity by facilitating ion flux across membranes. For obligate intracellular pathogens like microsporidia, adapting to changes in host environment is crucial for survival and propagation. Despite representing a eukaryote of extreme genome reduction, microsporidia have expanded the gene family of mechanosensitive ion channels of small conductance (mscS) through repeated gene duplication and horizontal gene transfer. All microsporidian genomes that are characterized to-date contain mscS genes of both eukaryotic and bacterial origin, and have at least 5 different mscS copies. Here, we investigated the cryo-electron microscopy structure of the bacterially derived mechanosensitive ion channel of small conductance 2 (MscS2) from Nematocida displodere, an intracellular pathogen of Caenorhabditis elegans. MscS2 is the most compact MscS known, and assembles into a unique superstructure in vitro with six heptameric MscS2 channels oligomerizing through their transmembrane domains. Individual MscS2 channels are oriented in a heterogeneous manner to one another, resembling an asymmetric, flexible six-way cross joint. Finally, we show that, despite the extreme compaction, microsporidian MscS2 still forms a heptameric membrane channel, conserving the most important structural features of bacterial MscS.

biochemistry↗

bioRxiv2023

Functional annotation of a divergent genome using sequence and structure-based homology.

BackgroundMicrosporidia are a large taxon of intracellular pathogens characterized by extraordinarily streamlined genomes with unusually high sequence divergence and many species-specific adaptations. These unique factors pose challenges for traditional genome annotation methods based on sequence homology. As a result, many of the microsporidian genomes sequenced to date contain numerous genes of unknown function. Recent innovations in rapid and accurate structure prediction and comparison, together with the growing amount of data in structural databases, provide new opportunities to assist in the functional annotation of newly sequenced genomes. ResultsIn this study, we established a workflow that combines sequence and structure-based functional gene annotation approaches employing a ChimeraX plugin, allowing for visual inspection and manual curation. We employed this workflow on a high-quality telomere-to-telomere sequenced tetraploid genome of Vairimorpha necatrix. First, the 3080 predicted open reading frames, of which 89 % were confirmed with RNA sequencing data, were used as input. Next, ColabFold was used to create protein structure predictions, followed by a Foldseek search for structural matching to the PDB and AlphaFold databases. The subsequent manual curation, using sequence and structure-based hits, increased the accuracy and quality of the functional genome annotation compared to results using only traditional annotation tools. Our workflow resulted in a comprehensive description of the V. necatrix genome, along with a structural summary of the most prevalent protein groups, such as the ricin B lectin family. In addition, and to test our tool, we identified the functions of several previously uncharacterized Encephalitozoon cuniculi genes. ConclusionWe provide a new functional annotation tool for divergent organisms and employ it on a newly sequenced, high-quality microsporidian genome to shed light on this uncharacterized intracellular pathogen of Lepidoptera. The addition of a structure-based annotation approach can serve as a valuable template for studying other microsporidian or similarly divergent species.

genomics↗

bioRxiv2022

Intense light unleashes male courtship behaviorin wild-type Drosophila

Drosophila courtship studies have elucidated several principles of the neurogenetic organization of complex behavior. Through an integration across sensory modalities, males perform stereotypic patterns of chasing, courtship song production, and copulation attempts. Here we report a serendipitous finding that intense light not only enhances courtship toward female targets but also triggers unexpected courtship behaviors among male flies. Strikingly, in wild-type male-only chambers, we observed extreme behavioral manifestations, such as "chaining" and "wheeling", resembling previously reported male-male courtship behaviors in fruitless mutants and in transformants with ectopic mini-white+ overexpression. This male-male courtship was greatly diminished in a variety of visual system mutants, including disrupted phototransduction (norpA), eliminated eye-color screening pigments (white), or deletion of the R7 photoreceptor cells (sevenless). However, light-induced courtship was unhampered in wing-cut flies, despite their inability to produce courtship song, a major acoustic signal during courtship. Unexpectedly the olfactory mutants orco and sbl displayed unrestrained male-male courtship. Particularly, orco males attained maximum courtship scores under either dim or intense light conditions. Together, our observations support the notion that the innate male courtship behavior is restrained by olfactory cues under normal conditions but can be unleashed by strong visual stimulation in Drosophila.

neuroscience↗

bioRxiv2022

Structure of trimeric pre-fusion rabies virus glycoprotein in complex with two protective antibodies

Rabies virus (RABV) causes lethal encephalitis and is responsible for approximately 60,000 deaths per year. As the sole virion-surface protein, the rabies virus glycoprotein (RABV-G) mediates host-cell entry. RABV-Gs pre-fusion trimeric conformation displays epitopes bound by protective neutralizing antibodies which can be induced by vaccination or passively administered for post-exposure prophylaxis. We report a 2.8-[A] structure of a RABV-G trimer in the pre-fusion conformation, in complex with two neutralizing and protective monoclonal antibodies, 17C7 and 1112-1. One of these antibodies is a licensed prophylactic (17C7, Rabishield), which we show locks the protein in pre-fusion conformation. We demonstrate that targeted mutations can stabilize RABV-G in the pre-fusion conformation, a key step towards structure-guided vaccine design. These data reveal the higher-order architecture of a key therapeutic target and the structural basis of neutralization by antibodies binding two key antigenic sites, and will facilitate the development of improved vaccines and prophylactic antibodies.

microbiology↗

bioRxiv2021

Accelerating manufacturing to start large-scale supply of a new adenovirus-vectored vaccine within 100 days

The Coalition for Epidemic Preparedness Innovations 100-day moonshot aspires to launch a new vaccine within 100 days of pathogen identification. Here, we describe work to optimize adenovirus vector manufacturing for rapid response, by minimizing time to clinical trial and first large-scale supply, and maximizing the output from the available manufacturing footprint. We describe a rapid viral seed expansion workflow that allows vaccine release to clinical trials within 60 days of antigen sequence identification, followed by vaccine release from globally distributed sites within a further 40 days. We also describe a new perfusion-based upstream production process, designed to maximize output while retaining simplicity and suitability for existing manufacturing facilities. This improves upstream volumetric productivity of ChAdOx1 nCoV-19 by around four-fold and remains compatible with the existing downstream process, yielding drug substance sufficient for 10000 doses from each liter of bioreactor capacity. Transition to a new production process across a large manufacturing network is a major task. In the short term, the rapid seed generation workflow could be used with the existing production process. We also use techno-economic modelling to show that, if linear scale-up were achieved, a single cleanroom containing two 2000 L bioreactors running our new perfusion-based process could supply bulk drug substance for around 120 million doses each month, costing <0.20 EUR/dose. We estimate that a manufacturing network with 32000 L of bioreactor capacity could release around 1 billion doses of a new vaccine within 130 days of genomic sequencing of a new pathogen, in a hypothetical surge campaign with suitable prior preparation and resources, including adequate fill-and-finish capacity. This accelerated manufacturing process, along with other advantages such as thermal stability, supports the ongoing value of adenovirus-vectored vaccines as a rapidly adaptable and deployable platform for emergency response.

bioengineering↗

bioRxiv2021

Model-Based Meta-Analysis of Relapsing Mouse Model Studies from the Critical Path to Tuberculosis Drug Regimens Initiative Database

Tuberculosis (TB), the disease caused by Mycobacterium tuberculosis (Mtb), remains a leading infectious disease-related cause of death worldwide, necessitating the development of new and improved treatment regimens. Non-clinical evaluation of candidate drug combinations via the relapsing mouse model (RMM) is an important step in regimen development, through which candidate regimens that provide the greatest decrease in probability of relapse following treatment in mice may be identified for further development. Although RMM studies are a critical tool to evaluate regimen efficacy, making comprehensive "apples to apples" comparisons of regimen performance in the RMM has been a challenge, in large part due to the need to evaluate and adjust for variability across studies arising from differences in design and execution. To address this knowledge gap, we performed a model-based meta-analysis on data for 17 unique regimens obtained from a total of 1592 mice across 28 RMM studies. Specifically, a mixed-effects logistic regression model was developed that described the treatment duration-dependent probability of relapse for each regimen and identified relevant covariates contributing to inter-study variability. Using the model, covariate-normalized metrics of interest, namely treatment duration required to reach 50% and 10% relapse probability, were derived and used to compare relative regimen performance. Overall, the model-based meta-analysis approach presented herein enables cross-study comparison of efficacy in the RMM, and provides a framework whereby data from emerging studies may be analyzed in the context of historical data to aid in selecting candidate drug combinations for clinical evaluation as TB drug regimens.

pharmacology and toxicology↗

bioRxiv2021

Protein-lipid interaction at low pH induces oligomerisation of the MakA cytotoxin from Vibrio cholerae

Many pathogenic bacteria produce protein toxins that target and perturb host cell membranes. The secreted -pore-forming toxins (-PFTs) cause membrane damage via pore formation. This study demonstrates a remarkable, hitherto unknown mechanism by an -PFT protein from Vibrio cholerae. As part of the MakA/B/E tripartite toxin, MakA is involved in membrane pore formation similar to other -PFTs. In contrast, MakA protein alone induces tube-like structures in the acidic lysosomal host cell compartment. In vitro studies unravel the dynamics of tubular growth, which occur in a pH-, lipid- and concentration-dependent manner. A 3.7-[A] cryo-electron microscopy structure of MakA filaments reveals a unique protein-lipid superstructure. In its active -PFT conformation, MakA embeds its transmembrane helices into a thin annular lipid bilayer and spirals around a central cavity. Our study provides molecular insights into a novel tubulation mechanism of an -PFT protein, revealing a new mode of action by a secreted bacterial toxin.

cell biology↗

bioRxiv2021

Metatranscriptomic comparison of endophytic and pathogenic Fusarium-Arabidopsis interactions reveals plant transcriptional plasticity

Plants are continuously exposed to beneficial and pathogenic microbes, but how plants recognize and respond to friends versus foes remains poorly understood. Here, we compared the molecular response of Arabidopsis thaliana independently challenged with a Fusarium oxysporum endophyte Fo47 versus a pathogen Fo5176. These two Fusarium oxysporum strains share a core genome of about 46 Mb, in addition to unique 1,229 and 5,415 accessory genes. Metatranscriptomic data reveal a shared pattern of expression for most plant genes ([~]80%) in responding to both fungal inoculums at all time points from 12 to 96 h post inoculation (HPI). However, the distinct responding genes depict transcriptional plasticity, as the pathogenic interaction activates plant stress responses and suppresses plant growth/development related functions, while the endophytic interaction attenuates host immunity but activates plant nitrogen assimilation. The differences in reprogramming of the plant transcriptome are most obvious in 12 HPI, the earliest time point sampled and are linked to accessory genes in both fungal genomes. Collectively, our results indicate that the A. thaliana and F. oxysporum interaction displays both transcriptome conservation and plasticity in the early stages of infection, providing insights into the fine-tuning of gene regulation underlying plant differential responses to fungal endophytes and pathogens. One-sentence summaryMultiomics analysis reveals the regulatory plasticity of plants in response to beneficial and antagonistic microbes, resulting in distinct phenotypes and rewired transcriptional networks.

plant biology↗

bioRxiv2020

Cuticular Hydrocarbons on Old Museum Specimens of the Spiny Mason Wasp, Odynerus spinipes, (Hymenoptera: Vespidae: Eumeninae) Shed Light on the Distribution and on Regional Frequencies of Distinct Chemotypes

The mason wasp Odynerus spinipes shows an exceptional case of intrasexual CHC dimorphism. Females of this species express one of two cuticular hydrocarbon (CHC) profiles (chemotypes) that differ qualitatively and quantitatively from each other. The ratio of the two chemotypes was previously shown to be close to 1:1 at three sites in Southern Germany, which might not be representative given the Palearctic distribution of the species. To infer the frequency of the two chemotypes across the entire distributional range of the species, we analyzed with GC-MS the CHC profiles of 1,042 dry-mounted specimens stored in private and museum collections. We complemented our sampling by including 324 samples collected and preserved specifically for studying their CHCs. We were capable of reliably identifying the chemotypes in 91% of dry-mounted samples, some of which collected almost 200 years ago. We found both chemotypes to occur in the Far East, the presumed glacial refuge of the species, and their frequency to differ considerably between sites and geographic regions. The geographic structure in the chemotype frequencies could be the result of differential selection regimes and/or different dispersal routes during the colonization of the Western Palearctic. The presented data pave the route for disentangling these factors by providing information where to geographically sample O. spinipes for population genetic analyses. They also form the much-needed basis for future studies aiming to understand the evolutionary and geographic origin as well as the genetics of the astounding CHC dimorphism that O. spinipes females exhibit.

ecology↗

bioRxiv2017

Goodness of fit checks for binomial N-mixture models

O_LIBinomial N-mixture models are commonly applied to analyze population survey data. By estimating detection probabilities, N-mixture models aim at extracting information about abundances in terms of actual and not just relative numbers. This separation of detection probability and abundance relies on parametric assumptions about the distribution of individuals among sites and of detections of individuals among repeat visits to sites. Current methods for checking assumptions are limited, and their computational complexity have hindered evaluations of their performances.\nC_LIO_LIWe develop computationally efficient graphical goodness of fit checks and measures of overdispersion for binomial N-mixture models. These checks are illustrated in a case study, and evaluated in simulations under two scenarios. The two scenarios assume overdispersion in the abundance distribution via a negative binomial distribution or in the detection probability via a beta-binomial distribution. We evaluate the ability of the checks to detect lack of fit, and how lack of fit affects estimates of abundances.\nC_LIO_LIThe simulations show that if the parametric assumptions are incorrect there can be severe biases in estimated abundances: negatively if there is overdispersion in abundance relative to the fitted model and positively if there is overdispersion in detection. Our goodness of fit checks performed well in detecting lack of fit when the abundance distribution is overdispersed, but struggled to detect lack of fit when detections were overdispersed. We show that the inability to detect lack of fit due to overdispersed detection is caused by a fundamental similarity between N-mixture models with beta-binomial detections and N-mixture models with negative binomial abundances.\nC_LIO_LIThe strong biases in estimated abundances that can occur in the binomial N-mixture model when the distribution of individuals among sites, or the detection model, is mis-specified implies that checking goodness of fit is essential for sound inference in ecological studies that use these methods. To check the assumptions we provide computationally efficient goodness of fit checks that are available in an R-package nmixgof. However, even when a binomial N-mixture model appears to fit the data well, estimates are not robust in the presence of overdispersion unless additional information about detection is collected.\nC_LI

ecology↗