Biology subjects

Bonsall, M. B.

Publications and source records attributed to Bonsall, M. B..

17 recordsLinked to original sources

bioRxiv2026

From Recovery to Risk: Intensifying ENSO Events Drive Extirpation Risk in a Marine Predator

Climate change poses a major threat to marine mammal populations, many of which remain vulnerable after years of overexploitation during the 17th to 20th centuries. Extreme climate events have grown in both frequency and severity in recent decades, and this trend is projected to accelerate under continued greenhouse gas emissions. Here, we assess how this intensification affects a top marine predator at the epicentre of extreme El Nino events - the Peruvian population of Otaria byronia (South American sea lion). We first apply a Bayesian population model that best predicts observed population dynamics to reconstruct female O. byronia population trends, estimate vital rates, and evaluate the effects of environmental drivers on survival and reproduction. We then use the same model to project extirpation risk under multiple future climate scenarios reflecting anticipated increases in both the intensity and frequency of extreme El Nino events. Our reconstruction reveals that the Peruvian O. byronia population has shown considerable resilience to episodic El Nino events over the past quarter-century, likely sustained by high female survival during normal and favourable years. However, under a scenario of moderate increases in El Nino frequency and intensity, the probability of extirpation over the next 50 years is 83.4% higher than under current conditions. As disturbance regimes intensify globally, we suggest that resilience-oriented management frameworks, grounded in species-specific demographic data and environmental context, as demonstrated here, will be essential for safeguarding marine mammal populations against an increasingly volatile climate.

ecology↗

bioRxiv2026

Cross-species meta-analysis reveals determinants of homing gene drive performance

Homing gene drives can bias their inheritance above Mendelian expectations, but reported outcomes vary widely. We compiled a cross-species dataset of nearly one million scored progeny from 42 publications reporting CRISPR/Cas9 endonuclease-based gene drives in 10 model, pest, and vector species. Using multilevel meta-analytic models, we evaluate biological, cross, and transgene design factors as predictors of biased drive inheritance. Species is the strongest predictor, but most heterogeneity remains unexplained; design features each explain a modest fraction of the remaining variation, with large construct-to-construct differences pointing to the full combination of design choices rather than any single factor. Nuclease expression timing, the most common optimization target, has limited predictive value after accounting for correlated factors, and predictions do not transfer well between species. Maternal nuclease deposition has a marginal effect on drive inheritance but dramatically increases somatic phenotype rates in offspring, revealing a tissue-of-action rather than repair-outcome effect. An interactive web tool enables community analysis of this dataset, which will guide the design of more efficient gene drives for genetic vector control, invasive species management and other applications. https://sverkuijl.shinyapps.io/GeneDrive/

bioengineering↗

bioRxiv2025

Polygenic viral factors enable efficient mosquito-borne transmission of African Zika virus

Zika virus (ZIKV) is a mosquito-borne flavivirus primarily transmitted among humans by Aedes aegypti. Over the past two decades, it has caused significant outbreaks associated with birth defects and neurological disorders. Phylogenetically, ZIKV consists of two main genotypes referred to as the African and Asian lineages, each exhibiting distinct biological properties. African lineage strains are transmitted more efficiently by mosquitoes, but pinpointing the genetic basis of this difference has remained challenging. Here, we address this question by comparing recent African and Asian strains using chimeric viruses, in which segments of the parental genomes are swapped. Our results show that the structural genes from the African strain enhance viral internalization, while the non-structural genes improve genome replication and infectious particle production in mosquito cells. In vivo mosquito transmission is most significantly influenced by the structural genes, although no single viral gene alone determines this effect. Additionally, we develop a stochastic model of in vivo viral dynamics in mosquitoes that mirrors the observed patterns, suggesting that the primary difference between the African and Asian strains lies in their ability to traverse the mosquito salivary glands. Overall, our findings suggest that the polygenic nature of ZIKV transmissibility has prevented Asian lineage strains from achieving the same epidemic potential as African lineage strains, underscoring the importance of lineage-specific adaptive landscapes in shaping ZIKV evolution and emergence.

microbiology↗

bioRxiv2024

How does host age and nutrition affect density regulation of obligate versus facultative bacterial symbionts? Insights from the tsetse fly

The relationships between insect hosts and their symbionts can vary tremendously in the extent to which hosts depend on and control their symbionts. Obligate symbionts that provide micronutrients to their host are often compartmentalised to specialised host organs and depend on their hosts for survival, whereas facultative symbionts retain the ability to survive outside of their hosts. Few studies compare the extent to which a host controls and adjusts the density of obligate and facultative symbionts directly. Here, we used tsetse as a model for teasing apart the relationships between a host (Glossina morsitans morsitans) and obligate (Wigglesworthia glossinidia) and facultative (Sodalis glossinidius) symbionts. We hypothesised that tsetse actively regulate the density of Wigglesworthia according to the hosts requirements, depending on their current nutritional state and developmental age. In contrast, we postulated that Sodalis retains some independence from host control, and that the growth of this symbiont is dependent on the conditions of the immediate environment, such as nutrient availability. Using qPCR, we examined how symbiont densities change across host age and the hunger cycle. Additionally, we investigated how host nutrition influences symbiont density, by comparing tsetse that were fed diluted blood (poor nutrition) or blood supplemented with yeast extract (vitamin enriched). We found that the density of Wigglesworthia did not reflect the nutritional status of the host, but was optimised to accommodate long-term host requirements (in terms of nutrient provisioning). In contrast, the density of facultative Sodalis was influenced by the ecological context (i.e. nutrient availability). This suggests that tsetse regulate the abundance of Wigglesworthia to a greater extent than Sodalis. We propose that tsetse exert only partial control over Sodalis growth due to the relatively recent transition of this symbiont to host-associated living. Author summarySymbiotic microbes have the potential to significantly impact the wider ecosystem by affecting the fitness and behaviour of their animal hosts. The density of a particular symbiont population within host tissues is likely an important factor influencing the effect it has on the host, however, little is known about the factors which determine how symbiont density is regulated, and how these differ between symbionts with different degrees of host-association (e.g. obligate and facultative symbionts). Here, we found that Wigglesworthia and Sodalis, two bacterial tsetse symbionts, demonstrate distinct trends in density according to host age and nutrition. We discuss how the evolutionary histories of these symbionts with their host potentially explain these results, highlighting the complexity and dynamic nature of host-symbiont interactions. Our findings contribute to our understanding of the extent to which hosts and symbionts control symbiont density and how symbiont density regulation can be affected by the ecological context.

evolutionary biology↗

bioRxiv2024

Immunisation of chickens with inactivated and/or infectious H9N2 avian influenza virus leads to differential immune B cell repertoire development

Avian influenza viruses (AIVs) are a major economic burden to the poultry industry, and pose serious zoonotic risk, with human infections being reported every year. To date, the vaccination of birds remains the most important method for the prevention and control of AIV outbreaks. Most national vaccination strategies against AIV infection use whole-virus inactivated vaccines, which predominantly trigger a systemic antibody-mediated immune response. There are currently no studies that have examined the antibody repertoire of birds that were infected with and/or vaccinated against AIV. To this end, we evaluate the changes in the H9N2-specific IgM and IgY repertoires in chickens subjected to vaccination(s) and/or infectious challenge. We show that a large proportion of the IgM and IgY clones were shared across multiple individuals, and these public clonal responses are dependent on both the immunisation status of the birds and the specific tissue that was examined. Furthermore, analysis reveals specific clonal expansions which are restricted to particular H9N2 immunisation regimes. These results indicate that both the nature and number of immunisations are important drivers of the antibody responses and repertoire profiles in chickens following H9N2 antigenic stimulation. We discuss how the repertoire biology of avian B cell responses may affect the success of AIV vaccination in chickens, in particular the implications of public versus private clonal selection.

immunology↗

bioRxiv2024

The potential impacts of vector host species fidelity on zoonotic arbovirus transmission

The interaction between vector host preference and host availability on vector blood feeding behaviour has important implications for the transmission of vector-borne pathogens. In particular in multi-host disease systems the fidelity of the vector biting behaviour has the potential to have important implications to disease outcomes, particularly when there are amplifying and dead-end hosts. Using a mathematical model we showed that vector fidelity to the host species they take a first blood meal from leads to non-homogeneous mixing between hosts and vectors. Taking Japanese encephalitis virus (JEV) as a case study, we investigated how vector preference for amplifying vs dead-end hosts and fidelity can influence JEV transmission. We show that in regions where pigs (amplifying hosts) are scarce compared to cattle (dead-end hosts preferred by common JEV vectors), JEV can still be maintained through vector fidelity. Our findings demonstrate the importance of considering fidelity as a potential driver of transmission, particularly in scenarios such as Bangladesh and India where the composition of the host community might initially suggest that transmission is not possible.

ecology↗

bioRxiv2024

Life Histories and Study Duration matter less than Prior Knowledge of Vital Rates to Inverse Integral Projection Models

O_LIEcology has been surprisingly slow to address the uncertainty and bias that results from using short-term time series to draw long-term inference. To improve our understanding of assumptions around the temporal structure of vital rates (e.g., survival, reproduction), we need tools that are feasible and capture longer-term, state-structured population dynamics. C_LIO_LIHere, we use inverse modelling of a set of integral projection models (IPMs) to show how demographic rates can be accurately reconstructed from state-structure fluctuations in a population time-series. We use a particle-filtering optimisation algorithm to fit vital rates from time-series of varying length, parameter combinations, priors, and life histories. C_LIO_LIWe show how key life history traits such as generation time have little effect on the ability of our approach to accurately identify vital rates using state structure over time. Further, contrary to our expectations, the duration of our time-series data has relatively modest impact on the estimation of vital rates compared to the critical role of prior knowledge on vital rates. C_LIO_LIur framework to estimate IPM vital rates highlights the potential of inverse models to extend time-series for demographic models, but also demonstrates that long-term time-series are not a perfect surrogate for detailed demographic inference. We discuss the need for more work exploring the conditions when inverse modelling is an adequate tool based on species traits. C_LI

ecology↗

bioRxiv2023

Temporal dynamics of trauma memory persistence

Traumatic events lead to distressing memories, but such memories are made all the worse when they intrude to mind unbidden and recurrently. Intrusive memories are a hallmark of several mental health disorders including posttraumatic stress disorder (PTSD) and can persist for years. Critically, the reduction of intrusive memories provides a treatment target. While cognitive models for psychological trauma exist, these lack formal quantitative structure and robust empirical validation. Here we develop a mechanistically-driven, quantitative framework to extend understanding of the temporal dynamic processes of trauma memory. We show how the marginal gains of interventions for intrusive memories can be enhanced as key properties of the intervention vary. Validating the framework against empirical data highlights that while emerging interventions to reduce occurrence of intrusive memories can be effective, counter-intuitively, maintaining these memories in a sufficiently reactivated state is essential for preventing their persistence. Author SummaryIntrusive memories and flashbacks after trauma are prominent in several mental disorders. Quantifying these intrusions is the aim of the current study. While many conceptual models for trauma memory exist, none provide a mechanistic framework for validating experimental or clinical evidence. Our approach is to develop a probabilistic description of memory mechanisms to link to the broader goals of trauma treatment. Analysis shows how critical attributes of the framework such as intervention strength and reminder strength determine success in managing intrusive memories. Validation with empirical data shows how the framework can be parameterized and predictions evaluated against observed outcomes. In this way neural mechanisms associated with memory can be combined with broader cognitive processes.

neuroscience↗

bioRxiv2022

Inclusive fitness forces of selection in an age-structured population

Current evolutionary theories of senescence predict that the force of selection on survival will decline from maturity to zero at the age of last reproduction, and the force of selection on reproduction will decline monotonically from birth. These predictions rest upon the assumption that individuals within a population do not interact with one another. This assumption, however, is violated in social species, where an individuals survival and/or reproduction may shape the fitness of other group members. In such species, it is inclusive fitness that natural selection optimises. Yet, it remains unclear how the forces of selection on survival and reproduction might be modified when inclusive fitness, rather than population growth rate, is considered the appropriate metric for fitness. Here, we derive inclusive fitness forces of selection for hypothetical populations of social species. We show that selection on survival is not always constant before maturity, and can remain above zero in post-reproductive age classes, contrary to conventional models of senescence. We also show how the trajectory of the force of selection on reproduction does not always decline monotonically from birth, as predicted by classical theory, but instead depends on the balance of benefits to direct fitness and costs to indirect fitness. Our theoretical framework provides the unique opportunity to expand our understanding of senescence across social species, with important implications to species with variable life histories.

evolutionary biology↗

bioRxiv2021

BugSplit: highly accurate taxonomic binning of metagenomic assemblies enables genome-resolved metagenomics

A large gap remains between sequencing a microbial community and characterizing all of the organisms inside of it. Here we develop a novel method to taxonomically bin metagenomic assemblies through alignment of contigs against a reference database. We show that this workflow, BugSplit, bins metagenome-assembled contigs to species with a 33% absolute improvement in F1-score when compared to alternative tools. We perform nanopore mNGS on patients with COVID-19, and using a reference database predating COVID-19, demonstrate that BugSplits taxonomic binning enables sensitive and specific detection of a novel coronavirus not possible with other approaches. When applied to nanopore mNGS data from cases of Klebsiella pneumoniae and Neisseria gonorrhoeae infection, BugSplits taxonomic binning accurately separates pathogen sequences from those of the host and microbiota, and unlocks the possibility of sequence typing, in silico serotyping, and antimicrobial resistance prediction of each organism within a sample. BugSplit is available at https://bugseq.com/academic.

bioinformatics↗

bioRxiv2021

Mechanisms of biodiversity between Campylobacter sequence types in a flock of broiler-breeder chickens.

A long-term study of Campylobacter sequence types was used to investigate the competitive framework of the Campylobacter metacommunity, and understand how multiple sequence types simultaneously co-occur in a flock of chickens. A combination of matrix and patch-occupancy models were used to estimate parameters describing the competition, transmission, and mortality of each sequence type. It was found that Campylobacter sequence types form a strong hierarchical framework within a flock of chickens, and occupied a broad spectrum of transmission-mortality trade-offs. Upon further investigation of how biodiversity is thus maintained within the flock, it was found that the demographic capabilities of Campylobacter, such as mortality and transmission, could not explain the broad biodiversity of sequence types seen, suggesting that external factors such as host-bird health and seasonality are important elements in maintaining biodiversity of Campylobacter sequence types.

microbiology↗

bioRxiv2020

Three-dimensional random walk models of individual animal movement and their application to trap counts modelling

BackgroundRandom walks (RWs) have proved to be a powerful modelling tool in ecology, particularly in the study of animal movement. An application of RW concerns trapping which is the predominant sampling method to date in insect ecology, invasive species, and agricultural pest management. A lot of research effort has been directed towards modelling ground-dwelling insects by simulating their movement in 2D, and computing pitfall trap counts, but comparatively very little for flying insects with 3D elevated traps. MethodsWe introduce the mathematics behind 3D RWs and present key metrics such as the mean squared displacement (MSD) and path sinuosity, which are already well known in 2D. We develop the mathematical theory behind the 3D correlated random walk (CRW) which involves short-term directional persistence and the 3D Biased random walk (BRW) which introduces a long-term directional bias in the movement so that there is an overall preferred movement direction. In this study, we consider three types of shape of 3D traps, which are commonly used in ecological field studies; a spheroidal trap, a cylindrical trap and a rectangular cuboidal trap. By simulating movement in 3D space, we investigated the effect of 3D trap shapes and sizes and of movement diffusion on trapping efficiency. ResultsWe found that there is a non-linear dependence of trap counts on the trap surface area or volume, but the effect of volume appeared to be a simple consequence of changes in area. Nevertheless, there is a slight but clear hierarchy of trap shapes in terms of capture efficiency, with the spheroidal trap retaining more counts than a cylinder, followed by the cuboidal type for a given area. We also showed that there is no effect of short-term persistence when diffusion is kept constant, but trap counts significantly decrease with increasing diffusion. ConclusionOur results provide a better understanding of the interplay between the movement pattern, trap geometry and impacts on trapping efficiency, which leads to improved trap count interpretations, and more broadly, has implications for spatial ecology and population dynamics.

ecology↗

bioRxiv2020

A mathematical modelling approach to uncover factors influencing the spread of Campylobacter in a flock of chickens

Despite continued efforts into improving biosecurity protocol, Campylobacter continues to be detected in the majority of commercial chicken flocks across Europe. Using an extensive data set of Campylobacter prevalence within a chicken breeder flock for over a year, multiple Bayesian models are presented to explore the dynamics of the spread of Campylobacter in response to seasonal variation, species-specificity, bird health and total infection prevalence. It was found that birds within the flock varied greatly in their response to bacterial challenge, and that this phenomena had a large impact in the overall prevalence of different species of Campylobacter. Campylobacter jejuni appeared more frequently in the summer, while Campylobacter coli persisted for a longer duration, amplified by the most susceptible birds in the flock. Our study suggests that strains of Campylobacter that appear most frequently likely possess no demographic advantage, but are instead amplified due to the health of the birds that ingest it.

microbiology↗

bioRxiv2018

The Goldilocks Window of Personalized Chemotherapy: An Immune Perspective

The immune system is increasingly being recognized for its untapped potential in being recruited to attack tumors in cancer therapy. The main challenge, however, is that most tumors exist in a state of immune tolerance where the patients immune system has become insensitive to the cancer cells. In order to investigate the ability to use chemotherapy to break immune tolerance, we created a mathematical modeling framework for tumor-immune dynamics. Our results suggest that optimal chemotherapy scheduling must balance two opposing objectives: maximal tumor reduction and preserving patient immune function. Successful treatment requires therapy to operate in a Goldilocks Window where patient immune health is not overly compromised. By keeping therapy just right, we show that the synergistic effects of immune activation and chemotherapy can maximize tumor reduction and control.\n\nStatement of SignificanceIn order to maximize the synergy between chemotherapy and anti-tumor immune response, lymphodepleting therapy must be balanced in a Goldilocks Window of optimal dosing.

cancer biology↗

bioRxiv2018

Crystal Toxins and the volunteer’s dilemma in bacteria

1The growth and virulence of the bacteria Bacillus thuringiensis depends on the production of Cry toxins, which are used to perforate the gut of its host. Successful invasion of the host relies on producing a threshold amount of toxin, after which there is no benefit from producing more toxin. Consequently, the production of Cry toxin appears to be a different type of social problem compared with the public goods scenarios that bacteria often encounter. We show that selection for toxin production is a volunteers dilemma. We make the specific predictions that: (1) selection for toxin production depends upon an interplay between the number of bacterial cells that each host ingests, and the genetic relatedness between those cells; (2) cheats that do not produce toxin gain an advantage when at low frequencies, and at high bacterial density, allowing them to be maintained in a population alongside toxin producing cells. More generally, our results emphasise the diversity of the social games that bacteria play.

evolutionary biology↗

bioRxiv2018

Interaction Modifications Disrupt The Structure And Stability Of Ecological Communities

Trophic interaction modifications, where a consumer-resource interaction is influenced by an additional species, are established as being prevalent throughout ecological networks. Despite this, their influence on the structure of interaction distributions within communities has not yet been examined. Although empirical information about the distribution of interaction modifications is currently sparse, the non-trophic effects they induce will be structured by the underlying network of trophic interactions. Here we test the impact of interaction modifications, introduced under a range of distributional assumptions to artificial and empirical trophic networks, on the overall structure of interactions within communities. We show that local stability and reactivity is critically dependent on the inter-relationship between the trophic and non-trophic effects. Depending on their distribution, interaction modifications can generate significant additional structure to community interactions making analyses of the stability of ecological systems based solely on trophic networks unreliable. Empirical information on the topological and strength distributions of interaction modifications will be a key part of understanding the dynamics of communities.

ecology↗

bioRxiv2017

Identifying Important Interaction Modifications in Ecological Systems

Trophic interaction modifications, where a consumer-resource link is affected by additional species, are widespread and significant causes of indirect effects in ecological networks. The sheer number of potential interaction modifications in ecological systems poses a considerable challenge, making prioritisation for empirical study essential. Here, we introduce measures to quantify the topological relationship of individual interaction modifications relative to the underlying network. We use these, together with measures for the strength of trophic interaction modifications to identify modifications that are most likely to exert significant effects on the dynamics of whole systems. Using a set of simulated food webs and randomly distributed interaction modifications, we test whether a subset of interaction modifications important for the local stability and direction of species responses to perturbation of complex networks can be identified. We show that trophic interaction modifications affecting interactions with a high biomass flux, those that connect species otherwise distantly linked, and those where high trophic-level species modify to interactions lower in the web have particular importance for dynamics. In contrast, the centrality of modifications in the network provided little information. This work demonstrates that analyses of interaction modifications can be tractable at the network scale and highlights the importance of understanding the relationship between the distributions of trophic and non-trophic effects.

ecology↗