Biology subjects

Haydon, D. T.

Publications and source records attributed to Haydon, D. T..

8 recordsLinked to original sources

bioRxiv2026

Implications of the trade-offs between negative density-dependence and Allee effects for vector control

BackgroundUnderstanding population dynamics is fundamental to predicting species persistence and extinction, yet remains challenging due to the complex interplay between ecological, environmental and anthropogenic factors. Population dynamics are regulated by intrinsic factors such as negative density-dependence and Allee effects. While negative density-dependence is a well-understood process, Allee effects have received less attention but can have important implications for conservation and species management. For control of disease vectors, negative density-dependence and Allee effects can drive vectors to elimination or to rebound after control. For malaria mosquitoes, negative density-dependence at the larval stages is well known to limit population growth, but the implications of Allee effects and the trade-offs between negative density-dependence and Allee effects remain unknown. It is hypothesised that, depending on the vector control strategy, Allee effects could be triggered and push populations closer to extinction. MethodsA stochastic state-structured population simulation model was developed, which followed a simplified mosquito life cycle. Negative density-dependence and Allee effects were included as parameters influencing larval survival and total fecundity, respectively. The aims were addressed by varying the strength of negative density-dependence and Allee effects parameters, independently and simultaneously, under different vector control scenarios: control, sustained and shorter-term interventions (here, immolating larvicides) that reduced the larval population. ResultsWhile in isolation, the strength of negative density-dependence and Allee effects did not have a long-term impact on the population dynamics, their combination accelerated population extinction as both the strength of negative density-dependence and Allee effects increased. As Allee effects act on small population sizes, sustained interventions were able to activate Allee effects, increasing the probability of population extinction, but short-term interventions can lead to populations rebounding, driven by negative density-dependence. ConclusionUnderstanding less-studied regulatory processes like Allee effects can support vector control by highlighting aspects of the vectors life cycle that are either resilient or vulnerable to interventions. If present, Allee effects could potentially be harnessed to accelerate the elimination of vectors and diseases such as malaria.

ecology↗

bioRxiv2025

Rift Valley fever virus dynamics in a transhumant cattle system in The Gambia

Rift Valley fever (RVF) is a zoonotic disease of global concern, driven by environmental conditions, vector activity, and livestock mobility. Although RVF has been reported in The Gambia, its epidemiology remains poorly understood. This study developed a compartmental model to study RVF dynamics in the cattle population of the country. The model incorporated seasonally dynamic transmission parameters reflecting transhumant movement and ecological differences between two distinct ecoclimatic regions: the Sahelian area and the Gambia river. Parameterised using serological data linked to household survey data, the model predicted endemic RVF virus (RVFV) circulation within The Gambia, and captured temporal infection trends that closely match empirical data. Weak decay rates of seropositivity were required to match predicted and observed age-seroprevalence. Results indicated sustained RVFV transmission during the dry season in the Gambia river eco-region, with a high risk of seasonal virus introductions to the Sahelian eco-region at the start of the wet season via the returning transhumant cattle. Our study highlighted the role of livestock mobility in RVFV epidemiology in The Gambia and the need for targeted control strategies that might include, for example, targeted cattle vaccination or application of topical insecticide treatments for transhumant herds.

ecology↗

bioRxiv2025

Do identification guides hold the key to speciesmisclassification by citizen scientists?

1O_LICitizen science data often contain high levels of species misclassification that can bias inference and conservation decisions. Current approaches to address mislabelling rely on expert taxonomists validating every record. This approach makes intensive use of a scarce resource and reduces the role of the citizen scientist. C_LIO_LISpecies, however, are not confused at random. If two species appear more similar, it is probable they will be more easily confused than two highly distinctive species. Identification guides are intended to use these patterns to aid correct classification, but misclassifications still occur due to user-error and imperfect guidebook design. Statistical models should be able to exploit this non-randomness to learn confusion patterns from small validation datasets provided by expert taxonomists, yielding a much-needed reduction in expert workload. Here, we use a variety of Bayesian hierarchical models to probabilistically classify species based on the species-label provided by the citizen scientist. We also explore the utility of guidebooks provided by the citizen science schemes as a prior for species similarity, and hence draw conclusions for their future improvement. C_LIO_LIWe find that the species-label assigned to a record by a citizen scientist, even when incorrect, contains useful information about the true species-identity. The citizen scientists correctly identify the species in around 58% of records. Using models trained on only 10% of these records (validated by experts), we can correctly predict species-identity for 69 (90%CI: 64-73)% of records when the guidebook is used, vs 64 (58-69)% for models that do not use the guidebook. The fact that misclassifications can be predicted systematically indicates that improvements could be made to the guidebook to reduce misclassification. C_LIO_LIBy using Bayesian, hierarchical models we can greatly reduce the workload for experts by providing a probabilistic correction to citizen science records, rather than requiring manual review. This is increasingly important as the number of citizen science schemes grows and the relative number of taxonomists shrinks. By learning confusion patterns statistically, we open up future avenues of research to identify what causes these confusions and how to better address them. C_LI

ecology↗

bioRxiv2025

Sero-epidemiology of Rift Valley fever virus in ruminant livestock in The Gambia

Rift Valley fever (RVF) virus is a globally significant zoonotic pathogen primarily transmitted by mosquitoes, causing abortion storms and neonatal mortality in ruminant livestock and haemorrhagic encephalitis in humans. Although localized RVF outbreaks occur frequently in the West Africa Sahel, the complex interplay between vectors, ruminant hosts, human behaviours, and ecoclimatic factors driving these outbreaks remains unclear. In 2022, we conducted a cross-sectional study across The Gambia that collected serum samples linked to questionnaire data from 202 randomly selected livestock-owning households to estimate population-level seroprevalence, investigate the patterns of, and identify risk factors associated with RVFV seropositivity in ruminant livestock. Design adjusted seroprevalence estimates were 36.8% (95% Confidence Interval [CI]: 31.6-40.0) for cattle (n = 1416), 2.1% (95% CI: 0.5-3.7) for goats (n = 1101) and 4.3% (95% CI: 1.2-7.4) for sheep (n = 1085) using the IDScreen(R) RVF c-ELISA assay. The intracluster correlation coefficients for RVFV seropositivity at the herd level were 0.13 (95% CI: 0.09-0.18) in cattle and 0.22 (95% CI: 0.06-0.31) in small ruminants on the logit scale. Risk factors associated with RVFV seropositivity were investigated using a LASSO regression, with transhumant movement to the Gambia river valley, increasing age, introduction of new ruminants, and proximity to water identified as most strongly associated with seropositivity. By fitting the serologic data to a catalytic force of infection (FOI) model, age-independent FOI estimates of 0.12 (95% Credible Interval [CrI]: 0.10-0.16) for cattle and 0.013 (95% CrI: 0.01-0.02) for small ruminants were obtained. The observed patterns of RVFV seropositivity indicate widespread and endemic viral circulation, with livestock management practices and the Gambia river floodplains likely sustaining transmission. The high seroprevalence in cattle raises concerns that sporadic outbreaks may have occurred unnoticed or unreported, underscoring the critical need for comprehensive One Health surveillance to identify potential clinical cases.

ecology↗

bioRxiv2024

Food webs can deliver win-win strategies for tropical agroforestry and biodiversity conservation

Balancing biodiversity conservation and agricultural productivity is commonly regarded as a trade-off, but such analyses overlook ecosystem services that functional biodiverse communities provide in agroecosystems, and the possibility that win-win strategies may exist. We developed a dynamic mechanistic community model of the bird-insect food web associated with African cocoa agroforestry, structurally informed by metabarcoding data on bird diets, and fitted to trapping data on species abundances. We used the model to predict equilibrium community composition under varying intensities of shade management and pesticide use. Our results indicate that low-intensity farming favours forest bird species, and potential pollinator abundance, with no increase in pest biomass. Furthermore, using simulations of pesticide application, we found that pesticides do not effectively reduce pest biomass, and result in forest bird extinction. Our mechanistic framework combines the influence of management and the direct and indirect effects of species interactions, and demonstrates that low intensity agriculture may provide a win-win for biodiversity and ecosystem services.

ecology↗

bioRxiv2021

Spatial scale of transmission explains how acute infections circulate at low prevalence

Fundamental questions remain about the regulation of acute pathogens in the absence of acquired immunity. This is especially true for canine rabies, a universally fatal zoonosis. From tracing rabies transmission in a population of 50,000 dogs in Tanzania between 2002-2016 we unravel the processes through which rabies is regulated and persists, fitting individual-based models to spatially-resolved data to investigate the mechanisms modulating transmission and the scale over which they operate. We find that while prevalence never exceeds 0.15%, we detect significant susceptible depletion at local scales commensurate with rabid dog movement, reducing transmission through clustering of rabies deaths and individuals incubating infection. Individual variation in rabid dog behaviour facilitates virus dispersal and co-circulation of lineages, enabling metapopulation persistence. These mechanisms likely operate in many pathogens circulating in spatially structured populations, with important implications for prediction and control, yet are unobservable unless the scale of host interactions is identified. One-Sentence SummaryIdentifying the spatial scale of contact reveals the mechanisms that limit the size of rabies outbreaks and that are critical for predicting transmission dynamics.

ecology↗

bioRxiv2018

Macarthurs 1955 Stability Function is Related to Formal Dynamic Measures of Food Web Stability

Community complexity-stability relationships have been at the centre of ecological thinking for many decades. MacArthur (1955) proposed a measure of stability that reflected the diversity in the number of pathways energy can flow up through a food web but how this index correlates with more formal ideas of dynamical stability remains unexplored. Here, we examine the relationship between MacArthurs proposed index and measures of local and global stability in Lotka-Volterra food web models. Our results provide support for MacArthurs intuitive hypothesis that increasing the diversity of energy pathways through food webs endows them with greater stability, as measured by both the probability of local and global point stabilities, and the return time to stable equilibria following perturbation.

ecology↗

bioRxiv2016

Surveillance to Establish Elimination of Transmission and Freedom from Dog-mediated Rabies

BackgroundWith a global target set for zero human deaths from dog-mediated rabies by 2030 and some regional programmes close to eliminating canine rabies, there is an urgent need for enhanced surveillance strategies suitable for declaring freedom from disease and elimination of transmission with known confidence.\n\nMethodsUsing exhaustive contact tracing across settings in Tanzania we generated detailed data on rabies incidence, rabid dog biting behaviour and health-seeking behaviour of bite victims. Using these data we compared case detection of sampling-based and enhanced surveillance methodologies and investigated elimination verification procedures.\n\nFindingsWe demonstrate that patients presenting to clinics with bite injuries are sensitive sentinels for identifying dog rabies cases. Triage of patients based on bite history criteria and investigation of suspicious incidents can confirm >10% of dog rabies cases and is an affordable approach that will enable validation of disease freedom following two years without case detection. Approaches based on sampling the dog population without using bite-injury follow-up were found to be neither sensitive nor cost-effective.\n\nInterpretationThe low prevalence of rabies, and short window in which disease can be detected, preclude sampling-based surveillance. Instead, active case finding guided by bite-patient triage is needed as elimination is approached. Our proposed methodology is affordable, practical and supports the goal of eliminating human rabies deaths by improving administration of lifesaving post-exposure prophylaxis for genuinely exposed but untreated contacts. Moreover, joint investigations by public health and veterinary workers will strengthen intersectoral partnerships and capacity for control of emerging zoonoses.

epidemiology↗