Biology subjects

Abbate, J. L.

Publications and source records attributed to Abbate, J. L..

3 recordsLinked to original sources

bioRxiv2026

Towards the automation of Species Distribution Modelling: The AutoMaxEnt routine

Species distribution models are widely used for the evaluation and analysis of species spatial distributions and responses to environmental changes. Due to this, there's a wide diversity of tools and algorithms to perform these types of analyses. However, despite being a mature field of study, SDM still requires a large amount of research intervention and decision-making to produce reliable models. This is a natural consequence of each species unique response to environmental factors, but in practice it hinders the potential of SDMs to be used effectively and with confidence across large sets of species. Here we present the AutoMaxEnt repository, a collection of functions and tools for the automation of maximum entropy species distribution models. AutoMaxEnt offers a flexible environment to model species distribution models, automating most of the data pre-processing and preparation and giving the user the possibility of exploring multiple model scenarios automatically or with control over how those scenarios are generated. AutoMaxent offers model fit control, multiple background points generation algorithms, automatic model and variable selection, and study area configuration, among other parameters. AutoMaxEnt allows for the automation of model fitting, evaluation and model selection across different species, study areas and time periods.

ecology↗

bioRxiv2026

To cull or not to cull: a model-based evaluation of response strategies against Lumpy Skin Disease outbreaks

With high risk of sustained transmission and substantial associated morbidity, Lumpy Skin Disease (LSD) of cattle presents a major emerging threat to bovine herds worldwide, and has the potential to cause huge losses for farmers, producers, and the wider bovine and dairy trade industries. The epidemic which started in June 2025 in France illustrates this threat, as the government-imposed mass culling strategy has led to protests by farmers and social unrest throughout the country. Here, we developed an infectious disease modelling framework for evaluating different intervention strategies in an effort to critically evaluate the evidence behind the drastic measures being taken. By simulating epidemics under different response settings, we found that control strategies employing targeted culling were essentially as effective as those requiring mass culling, and did not require significantly more vaccination. These results question the response strategy currently imposed by the French government, and suggest avenues for alternative response strategies which could gain better support from the affected communities. Our results are entirely reproducible using a new free, open-source simulation tool which can be used for further evaluation of public health interventions against LSD epidemics.

ecology↗

bioRxiv2020

Pathogen community composition and co-infection patterns in a wild community of rodents

Rodents are major reservoirs of pathogens that can cause disease in humans and livestock. It is therefore important to know what pathogens naturally circulate in rodent populations, and to understand the factors that may influence their distribution in the wild. Here, we describe the occurrence and distribution patterns of a range of endemic and zoonotic pathogens circulating among rodent communities in northern France. The community sample consisted of 713 rodents, including 11 host species from diverse habitats. Rodents were screened for virus exposure (hantaviruses, cowpox virus, Lymphocytic choriomeningitis virus, Tick-borne encephalitis virus) using antibody assays. Bacterial communities were characterized using 16S rRNA amplicon sequencing of splenic samples. Multiple correspondence (MCA), multiple regression and association screening (SCN) analyses were used to determine the degree to which extrinsic factors (study year and site; host habitat, species, sex and age class) contributed to pathogen community structure, and to identify patterns of associations between pathogens within hosts. We found a rich diversity of bacterial genera, with 36 known or suspected to be pathogenic. We revealed that host species is the most important determinant of pathogen community composition, and that hosts that share habitats can have very different pathogen communities. Pathogen diversity and co-infection rates also vary among host species. Aggregation of pathogens responsible for zoonotic diseases suggests that some rodent species may be more important for transmission risk than others. Moreover, we detected positive associations between several pathogens, including Bartonella, Mycoplasma species, Cowpox virus (CPXV) and hantaviruses, and these patterns were generally specific to particular host species. Altogether, our results suggest that host and pathogen specificity is the most important driver of pathogen community structure, and that interspecific pathogen-pathogen associations also depend on host species.

ecology↗