Model-based extrapolation of ecological systems under future climate scenarios: The example of Ixodes ricinus ticks.

Models can be applied to extrapolate consequences of climate change for complex ecological systems in the future. The acknowledged systems' behaviour at present is projected into the future considering climate projection data. Such an approach can be used to addresses the future activity and density of the castor bean tick Ixodes ricinus, the most widespread tick species in Europe. It is an important vector of pathogens causing Lyme borreliosis and tick-borne encephalitis. The population dynamics depend on several biotic and abiotic factors. Such complexity makes it difficult to predict the future dynamics and density of I. ricinus and associated health risk for humans. The objective of this study is to force ecological models with high-resolution climate projection data to extrapolate I. ricinus tick density and activity patterns into the future. We used climate projection data of temperature, precipitation, and relative humidity for the period 1971-2099 from 15 different climate models. Tick activity was investigated using a climate-driven cohort-based population model. We simulated the seasonal population dynamics using climate data between 1971 and 2099 and observed weather data since 1949 at a specific location in southern Germany. We evaluated derived quantities of local tick ecology, e.g. the maximum questing activity of the nymphal stage. Furthermore, we predicted spatial density changes by extrapolating a German-wide tick density model. We compared the tick density of the reference period (1971-2000) with the counter-factual densities under the near-term scenario (2012-2041), mid-term scenario (2050-2079) and long-term scenario (2070-2099). We found that the nymphal questing peak would shift towards early seasons of the year. Also, we found high spatial heterogeneity across Germany, with predicted hotspots of up to 2,000 nymphs per 100 m2 and coldspots with constant density. As our results suggest extreme changes in tick behaviour and density, we discuss why caution is needed when extrapolating climate data-driven models into the distant future when data on future climate drive the model projection.

The Irish cattle population structured by enterprise type: overview, trade & trends.

BACKGROUND: The cattle sector is the most important economic production unit of the Irish farming and agri-food sector. Despite its relevance, there has been limited quantitative information about the structure of differing cattle production types and of the connections between them. This paper addresses this gap by providing, for the first time, an overview of the Irish cattle population structured by enterprise type. METHODS & RESULTS: We collected data from the cattle register for the period 2015 to 2019 and assigned registered herds to one of 18 different herd types using a recently published herd type classification approach. This allows, for the first time, to exploring changes in enterprise types and subtypes over time, and describing the movements between these subtypes and from these subtypes to slaughter. CONCLUSIONS: The overview and associated classification presented in this study will form the basis for a number of future comparative studies, including cross-sectoral assessments of profitability, estimation of the extent of animal health losses on Irish cattle farms or structural analysis of Greenhouse Gas (GHG) emissions across production systems.

A large-scale epidemiological model of BoHV-1 spread in the Irish cattle population to support decision-making in conformity with the European Animal Health Law.

We present a new modelling framework to address the evaluation of national control/surveillance programs planned in line with the European Animal Health Law (AHL) for livestock diseases. Our modelling framework is applied to the cattle sector in Ireland where there is need for policy support to design an optimal programme to achieve bovine herpesvirus type 1 (BoHV-1) free status under the AHL. In this contribution, we show how our framework establishes a regional model that is able to mechanistically reproduce the demography, management practices and transport patterns of an entire cattle population without being dependent on continuous livestock registry data. An innovative feature of our model is the inclusion of herd typing, thereby extending these beyond the categories of dairy, beef and mixed herds that are frequently considered in other regional modelling studies. This detailed representation of herd type-specific management facilitates comparative assessment of BoHV-1 eradication strategies targeting different production types with individual strategy protocols. Finally, we apply our model to support current discussions regarding the structure and implementation of a potential national BoHV-1 eradication programme in Ireland.

Combining expert knowledge and machine-learning to classify herd types in livestock systems.

A detailed understanding of herd types is needed for animal disease control and surveillance activities, to inform epidemiological study design and interpretation, and to guide effective policy decision-making. In this paper, we present a new approach to classify herd types in livestock systems by combining expert knowledge and a machine-learning algorithm called self-organising-maps (SOMs). This approach is applied to the cattle sector in Ireland, where a detailed understanding of herd types can assist with on-going discussions on control and surveillance for endemic cattle diseases. To our knowledge, this is the first time that the SOM algorithm has been used to differentiate livestock systems. In compliance with European Union (EU) requirements, relevant data in the Irish livestock register includes the birth, movements and disposal of each individual bovine, and also the sex and breed of each bovine and its dam. In total, 17 herd types were identified in Ireland using 9 variables. We provide a data-driven classification tree using decisions derived from the Irish livestock registration data. Because of the visual capabilities of the SOM algorithm, the interpretation of results is relatively straightforward and we believe our approach, with adaptation, can be used to classify herd type in any other livestock system.

Epidemiology of age-dependent prevalence of Bovine Herpes Virus Type 1 (BoHV-1) in dairy herds with and without vaccination.

Many studies report age as a risk factor for BoHV-1 infection or seropositivity. However, it is unclear whether this pattern reflects true epidemiological causation or is a consequence of study design and other issues. Here, we seek to understand the age-related dynamics of BoHV-1 seroprevalence in seasonal calving Irish dairy herds and provide decision support for the design and implementation of effective BoHV-1 testing strategies. We analysed seroprevalence data from dairy herds taken during two Irish seroprevalence surveys conducted between 2010 and 2017. Age-dependent seroprevalence profiles were constructed for herds that were seropositive and unvaccinated. Some of these profiles revealed a sudden increase in seroprevalence between adjacent age-cohorts, from absent or low to close to 100% of seropositive animals. By coupling the outcome of our data analysis with simulation output of an individual-based model at the herd scale, we have shown that these sudden increases are related to extensive virus circulation within a herd for a limited time, which may then subsequently remain latent over the following years. BoHV-1 outbreaks in dairy cattle herds affect animals independent of age and lead to almost 100% seroconversion in all age groups, or at least in all animals within a single epidemiological unit. In the absence of circulating infection, there is a year-on-year increase in the age-cohort at which seroprevalence changes from low to high. The findings of this study inform recommendations regarding testing regimes in the context of contingency planning or an eradication programme in seasonal calving dairy herds.

Reviewing age-structured epidemiological models of cattle diseases tailored to support management decisions: Guidance for the future.

Mechanistic simulation models are being increasingly used as tools to assist with animal health decision-making in the cattle sector. We reviewed scientific literature for studies reporting age-structured cattle management models in application to infectious diseases. Our emphasis was on papers dedicated to support decision making in the field. In this systematic review we considered 1290 manuscripts and identified 76 eligible studies. These are based on 52 individual models from 10 countries addressing 9 different pathogens. We provide an overview of these models and present in detail their theoretical foundations, design paradigms and incorporated processes. We propose a structure of the characteristics of cattle disease models using three main features: [1] biological processes, [2] farming-related processes and [3] pathogen-related processes. It would be of benefit if future cattle disease models were to follow this structure to facilitate science communication and to allow increased model transparency.