Upscaling disease risk estimates Karen Garrett Kansas State University

Recruitment We are seeking a collaborator who can authoritatively address scaling of weather/climate data relevant to pathogens

Outline Upscaling disease forecasting models based on weather Network models at national scale Network model for soybean rust incorporating wind speed and direction

Garrett et al. 2006

From Sparks, Hijmans, Forbes, and Garrett, in preparation Adam Sparks

Outline Upscaling disease forecasting models based on weather Network models at national scale Network model for soybean rust incorporating wind speed and direction

Many predictive models of plant disease rely upon fine-scale weather data This data requirement is a major constraint when applying disease prediction models in areas of the world where hourly weather data are unreliable or unavailable. We developed a framework to adapt an existing potato late blight forecast model, SimCast for use with coarse scale weather data.

Objectives Develop disease prediction models based on daily and monthly weather means and compare to results based on hourly weather data. Compare risk predictions based on hourly, daily, and monthly weather data to late blight severity data sets from several countries. Predict disease for resistant and susceptible cultivars under climate change scenarios.

Methods – development of models Hourly weather data from the US National Climatic Data Center were used in SimCast to calculate blight units, a daily measure of disease risk. Generalized additive models (GAM) were created to estimate blight units based on daily or monthly averages of weather data.

Blight units predicted by SimCast Daily Means susceptible cultivars. “Observed” blight units are SimCast estimates based on hourly observations.

Blight units predicted by SimCast Monthly Means susceptible cultivars. “Observed” blight units are SimCast estimates based on hourly observations.

Comparison of estimates for blight units at two levels weather data resolution vs. late blight severity (AUDPC) from 19 cultivar-site-year combinations Observed: p>0.01, R 2 =0.56 Predicted: p>0.01, R 2 =0.62

Methods – climate change scenarios Maps of disease risk were produced using WorldClim ( datasets that include the IPCC A2a (high growth carbon emission) climate change scenario for We applied SimCast Monthly Means to this data to compare current and future risk estimates. We have low confidence in our estimation of relative humidity – thus seek a collaborator with expertise in this area

Late blight severity for February for current conditions and 2080 a2a climate scenario Peru Bolivia Peru Bolivia

Upshot Using this approach we have created models that can quickly estimate late blight risk over large areas using readily available weather data sets. Although the models underpredict, they are useful for evaluating relative levels of risk.

Outline Upscaling disease forecasting models based on weather Network models at national scale Network model for soybean rust incorporating wind speed and direction

The connectivity of the American agricultural landscape Peg Margosian, Shawn Hutchinson, and Kim With Margosian et al. BioScience 2009 Applying graph theory to assess the national risk of crop pest and disease spread

The potential for movement through landscapes can be modeled by evaluating nodes and the edges that connect them Node and edge characteristics may influence the potential for movement

Maize

Soybean

Wheat

Cotton

Outline Upscaling disease forecasting models based on weather Network models at national scale Network model for soybean rust incorporating wind speed and direction

Dynamic network models of a national epidemic: soybean rust Sweta Sutrave Sweta Sutrave, Caterina Scoglio, Scott Isard, and Karen Garrett

Objectives Develop a framework for estimating edge weights using observed epidemic time series in dynamic network models Apply the model to the spread of soybean rust in the US. Evaluate the estimation framework potential for epidemic modeling.

Data Sets Rust status data: 2005 to 2008, from Dr.Scott Isard. Host density data: 2005 to 2008, from US National Agricultural Statistics Service. Wind data: Wind speed and direction, National Climatic Data Center’s website.

Model SI model which classifies nodes as being susceptible or infected. We consider the centroid of each county of the United states as a node or vertex. We assume that the sentinel plot and the area around it behave in a similar manner and begin by modeling dynamics within a single season.

Edge weight function u ji : Edge-weight between two nodes A function of the following - Distance between the sentinel plots. - Crop density and kudzu density. - Speed and direction of wind w.r.t the link

Example of Epidemic Prediction Soybean rust model realization Green = no rust predicted Red shading = likelihood of infection

Looking toward the future Developing global model for general environmental-response classes of pathogens Seeking a collaborator who can authoritatively address scaling of weather/climate data relevant to pathogens

Sparks et al., in prep Mapping disease risk based on: -Climate -Historical disease distribution -Host availability Rival models for consideration