Research Article |
Corresponding author: Roger Magarey ( rdmagare@ncsu.edu ) Academic editor: Richard Shaw
© 2015 Seung Cheon Hong, Roger Magarey, Daniel M. Borchert, Roger I. Vargas, Steven Souder.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Hong SC, Magarey RD, Borchert DM, Vargas RI, Souder SK (2015) Site-specific temporal and spatial validation of a generic plant pest forecast system with observations of Bactrocera dorsalis (oriental fruit fly). NeoBiota 27: 37-67. doi: 10.3897/neobiota.27.5177
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This study introduces a simple generic model, the Generic Pest Forecast System (GPFS), for simulating the relative populations of non-indigenous arthropod pests in space and time. The model was designed to calculate the population index or relative population using hourly weather data as influenced by developmental rate, high and low temperature mortalities and wet soil moisture mortality. Each module contains biological parameters derived from controlled experiments. The hourly weather data used for the model inputs were obtained from the National Center of Environmental Prediction Climate Forecast System Reanalysis (NCEP-CFSR) at a 38 km spatial resolution. A combination of spatial and site-specific temporal data was used to validate the GPFS models. The oriental fruit fly, Bactrocera dorsalis (Hendel), was selected as a case study for this research because it is climatically driven and a major pest of fruit production. Results from the GPFS model were compared with field B. dorsalis survey data in three locations: 1) Bangalore, India; 2) Hawaii, USA; and 3) Wuhan, China. The GPFS captured the initial outbreaks and major population peaks of B. dorsalis reasonably well, although agreement varied between sites. An index of agreement test indicated that GPFS model simulations matched with field B. dorsalis observation data with a range between 0.50 and 0.94 (1.0 as a perfect match). Of the three locations, Wuhan showed the highest match between the observed and simulated B. dorsalis populations, with indices of agreement of 0.85. The site-specific temporal comparisons implied that the GPFS model is informative for prediction of relative abundance. Spatial results from the GPFS model were also compared with 161 published observations of B. dorsalis distribution, mostly from East Asia. Since parameters for pupal overwintering and survival were unknown from the literature, these were inferred from the distribution data. The study showed that GPFS has promise for estimating suitable areas for B. dorsalis establishment and potentially other non-indigenous pests. It is concluded that calibrating prediction models with both spatial and site-specific temporal data may provide more robust and reliable results than validations with either data set alone.
Risk analysis, invasive species, modeling, climate
The increase in international trade has exacerbated the problem of non-indigenous species moving between continents (
In addition to the need for potential distribution maps, other phytosanitary applications of weather or climate-based models include predictions of: i) the frequency of years favorable to crop losses or epidemics (
In order to address this problem, there is benefit in creating a simple generic model framework that is a compromise between ease of use and capabilities for additional phytosanitary and pest management applications. In this study, we introduce the Generic Pest Forecast System (GPFS), for simulating relative pest populations in space and time. The GPFS model presented in this study has the following components: i) Developmental rate estimated from cardinal temperatures (
The oriental fruit fly (OFF) (Bactrocera dorsalis) was chosen as a study pest to test the GPFS model because there is an extensive amount of literature data available for model development and validation. B. dorsalis lays eggs below the skin of the host fruit and develops from egg to adult in as little as 17 days but development can be substantially delayed under cooler conditions (
In summary, the objective of this study is to introduce the GPFS model and validate it for B. dorsalis using site-specific observations and distribution data. In addition, we wished to use the GPFS model to investigate the potential for establishment in the United States. No information collected on site was used to parameterize the model with the exception of food availability. In addition, no local weather data were used as input into the models to investigate the potential for gridded global hourly weather data to be used for historical pest predictions.
Pest observations. Site-specific temporal pest observations were obtained from three studies in which adult oriental fruit fly were trapped (
Comparison of observed (straight line with markers) and GPFS predicted (dashed line without markers) population of the adult oriental fruit fly, Bactrocera dorsalis, at three locations: A Bangalore, India B Hawaii, USA; and C Wuhan, China. Raw data of B. dorsalis field observations were converted to a population index (range: 0 to 1) to facilitate the comparisons
Locations of case studies.
Reference | Location | Latitude | Longitude | Data period |
---|---|---|---|---|
Hawaii Island, HI, USA |
19.42942 (19°25'45.912") |
-154.882 (-154°52'55.2") |
2006–2008 | |
Wuhan, China |
30.42915 (30°25'44.9394") |
114.3639 (114°21'50.04") |
2007–2009 | |
Bangalore, India |
12.93686 (12°56'12.6954") |
77.62111 (77°37'15.996") |
1999–2002 |
The Hawaii data were obtained from the authors whereas the observations for Bangalore and Wuhan were extracted directly from figures in the papers. Data extraction was conducted using a spreadsheet program (Excel 2010, Microsoft, Redmond, WA). The figure from the paper was scanned and copied into the spreadsheet and overlaid with a finer scale transparent grid-shaped graph with the same range of x- and y-axes to improve the ease of reading the data.
In addition to the site-specific observations, pest distribution data were also obtained from the literature (Suppl. material
GPFS model. The GPFS model is designed as a simple generic tool for pest prediction for both arthropods and pathogens. The model is designed to run from hourly weather data inputs and to make predictions of the influence of weather on the relative pest population (population index) and phenological stages. For oriental fruit fly, GPFS only utilizes modules for development rate, high and cold temperature mortality, wet soil moisture mortality, and population index (Table
Parameters and abbreviation used in the GPFS model for oriental fruit fly.
Symbol | Parameter name | Value | Reference |
---|---|---|---|
Development rate | |||
Ambient temperature, °C | |||
Minimum temperature | 13.3 | ||
Low optimum temperature | 24 | ||
High optimum temperature | 34 | ||
Maximum temperature | 41 | ||
Low temperature mortality | |||
Threshold | 13.3 |
|
|
Constant for |
1101.7 | ||
Coefficient for |
-49892 | ||
Coefficient for |
-162.9 | ||
High temperature mortality | |||
Threshold | 33 |
|
|
Constant for |
25.9595 | ||
Coefficient of degree one for |
-0.4959 | ||
Coefficient of degree two for |
0 | ||
Wet soil moisture mortality |
|
||
Constant for |
50.4 |
|
|
Proportion of population in soil inhabiting life stages for |
0.36 | ||
Population index | |||
Reciprocal of number of hours required to reach maximum population for |
0.008 | ||
Generations to reach maximum population under optimum conditions for |
4 | ||
Hours to complete one generation under optimum conditions for |
30.4 d | ||
Extinction threshold | 0, 0.0001 |
Developmental rate. The hourly developmental rate (
If
If
If
If
where
Low temperature mortality. The hourly low temperature mortality was estimated from an exponential equation (
where
Puparia of B. dorsalis can survive freezing conditions and overwinter at low levels in China (
High temperature mortality. The hourly high temperature mortality is given by a polynomial equation with parameters
where
Wet soil moisture mortality. Excessive soil moisture i.e. flooding can reduce the populations of some fruit flies including B. dorsalis (
where
Population index. The population index is a measure of relative population as influenced by weather conditions and is a function of the developmental rate, the mortality rates and the population index in the current hour (
where
where
Host fruit availability. The period when host fruits are available is an important factor in determining B. dorsalis population increase (
Pupal cold mortality. There is evidence to suggest that pupae survive lower cold temperatures than larvae. In Wuhan, pupae were shown to successfully overwinter although survival was dependent upon the time of year when pupae where placed in the soil (
Dry exclusion. In addition to cold exclusion, a dry exclusion map was generated to mask dry/desert areas from the global distribution map using the ArcGIS. If annual precipitation was less than 254 mm, then the areas were defined as arid and unsuitable for oriental fruit fly habitats. This limit is commonly defined as limit for aridity (
Model runs. The hourly weather data used for the model comparison and the creation of maps were produced by the National Center of Environmental Prediction Climate Forecast System Reanalysis (NCEP-CFSR) at a 38 km spatial resolution (
Site-specific temporal comparisons. Several accuracy measurements were calculated to determine how well GPFS predictions fit the observed population changes at the study locations. To facilitate comparisons with the predicted populations, the trap catch data were scaled between 0 and 1. The scaled values were calculated by dividing each observation by the 99th percentile of data from all years at each location. The statistical tests included mean error (
The index of agreement (
Spatial distribution comparisons. Model accuracy measures, modeled prevalence and sensitivity, were estimated using the final GPFS risk map. Raster cell values were extracted using ArcGIS. No data values (i.e., -9999), mainly assigned to oceans, were excluded from the analysis. The modeled prevalence is the proportion of raster cells classified as suitable. To estimate prevalence, the least presence threshold was used to classify raster cells as suitable or unsuitable. In species distribution modeling, the lowest presence threshold (LPT) is commonly defined as the predicted value of lowest training observation (
Site-specific temporal validations. At the China and India sites, the GPFS model populations went extinct due to cold and/or heat mortality with the extinction threshold set at 0.0001. Since the parameters for pupal cold mortality were unknown, the cold mortality threshold was not able to be estimated. Instead the model was run with an extinction threshold set to 0. For high temperature mortality, a correction was made to the threshold,
The GPFS population predictions at Bangalore, India matched relatively well with the observed population (Figure
For Hawaii, USA, the GPFS model simulated population dynamics relatively poorly compared to the other two locations (Figure
The GPFS predictions matched the observed oriental fruit fly population comparatively well in Wuhan (Figure
Spatial distribution validations. The cold and dry exclusions eliminated large portions of Northern Europe, Asia and America and desert regions of Africa and Asia (Figure
Cold and dry exclusions based on one or more occurrence of minimum temperatures of -10 °C (A) and annual precipitation less than 254 mm (B).
GPFS model prediction of potential global population index of oriental fruit fly, Bactrocera dorsalis (including observations of B. invadens), based on most recent 10 years (2003–2012) weather data from National Centers for Environmental Prediction – Climate Forecast System Reanalysis (NCEP-CFSR) at a 38 km resolution. The predictions are on a scale of 0-1 and do not account for the presence or absence of suitable hosts. The map is the highest population index of any month averaged over ten years with initial populations in each year being independent. The map also includes the cold and dry exclusions from Figure
GPFS model prediction for potential population index of oriental fruit fly, Bactrocera dorsalis (including observations of Bactrocera invadens) in A) Africa and B) Asia based on most recent 10 years (2003-2012) weather data from National Centers for Environmental Prediction – Climate Forecast System Reanalysis (NCEP-CFSR) at a 38 km resolution. Locations where B. dorsalis or B. invadens has been observed in the literature are shown as black dots. The predictions are on a scale of 0–1 and do not account for the presence or absence of suitable hosts. The map is the highest population index of any month averaged over ten years with initial populations in each year being independent. The maps also include the cold and dry exclusions from Figure
GPFS predictions of potential population index of oriental fruit fly, Bactrocera dorsalis, in the United States based on A. Real-Time Mesoscale Analysis weather data (2007–2012) with a 5 km resolution. The predictions are on a scale of 0-1 and do not account for the presence or absence of suitable hosts. The map is the final population index in December 2012 that resulted from the simulation of population change beginning with an initial population in January 2007. The map also includes the cold exclusion from Figure
In this study, we introduced a new pest prediction model, the Generic Pest Forecast System (GPFS) and validated it against site-specific observations and spatial distribution. Importantly, no site-specific information was used to parameterize the model, with the exception of host fruit availability used in both models. In addition, no local weather data were used as inputs into the models to investigate the potential for a gridded global weather database to be used for historical pest predictions.
The goal of the team developing the GPFS model was to create a simple weather-based pest model that would have application for predicting potential distribution. In addition, the model was conceived also to have application to other risk based questions such as time of pest emergence and potential impacts in managed crop systems for both indigenous and non-indigenous pests. This additional information may enable decision makers to better understand the consequences of a newly established pest. One of the precedents for the GPFS model is weather-based pest forecast models which are routinely used in pest forecasting (
The GPFS model appears to have a number of useful features. It has a relatively simple formulation, few parameters and can be used to investigate population changes during the seasons as well as produce overall suitability maps. The simplicity of the model makes it easy to adapt to a new pest, assuming these parameters are available or can be determined from a closely related pest (the latter which would increase the uncertainties associated with the simulation). Adaptability of a model to a new species is important since phytosanitary agencies must often develop risk assessments at short notice.
Although GPFS is a generic model, it is still not as flexible as the generic pest simulation model in the CLIMEX family, DYMEX (
The ease of parameterization is another key consideration for the use of a pest model. One limitation for the modeling of exotic species is the lack of published experimental data to parameterize the model. A useful feature of CLIMEX-CL is that parameter values can be estimated from the experimental literature, from the distribution data or as recommended using both in combination. A disadvantage of CLIMEX-CL is the weekly model time step, which can make the parameterization process more difficult since some experimental data such as mortality may have observations made at an hourly time step. The GPFS requires biological parameters, including information on development rate and mortalities due to heat, cold, and wet soil moisture. Consequently, it would not be possible to make a GPFS model for some pest species at present. One option is to parameterize the model from a related species, which increases the level of uncertainty associated with the modeling process. One possible solution is to use the distribution data to fit the parameters using an automated process. Such a method has been employed to fit a mechanistic model to predict forest species distributions (Higgins, Mullen et al. 2011).
Accuracy is another key consideration for evaluating models. The results from this study need to be kept in context with the limited amount of site-specific information (including weather data) that was used to inform the model. Information on other factors such as pest migration, food quantity, species competition and/or existing natural enemies, and management factors were not included. A more sophisticated simulation model may be able to have superior results using this kind of site-specific variables. When these kinds of site-specific parameters are included in a simulation model it is prudent to check the model is portable to other sites (
The GPFS model might also be improved by adding modules to account for the population of individual pest stages. This would allow it to be used for other applications for example predicting the timing of a particular phenological stage for scheduling trapping or scouting applications. Another module that could be improved is the food supply model, which was highly simplistic and also relied on a monthly time-step. In some cases the phenological susceptibility of a host may be more precisely estimated from an observed biofix and a degree day model. In phytosanitary risk analysis, there is sometimes a need to simulate potential impacts and spread of pest in order to assess mitigation or response options (
One limitation with process models that require hourly weather inputs has been the lack of reliable, consistent, and dense global historical weather station data for use in validating models against published historical data of pest populations. This situation changed in 2010 when the National Center of Environmental Prediction (NCEP) introduced the Climate Forecast System Reanalysis (CFSR) (
Site-specific temporal observations can play a useful role for model validation by providing an additional level of confidence that the model is providing realistic results. These types of validations may not be possible or can be difficult for some species due to pest and host phenology. That is that the number of individuals caught in a trap is a function of pest or host phenology and not just pest abundance. In this version of the GPFS model, we ignored pest phenology although it is incorporated into a newer version (Magarey unpublished data). However, including pest stages into the model greatly adds to complexity including the required parameters. In addition, for a pest with many generations and overlapping stages such as OFF it may not contribute much additional information. For example, including a stage specific model into the GPFS did not improve prediction accuracy for light brown apple moth (Epiphyas postvittana) (Hong and Magarey, unpublished data). The prediction of pest population index at specific sites can be revealing. For example, it might help identify sites where a pest is not expected to overwinter even if the summer climate is suitable. This is important since some distribution (spatial) records may be unreliable or the record may have corresponded with a rare or ephemeral observation of the species (
One important factor for site-specific validation is choosing representative locations. For example, predicted population indexes of B. dorsalis oriental fruit fly population in Wuhan, China were relatively superior compared to the two other locations (Figures
Model accuracy measures between observation and predictions of GPFS.
Bangalore, India | Hawaii, USA | Wuhan, China | |
---|---|---|---|
Observation | |||
N | 50 | 24 | 73 |
Mean | 0.32 | 0.44 | 0.12 |
Standard deviation | 1.75 | 1.18 | 1.77 |
GPFS | |||
Host/food availability | Jan–Dec | Jan–Dec | Jul–Dec |
Prediction mean | 0.40 | 0.85 | 0.13 |
Mean absolute error (MAE) (>= 0) | 0.23 | 0.41 | 0.08 |
Mean error (ME) (-Inf to +Inf) | -0.08 | -0.41 | -0.02 |
Mean square error (MSE) (>= 0) | 0.08 | 0.20 | 0.02 |
Index of agreement (d) | 0.58 | 0.50 | 0.85 |
Utility of spatial distribution validation. Since site-specific temporal validation often includes relatively few locations, spatial validation is critical. Spatial validation of the GPFS showed the utility of the GPFS model but also the need for the cold exclusion layer to prevent over-prediction in higher latitudes due to the lack of experimental data to parameterize the low temperature mortality. This shows that the combination of both complex (i.e., GPFS) and simple (i.e., exclusion) modeling techniques may be useful for defining the non-suitable areas (Figures
The GPFS predicted population can also be compared to a description of B. dorsalis populations found in an environmental chamber study in which temperature and humidity were maintained at levels representative of six U.S. cities (
Ideally, host abundance and phenology are also required for prediction of the population index (or relative abundance), but this information is very rarely available, especially on global scales. We investigated the use of global crop maps (http://capra.eppo.org/maps.php) (
The GPFS model was introduced as a simple weather-based model for predicting potential distribution. The model was shown to be able to simulate relative pest populations in some locations, which could have potential to estimate potential impacts of a pest when combined with other biological and management variables. The model requires literature data to estimate model parameters and as such will not be usable for all species unless alternative methods of parameterization are added in improved versions of the GPFS model. This study also shows the potential for improving pest risk models by conducting spatial and site-specific temporal validations against published observations. Although these kinds of temporal validations will not be possible for every species, they can provide insight into the spatial domain by suggesting why a species might not persist or provide an indication of the risk. It can also be helpful for calibrating model parameter values. Importantly, the arrival of high quality global gridded historical weather databases can make site-specific temporal validations from published observations easier for hourly weather-based models. The downloading and archival of gridded data sets are a large undertaking requiring considerable resources. However, smaller organizations have the opportunity to purchase hourly data sets from commercial weather providers for specific sites of interest. Ultimately as computer power improves these costs will decrease. Additionally, the model could be run in real time to support surveillance activities given the concern about low level or cryptic invasions escaping pest detection programs (
We appreciate ArcGIS technical support from Yu Takeuchi and David Christie at the Center of Integrated Pest Management in North Carolina State University. ZedX, Inc. (Bellefonte, PA), a commercial information technology (IT) company, prepared the NCEP-RTMA and NCEP-CFSR hourly weather data sets for specific years and locations in the United States and globally. Special thanks to Nicholas Manoukis, USDA-ARS and Ashley Franklin USDA-APHIS-PPQ-CPHST Raleigh for critical comments and manuscript editing, respectively. We thank Marc De Meyer, Royal Museum for Central Africa, Tervuren, Belgium for Bactrocera invadens data. The authors also thank Darren Kriticos, CSIRO, Australia, Richard Baker, DEFRA, UK. Gericke Cook, USDA-APHIS-PPQ-CPHST Fort Collins and two anonymous reviewers for their valuable comments on the manuscript. This project was supported by the USDA-APHIS-PPQ Pest Detection program. This material was made possible, in part, by a Cooperative Agreement from the United States Department of Agriculture’s Animal and Plant Health Inspection Service (APHIS). It may not necessarily express APHIS’ views.