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Species distribution models: Administrative boundary centroid occurrences require careful interpretation

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  • Barker, Justin R.
  • MacIsaac, Hugh J.

Abstract

Describing and understanding species distributions and the factors driving them is fundamental to ecology and biogeography. Species distribution models (SDMs) allow one to investigate objectives of identifying ecologically important factors to the distribution, estimating species-environment responses, predicting the probability of species occurrence, and predicting species presence or absence. Mosquito occurrence records used in SDMs are often imprecise and represented as a centroid of a geopolitical/administrative boundary. Using a virtual species, we investigated the effect of centroids on SDMs and determined which methodology was best suited to provide accurate and applicable conclusions for each of the objectives. We compared 12 distinct algorithms, four levels of pseudo-absences, and three predictor sets to determine the optimal SDM methodology for each objective. The ability of methodology considerations to account for the effects of centroids varied for each objective. Ecologically important predictors were misidentified but could be best approximated by generalized additive models with 10,000 pseudo-absences. Response curves only captured the expected positive or negative trends. Centroids limited SDMs’ ability to differentiate expected probabilities, resulting in overprediction of high probability areas. Response curves and occurrence probabilities were best estimated by generalized boosting regression models. Species presence was largely over-estimated within southern regions, but underpredicted in northern regions, and was best estimated by weighted mean ensembles. Overall, generalized boosting regression methods and (weighted) mean ensembles provided the most reliable conclusions across all four objectives. Further, the most reliable conclusions were consistently observed with equal pseudo-absences when considered with the removal of low-contributing predictors, except for predictor identification.

Suggested Citation

  • Barker, Justin R. & MacIsaac, Hugh J., 2022. "Species distribution models: Administrative boundary centroid occurrences require careful interpretation," Ecological Modelling, Elsevier, vol. 472(C).
  • Handle: RePEc:eee:ecomod:v:472:y:2022:i:c:s0304380022002101
    DOI: 10.1016/j.ecolmodel.2022.110107
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    References listed on IDEAS

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    1. Boria, Robert A. & Blois, Jessica L., 2018. "The effect of large sample sizes on ecological niche models: Analysis using a North American rodent, Peromyscus maniculatus," Ecological Modelling, Elsevier, vol. 386(C), pages 83-88.
    2. Ryan A. Peterson & Joseph E. Cavanaugh, 2020. "Ordered quantile normalization: a semiparametric transformation built for the cross-validation era," Journal of Applied Statistics, Taylor & Francis Journals, vol. 47(13-15), pages 2312-2327, November.
    3. Hsu, Wu-ron & Murphy, Allan H., 1986. "The attributes diagram A geometrical framework for assessing the quality of probability forecasts," International Journal of Forecasting, Elsevier, vol. 2(3), pages 285-293.
    4. Santika, Truly & Hutchinson, Michael F., 2009. "The effect of species response form on species distribution model prediction and inference," Ecological Modelling, Elsevier, vol. 220(19), pages 2365-2379.
    5. Johnson, Chris J. & Gillingham, Michael P., 2008. "Sensitivity of species-distribution models to error, bias, and model design: An application to resource selection functions for woodland caribou," Ecological Modelling, Elsevier, vol. 213(2), pages 143-155.
    6. Grimmett, Liam & Whitsed, Rachel & Horta, Ana, 2020. "Presence-only species distribution models are sensitive to sample prevalence: Evaluating models using spatial prediction stability and accuracy metrics," Ecological Modelling, Elsevier, vol. 431(C).
    7. Barve, Narayani & Barve, Vijay & Jiménez-Valverde, Alberto & Lira-Noriega, Andrés & Maher, Sean P. & Peterson, A. Townsend & Soberón, Jorge & Villalobos, Fabricio, 2011. "The crucial role of the accessible area in ecological niche modeling and species distribution modeling," Ecological Modelling, Elsevier, vol. 222(11), pages 1810-1819.
    8. Yu, Hao & Cooper, Arthur R. & Infante, Dana M., 2020. "Improving species distribution model predictive accuracy using species abundance: Application with boosted regression trees," Ecological Modelling, Elsevier, vol. 432(C).
    9. Murphy, Allan H. & Winkler, Robert L., 1992. "Diagnostic verification of probability forecasts," International Journal of Forecasting, Elsevier, vol. 7(4), pages 435-455, March.
    10. Jesús Aguirre-Gutiérrez & Luísa G Carvalheiro & Chiara Polce & E Emiel van Loon & Niels Raes & Menno Reemer & Jacobus C Biesmeijer, 2013. "Fit-for-Purpose: Species Distribution Model Performance Depends on Evaluation Criteria – Dutch Hoverflies as a Case Study," PLOS ONE, Public Library of Science, vol. 8(5), pages 1-11, May.
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    1. Benkendorf, Donald J. & Schwartz, Samuel D. & Cutler, D. Richard & Hawkins, Charles P., 2023. "Correcting for the effects of class imbalance improves the performance of machine-learning based species distribution models," Ecological Modelling, Elsevier, vol. 483(C).

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