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    Species Distribution Model Class 01: Documentation

    Models available through the Modeling section of the FoTX website are considered the first class of models available. Future derivations and alternate model versions will be indicated as subsequent classes. Below are specific methods of construction for model class 01.

    Model Class 01

    Suggested Interpretation

    Species Distribution Models (SDMs) predict the potential geographic distribution of a species based on occurrence points of a species and predictive environmental variables; they are sometimes interpreted as approximating the ecological niche for that species (Guisan & Thuiller 2005). For the last decade SDMs have often been constructed using machine–learning algorithms that use the co-occurrence of species occurrence points and environmental data to predict the environmental conditions in which a species is likely to occur. These are then projected back to geographical space to obtain the potential distribution. When constraints on dispersal due to geography or behavior (Margules & Sarkar 2007) are taken into account in model development, the realized distributions are predicted (Pawar et al. 2007).

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    This technique converts disparate occurrence records into continuous probabilities of occurrence that predict habitat suitability. SDMs are therefore more amenable to diverse mathematical analyses as performed in geographical information systems than are the raw occurrence data (Guisan & Thuiller 2005), which typically lack proper temporal and spatial representation for direct use in most comparative or trend analyses commonly used for assessing changes in biological communities. Through the incorporation of these disparate and temporally diverse historical occurrence data with environmental variables accounting for only broad-scale physiological and biogeographical constraints, we propose that SDMs constructed as described here provide a robust and quantifiable estimation of historical habitat suitability (Labay et al. 2011).

    Some things to keep in mind while using and viewing models:

    • The models do not directly incorporate anthropogenic influence such as dams or land use. Model results should be carefully interpreted with this in mind; for example, modeling results for a species found primarily in lotic habitat that indicate high probabilities within a reservoir should be viewed as potential occurrence probability in the absence of reservoir conditions.
    • The models do not directly incorporate biotic interactions.
    • The model images (jpgs) available through this site (here) only display the occurrence probability range of 0.5 to 1, which generally indicates high probability of occurrence. To view the full range of probabilities, the ascii file must be downloaded, incorporated into a GIS and symbolized as desired. It must be noted that the symbology (e.g., range of values shown, whether displayed as categories or stretched, color scale) used to view the models has a large influence on interpretation. We display only high probabilities (0.5 - 1) in an effort to highlight the modeling technique's capabilities in identifying primary suitable habitat.

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    Example species distribution model; Notropis oxyrhynchus (Sharpnose Shiner) in the upper Brazos River.

    Model Construction

    The general construction protocol that was used for models has been previously published (Sarkar et al. 2010, Labay et al. 2011), so the description here will be cursory. A wide variety of machine–learning algorithms have been used for SDM construction (reviewed in Elith et al. 2006). This project used a maximum entropy algorithm incorporated in the Maxent software package (Phillips & Dudik 2008, Phillips et al. 2006) because it directly provides probabilistic output (unlike the genetic algorithm of GARP (Stockwell 1999)) that can be used without further treatment for subsequent analyses, and because a variety of recent studies have concluded that its performance is superior to those of other methods (Elith et al. 2006, Wisz et al. 2008). Maxent was parameterized following published recommendations (Phillips et al. 2006), with models replicated 100 times withholding randomly in each replicate 40% of localities as ‘test’ records, with the remaining 60% serving as model ‘training’ records. Model performance was evaluated using a (threshold-independent) receiver operating characteristic (ROC) analysis and 11 internal binomial analyses of ‘training’ and ‘test’ occurrence omission. The ROC analysis characterizes model performance at all possible thresholds using the area under the curve (AUC), a measure of model performance independent of any threshold (Hanley & McNeil 1982). An optimal model with perfect discrimination would have an AUC of 1 while a model that predicted species occurrences at random would have an AUC of 0.5 (Hanley & McNeil 1982).

    Biological and Environmental Data

    Occurrence data input consists of FoTX records. Records with > one km potential georeferencing error (radius, see Georeferencing and Geographic Units) were excluded to assure input occurrences closely corresponded in spatial resolution to environmental layers used in modeling. This spatial error threshold of one km approximately matches the grid cell resolution of 30 arc-seconds (which approximates one km at the Equator), but is slightly larger than the longitudinal boundary of the average cell size (0.73 km2) due to geographic projection at the latitude of Texas. However, the maximum entropy algorithm used for analysis (see Model Construction above) has been shown not to be affected by spatial errors in occurrence datasets with standard deviations up to five km (Hernandez et al. 2006, Wisz et al. 2008). Occurrence records before 1950 were similarly excluded so that occurrence data were temporally congruent with climatic variables used (see Table 1 below). Finally, since model performance stabilizes with respect to accuracy of prediction at about 10 records when using the maximum entropy model construction algorithm (Phillips & Dudik 2008, Phillips et al. 2006), models were produced only for those species for which we had a minimum of 10 occurrences corresponding to at least 10 unique cells on the environmental layer grids.

    Table 1. Environmental Layers used in models

    Layer Category Layer Type Description Source
    Topological Continuous aspect 1km DEM
    Topological Continuous slope 1km DEM
    Topological Continuous compound topological index (ln(acc.flow/tan[slope])) 1km DEM
    Topological Continuous altitude 1km DEM
    Climate Continuous annual mean temperature Wordclim variable 1
    Climate Continuous mean diurnal range (mean of monthly (max temp - min temp)) Wordclim variable 2
    Climate Continuous isothermality (P2/P7)(*100) Wordclim variable 3
    Climate Continuous (temperature seasonality (sd *100) Wordclim variable 4
    Climate Continuous max temperature of warmest month Wordclim variable 5
    Climate Continuous min temperature of coldest month Wordclim variable 6
    Climate Continuous temperature annual range (P5-P6) Wordclim variable 7
    Climate Continuous annual precipitation Wordclim variable 12
    Climate Continuous precipitation of wettest month Wordclim variable 13
    Climate Continuous precipitation of driest month Wordclim variable 14
    Climate Continuous precipitation seasonality (coefficient of variation) Wordclim variable 15
    Climate Continuous precipitation of wettest quarter Wordclim variable 16
    Climate Continuous precipitation of driest quarter Wordclim variable 17
    Climate Continuous precipitation of warmest quarter Wordclim variable 18
    Climate Continuous precipitation of coldest quarter Wordclim variable 19
    Geographic Categorical major river basins Texas Water Development Board
    Geographic Categorical 8-digit hydrologic unit code (HUC) Texas Water Development Board
    Hydrologic Continuous cumulative drainage National Hydrology Dataset plus
    Hydrologic Continuous mean annual flow National Hydrology Dataset plus
    Hydrologic Continuous mean annual velocity National Hydrology Dataset plus

    References

    Guisan A, Thuiller W (2005) Predicting species distribution: offering more than simple habitat models. Ecology Letters 8: 993-1009.

    Elith J, Graham CH, Anderson RP, Dudık M, Ferrier S, et al., others (2006) Novel methods improve prediction of species’ distributions from occurrence data. Ecography 29: 129–151.

    Margules C, Sarkar S (2007) Systematic conservation planning. Systematic conservation planning.

    Hernandez PA, Graham CH, Master LL, Albert DL (2006) The effect of sample size and species characteristics on performance of different species distribution modeling methods. Ecography 29: 773–785.

    Pawar S, Koo MS, Kelley C, Ahmed MF, Chaudhuri S, et al. (2007) Conservation assessment and prioritization of areas in Northeast India: priorities for amphibians and reptiles. Biological Conservation 136: 346–361.

    Labay, B.J., A.E. Cohen, B. Sissel, D.A. Hendrickson, F.D. Martin, and S. Sarkar., 2011. Assessing historical fish community composition using surveys, historical collection data, and species distribution models. PLoS ONE 6, e25145.

    Illoldi-Rangel P, Fuller T, Linaje M, Pappas C, Sánchez-Cordero V, et al. (2008) Solving the maximum representation problem to prioritize areas for the conservation of terrestrial mammals at risk in Oaxaca. Diversity and distributions 14: 493–508.

    González C, Wang O, Strutz SE, González-Salazar C, Sánchez-Cordero V, et al. (2010) Climate Change and Risk of Leishmaniasis in North America: Predictions from Ecological Niche Models of Vector and Reservoir Species.

    Wisz MS, Hijmans RJ, Li J, Peterson AT, Graham CH, et al. (2008) Effects of sample size on the performance of species distribution models. Diversity and Distributions 14: 763–773.

    Sarkar S, Sánchez-Cordero V, Londoño M, Fuller T (2009) Systematic conservation assessment for the Mesoamerica, Chocó, and Tropical Andes biodiversity hotspots: a preliminary analysis. Biodiversity and Conservation 18: 1793-1828.

    Phillips SJ, Dudík M (2008) Modeling of species distributions with Maxent: new extensions and a comprehensive evaluation. Ecography 31: 161–175.

    Phillips SJ, Anderson RP, Schapire RE (2006) Maximum entropy modeling of species geographic distributions. Ecological Modelling 190: 231–259.

    Stockwell D (1999) The GARP modelling system: problems and solutions to automated spatial prediction. International Journal of Geographical Information Science 13: 143–158.

    Hanley JA, McNeil BJ (1982) The meaning and use of the area under a receiver operating characteristic (ROC) curve. Radiology 143: 29.

    Sarkar S, Strutz SE, Frank DM, Rivaldi C, Sissel B, et al. (2010) Chagas Disease Risk in Texas. PLoS Neglected Tropical Diseases 4: e836. Accessed 8 October 2010.