Effect of species rarity on the accuracy of species distribution models for reptiles and amphibians in southern California

Janet Franklin, Katherine E. Wejnert, Stacie A. Hathaway, Carlton J. Rochester, Robert N. Fisher

Research output: Contribution to journalArticlepeer-review

106 Scopus citations


Aim: Several studies have found that more accurate predictive models of species' occurrences can be developed for rarer species; however, one recent study found the relationship between range size and model performance to be an artefact of sample prevalence, that is, the proportion of presence versus absence observations in the data used to train the model. We examined the effect of model type, species rarity class, species' survey frequency, detectability and manipulated sample prevalence on the accuracy of distribution models developed for 30 reptile and amphibian species. Location: Coastal southern California, USA. Methods: Classification trees, generalized additive models and generalized linear models were developed using species presence and absence data from 420 locations. Model performance was measured using sensitivity, specificity and the area under the curve (AUC) of the receiver-operating characteristic (ROC) plot based on twofold cross-validation, or on bootstrapping. Predictors included climate, terrain, soil and vegetation variables. Species were assigned to rarity classes by experts. The data were sampled to generate subsets with varying ratios of presences and absences to test for the effect of sample prevalence. Join count statistics were used to characterize spatial dependence in the prediction errors. Results: Species in classes with higher rarity were more accurately predicted than common species, and this effect was independent of sample prevalence. Although positive spatial autocorrelation remained in the prediction errors, it was weaker than was observed in the species occurrence data. The differences in accuracy among model types were slight. Main conclusions: Using a variety of modelling methods, more accurate species distribution models were developed for rarer than for more common species. This was presumably because it is difficult to discriminate suitable from unsuitable habitat for habitat generalists, and not as an artefact of the effect of sample prevalence on model estimation.

Original languageEnglish (US)
Pages (from-to)167-177
Number of pages11
JournalDiversity and Distributions
Issue number1
StatePublished - Jan 1 2009


  • Classification tree
  • Generalized additive model
  • Generalized linear model
  • Herpetofauna
  • Prevalence
  • Rarity

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics


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