Mesoamerica, Chocó and the tropical Andes are recognized as biodiversity hotspots where conservation action is urgently needed. Because World Wildlife Fund for Nature (WWF) ecoregions are commonly used as the basis for conservation decisions, an understanding of WWF ecoregions’ environmental heterogeneity and their representation in current protected areas (PAs) is important for identifying priority areas for conservation. Thirteen environmental domain classifications based on 22 climatic and topographical variables and the Shannon diversity index were used to quantify environmental diversity for each WWF ecoregion. The area of each environmental domain and ecoregion was compared with the World Database on Protected Areas 2007. The most environmentally-diverse ecoregions were poorly represented in the PAs and several ecoregions showed low environmental heterogeneity representation inside PAs, for example the Balsas depression, Sierra Madre del Sur and the Chiapas Sierras in Mexico, some sierras in Central America, the Middle Magdalena, inter-Andean valleys, the Eastern Cordillera of Colombia and the Western Moist Forest of Ecuador. Using WWF ecoregions as equivalent units for conservation and management can be misleading, given their environmental heterogeneity; therefore, they have limited usefulness in assessing environmental representation in PAs. An underestimation of environmental heterogeneity representation in PAs can have misleading implications for conservation actions in regions where detailed biological information is lacking. Conservation efforts should focus on the environmental domains and ecoregions showing high environmental heterogeneity that is poorly represented in PAs.
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