Assessment of conservation effectiveness in biodiversity ecological function zones (BEFZs) is important for biodiversity in China. However, a scientific and practical method for effectively comparing biodiversity conservation between different BEFZs is lacking. In this study, a reference condition index that can represent the optimum value of biodiversity in one BEFZ and a conservation effectiveness index that can reflect the effect of conservation measures were developed. Then a method to compare the biodiversity conservation effectiveness between different BEFZs on both temporal and spatial scales was developed. The method was applied to three BEFZs in China—Yili-Tianshan Mountain, San Jiang Plain Wetland and Minshan-Qionglai Mountain—which are located in different geographic environments. The main conclusions are as follows: (1) the reference condition index can reflect differences in the background of conservation capacity among BEFZs examined, allowing comparison of the biodiversity conservation effectiveness between different BEFZs; (2) the conservation effectiveness index is a useful quantitative measure of the biodiversity conservation effectiveness in BEFZs; and (3) application of this method to the three BEFZs indicated that the method can provide a powerful tool for the management of biodiversity conservation in BEFZs at a macroscale in China. Meanwhile, this method can also provide a reference for building strategies for protecting the ecological environments in other countries on a case-by-case basis.
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