Previous research has indicated that a substantial portion of native flora and fauna may persist in agricultural mosaics in the Neotropics. However, understanding the relative importance of different habitat factors and management practices at different scales for sustaining this biodiversity has proven somewhat elusive. In addition, most such research has taken place in only a few fairly well-studied landscapes, thus limiting our ability to infer broader patterns that might be transferred to unstudied locales. This study expands the geographic breadth of prior research by evaluating bird and butterfly assemblages in an agricultural landscape in the Rıo Copan watershed of western Honduras. The study also provides a systematic assessment of the relative influence of categorical and continuous habitat variables across a range of scales likely to be significant for birds and butterflies. Overall, we recorded 145 tree species, 139 bird species, and 119 butterfly species. Birds and butterflies displayed contrasting responses to land cover: birds were most strongly associated with dense vegetation in broadleaf forests, forest fallows, shade-grown coffee farms, and live fences, while butterflies were most abundant in live fences, pastures, and riparian forests. Bird assemblages were heavily skewed toward common and non-forest-dependent species, likely due to the young age and high disturbance level of forest plots. In contrast, butterfly assemblages contained a substantial proportion of forest-dependent species, which were observed in forests as well as pastures and live fences. Contrary to expectations, categorical land cover descriptors were more effective at explaining faunal assemblage patterns than continuous habitat descriptors related to vegetation and landscape context. In addition, plot scale (25100 m) habitat features had a greater influence on faunal assemblages than did neighborhood scale (2003000 m) landscape composition or structure, although differences in management intensity at the scale of the entire watershed (520 km) also exerted a strong influence on conservation outcomes.
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