ABSTRACT
Diversified smallholder agriculture is the main land-use affecting the western Amazon, home to the world’s richest terrestrial biota, yet the decades-long debate over the conservation value of smallholder agriculture relies almost entirely on data collected in less biodiverse settings. Habitat specialization in hyperdiverse Amazonian assemblages might predispose species towards sensitivity to habitat degradation, and degradation might homogenize distinctive communities in different forest-types. We comprehensively surveyed birds and trees in primary forest and smallholder mosaics spanning major edaphic and hydrological gradients in northern Peru to quantify how Amazonian biodiversity responds to smallholder agriculture. We found that smallholder agriculture devastates tree richness and reduces bird richness via beta-diversity losses across distinct forest-types. Many of the tree and bird species that persist in disturbed sites do so at greatly reduced densities. Their persistence is associated with extensive forest cover at disturbed sites, including local secondary forest and nearby primary forest, suggesting that our results represent a best-case scenario for Amazonian agricultural biodiversity. Thus, regional conservation efforts should focus on preserving primary forest. For birds, this conclusion emerges only after extensive sampling across multiple forest types, suggesting that existing literature’s focus on upland (terra firme) forest masks the true biodiversity cost of slash-and-burn agriculture.