A key challenge for ecological science is to understand how biodiversity loss is changing ecosystem structure and function at scales that are relevant for policy1. Almost all biodiversity metrics are challenging to disaggregate into animal-mediated ecosystem functions such as pollination, seed and nutrient dispersal, and predation. Here we adopt an ecosystem energetics approach2 as a physically meaningful method of translating animal species composition into a suite of ecosystem functions. Drawing on new datasets that estimate biodiversity intactness and species population densities3–5, we quantify historical changes to energy flows through mammal- and bird-mediated ecosystem functions across sub-Saharan Africa. In total, trophic energy flows have decreased by more than one-third. The pattern of decreasing function varies by historical biome, driven by arboreal birds and primates in forests, terrestrial herbivores in grassy systems, and burrowing mammals in arid systems. Functions performed by megafauna in particular have collapsed outside protected areas. Compared with other biodiversity metrics, an energetics approach highlights the ecological importance of smaller animals and keystone species. The results can help practitioners conserve and restore functionally diverse, energetically intact ecosystems across land uses and biomes. By relating biodiversity intactness to energy and material flows, ecosystem energetics can also advance efforts to integrate animal-driven functions into biosphere and earth system models, helping us to understand possible regional or planetary boundaries6 for biodiversity.
