Extended Data Fig. 1: Recovery trajectories of abundance.

Blue and orange dots represent abundance (number of all individuals of each taxon group) in agriculture plots or recovering plots with cacao or pasture land use legacy. Green dots indicate abundance in old-growth forest plots. The blue and orange curves represent the estimated recovery trajectories for cacao and pasture legacy plots according to Eq. 5 (see Methods). Dashed lines indicate curves with λ not significantly different from 0. The light blue and orange curves indicate 95% confidence intervals estimated using a jackknife procedure (see Methods) based on n-1 iterations with n being the number of independent plots sampled per taxon and legacy, with n = 39 for cacao and n = 40 for pasture plots in all cases, except bacteria in 10 cm depth: n = 18/20; bacteria in 50 cm depth: n = 14/14; leaf-litter arthropods: n = 19/19; frogs: n = 23/23; seedlings: n = 24/24; nocturnal insects: n = 39/38 for cacao/pasture plots. Boxplots are provided for n = 6 active cacao plots and n = 6 active pasture plots (except for bacteria in 10 cm depth: n = 3/3; bacteria in 50 cm depth: n = 2/1; leaf-litter arthropods: n = 3/3; frogs: n = 6/6; seedlings: n = 4/4 for cacao/pasture). Boxplots for old-growth (OG) forest plots are based on n = 17 plots (except for bacteria in 10 cm depth: n = 8; bacteria in 50 cm depth: n = 6; leaf-litter arthropods: n = 8; frogs: n = 8; seedlings: n = 9). Orange line in boxplots shows median, boxes show data in 25th and 75th quartile and whiskers indicate 1.5x the interquartile range. Silhouettes of saproxylic beetle, bee, moth, dung beetle, nocturnal insect, ant, bird and ground bird were created by G. Brehm under a CC BY-SA 4.0 licence. The following silhouettes were reproduced from PhyloPic (https://www.phylopic.org/): frog and ground mammal, created by M. Michaud under a CC0 1.0 Universal Public Domain licence; bat, created by Y. Wong under a CC0 1.0 Universal Public Domain licence; frugivorous bird, created by E. Price under a CC BY 4.0 licence; seedling, created by M. Hofstetter under a CC BY 3.0 licence; tree, created by T. M. Keesey under a CC0 1.0 Universal Public Domain licence; leaf-litter arthropod, created by B. Lang under a CC BY 3.0 licence; bacteria 10-cm depth and bacteria 50-cm depth, created by L. Simons under a CC0 1.0 Universal Public Domain licence.