Fig. 3: Recovery trajectories of species composition.

Blue and orange dots represent the species composition similarity between cacao or pasture plots (either still in use at time t = 0 or recovering) and old-growth forest plots. Green dots indicate species composition similarity among old-growth forest plots. The blue and orange curves represent the estimated recovery trajectories for cacao and pasture legacy plots according to equation (5) (Methods). Dashed lines indicate curves with λ not significantly different from 0. The light blue and orange curves indicate 95% CIs estimated using a jackknife procedure (Methods) based on n − 1 iterations with n being the number of sampled plots per taxon and legacy (caption of Fig. 2). Note that the y axis has different ranges for different taxa. Boxplots are provided for n = 6 active cacao plots and n = 6 active pasture plots (except 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; given for cacao/pasture plots). 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 1.5× 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.