Disparate recovery of phylogenetic diversity across taxa during tropical rainforest regeneration
Data files
Jan 20, 2026 version files 2.35 MB
-
12862_2016_822_MOESM10_ESM.tree
38.26 KB
-
15K_FBD_crown_mcc.tre
705.50 KB
-
ant_list.csv
3.71 KB
-
ant_matrix.csv
41.93 KB
-
bat_list.csv
1.78 KB
-
bat_matrix.csv
6.50 KB
-
bee_list.csv
2.29 KB
-
BEE_mat7_fulltree_tplo35_sf20lp.nwk
261.04 KB
-
bee_matrix.csv
24.26 KB
-
beetle_list.csv
514 B
-
beetle_matrix.csv
3.49 KB
-
bird_megatree_Jin-Qian2023.tre
463.53 KB
-
cultivated_trees.csv
532 B
-
ferns.csv
59 B
-
frog_list.csv
652 B
-
frog_matrix.csv
2.35 KB
-
frugi_bird_list.csv
2.06 KB
-
frugi_bird_matrix.csv
10.10 KB
-
inverti_bird_list.csv
5.59 KB
-
inverti_bird_matrix.csv
24.44 KB
-
phylo_div.R
55.60 KB
-
plot_data.csv
13.10 KB
-
README.md
6.68 KB
-
Shi-Rabosky2015_tree.tre
32.71 KB
-
tree_data_250625.csv
395.32 KB
-
tree_list.csv
20.30 KB
-
TreePL-Rooted_Anura_bestTree.tre
223.28 KB
Feb 09, 2026 version files 2.35 MB
-
12862_2016_822_MOESM10_ESM.tree
38.26 KB
-
15K_FBD_crown_mcc.tre
705.50 KB
-
ant_list.csv
3.71 KB
-
ant_matrix.csv
41.93 KB
-
bat_list.csv
1.78 KB
-
bat_matrix.csv
6.50 KB
-
bee_list.csv
2.29 KB
-
BEE_mat7_fulltree_tplo35_sf20lp.nwk
261.04 KB
-
bee_matrix.csv
24.26 KB
-
beetle_list.csv
514 B
-
beetle_matrix.csv
3.49 KB
-
bird_megatree_Jin-Qian2023.tre
463.53 KB
-
cultivated_trees.csv
532 B
-
ferns.csv
59 B
-
frog_list.csv
652 B
-
frog_matrix.csv
2.35 KB
-
frugi_bird_list.csv
2.06 KB
-
frugi_bird_matrix.csv
10.10 KB
-
inverti_bird_list.csv
5.59 KB
-
inverti_bird_matrix.csv
24.44 KB
-
phylo_div.R
55.60 KB
-
plot_data.csv
13.10 KB
-
README.md
6.68 KB
-
Shi-Rabosky2015_tree.tre
32.71 KB
-
tree_data_250625.csv
395.32 KB
-
tree_list.csv
20.30 KB
-
TreePL-Rooted_Anura_bestTree.tre
223.28 KB
Abstract
Tropical forests are highly threatened habitats with the capacity to recover after disturbance. We studied the recovery of phylogenetic diversity (PD) and phylogenetic community structure in plants and animals along a chronosequence of regeneration. We tested expected phylogenetic patterns through succession, including a slower recovery of PD compared to species richness (SR), increasing phylogenetic overdispersion with regeneration time, and the role of environmental filtering and landscape in promoting phylogenetic clustering and overdispersion. Phylogenetic diversity recovery occurred after SR for only four out of eight groups. Frugivorous and invertivorous birds showed increasing phylogenetic overdispersion during succession, while frogs, bees, and trees instead showed a tendency for increasing phylogenetic clustering. Phylogenetic clustering was mainly related to environmental factors during early and late regeneration. Phylogenetic overdispersion during late regeneration was driven by the distance to old-growth forests only in frugivorous birds. Our results show the complex nature of succession in tropical forests, reflecting idiosyncratic patterns of PD and phylogenetic community structure recovery after disturbance for plants and animals. However, they also show that PD can recover relatively rapidly under natural regeneration, suggesting that the studied communities are resilient to disturbance from an evolutionary perspective.
Description of the data and file structure
This dataset is associated with the accepted manuscript Sebastián Escobar, Juan E. Guevara-Andino, Nico Blüthgen, Gunnar Brehm, Santiago F. Burneo, Ugo Diniz, David A. Donoso, Santiago Erazo, Heike Feldhaar, Nina Grella, Alexander Keller, Anna R. Landim, Sara D. Leonhardt, Diego Marín-Armijos, Jörg Müller, Karla Neira-Salamea, Eike Lena Neuschulz, Felicity L. Newell, Karen M. Pedersen, Mark-Oliver Roedel, Matthias Schleuning, Marco Tschapka, María-José Endara. Proceedings of the Royal Society B. 2026.
The repository contains one R script and several documents with raw data to replicate the analyses and figures in the manuscript. All analyses were performed during 2024-2025 using R version 4.4.2 (2024-10-31 ucrt).
Files and variables
File: phylo_div.R
Description: This R script is used to replicate the statistical analyses performed in the manuscript. This scripts also allows obtaining phylogenetic diversity and structure measures, as well as performiong statistical analysis and figures. With this file, phylogenetic trees are built for all groups. THIS SCRIPT WORKS WITH ALL THE OTHER FILES UPLOADED.
File: plot_data.csv
Description: This files contains baseline and environmental data collected in the plots, and is a subset of the data presented in Escobar et al. 2025. Reassembly of a tropical rainforest: A new chronosequence in the Chocó tested with the recovery of tree attributes. Ecosphere. https://doi.org/10.1002/ecs2.70157
- Plot_ID Unique code assigned to each plot based on their Treatment.
- Treatment Category of the plots based on their Legacy and Regeneration.
- Legacy Category of the plots depending on whether they used to be cacao plantations, pastures, or they have remained as old growth forests.
- Regeneration: Regeneration status of the plots depending whether they are still active cacao plantations or pastures, they are during early (Reg. I) or late (Reg. II) regeneration, or they are old-growth forests (OG).
- Reg_year Year at which plots were abandoned for regeneration. Active and old-growth forest plots do not have a regeneration year because they have not been left abandoned for regeneration.
- Latitude Latitude of the plots.
- Longitude Longitude of the plots.
- Elevation Elevation of the plots in m above sea level.
- Rain_chirps Precipitation data in the plots in mm measured from CHIRPS.
- Temperature Temperature data in the plots in °C measured with in-situ loggers.
- Humidity: Humidity data in the plots as % measured with in-situ loggers.
- Solar_annual Solar incidence received by the plots extracted from satellite data.
- Distance_forest Distance to the nearest forest in m extracted from satellite data.
- Soil texture 10 cm Texture data of the soil from the plots at 10 cm depth.
- pH 10 cm pH data of the soil from the plots at 10 cm depth.
- N 10 cm Nitrogen content of the soil from the plots at 10 cm depth.
- C 10 cm Carbon content of the soil from the plots at 10 cm depth.
- Ca 10 cm Calcium content of the soil from the plots at 10 cm depth.
- Fe 10 cm Iron content of the soil from the plots at 10 cm depth.
- K 10 cm Potassium content of the soil from the plots at 10 cm depth.
- Na 10 cm Sodium content of the soil from the plots at 10 cm depth.
- Mg 10 cm Magnesium content of the soil from the plots at 10 cm depth.
- Mn 10 cm Manganese content of the soil from the plots at 10 cm depth.
- P 10 cm Phosphorus content of the soil from the plots at 10 cm depth.
File: cultivated_trees.csv
Description: This file contains a list of 11 cultivated tree species and it is used to filter these species in case only wild trees want to be analyzed.
File: ferns.csv
Description: This file contains a list of 1 cultivated fern species and it is used to filter this species in case only Angiosperm trees want to be analyzed.
File: tree_list.csv
Description: This file contains a list of tree species for building a phylogenetic tree
File: frog_list.csv
Description: This file contains a list of frog species for building a phylogenetic tree
File: frugi_bird_list.csv
Description: This file contains a list of frugivorous bird species for building a phylogenetic tree
File: inverti_bird_list.csv
Description: This file contains a list of vocalizing bird species for building a phylogenetic tree
File: bat_list.csv
Description: This file contains a list of bat species for building a phylogenetic tree
File: ant_list.csv
Description: This file contains a list of ant species for building a phylogenetic tree
File: beetle_list.csv
Description: This file contains a list of dung beetle species for building a phylogenetic tree
File: bee_list.csv
Description: This file contains a list of bee species for building a phylogenetic tree
File: tree_data_250625.csv
Description: This file contains a list of tree species for building a matrix of the tree community
File: frog_matrix.csv
Description: This file is a community matrix of frog species for analysis
File: frugi_bird_matrix.csv
Description: This file is a community matrix of frugivorous bird species for analysis
File: inverti_bird_matrix.csv
Description: This file is a community matrix of vocalizing bird species for analysis
File: bat_matrix.csv
Description: This file is a community matrix of bat species for analysis
File: ant_matrix.csv
Description: This file is a community matrix of ant species for analysis
File: beetle_matrix.csv
Description: This file is a community matrix of dung beetle species for analysis
File: bee_matrix.csv
Description: This file is a community matrix of bee species for analysis
File: 15K_FBD_crown_mcc.tre
Description: This file is a mega phylogenetic tree of ants for analysis
File: 12862_2016_822_MOESM10_ESM.tree
Description: This file is a mega phylogenetic tree of dung beetles for analysis
File: BEE_mat7_fulltree_tplo35_sf20lp.nwk
Description: This file is a mega phylogenetic tree of bees for analysis
File: bird_megatree_Jin-Qian2023.tre
Description: This file is a mega phylogenetic tree of birds for analysis
File: Shi-Rabosky2015_tree.tre
Description: This file is a mega phylogenetic tree of bats for analysis
File: TreePL-Rooted_Anura_bestTree.tre
Description: This file is a mega phylogenetic tree of frogs for analysis
Date of data collection
2021 - 2023
Missing data/not determined: NA/ND
In this study, we aim to test expected phylogenetic patterns during forest succession for one plant and seven animal groups along a chronosequence of tropical rainforest regeneration in order to raise generalizations on phylogenetic recovery. This approach provides a unique opportunity to study the recovery of multiple communities simultaneously, allowing a better comprehension of forest regeneration and community assembly from different taxonomic perspectives. Although previous research on phylogenetic dynamics has been done for individual taxonomic groups, this study represents the first synthesis across multiple taxa, including trees, flying and ground-dwelling vertebrates, and insects. Our goal is to determine phylogenetic diversity and community structure patterns during succession across taxa with different life histories and strategies,s which could influence how these communities respond to disturbance. Phylogenetic diversity recovered with regeneration time, and it occurred after species richness for four out of eight studied groups. Flying vertebrates showed a tendency for increasing phylogenetic overdispersion during succession, but only frugivorous birds strictly followed it. Insects and low dispersal capacity groups (trees and frogs) instead showed a tendency for increasing phylogenetic clustering. Phylogenetic clustering was mainly related to environmental factors during early and late regeneration. Phylogenetic overdispersion during late regeneration was driven by the distance to old-growth forests only in frugivorous birds. Our results show the complex nature of succession in tropical forests, reflecting idiosyncratic patterns of PD and phylogenetic community structure recovery after disturbance for plants and animals. However, they also show that PD can recover relatively rapidly under natural regeneration, suggesting that the studied communities are resilient to disturbance from an evolutionary perspective.
Changes after Jan 20, 2026:
A typo was corrected in the plot_data.csv file.