DOI: 10.5061/dryad.cjsxksnhm
title: Disparate recovery of phylogenetic diversity across taxa during tropical rainforest regeneration

description: 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: 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.
description: # Disparate recovery of phylogenetic diversity across taxa during tropical
 rainforest regeneration **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](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