Disparate recovery of phylogenetic diversity across taxa during tropical rainforest regeneration

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 drive..., 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 aft..., # 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 perform..., , **Changes after Jan 20, 2026:** 

A typo was corrected in the plot_data.csv file.