DOI: 10.5061/dryad.3bp51
title: Data from: How ecology and landscape dynamics shape phylogenetic trees

description: Whether biotic or abiotic factors are the dominant drivers of clade
 diversification is a long-standing question in evolutionary biology. The
 ubiquitous patterns of phylogenetic imbalance and branching slowdown have
 been taken as supporting the role of ecological niche filling and spatial
 heterogeneity in ecological features, and thus of biotic processes, in
 diversification. However, a proper theoretical assessment of the relative
 roles of biotic and abiotic factors in macroevolution requires models that
 integrate both types of factors, and such models have been lacking. In
 this study, we use an individual-based model to investigate the temporal
 patterns of diversification driven by ecological speciation in a
 stochastically fluctuating geographic landscape. The model generates
 phylogenies whose shape evolves as the clade ages. Stabilization of tree
 shape often occurs after ecological saturation, revealing species turnover
 caused by competition and demographic stochasticity. In the initial phase
 of diversification (allopatric radiation into an empty landscape), trees
 tend to be unbalanced and branching slows down. As diversification
 proceeds further due to landscape dynamics, balance and branching tempo
 may increase and become positive. Three main conclusions follow. First,
 the phylogenies of ecologically saturated clades do not always exhibit
 branching slowdown. Branching slowdown requires that competition be wide
 or heterogeneous across the landscape, or that the characteristics of
 landscape dynamics vary geographically. Conversely, branching acceleration
 is predicted under narrow competition or frequent local catastrophes.
 Second, ecological heterogeneity does not necessarily cause phylogenies to
 be unbalanced—short time in geographical isolation or frequent local
 catastrophes may lead to balanced trees despite spatial heterogeneity.
 Conversely, unbalanced trees can emerge without spatial heterogeneity,
 notably if competition is wide. Third, short isolation time causes a
 radically different and quite robust pattern of phylogenies that are
 balanced and yet exhibit branching slowdown. In conclusion, biotic factors
 have a strong and diverse influence on the shape of phylogenies of
 ecologically saturating clades and create the evolutionary template in
 which branching slowdown and tree imbalance may occur. However, the
 contingency of landscape dynamics and resource distribution can cause wide
 variation in branching tempo and tree balance. Finally, considerable
 variation in tree shape among simulation replicates calls for caution when
 interpreting variation in the shape of real phylogenies.
description: Tree_shape_ModelV2_codeCodes of the refined version of the model (which accounts for genetic incompatibilities to delineate species and follow their evolutionary history).AppendixThis document contains all the supplementary information.Tree_shape_model.V2This document explains why we created a new version of the model, what was modified in this new version, and shows updates of all the results of the article "How Ecology and Landscape Dynamics Shape Phylogenetic Trees" based on this new version (identical results).