DOI: 10.5061/dryad.1sf007b
title: Data from: Species Selection Regime and Phylogenetic Tree Shape

description: Species selection, the effect of heritable traits in generating
 between-lineage diversification rate differences, provides a valuable
 conceptual framework for understanding the relationship between traits,
 diversification and phylogenetic tree shape. An important challenge,
 however, is that the nature of real diversification landscapes – curves or
 surfaces which describe the propensity of species-level lineages to
 diversify as a function of one or more traits – remains poorly understood.
 Here we present a novel, time-stratified extension of the QuaSSE model in
 which speciation/extinction rate is specified as a static or
 temporally-shifting Gaussian or skewed-Gaussian function of the
 diversification trait. We then use simulations to show that the generally
 imbalanced nature of real phylogenetic trees, as well as their generally
 greater-than-expected frequency of deep branching events, are typical
 outcomes when diversification is treated as a dynamic, trait-dependent
 process. Focusing on four basic models (Gaussian-speciation with and
 without background extinction; skewed-speciation; Gaussian-extinction), we
 also show that particular features of the species selection regime produce
 distinct tree shape signatures and that, consequently, a combination of
 tree shape metrics has the potential to reveal the species selection
 regime under which a particular lineage diversified. We evaluate this idea
 empirically by comparing the phylogenetic trees of plant lineages
 diversifying within climatically- and geologically-stable environments of
 the Greater Cape Floristic Region, with those of lineages diversifying in
 environments that have experienced major change through the Late
 Miocene-Pliocene. Consistent with our expectations, the trees of lineages
 diversifying in a dynamic context are less balanced, show a greater
 concentration of branching events close to the present, and display
 stronger diversification rate-trait correlations. We suggest that species
 selection plays an important role in shaping phylogenetic trees but
 recognize the need for an explicit probabilistic framework within which to
 assess the likelihoods of alternative diversification scenarios as
 explanations of a particular tree shape.
description: Appendix
 1This
 file contains supplementary figures and tables referred to as online
 Appendix 1 in the main text.Phylogenetic
 treesThis file contains
 newick-format phylogenetic trees for the 15 lineages included in the
 empirical component of the study. Table 1 and Fig. 7 draw on these
 data.phylogenetic_trees.txtSpecies vegetation scoresThis file contains the vegetation-association scores of Cape species belonging to the 15 lineages included in the empirical component of the study. Table 1 and Fig. 7 draw on these data.habitat_scorings.xlsxSpecies precipitation scores and nodal distanceThis file contains mean precipitation seasonality and mean summer precipitation amount of species in 11 of the 15 lineages included in the empirical component of the study. It also provides the number of nodes separating each species from the crown node of the clade to which it belongs. Table 1 and Fig. 7 draw on these data.Species_enviro_data.xlsxShifting sim results by individual runThis file provides the size and shape characteristics of trees generated by replicate simulations with a shifting diversification function (Rshift = [0,1]) under each model/parameter combination. Fig. 5 is based on these data.shift_sims_by_individ_run.csvShift sim results (means) by parameter combinationThis file provides the mean size and shape characteristics of trees generated of trees generated with a shifting diversification function (Rshift = [0,1]) under each model/parameter combination. Table 2(c) and Figs. 3 and 4 are based on these data.shift_sims_by_param_comb_means.csvSimulation scriptsThe zip file simulation_scripts.zip contains all the scripts needed to run the simulations under the range of models explored in the paper.simulation_scripts.zipstatic sim results (means) by parameter combinationThis file provides the mean size and shape characteristics of trees generated of trees generated with a static diversification function (Rshift = [0,1]) under each model/parameter combination. Tables 2(a) and 2(b) and Fig. 2 are based on these data.static_sims_by_param_comb_means.csv