DOI: 10.5061/dryad.486c0
title: Data from: Non-equilibrium dynamics and floral trait interactions shape extant angiosperm diversity

description: Why are some traits and trait combinations exceptionally common across the
 tree of life, whereas others are vanishingly rare? The distribution of
 trait diversity across a clade at any time depends on the ancestral state
 of the clade, the rate at which new phenotypes evolve, the differences in
 speciation and extinction rates across lineages, and whether an
 equilibrium has been reached. Here we examine the role of transition
 rates, differential diversification (speciation minus extinction), and
 non-equilibrium dynamics on the evolutionary history of angiosperms, a
 clade well known for the abundance of some trait combinations and the
 rarity of others. Our analysis reveals that three character states
 (corolla present, bilateral symmetry, reduced stamen number) act
 synergistically as a key innovation, doubling diversification rates for
 lineages in which this combination occurs. However, this combination is
 currently less common than predicted at equilibrium because the individual
 characters evolve infrequently. Simulations suggest that angiosperms will
 remain far from the equilibrium frequencies of character states well into
 the future. Such non-equilibrium dynamics may be common when major
 innovations evolve rarely, allowing lineages with ancestral forms to
 persist, and even outnumber those with diversification-enhancing states,
 for tens of millions of years.
description: Summary files for
 testing simsThis includes the
 summary files from the simulations used to test
 faMUSSE.FloralFilesForDryad.zipScriptsThese are the R scripts for doing all the analyses in the paper. Note that we include a copy of diversitree with slight modifications (look for BCO in the code).Performance check resultsThese files are the result of simulations followed by pruning and analyses to test the new approach. The only modification was to remove (for space concerns) the files associated with batching each of the many jobs.PerformanceCheck_May2015_forDryad.zipForward in time simulationsThese are the output of doing simulations forward in time to predict floral evolution.SimsMay2013FINAL.zipMain analysis: source dataThe data used in the main analysis of floral evolution.SourceData.zipMain analysis: summariesSummaries of rates, likelihoods, and AIC values for the over 19K models analyzed.Summaries.zipMain analysis: analyses under transition model 1The models were broken up by transition model, then diversification model, then focal area.T1.zipMain analysis: analyses under transition model 2The models were broken up by transition model, then diversification model, then focal area.T2.zipMain analysis: analyses under transition model 3The models were broken up by transition model, then diversification model, then focal area.T3.zipMain analysis: analyses under transition model 4The models were broken up by transition model, then diversification model, then focal area.T4.zipMain analysis: analyses under transition model 5The models were broken up by transition model, then diversification model, then focal area.T5.zip