Recognizing the forest for the trees: testing temporal patterns of cladogenesis using a null model of stochastic diversification

Computer simulations are developed and employed to examine the expectedtemporal distributions of nodes under a null model of stochastic lineagebifurcation and extinction. These Markovian models of phylogenetic processwere constructed so as to permit direct comparisons against empiricalphylogenetic trees generated from molecular or other information availablesolely from extant species. For replicate simulated phylads with n extantspecies, cumulative distribution functions (cdf's) of branching times werecalculated, and compared (using the Kolmogorov-Smirnov test statistic D) tothose from three published empirical trees. Molecular phylogenies forcolumbine plants and avian cranes showed statistically significantdepartures from the null expectations, in directions indicating recent andancient species' radiations, respectively, whereas a molecular phylogenyfor the Drosophila virilis species group showed no apparent historicalclustering of branching events. Effects of outgroup choice and phylogeneticframe of reference were investigated for the columbines and found to have apredictable influence on the types of conclusions to be drawn from suchanalyses. To enable other investigators to statistically test fornonrandomness in temporal cladogenetic pattern in empirical trees generatedfrom data on extant species, we present tables of mean cdf's and associatedprobabilities under the null model for expected branching times in phyladsof varying size. The approaches developed in this report complement andextend those of other recent methods for employing null models to assessthe statistical significance of pattern in evolutionary trees.