Data from: Microevolutionary processes generate phylogenomic discordance at ancient divergences

Angiosperm trees used for simulations, based on estimate of Bell et al. 2010.Phylogenetic estimate of flowering plants and phylogenies used in simulations. Original tree is in 'Original Tree' tree block. 'Trees for simulation' tree block contains 100 trees with (i) branch lengths scaled to generation time and (ii) branch widths scaled to effective population size as described in Oliver (2013). Dated phylogenetic estimate was originally published in: Bell, C. D., D. E. Soltis, and P. S. Soltis. 2010. The age and diversification of the angiosperms re-revisited. Am. J. Bot. 97:1296-1303.Angiosperms.nexBird trees used for simulations, based on estimate of Hackett et al. 2008.Phylogenetic estimate of modern birds and phylogenies used in simulations. Original tree is in 'Original Tree' tree block. 'Trees for simulation' tree block contains 100 trees with (i) branch lengths scaled to generation time and (ii) branch widths scaled to effective population size as described in Oliver (2013). Dated phylogenetic estimate was originally published in: Hackett, S. J., R. T. Kimball, S. Reddy, R. C. K. Bowie, E. L. Braun, M. J. Braun, J. L. Chojnowski, W. A. Cox, K.-L. Han, J. Harshman, et al. 2008. A phylogenomic study of birds reveals their evolutionary history. Science 320:1763-1768.Birds.nexHarpaline beetle trees used for simulations, based on estimate of Ober and Heider 2010.Phylogenetic estimate of harpaline beetles and phylogenies used in simulations. Original tree is in 'Original Tree' tree block. 'Trees for simulation' tree block contains 100 trees with (i) branch lengths scaled to generation time and (ii) branch widths scaled to effective population size as described in Oliver (2013). Dated phylogenetic estimate was originally published in: Ober, K.A. and T. N. Heider. 2010. Phylogenetic diversification patterns and divergence times in ground beetles (Coleoptera: Carabidae: Harpalinae). BMC Evol. Biol. 10:262.Harpalines.nexMammal trees used for simulations, based on estimate of Meredith et al. 2011.Phylogenetic estimate of mammals and phylogenies used in simulations. Original tree is in 'Original Tree' tree block. 'Trees for simulation' tree block contains 100 trees with (i) branch lengths scaled to generation time and (ii) branch widths scaled to effective population size as described in Oliver (2013). Dated phylogenetic estimate was originally published in: Meredith, R. W. J. E. Janečka, J. Gatesy, O. A. Ryder, C. A. Fisher, E. C. Teeling, A. Goodbla, E. Eizirik, T. L. L. Simão, T. Stadler, et al. 2011. Impacts of the Cretaceous terrestrial revolution and KPg extinction on mammal diversification. Science 334:521-524.Mammals.nexNymphalid butterfly trees used for simulations, based on estimate of Wahlberg et al. 2009.Phylogenetic estimate of nymphalid butterflies and phylogenies used in simulations. Original tree is in 'Original Tree' tree block. 'Trees for simulation' tree block contains 100 trees with (i) branch lengths scaled to generation time and (ii) branch widths scaled to effective population size as described in Oliver (2013). Dated phylogenetic estimate was originally published in: Wahlberg, N., J. Leneveu, U. Kodandaramaiah, C. Peña, S. Nylin, A. V. L. Freitas, and A. V. Z. Brower. 2009. Nymphalid butterflies diversify following near demise at the Cretaceous/Tertiary boundary. Proc. R. Soc. B 276:4295-4302.Nymphalids.nex