DOI: 10.5061/dryad.88qf4
title: Data from: Microevolutionary processes generate phylogenomic discordance at ancient divergences

description: Stochastic population processes may cause differences between species
 histories and gene histories. These processes are assumed to only
 influence the most recent divergences in the tree of life; however, there
 may be under-appreciated potential for microevolutionary processes to
 impact deep divergences. I used multispecies coalescent models to
 determine the impact of stochastic processes on deep phylogenomic
 histories. Here I show phylogenomic discordance between gene histories and
 species histories is expected at deep divergences for many eukaryotic
 taxa, and the probability of discordance increases with population size,
 generation time, and the number of species in the tree. Five eukaryotic
 clades (angiosperms, birds, harpaline beetles, mammals, and nymphalid
 butterflies) demonstrate significant discordance potential at divergences
 over 50 million years old, and this discordance potential is independent
 of the age of divergence. These findings demonstrate population processes
 acting over very short timescales will leave a lasting impact on genomic
 histories, even for divergence events occurring tens to hundreds of
 millions of years ago.
description: 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