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.
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.nex
Bird 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.nex
Harpaline 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.nex
Mammal 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.nex
Nymphalid 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