Geko Small Tree Of Life Clock, 30cm.

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Knoll, A. H. Paleobiological perspectives on early eukaryotic evolution. Cold Spring Harb. Perspect. Biol. 6, a0161211 (2014). Further information on experimental design is available in the Life Sciences Reporting Summary. Data availability The names of all organisms that are represented in the genetic databases with at least one nucleotide or protein sequence, arranged hierarchically. Szöllősi, G. J. & Daubin, V. Modeling gene family evolution and reconciling phylogenetic discord. Methods Mol. Biol. 856, 29–51 (2012). Nee S, May RM. Extinction and the loss of evolutionary history. Science. 1997; 278(5338):692–694. [ PubMed] [ Google Scholar]

Knoll, A. H. in Fundamentals of Geobiology (eds Knoll, A. H., Canfield, D. E. & Konhauser, K. O.) Ch. 16 (John Wiley, Chichester, 2012). dos Reis, M. et al. Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny. Proc. Biol. Sci. 279, 3491–3500 (2012). Here, we have taken an approach to build a global TTOL by means of a data-driven synthesis of published timetrees into a large hierarchy. We have synthesized timetrees and related information in 2,274 molecular studies, which we collected and curated in a knowledgebase ( Hedges et al. 2006) ( supplementary Materials and Methods, Supplementary Material online). We mapped timetrees and divergence data from those studies on a robust and conservative guidetree based on community consensus ( National Center for Biotechnology Information 2013) and used those times to resolve polytomies and derive nodal times in the TTOL ( supplementary fig. S2, Supplementary Material online). We present this synthesis here, for use by the community, and explore how it bears on evolutionary hypotheses and mechanisms of speciation and diversification. Results A Global Timetree of Species

Tomitani, A., Knoll, A. H., Cavanaugh, C. M. & Ohno, T. The evolutionary diversification of Cyanobacteria: molecular–phylogenetic and paleontological perspectives. Proc. Natl Acad. Sci. USA 103, 5442–5447 (2006). Huang, J., Xu, Y. & Gogarten, J. P. The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic. Mol. Biol. Evol. 22, 2142–2146 (2005). column) Temporal relationships of Linnaean ranks of eukaryotes, showing mode and 95% confidence intervals. Prokaryotes are not shown because of large differences in scale ( supplementary Materials and Methods, Supplementary Material online). Diversification

Tamura K, Battistuzzi FU, Billing-Ross P, Murillo O, Filipski A, Kumar S. Estimating divergence times in large molecular phylogenies. Proc Natl Acad Sci U S A. 2012; 109(47):19333–19338. [ PMC free article] [ PubMed] [ Google Scholar] Rabosky DL. Diversity-dependence, ecological speciation, and the role of competition in macroevolution. Annu Rev Ecol Evol Syst. 2013; 44:481–502. [ Google Scholar] Nei M, Kumar S. Molecular evolution and phylogenetics. New York: Oxford University Press; 2000. [ Google Scholar] There are challenges in synthesizing a global TTOL. The most common approach for constructing a large timetree using a sequence alignment or super alignment is possible ( Smith and O'Meara 2012; Tamura et al. 2012), but not generally practical because of data matrix sparseness. For example, genes appropriate for closely related species are unalignable at higher levels, and those appropriate for higher levels are too conserved for resolving relationships of species. Disproportionate attention to some species, such as model organisms and groups of general interest (e.g., mammals and birds), also results in an uneven distribution of knowledge. In addition, computational limits are reached for Bayesian timing methods involving more than a few hundred species ( Battistuzzi et al. 2011; Jetz et al. 2012). Rabosky DL. Automatic detection of key innovations, rate shifts, and diversity-dependence on phylogenetic trees. PLoS One. 2014; 9:e89543. [ PMC free article] [ PubMed] [ Google Scholar]The consistency in TTS among groups found here suggests that the time-based acquisition of GIs, and not adaptive change, is driving reproductive isolation, almost in a neutral process. By implication, geographically isolated populations, even if morphologically different and diagnosable, are not expected to be species until they have reached the point of no return. This is because some differentiation and adaptive change should occur in isolation, and many isolates will be ephemeral ( Rosenblum et al. 2012), merging with other isolates or disappearing and never becoming species that enter the tree of life. More population data are needed before it is possible to identify the point of no return with precision. Nonetheless, these data suggest that, in most cases, described species separated by only tens of thousands of years are not real species. The Linnaean rank of subspecies, which has declined in use for decades, might be appropriate for such diagnosable isolates that have not yet reached the point of no return. Oversplitting of species by taxonomists may explain the sharp peak in diversification (hyper-expansion) in the last 10 My of eukaryote history ( fig. 4 b). On the other hand, it could also result from statistical (small sample) artifacts that were published in many different studies (summarized in the TTOL). Therefore, further analysis of that unusual rate spike is warranted.