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An international initiative devoted to developing DNA barcoding as a global standard for the identification of biological species. For the mammal tree ( supplementary fig. S4 b, Supplementary Material online), the models with zero, one, two, or three rate shifts are rejected in favor of a model with four rate shifts ( P< 0.05) ( supplementary table S9, Supplementary Material online). A model with four rate shifts is not rejected in favor of a model with five rate shifts ( P = 0.123). The 4 shifts are detected, at 2.1, 9.6, 42.4 and 105 Ma ( supplementary table S10, Supplementary Material online). The parameters obtained for the 4 shifts model between 105 and 42.4 Ma (λ−μ = 0.05186 and μ/λ = 0.3528) were used to plot the confidence interval of the null distribution ( supplementary fig. S4 b, Supplementary Material online). Szöllősi, G. J., Davín, A. A., Tannier, E., Daubin, V. & Boussau, B. Genome-scale phylogenetic analysis finds extensive gene transfer among fungi. Phil. Trans. R. Soc. B 370, 20140335 (2015). We used a hierarchical average linkage method of estimating divergence times ( T s) of clade pairs to build a Super Timetree, along with a procedure for testing and updating topological partitions to ensure the highest degree of consistency with individual timetrees in every study. For the TTOL, uncertainty derived from individual studies is available for each node ( supplementary table S2, Supplementary Material online). Branch time modes of different Linnaean categories were estimated ( supplementary table S3, Supplementary Material online). Diversification Analyses Chauve, C. et al. MaxTiC: Fast ranking of a phylogenetic tree by maximum time consistency with lateral gene transfers. Preprint at https://www.biorxiv.org/content/early/2017/10/06/127548 (2017).

Timetree of Life (2009) Download (1,610 families)

Jetz W, Thomas GH, Joy JB, Hartmann K, Mooers AO. The global diversity of birds in space and time. Nature. 2012; 491(7424):444–448. [ PubMed] [ Google Scholar] Kimura M. Evolutionary rate at the molecular level. Nature. 1968; 217:624–626. [ PubMed] [ Google Scholar]

For the bird tree ( supplementary fig. S4a, Supplementary Material online), the models with zero, one, two, three, four, and five rate shifts are rejected in favor of a model with six rate shifts ( P< 0.05) ( supplementary table S9, Supplementary Material online). A model with six rate shifts is not rejected in favor of a model with seven rate shifts ( P = 0.091). The 6 shifts are detected at 1, 3.4, 14.4, 48.2, 73.3, and 84.4 Ma ( supplementary table S10, Supplementary Material online). The parameters obtained for the 6 shifts model between 73.3 and 48.2 Ma (λ−μ = 0.04058 and μ/λ = 0.0395) were used to plot the confidence interval of the null distribution ( supplementary fig. S4a, Supplementary Material online). Coyne JA, Orr HA. Patterns of speciation in Drosophila. Evolution. 1989; 43(2):362–381. [ PubMed] [ Google Scholar] Soo, R. M., Hemp, J., Parks, D. H., Fischer, W. W. & Hugenholtz, P. On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria. Science 355, 1436–1440 (2017). Doolittle, W. F. Phylogenetic classification and the Universal Tree. Science 284, 2124–2128 (1999). Szöllősi, G. J., Tannier, E., Daubin, V. & Boussau, B. The inference of gene trees with species trees. Syst. Biol. 64, e42–e62 (2015).

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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]

For the TTOL, we estimated node time uncertainty in both the LTT curve and rate test by producing 500 replicates of the TTOL, sampling a time between the confidence intervals at each node under a uniform distribution. These replicates were then used in the TREEPAR analysis to estimate and test rate change, with the uncertainty shown in figure 4 and the significant shifts by time interval (20 My) shown in supplementary table S8, Supplementary Material online. 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

Timetree of Life (2015) Download (>50,000 species)

Benton, M. J. & Donoghue, P. C. J. Paleontological evidence to date the tree of life. Mol. Biol. Evol. 24, 26–53 (2007).

The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. column) Diversification analyses of major Linnaean clades in the timetree of life. ( a–b) Results of coalescent analyses testing models of diversification. Of 48 tetrapod clades, 37 showed significant model selected and they were used in these analyses. ( a) Effect of clade size (number of described species). ( b) Effect of clade age. ( c) Diagram illustrating difference between stem and crown age for two clades. ( d–e) Relationship of stem branch and crown age in mammals ( d; r 2 = 0.07) and birds ( e; r 2 = 0.04). Moen D, Morlon H. Why does diversification slow down? Trends Ecol Evol. 2014; 29(4):190–197. [ PubMed] [ Google Scholar] Smith SA, O'Meara BC. treePL: divergence time estimation using penalized likelihood for large phylogenies. Bioinformatics. 2012; 28(20):2689–2690. [ PubMed] [ Google Scholar]Knoll, A. H. Paleobiological perspectives on early eukaryotic evolution. Cold Spring Harb. Perspect. Biol. 6, a0161211 (2014). Our results show that it is best to avoid stem branch time, because the length of any (stem) branch in the tree should not be related to the time depth of the descendant node (crown age; fig. 5 d and e). Therefore, the use of stem branch time will introduce large statistical noise and make the test extremely conservative. For example, when considering every node in a timetree of species, the coefficient of variation of stem branch length relative to crown age is over 200% in the best sampled groups, mammals (208%) and birds (224%). That noise is further weighted by the pull of the present ( Nee et al. 1994), which, we determined, adds 40% time (median) to crown age at any given node (if stem age is used instead of crown age), in separate analyses of birds, mammals, and all eukaryotes. This is because the pull of the present creates longer internal branches deeper in a tree, as more lineages are pruned by extinction. Therefore, the use of stem branches in diversification analyses adds noise (variance) and gives increased weight to that noise. We believe that the stronger signal of constant expansion in our results, compared with earlier studies that have supported hypo-expansion and saturation, is in part because we have identified and avoided some biases (e.g., sampling effort, clade size, and stem age) that can impact diversification analyses. Speciation Knoll, A. H., Bergmann, K. D. & Strauss, J. V. Life: the first two billion years. Phil. Trans. R. Soc. B 371, 20150493 (2016). Etienne RS, Rosindell J. Prolonging the past counteracts the pull of the present: protracted speciation can explain observed slowdowns in diversification. Syst Biol. 2012; 61(2):204–213. [ PMC free article] [ PubMed] [ Google Scholar] A unique collection of thousands of videos, images and fact-files illustrating the world's species.