Geko Small Tree Of Life Clock, 30cm.

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Shih, P. M., Hemp, J., Ward, L. M., Matzke, N. J. & Fischer, W. W. Crown group Oxyphotobacteria postdate the rise of oxygen. Geobiology 15, 19–29 (2017). Knoll, A. H., Bergmann, K. D. & Strauss, J. V. Life: the first two billion years. Phil. Trans. R. Soc. B 371, 20150493 (2016). 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 Sjöstrand, J. et al. A Bayesian method for analyzing lateral gene transfer. Syst. Biol. 63, 409–420 (2014). 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).

Spatafora, J. W. et al. A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data. Mycologia 108, 1028–1046 (2016).

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

Puillandre N, Lambert A, Brouillet S, Achaz G. ABGD, Automatic Barcode Gap Discovery for primary species delimitation. Mol Ecol. 2011; 21:1864–1877. [ PubMed] [ Google Scholar] 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). Detailed methods are described in supplementary Materials and Methods, Supplementary Material online. TTOL Data Collection

Blank, C. E. & Sánchez-Baracaldo, P. Timing of morphological and ecological innovations in the cyanobacteria — a key to understanding the rise in atmospheric oxygen. Geobiology 8, 1–23 (2010). Stadler T. Mammalian phylogeny reveals recent diversification rate shifts. Proc Natl Acad Sci U S A. 2011; 108(15):6187–6192. [ PMC free article] [ PubMed] [ Google Scholar] An online database of animal natural history, distribution, classification, and conservation biology. Information about all known species, including their taxonomy, geographic distribution, collections, genetics, evolutionary history, morphology, behavior, ecological relationships, etc. The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.A collection of information about biodiversity compiled collaboratively by hundreds of expert and amateur contributors. 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 Ueno, Y., Yamada, K., Yoshida, N., Maruyama, S. & Isozaki, Y. Evidence from fluid inclusions for microbial methanogenesis in the early Archaean era. Nature 440, 516–519 (2006). Benton, M. J. & Donoghue, P. C. J. Paleontological evidence to date the tree of life. Mol. Biol. Evol. 24, 26–53 (2007).