Abby, S. S., Tannier, E., Gouy, M. & Daubin, V. Lateral gene transfer as a support for the tree of life. Proc. Natl Acad. Sci. USA 109, 4962–4967 (2012). Huang, J. & Gogarten, J. P. Ancient gene transfer as a tool in phylogenetic reconstruction. Methods Mol. Biol. 532, 127–139 (2009). The Genome database provides views for a variety of genomes, complete chromosomes, sequence maps with contigs, and integrated genetic and physical maps. Nagy, L. G. et al. Latent homology and convergent regulatory evolution underlies the repeated emergence of yeasts. Nat. Commun. 5, 4471 (2014).

O’Leary, M. A. et al. The placental mammal ancestor and the post-K-Pg radiation of placentals. Science 339, 662–667 (2013).Cohan FM. What are bacterial species? Ann Rev Microbiol. 2002; 56:457–487. [ PubMed] [ Google Scholar] 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] The large TTOL afforded us the opportunity to examine patterns of lineage splitting across the diversity of eukaryotes (we omit prokaryotes in our TTOL analyses because they have an arbitrary species definition). Under models of “expansion,” diversity will continue to expand, either at an increasing diversification rate (hyper-expansion), the same rate (constant expansion), or decreasing rate (hypo-expansion). Saturation, on the other hand, refers to a drop in rate to zero as diversity reaches a plateau (equilibrium), possibly because of density-dependent biotic factors such as species interactions ( Morlon 2014). Most recent analyses, but not all ( Venditti et al. 2010; Jetz et al. 2012), have suggested that hypo-expansion is the predominant pattern in the tree of life, although there has been considerable debate as to the importance of timescales, biotic or abiotic factors, and potential biases in the analyses ( Sepkoski 1984; Benton 2009; Morlon et al. 2010; Rabosky et al. 2012; Cornell 2013; Rabosky 2013). An online system to search and retrieve information relating to amphibian biology and conservation.

Spatafora, J. W. et al. A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data. Mycologia 108, 1028–1046 (2016). Szöllősi, G. J., Tannier, E., Lartillot, N. & Daubin, V. Lateral gene transfer from the dead. Syst. Biol. 62, 386–397 (2013). Nee S, May RM. Extinction and the loss of evolutionary history. Science. 1997; 278(5338):692–694. [ PubMed] [ Google Scholar]

Site Customisation

For the eukaryote tree ( fig. 4), 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 = 0.055). Six shifts are thus detected at 1, 11, 21, 121, 14,1 and 151 Ma ( supplementary table S10, Supplementary Material online). The parameters obtained for the 6 shifts model between 2,100 and 151 Ma (λ−μ = 0.00307 and μ/λ = 0.9581) were used to plot the confidence interval of the null distribution ( fig. 4). 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. in Fundamentals of Geobiology (eds Knoll, A. H., Canfield, D. E. & Konhauser, K. O.) Ch. 16 (John Wiley, Chichester, 2012).

A unique collection of thousands of videos, images and fact-files illustrating the world's species. Information about all known species, including their taxonomy, geographic distribution, collections, genetics, evolutionary history, morphology, behavior, ecological relationships, etc.

Required Cookies & Technologies

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). 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). 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). 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