Geko Small Tree Of Life Clock, 30cm.

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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 The names of all organisms that are represented in the genetic databases with at least one nucleotide or protein sequence, arranged hierarchically. 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). 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).

Knoll, A. H. Paleobiological perspectives on early eukaryotic evolution. Cold Spring Harb. Perspect. Biol. 6, a0161211 (2014). Szöllősi, G. J., Tannier, E., Daubin, V. & Boussau, B. The inference of gene trees with species trees. Syst. Biol. 64, e42–e62 (2015).These results have implications for patterns of species diversification and the interpretation of timetrees. If adaptation is largely decoupled from speciation, we should not expect it to be a driver of speciation as is frequently assumed. Also, we should not expect to see major diversification rate increases following mass extinction events, even though large adaptive changes took place at those times. That expectation is realized in our analyses ( fig. 4) where we see constant splitting through time across the two major Phanerozoic extinction events (251 and 66 Ma). Likewise, our diversification analyses of smaller groups, such as birds and mammals ( supplementary fig. S4, Supplementary Material online), and past studies of those groups ( Bininda-Emonds et al. 2007; Meredith et al. 2011; Jetz et al. 2012) have not found rate increases immediately following the end-Cretaceous mass extinction event (66 Ma). Rate decreases from the extinction events themselves are not expected because of the inability to detect, in trees, a large proportion of species extinctions that occurred ( Nee and May 1997). Our diversification results for birds are similar to an earlier analysis ( Jetz et al. 2012), with a strong increase in diversification from ∼45 Ma to the present. The mammal results are also generally similar to past mammal analyses in showing the absence of any rate increase immediately after the end-Cretaceous extinctions ( Bininda-Emonds et al. 2007; Meredith et al. 2011). We did not find a sharp mid-Cenozoic increase in rate that was found in one other analysis ( Stadler 2011), although we determined that the cause of that rate increase was from a polytomy in the mammal timetree used in that study ( Stadler 2011); otherwise our results are comparable. 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).

Rabosky DL. Diversity-dependence, ecological speciation, and the role of competition in macroevolution. Annu Rev Ecol Evol Syst. 2013; 44:481–502. [ Google Scholar] An online database of animal natural history, distribution, classification, and conservation biology. 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). Gogarten, J. P., Murphey, R. D. & Olendzenski, L. Horizontal gene transfer: pitfalls and promises. Biol. Bull. 196, 359–362 (1999).Benton MJ. The Red Queen and the Court Jester: species diversity and the role of biotic and abiotic factors through time. Science. 2009; 323(5915):728–732. [ PubMed] [ Google Scholar] A collection of sequences from several sources, including SwissProt, PIR, PRF, PDB, and translations from annotated coding regions in GenBank and RefSeq. Szöllősi, G. J., Rosikiewicz, W., Boussau, B., Tannier, E. & Daubin, V. Efficient exploration of the space of reconciled gene trees. Syst. Biol. 62, 901–912 (2013). Morlon H, Potts MD, Plotkin JB. Inferring the dynamics of diversification: a coalescent approach. PLoS Biol. 2010; 8(9):e1000493. [ PMC free article] [ PubMed] [ Google Scholar] Groussin, M. et al. Unraveling the processes shaping mammalian gut microbiomes over evolutionary time. Nat. Commun. 8, 14319 (2017).