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TimeTree
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<h2 id="features">Features</h2> <p>TimeTree users can search for the names of two species, such as cat and dog, to obtain the mean and median time estimates for their divergence, in millions of years. The results also show all individual time estimates, from each study, next to a geologic timescale, indicating geologic periods. Different aspects of the Earth's environment are shown next to the timescale for comparison, including Earth impacts, solar luminosity, carbon dioxide levels, and oxygen levels. Separately, a table lists the time estimates, downloadable as a spreadsheet, from each study along with references and links to the abstracts of the original articles. Users can download the original study data as <a href="/facts/Newick_format/CpLFja9e">Newick</a>-formatted timetrees for further research. In the timeline search, users type the name of a taxon, and all divergences back to the origin of life are show with their taxon names, in a vertical ladder-like figure. Timepanels of Earth's environment also are shown next to the geological timescale, as in all three search options. The third search option, <a href="/facts/Timetree/7fYX9X8o">timetree</a> search, involves building a <a href="/facts/Timetree/7fYX9X8o">timetree</a> by either specifying a taxon (group) name or uploading a list of species or other taxa. After specifying a group name, the user can choose which taxonomic level they prefer to view. For example, with a family group name, either a species-level or genus-level timetree can be selected. Then, the <a href="/facts/Timetree/7fYX9X8o">timetree</a> is show and can be output as a <a href="/facts/Newick_format/CpLFja9e">Newick</a> file or image for publication. Times on the tree can be explored by clicking on nodes, and obtaining tables of data pertaining to the node. The database also allows search of <a href="/facts/Timetree/7fYX9X8o">timetree</a> articles by author name. The entire open-access book <i>Timetree of Life</i><a class="footnote-ref" id="fnref:12" href="#fn:12"><sup>12</sup></a> is presented on the site. </p> <h2 id="external-links">External links</h2> <ul><li><a href="http://www.timetree.org/">Official website</a> </li></ul> <h2 id="references">References</h2> <ol> <li id="fn:1"><p>Hedges, S. Blair; Dudley, Joel; Kumar, Sudhir (4 October 2006). "TimeTree: a public knowledge-base of divergence times among organisms" (PDF). Bioinformatics. 22 (23). Oxford University Press: 2971–2972. doi:10.1093/bioinformatics/btl505. ISSN 1367-4811. PMID 17021158. <a href="http://www.hedgeslab.org/pubs/180.pdf" target="_blank">http://www.hedgeslab.org/pubs/180.pdf</a> <a href="#fnref:1" class="footnote-back-ref">↩</a></p></li> <li id="fn:2"><p>Kumar, Sudhir; Hedges, S. Blair (2011-07-15). "TimeTree2: species divergence times on the iPhone". Bioinformatics. 27 (14): 2023–2024. doi:10.1093/bioinformatics/btr315. ISSN 1367-4803. PMC 3129528. PMID 21622662. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129528" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129528</a> <a href="#fnref:2" class="footnote-back-ref">↩</a></p></li> <li id="fn:3"><p>Hedges, S. Blair; Kumar, Sudhir (2009-04-23). The Timetree of Life. Oxford, UK: Oxford University Press. ISBN 978-0-19-953503-3. <a href="978-0-19-953503-3" target="_blank">978-0-19-953503-3</a> <a href="#fnref:3" class="footnote-back-ref">↩</a></p></li> <li id="fn:4"><p>Hedges, S. Blair; Marin, Julie; Suleski, Michael; Paymer, Madeline; Kumar, Sudhir (2015). "Tree of Life Reveals Clock-Like Speciation and Diversification". Molecular Biology and Evolution. 32 (4): 835–845. arXiv:1412.4312. doi:10.1093/molbev/msv037. ISSN 1537-1719. PMC 4379413. PMID 25739733. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4379413" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4379413</a> <a href="#fnref:4" class="footnote-back-ref">↩</a></p></li> <li id="fn:5"><p>Kumar, Sudhir; Hedges, S. Blair (2011-07-15). "TimeTree2: species divergence times on the iPhone". Bioinformatics. 27 (14): 2023–2024. doi:10.1093/bioinformatics/btr315. ISSN 1367-4803. PMC 3129528. PMID 21622662. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129528" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129528</a> <a href="#fnref:5" class="footnote-back-ref">↩</a></p></li> <li id="fn:6"><p>Kumar, Sudhir; Suleski, Michael; Craig, Jack; Kasprowicz, Adrienne; Sanderford, Maxwell; Li, Michael; Stecher, Glen; Hedges, S. Blair (2022). "TimeTree 5: An Expanded Resource for Species Divergence Times". Molecular Biology and Evolution. 39 (8). doi:10.1093/molbev/msac174. PMC 9400175. PMID 35932227. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9400175" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9400175</a> <a href="#fnref:6" class="footnote-back-ref">↩</a></p></li> <li id="fn:7"><p>Metzger KJ (2011). "Helping Students Conceptualize Species Divergence Events using the Online Tool "TimeTree: The Timescale of Life"". The American Biology Teacher. 73 (2): 106–108. doi:10.1525/abt.2011.73.2.9. S2CID 85026876. <a href="/wiki/Doi_(identifier)" target="_blank">/wiki/Doi_(identifier)</a> <a href="#fnref:7" class="footnote-back-ref">↩</a></p></li> <li id="fn:8"><p>Babaian, Caryn; Kumar, Sudhir (2018). "Time travel and the naturalist's notebook: Vladimir Nabokov meets the TimeTree of Life". The American Biology Teacher. 80 (9): 650–658. doi:10.1525/abt.2018.80.9.650. S2CID 91951552. <a href="https://doi.org/10.1525%2Fabt.2018.80.9.650" target="_blank">https://doi.org/10.1525%2Fabt.2018.80.9.650</a> <a href="#fnref:8" class="footnote-back-ref">↩</a></p></li> <li id="fn:9"><p>Babaian, Caryn; Kumar, Sudhir (2020). "Molecular memories of a Cambrian fossil". The American Biology Teacher. 82 (9): 586–595. doi:10.1525/abt.2020.82.9.586. PMC 8104914. PMID 33967280. S2CID 227304077. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8104914" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8104914</a> <a href="#fnref:9" class="footnote-back-ref">↩</a></p></li> <li id="fn:10"><p>Hedges, S. Blair; Kumar, Sudhir (2009-04-23). The Timetree of Life. Oxford, UK: Oxford University Press. ISBN 978-0-19-953503-3. <a href="978-0-19-953503-3" target="_blank">978-0-19-953503-3</a> <a href="#fnref:10" class="footnote-back-ref">↩</a></p></li> <li id="fn:11"><p>Kumar, Sudhir; Suleski, Michael; Craig, Jack; Kasprowicz, Adrienne; Sanderford, Maxwell; Li, Michael; Stecher, Glen; Hedges, S. Blair (2022). "TimeTree 5: An Expanded Resource for Species Divergence Times". Molecular Biology and Evolution. 39 (8). doi:10.1093/molbev/msac174. PMC 9400175. PMID 35932227. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9400175" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9400175</a> <a href="#fnref:11" class="footnote-back-ref">↩</a></p></li> <li id="fn:12"><p>Hedges, S. Blair; Kumar, Sudhir (2009-04-23). The Timetree of Life. Oxford, UK: Oxford University Press. ISBN 978-0-19-953503-3. <a href="978-0-19-953503-3" target="_blank">978-0-19-953503-3</a> <a href="#fnref:12" class="footnote-back-ref">↩</a></p></li> </ol>