TimeTree :: The Timescale of Life

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</div>  <a name="Biodiversity Sites"></a> <h2 class="resource-category-heading text-center">Biodiversity Sites</h2> <div class="resource-container grid">  <section class="resource"> <h2 class="resource-name"> <a href="http://amphibiaweb.org/" target="_blank">AmphibiaWeb</a> </h2> <p class="resource-description"> An online system to search and retrieve information relating to amphibian biology and conservation. </p> </section> <section class="resource"> <h2 class="resource-name"> <a href="http://animaldiversity.ummz.umich.edu/site/index.html" target="_blank">Animal Diversity</a> </h2> <p class="resource-description"> An online database of animal natural history, distribution, classification, and conservation biology. </p> </section> <section class="resource"> <h2 class="resource-name"> <a href="http://www.antweb.org/" target="_blank">AntWeb</a> </h2> <p class="resource-description"> An advanced biodiversity information system at species level dedicated to ants. </p> </section> <section class="resource"> <h2 class="resource-name"> <a href="http://www.arkive.org/" target="_blank">Arkive</a> </h2> <p class="resource-description"> A unique collection of thousands of videos, images and fact-files illustrating the world's species. </p> </section> <section class="resource"> <h2 class="resource-name"> <a href="http://www.catalogueoflife.org" target="_blank">Catalogue of Life</a> </h2> <p class="resource-description"> An informal partnership dedicated to creating an index of the world's organisms. </p> </section> <section class="resource"> <h2 class="resource-name"> <a href="http://www.catalogueoflife.org" target="_blank">Encyclopedia of Life</a> </h2> <p class="resource-description"> Information about all known species, including their taxonomy, geographic distribution, collections, genetics, evolutionary history, morphology, behavior, ecological relationships, etc. </p> </section> <section class="resource"> <h2 class="resource-name"> <a href="http://www.fishbase.org/" target="_blank">FishBase</a> </h2> <p class="resource-description"> A global information system about fishes. </p> </section> <section class="resource"> <h2 class="resource-name"> <a href="http://www.gbif.org/" target="_blank">Global Biodiversity Information Facility</a> </h2> <p class="resource-description"> A source for information on biological specimen and observational data with access to more than 135 million data records from around the world. </p> </section> <section class="resource"> <h2 class="resource-name"> <a href="http://www.iucn.org/about/work/programmes/species/red_list" target="_blank">IUCN Redlist</a> </h2> <p class="resource-description"> A comprehensive inventory of the global conservation status of plant and animal species. </p> </section> <section class="resource"> <h2 class="resource-name"> <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=taxonomy" target="_blank">Taxonomy Browser</a> </h2> <p class="resource-description"> The names of all organisms that are represented in the genetic databases with at least one nucleotide or protein sequence, arranged hierarchically. </p> </section> </div> <a name="Molecular and Phylogenetic Sites"></a> <h2 class="resource-category-heading text-center">Molecular and Phylogenetic Sites</h2> <div class="resource-container grid">  <section class="resource"> <h2 class="resource-name"> <a href="http://www.phylo.org/" target="_blank">CIPRES</a> </h2> <p class="resource-description"> Cyberinfrastructure for Phylogenetic Research (CIPRES) is an open collaboration funded by the National Science Foundation to enable large-scale phylogenetic reconstructions. </p> </section> <section class="resource"> <h2 class="resource-name"> <a href="http://www.barcoding.si.edu/" target="_blank">Consortium for the Barcode of Life</a> </h2> <p class="resource-description"> An international initiative devoted to developing DNA barcoding as a global standard for the identification of biological species. </p> </section> <section class="resource"> <h2 class="resource-name"> <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome" target="_blank">Genome</a> </h2> <p class="resource-description"> The Genome database provides views for a variety of genomes, complete chromosomes, sequence maps with contigs, and integrated genetic and physical maps. </p> </section> <section class="resource"> <h2 class="resource-name"> <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=nuccore" target="_blank">Nucleotide</a> </h2> <p class="resource-description"> A collection of sequences from several sources, including GenBank, RefSeq, and PDB. </p> </section> <section class="resource"> <h2 class="resource-name"> <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=protein" target="_blank">Protein</a> </h2> <p class="resource-description"> A collection of sequences from several sources, including SwissProt, PIR, PRF, PDB, and translations from annotated coding regions in GenBank and RefSeq. </p> </section> <section class="resource"> <h2 class="resource-name"> <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed" target="_blank">Pubmed</a> </h2> <p class="resource-description"> A service of the U.S. National Library of Medicine that includes over 18 million citations from MEDLINE and other life science journals for biomedical articles back to 1948. </p> </section> <section class="resource"> <h2 class="resource-name"> <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=taxonomy" target="_blank">Taxonomy Browser</a> </h2> <p class="resource-description"> The names of all organisms that are represented in the genetic databases with at least one nucleotide or protein sequence, arranged hierarchically. </p> </section> <section class="resource"> <h2 class="resource-name"> <a href="http://www.tolweb.org/tree/" target="_blank">Tree of Life Web Project</a> </h2> <p class="resource-description"> A collection of information about biodiversity compiled collaboratively by hundreds of expert and amateur contributors. </p> </section> <section class="resource"> <h2 class="resource-name"> <a href="http://www.treebase.org/" target="_blank">TreeBase</a> </h2> <p class="resource-description"> A relational database of phylogenetic information. </p> </section> </div> <a name="Software: Divergence Times"></a> <h2 class="resource-category-heading text-center">Software: Divergence Times</h2> <div class="resource-container grid">  <section class="resource"> <h2 class="resource-name"> <a href="http://beast.bio.ed.ac.uk/" target="_blank">BEAST</a> </h2> <p class="resource-description"> A cross-platform program for Bayesian MCMC analysis of molecular sequences. </p> </section> <section class="resource"> <h2 class="resource-name"> <a href="http://statgen.ncsu.edu/thorne/multidivtime.html" target="_blank">MULTIDIVTIME</a> </h2> <p class="resource-description"> Programs for studying rates of molecular evolution and for estimating divergence times. </p> </section> <section class="resource"> <h2 class="resource-name"> <a href="http://www.ncbi.nlm.nih.gov/pubmed/12538260" target="_blank">r8s</a> </h2> <p class="resource-description"> Program for estimating absolute rates of molecular evolution and divergence times on a phylogenetic tree. </p> </section> <section class="resource"> <h2 class="resource-name"> <a href="http://www.megasoftware.net/" target="_blank">MEGA7</a> </h2> <p class="resource-description"> Contains the RelTime method for estimating divergence times. </p> </section> </div> <a name="Software: Phylogeny"></a> <h2 class="resource-category-heading text-center">Software: Phylogeny</h2> <div class="resource-container grid">  <section class="resource"> <h2 class="resource-name"> <a href="http://www.megasoftware.net/" target="_blank">MEGA</a> </h2> <p class="resource-description"> A tool for conducting sequence alignment, tree construction, and other evolutionary analyses of molecular data. </p> </section> <section class="resource"> <h2 class="resource-name"> <a href="http://mrbayes.csit.fsu.edu/index.php" target="_blank">MrBAYES</a> </h2> <p class="resource-description"> A program for the Bayesian estimation of phylogeny. </p> </section> <section class="resource"> <h2 class="resource-name"> <a href="http://paup.csit.fsu.edu/" target="_blank">PAUP</a> </h2> <p class="resource-description"> Tools for inferring and interpreting evolutionary trees. </p> </section> <section class="resource"> <h2 class="resource-name"> <a href="http://www.atgc-montpellier.fr/phyml/" target="_blank">PHYML</a> </h2> <p class="resource-description"> A fast algorithm to estimate large phylogenies by maximum likelihood. </p> </section> <section class="resource"> <h2 class="resource-name"> <a href="http://phylobench.vital-it.ch/raxml-bb/" target="_blank">RAxML</a> </h2> <p class="resource-description"> A program for Maximum Likelihood-based inference of large phylogenetic trees. </p> </section> </div>  <h2 class="literature-heading text-center">Selected Literature</h2> <section class="literature-container grid"> <a name="Review Articles"></a> <h2 class="literature-category-heading">Review Articles</h2>  <div class="literature"> <p class="literature-info"> Hedges SB. 2002. The origin and evolution of model organisms. <strong>Nature Reviews Genetics</strong> 3:838-849. </p> </div> <div class="literature"> <p class="literature-info"> Hedges SB & Kumar S. 2003. Genomic clocks and evolutionary timescales. <strong>Trends In Genetics</strong> 19:200-206. </p> </div> <div class="literature"> <p class="literature-info"> Hedges SB & Kumar S. 2009. Discovering the timetree of life. <strong>Oxford University Press, New York</strong> Pp. 3-18 in The Timetree of Life. </p> </div> <div class="literature"> <p class="literature-info"> Kumar S. 2005. Molecular clocks: four decades of evolution. <strong>Nature Reviews Genetics</strong> 6:654-662. </p> </div> <div class="literature"> <p class="literature-info"> Rutschmann F. 2006. Molecular dating of phylogenetic trees: a brief review of current methods that estimate divergence times. <strong>Diversity and Distributions</strong> 12:35-48. </p> </div> <div class="literature"> <p class="literature-info"> Wray GA. 2001. Dating branches on the tree of life using DNA. <strong>Genome Biology</strong> 3:1.1-1.7. </p> </div> <a name="Technical Articles on Methodology"></a> <h2 class="literature-category-heading">Technical Articles on Methodology</h2>  <div class="literature"> <p class="literature-info"> Drummond AJ, Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. <strong>BMC Evolutionary Biology</strong> 7:21. </p> </div> <div class="literature"> <p class="literature-info"> Drummond AJ, Ho SYW, Phillips MJ & Rambaut A. 2006. Relaxed phylogenetics and dating with confidence. <strong>PLoS Biology</strong> 4:699-710. </p> </div> <div class="literature"> <p class="literature-info"> Hedges SB & Kumar S. 2004. Precision of molecular time estimates. <strong>Trends in Genetics</strong> 20:242-247. </p> </div> <div class="literature"> <p class="literature-info"> Hedges SB, Dudley J, & Kumar S. 2006. TimeTree: a public knowledge-base of divergence times among organisms. <strong>Bioinformatics</strong> 22:2971-2972. </p> </div> <div class="literature"> <p class="literature-info"> Kumar S, Filipski A, Swarna V, Walker A, & Hedges SB. 2005. Placing confidence limits on the molecular age of the human-chimpanzee divergence. <strong>Proceedings of the National Academy of Sciences</strong> 102:18842-18847. </p> </div> <div class="literature"> <p class="literature-info"> Near TJ & Sanderson MJ. 2004. Assessing the quality of molecular divergence time estimates by fossil calibrations and fossil-based model selection. <strong>Philosophical Transactions of the Royal Society of London B</strong> 359:1477-1483. </p> </div> <div class="literature"> <p class="literature-info"> Sanderson MJ. 1997. A nonparameteric approach to estimating divergence times in the absence of rate constancy. <strong>Molecular Biology and Evolution</strong> 14:1218-1231. </p> </div> <div class="literature"> <p class="literature-info"> Sanderson MJ. 2003. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. <strong>Bioinformatics</strong> 19:301-302. </p> </div> <div class="literature"> <p class="literature-info"> Takezaki N, Rzhetsky A, & Nei M. 1995. Phylogenetic test of the molecular clock and linearized trees. <strong>Molecular Biology and Evolution</strong> 12:823-833. </p> </div> <div class="literature"> <p class="literature-info"> Thorne JL, Kishino H, & Painter IS. 1998. Estimating the rate of evolution of the rate of molecular evolution. <strong>Molecular Biology and Evolution</strong> 15:1647-1657. </p> </div> <div class="literature"> <p class="literature-info"> Thorne JL, & Kishino H. 2002. Divergence time and evolutionary rate estimation with multilocus data. <strong>Systematic Biology</strong> 51:689-702. </p> </div> <div class="literature"> <p class="literature-info"> Yang Z, & Yoder AD. 2003. Comparison of likelihood and Bayesian methods for estimating divergence times using multiple loci and calibration points, with application to a radiation of cute-looking mouse lemur species. <strong>Systematic Biology</strong> 52:705-716. </p> </div> </section>  <a name="EducationResources"></a> <h2 class="resource-edu-stu-heading text-center">Resources for Educators and Students</h2> <section class="resource-container grid"> <div class="resource"> <h2 class="resource-name"> TTOL Lesson plans </h2> <ul class="resource-edu-stu-info"> <li><a href="https://online.ucpress.edu/abt/article/81/8/543/20716/Adventures-in-Evolution-The-Narrative-of" target="_blank">Adventures in Evolution: The Narrative of Tardigrada, Trundlers in Time</a></li> <li><a href="https://online.ucpress.edu/abt/article/82/9/586/114329/Molecular-Memories-of-a-Cambrian-Fossil" target="_blank">Molecular Memories of a Cambrian Fossil</a></li> <li><a href="https://online.ucpress.edu/abt/article/80/9/650/19098/Time-Travel-and-the-Naturalist-s-Notebook-Vladimir" target="_blank">Time Travel and the Naturalist鈥檚 Notebook: Vladimir Nabokov Meets the TimeTree of Life</a></li> <li><a href="https://online.ucpress.edu/abt/article/83/3/138/116457/How-to-Build-a-Super-PredatorFrom-Genotype-to" target="_blank">How to Build a Super Predator: From Genotype to Phenotype</a></li> </ul> </div> <div class="resource"> <h2 class="resource-name"> What are Phylogenetic Trees? </h2> <ul class="resource-edu-stu-info"> <li><a href="https://evolution.berkeley.edu/the-tree-room/" target="_blank">The Tree Room Project</a></li> <li><a href="https://www.pbs.org/wgbh/nova/labs/lab/evolution/" target="_blank">PBS Evolution Lab</a></li> </ul> </div> <div class="resource"> <h2 class="resource-name"> TimeTree of Life Coloring Book </h2> <ul class="resource-edu-stu-info"> <li><a href="../public/data/pdf/TTOL_Coloring_Book.pdf" target="_blank">PDF Download</a></li> </ul> </div> </section> </div> </div> </div> </main> <footer> <div class="container"> <div class="row"> <div class="col-sm-2 col-sm-offset-1 hidden-xs"> <h2 class="footer-heading" id="site-links">Site Links</h2> <nav aria-labelledby="site-links"> <ul class="site-links-list"> <li class="site-links-link"> <a href="/about" class="">About</a> </li> <li class="site-links-link"> <a href="/book" class="">Book</a> </li> <li class="site-links-link"> <a href="/references" class="">Studies</a> </li> <li class="site-links-link"> <a href="/resources" class="active">Resources</a> </li> <li class="main-nav-link"> <a href="/movies" class="">Movie</a> </li> <li class="site-links-link"> <a href="/news" class="">News</a> </li> <li class="site-links-link"> <a href="/faqs" class="">FAQs</a> </li> <li class="site-links-link"> <a href="/contact" class="">Contact</a> </li> </ul> </nav> </div> <div class="col-xs-12 col-sm-4 col-sm-offset-1"> <h2 class="footer-heading" id="footer-contact">Contact</h2> <address class="footer-contact" aria-labelledby="footer-contact"> Institute for Genomics and Evolutionary Medicine<br /> Center of Biodiversity<br /> Temple University<br /> 1925 N. 12th Street<br /> Philadelphia, PA 19122-1801<br /> Email: <a href="mailto:info@timetree.org" target="_top">info@timetree.org</a> </address> </div> <div class="col-xs-12 col-sm-3"> <h2 class="footer-heading" id="ios-app">iOS App</h2> <p aria-labelledby="ios-app"> <a href="https://itunes.apple.com/us/app/timetree-4/id372842500?mt=8" target="_blank">Download the TimeTree app</a> on the App Store </p> </div> <div class="col-xs-12 col-sm-10 col-sm-offset-1"> <p class="copyright-info"> <small>Copyright © 2005 – 2025. Data and syntheses accessed from TimeTree are provided openly for personal research and teaching use. Requests to use these data for all other purposes must be sent to <a href="mailto:info@timetree.org">info@timetree.org</a>. Redistribution of TimeTree data and its transformations are not permitted. Publications utilizing the TimeTree resource or data are encouraged to include a citation to TimeTree. Please write to <a href="mailto:info@timetree.org">info@timetree.org</a> for clarifications.</small> </p> <p class="copyright-info"> <small>Note: copyright holders expressly disclaim any warranty for processed study timetrees and other data accessed from these resources. Data are provided 'As Is' without any express or implied warranty of any kind, including but not limited to any warranties of merchantability, non-infringement, or fitness for a particular purpose.</small> </p> <p class="citation-directions"> <small><strong>CITE THIS RESOURCE AS</strong>: S. Kumar, M. Suleski, J.E. Craig, A.E. Kasprowicz, M. Sanderford, M. Li, G. Stecher, and S.B. Hedges, 2022. <a class="pdflink" href="https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msac174/6657692" target="_blank">TimeTree 5: An Expanded Resource for Species Divergence Times</a>. Molecular Biology and Evolution, DOI: 10.1093/molbev/msac174.</small> </p> </div> </div> </div> </footer> <script> (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){ (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); ga('create', 'UA-4210986-3', 'auto'); ga('send', 'pageview'); </script> </body> </html>

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TimeTree :: The Timescale of Life