TimeTree

Web Resources

Biodiversity Sites
	AmphibiaWeb	An online system to search and retrieve information relating to amphibian biology and conservation.
	Animal Diversity	An online database of animal natural history, distribution, classification, and conservation biology.
	AntWeb	An advanced biodiversity information system at species level dedicated to ants.
	Arkive	A unique collection of thousands of videos, images and fact-files illustrating the world's species.
	Catalogue of Life	An informal partnership dedicated to creating an index of the world’s organisms.
	Encyclopedia of Life	Information about all known species, including their taxonomy, geographic distribution, collections, genetics, evolutionary history, morphology, behavior, ecological relationships, etc.
	FishBase	A global information system about fishes.
	Global Biodiversity Information Facility	A source for information on biological specimen and observational data with access to more than 135 million data records from around the world.
	IUCN Redlist	A comprehensive inventory of the global conservation status of plant and animal species.
	Micro*scope	Descriptive information and images about all kinds of microbes.
	Taxonomy Browser	The names of all organisms that are represented in the genetic databases with at least one nucleotide or protein sequence, arranged hierarchically.
Molecular and Phylogenetic Sites
	ATOL	Assembling the Tree of Life (ATOL) is a large research effort sponsored by the National Science Foundation to reconstruct the evolutionary origins of all living things.
	CIPRES	Cyberinfrastructure for Phylogenetic Research (CIPRES) is an open collaboration funded by the National Science Foundation to enable large-scale phylogenetic reconstructions.
	Consortium for the Barcode of Life	An international initiative devoted to developing DNA barcoding as a global standard for the identification of biological species.
	Genome	The Genome database provides views for a variety of genomes, complete chromosomes, sequence maps with contigs, and integrated genetic and physical maps.
	Nucleotide	A collection of sequences from several sources, including GenBank, RefSeq, and PDB.
	Protein	A collection of sequences from several sources, including SwissProt, PIR, PRF, PDB, and translations from annotated coding regions in GenBank and RefSeq.
	Pubmed	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.
	Taxonomy Browser	The names of all organisms that are represented in the genetic databases with at least one nucleotide or protein sequence, arranged hierarchically.
	Tree of Life Web Project	A collection of information about biodiversity compiled collaboratively by hundreds of expert and amateur contributors.
	TreeBase	A relational database of phylogenetic information.
Software: Divergence Times
	BEAST	A cross-platform program for Bayesian MCMC analysis of molecular sequences.
	MULTIDIVTIME	Programs for studying rates of molecular evolution and for estimating divergence times.
	r8s	Program for estimating absolute rates of molecular evolution and divergence times on a phylogenetic tree.
Software: Phylogeny
	MEGA	A tool for conducting sequence alignment, tree construction, and other evolutionary analyses of molecular data.
	MrBAYES	A program for the Bayesian estimation of phylogeny.
	PAUP	Tools for inferring and interpreting evolutionary trees.
	PHYML	A fast algorithm to estimate large phylogenies by maximum likelihood.
	RAxML	A program for Maximum Likelihood-based inference of large phylogenetic trees.

Selected Literature

Review Articles
	Hedges SB. 2002. The origin and evolution of model organisms. Nature Reviews Genetics 3:838-849.
	Hedges SB, & Kumar S. 2003. Genomic clocks and evolutionary timescales. Trends in Genetics 19:200-206.
	Hedges SB, & Kumar S. 2009. Discovering the timetree of life. Pp. 3–18 in The Timetree of Life, SB Hedges and S Kumar, Eds. Oxford University Press, New York.
	Kumar S. 2005. Molecular clocks: four decades of evolution. Nature Reviews Genetics 6:654-662.
	Rutschmann F. 2006. Molecular dating of phylogenetic trees: a brief review of current methods that estimate divergence times. Diversity and Distributions 12: 35–48
	Wray GA. 2001. Dating branches on the tree of life using DNA. Genome Biology 3:1.1–1.7.
Technical Articles on Methodology
	Drummond AJ, Rambaut A. 2007. "BEAST: Bayesian evolutionary analysis by sampling trees." BMC Evolutionary Biology 7:21.
	Drummond AJ, Ho SYW, Phillips MJ & Rambaut A. 2006. Relaxed phylogenetics and dating with confidence. PLoS Biology 4: 699-710.
	Hedges SB, & Kumar S. 2004. Precision of molecular time estimates. Trends in Genetics 20:242-247.
	Hedges SB, Dudley J, & Kumar S. 2006. TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics 22:2971-2972.
	Kumar S, Filipski A, Swarna V, Walker A, & Hedges SB. 2005. Placing confidence limits on the molecular age of the human-chimpanzee divergence. Proceedings of the National Academy of Sciences 102:18842-18847
	Near TJ & Sanderson MJ. 2004. Assessing the quality of molecular divergence time estimates by fossil calibrations and fossil-based model selection. Philosophical Transactions of the Royal Society of London B 359: 1477–1483.
	Sanderson MJ. 1997. A nonparameteric approach to estimating divergence times in the absence of rate constancy. Molecular Biology and Evolution 14: 1218–1231.
	Sanderson MJ. 2003. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 19: 301–302.
	Takezaki N, Rzhetsky A, & Nei M. 1995. Phylogenetic test of the molecular clock and linearized trees. Molecular Biology and Evolution 12: 823–833.
	Thorne JL, Kishino H, & Painter IS. 1998. Estimating the rate of evolution of the rate of molecular evolution. Molecular Biology and Evolution 15: 1647–1657.
	Thorne JL, & Kishino H. 2002. Divergence time and evolutionary rate estimation with multilocus data. Systematic Biology 51: 689–702.
	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. Systematic Biology 52: 705–716.

Copyright ©2005-2013. All Rights Reserved. Substantial duplication is not permitted. We encourage wide use of this resource, but until it is complete it should not be used to represent a synthesis for any taxonomic group. Currently large scale, automated, data-mining is not permitted. Consult the authors if you have any questions about appropriate use, or if you plan to publish results from the database.