Web Resources

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

Selected Literature

Review Articles
PDF Hedges SB. 2002. The origin and evolution of model organisms. Nature Reviews Genetics 3:838-849.
PDF Hedges SB, & Kumar S. 2003. Genomic clocks and evolutionary timescales. Trends in Genetics 19:200-206.
PDF 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.
PDF 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.
PDF Hedges SB, & Kumar S. 2004. Precision of molecular time estimates. Trends in Genetics 20:242-247.
PDF Hedges SB, Dudley J, & Kumar S. 2006. TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics 22:2971-2972.
PDF 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.