Daubin, V., and H. Ochman. (2004) Bacterial Genomes As New Gene Homes: The Genealogy of Orfans in E. Coli. Genome Res 14: 1,036—1,042.
Davidov, Y., and E. Jurkevitch. (2009) Predation Between Prokaryotes and the Origin of Eukaryotes. Bioessays 31: 748–757.
Daviter, T., K. B. Gromadski, and M. V. Rodnina. (2006) The Ribosome’s Response to Codon-Anticodon Mismatches. Biochimie 88: 1,001—1,011.
Dawkins, R. (1996) The Blind Watchmaker: Why the Evidence of Evolution Reveals a Universe Without Design. London: W.W. Norton & Co.
Dawkins, R. (2006) The Selfish Gene: 30th Anniversary Edition — with a New Introduction by the Author. Oxford: Oxford University Press.
Dayhoff, M. O., W. C. Barker, and L. T. Hunt. (1983) Establishing Homologies in Protein Sequences. Methods Enzymol 91: 524–545.
de Nooijer, S., B. R. Holland, and D. Penny. (2009) The Emergence of Predators in Early Life: There Was No Garden of Eden. PLoS ONE 4: e5507.
de Souza, S. J., M. Long, R. J. Klein, S. Roy, S. Lin, and W. Gilbert. (1998) Toward a Resolution of the Introns Early/Late Debate: Only Phase Zero Introns Are Correlated with the Structure of Ancient Proteins. Proc Natl Acad Sci USA 95: 5,094—5,099.
de Visser, J. A., and S. F. Elena. (2007) The Evolution of Sex: Empirical Insights into the Roles of Epistasis and Drift. Nat Rev Genet 8: 139–149.
Deckert, G., P. V. Warren, T. Gaasterland, W. G. Young, A. L. Lenox, D. E. Graham, R. Overbeek, M. A. Snead, M. Keller, M. Aujay, R. Huber, R. A. Feldman, J. M. Short, G. J. Olsen, and R. V. Swanson. (1998) The Complete Genome of the Hyperthermophilic Bacterium Aquifex Aeolicus. Nature 392: 353–358.
Delarue, M., O. Poch, N. Tordo, D. Moras, and P. Argos. (1990) An Attempt to Unify the Structure of Polymerases. Protein Eng 3: 461–467.
Delaye, L., and A. Moya. (2010) Evolution of Reduced Prokaryotic Genomes and the Minimal Cell Concept: Variations on a Theme. Bioessays 32: 281–287.
Deleuze, G., and F. Guattari. (1987) Thousand Plateaus: Capitalism and Schizophrenia. Minneapolis, MN: University of Minnesota Press.
Denamur E. and I. Matic. (2006) Evolution of Mutation Rates in Bacteria. Mol Microbiol 60: 820–827.
Dennett, D. C. (1996) Darwin‘s Dangerous Idea: Evolution and the Meanings of Life. New York: Simon & Schuster.
Deppenmeier, U., A. Johann, T. Hartsch, R. Merkl, R. A. Schmitz, R. Martinez-Arias, A. Henne, A. Wiezer, S. Baumer, C. Jacobi, H. Bruggemann, T. Lienard, A. Christmann, M. Bomeke, S. Steckel, A. Bhattacharyya, A. Lykidis, R. Overbeek, H. P. Klenk, R. P. Gunsalus, H. J. Fritz, and G. Gottschalk. (2002) The Genome of Methanosarcina Mazei: Evidence for Lateral Gene Transfer Between Bacteria and Archaea. J Mol Microbiol Biotechnol 4: 453–461.
Deveau, H., J. E. Garneau, and S. Moineau. (2010) CRISPR/Cas System and Its Role in Phage-Bacteria Interactions. Annu Rev Microbiol 64: 475–493.
Diaz, R., C. Vargas-Lagunas, M. A. Villalobos, H. Peralta, Y. Mora, S. Encarnacion, L. Girard, and J. Mora. (2011) argC Orthologs from Rhizobiales Show Diverse Profiles of Transcriptional Efficiency and Functionality in Sinorhizobium Meliloti. J Bacteriol 193: 460–472.
Ding, S. W. (2010) RNA-Based Antiviral Immunity. Nat Rev Immunol 10: 632–644.
Dlakic, M. and A. Mushegian. (2011) Prp8, the Pivotal Protein of the Spliceosomal Catalytic Center, Evolved from a Retroelement-Encoded Reverse Transcriptase. RNA [Epub ahead of print].
Dobzhansky, T. (1951). Genetics and the Origin of Species. New York: Columbia University Press.
Dobzhansky, T. (1973) Nothing in Biology Makes Sense Except in the Light of Evolution. The American Biology Teacher 35: 125–129.
Dong, H., and C. G. Kurland. (1995) Ribosome Mutants with Altered Accuracy Translate with Reduced Processivity. J Mol Biol 248: 551–561.
Doolittle, R. F. (1995) The Multiplicity of Domains in Proteins. Annu Rev Biochem 64: 287–314.
Doolittle, W. F. (1999a) Lateral Genomics. Trends Cell Biol 9: M5—8.
Doolittle, W. F. (1999b) Phylogenetic Classification and the Universal Tree. Science 284: 2,124—2,129.
Doolittle, W. F. (2000) Uprooting the Tree of Life. Sci Am 282: 90–95.
Doolittle, W. F., and E. Bapteste. (2007) Pattern Pluralism and the Tree of Life Hypothesis. Proc Natl Acad Sci USA 104: 2,043—2,049.
Doolittle, W. F., and J. R. Brown. (1994) Tempo, Mode, the Progenote, and the Universal Root. Proc Natl Acad Sci USA 91: 6,721—6,728.
Doolittle, W. F., and C. Sapienza. (1980) Selfish Genes, the Phenotype Paradigm and Genome Evolution. Nature 284: 601–603.
Doolittle, W. F., and O. Zhaxybayeva. (2009) On the Origin of Prokaryotic Species. Genome Res 19: 744–756.
Doudna, J. A., and T. R. Cech. (2002) The Chemical Repertoire of Natural Ribozymes. Nature 418: 222–228.
Douzery, E. J., E. A. Snell, E. Bapteste, F. Delsuc, and H. Philippe. (2004) The Timing of Eukaryotic Evolution: Does a Relaxed Molecular Clock Reconcile Proteins and Fossils? Proc Natl Acad Sci USA 101: 15,386—15,391.
Draghi, J. A., T. L. Parsons, G. P. Wagner, and J. B. Plotkin. (2010) Mutational Robustness Can Facilitate Adaptation. Nature 463: 353–355.
Drake, J. W. (1991) A Constant Rate of Spontaneous Mutation in DNA-Based Microbes. Proc Natl Acad Sci USA 88: 7,160—7,164.
Drake, J. W., and J. J. Holland. (1999) Mutation Rates Among RNA Viruses. Proc Natl Acad Sci USA 96: 13,910—13,913.
Dronamraju, K. R., ed. (1968) Haldane and Modern Biology. Baltimore, Johns Hopkins University Press.
Drummond, D. A., J. D. Bloom, C. Adami, C. O. Wilke, and F. H. Arnold. (2005) Why Highly Expressed Proteins Evolve Slowly. Proc Natl Acad Sci USA 102: 14,338—14,343.
Drummond, D. A., A. Raval, and C. O. Wilke. (2006) A Single Determinant Dominates the Rate of Yeast Protein Evolution. Mol Biol Evol 23: 327–337.
Drummond, D. A., and C. O. Wilke. (2008) Mistranslation-Induced Protein Misfolding As a Dominant Constraint on Coding-Sequence Evolution. Cell 134: 341–352.
