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D

Dayhoff, M. O., R. V. Eck and C. M. Park. 1972. A model of evolutionary change in proteins. In Atlas of Protein Sequence and Structure Vol. 5 (ed. M.O. Dayhoff), pp. 89-99. National Biomedical Research Foundation, Washington DC. aamodels

Dayhoff, M. O., R. M. Schwartz and B. C. Orcutt. 1978. A model of evolutionary change in proteins. In Atlas of Protein Sequence and Structure Vol. 5 suppl. 2 (ed. M.O. Dayhoff), pp. 345-352. National Biomedical Research Foundation, Washington DC. aamodels

Dennehy, J. J., N. A. Friedenberg, R. D. Holt, and P. E. Turner. Viral ecology and the maintenance of novel host use. Am. Nat. 167:429-439.

Derr, L. K., J. N. Strathern and D. J. Garfinkel. 1991. RNA-mediated recombination in S. cerevisiae. Cell 67:355-364.

Devos, K. M., J. K. Brown and J. L. Bennetzen. 2002. Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Research 12:1075-1079.

Donze, D., C. R. Adams, J. Rine, and R. T. Kamakaka. 1999. The boundaries of the silenced HMR domain in Saccharomyces cerevisiae. Genes Dev. 13:698-708

Douady C. J., F. Delsuc, Y. Boucher, W. F. Doolittle and E. J. P. Douzery. 2003. Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability. Mol. Biol. Evol. 20(2):248-254.

Douady C. J., F. Catzeflies, D.J. Kao, M.S. Springer, M.J. Stanhope 2002. Molecular evidence for the monophyly of Tenrecidae (Mammalia) and the timing of the colinization of Madagascar by Malagasy Tenrecs. Mol. Phylogenet. Evol. 22:357-363.

Drummond, A. J., S.Y.W. Ho, M.J. Phillips, A. Rambaut. 2006. Relaxed phylogenetics and dating with confidence. PLOS Biol. 4:e88.

Drummond, A. J., G. K. Nichols, A. G. Rodrigo and W. Solomon. 2002. Estimating mutation parameters, population history and genealogy simultaneously from temporarally spaced sequence data. Genetics. 161:1307-1320.

Drummond, A. J., and A.Rambaut. Bayesian evolutionary analysis by sampling trees. In The Phylogenetics Handbook, 2nd edition. Cambridge University Press, In Press.

Drummond, A. J., and A.Rambaut. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology 7:214.

Drummond, A. J., A. Rambaut, B. Shapiro and O. G. Pybus. 2005. Bayesian coalescent inference of past population dynamics from molecular sequences. Mol. Biol. Evol. 22:1185-1192.

Dunn, J. Bielawski, and Z. Yang. 2001. Rates and patterns of synonymous substitutions in Drosophila: Implications for translational selection. Genetics. 157:295-305.

Duffy, S., P. E. Turner, and C. L. Burch. 2006. Pleiotropic costs of niche expansion in the RNA bacteriophage phi6. Genetics 172:751-757.

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