Flanagan, N., A. Tobler, A. Davison, O. G. Pybus, D. D. Kapan, S. Planas, M. Linares, D. Heckel, and W. O. McMillan. (2003) The historical demography of Mullerian mimicry in Heliconius butterflies. Proceedings of the National Academy of Sciences USA (in prep).

Rivera, E., M. Aide, and W. O. McMillan. (2003) Small-scale patterns of genetic diversity in P. officinalis. Conservation Biology (submitted).

Bull, V., M. Beltrán, E. Bermingham, C. D. Jiggins, W. O. McMillan and J. Mallet. (2003) Molecular evidence for gene flow between species. Proceedings of the Royal Society of London, B (submitted).

Bennett, S. N., E. C. Holmes, M. Chirivella, D. M. Rodriguez, M. Beltran, V. Vorndam, D. Gubler, and W. O. McMillan. (2003) Selection-driven evolution of emergent dengue virus. Molecular Biology and Evolution (in press).

McCartney, M., J. Patricia, C. Rico, E. Bermingham, and W. O. McMillan. (2003) Genetic mosaic of a marine species flock. Molecular Ecology(in press).

Foster, J. E., S. N. Bennett, H. Vaughan, V. Vorndam, W.O. McMillan, and C.V.F. Carrington. (2003) Molecular evolution and phylogeny of Dengue Type 4 virus in the Caribbean. Journal of Virology (in press).

Flanagan, N.S., A. Davison, M. Blum, and W.O. McMillan . (2002) Characterization of microsatellite loci in neotropical Heliconius butterflies. Molecular Ecology (in press).

Beltrán M., C. D. Jiggins, V. Bull, M. Linares, W. O. McMillan, E. Bermingham and J.Mallet. (2002) Phylogenetic discordance at the species boundary: comparative gene genealogies among Heliconius butterflies. Molecular Biology and Evolution (in press).

Rivera, E., M. Aide, and W. O. McMillan. (2002) Regional patterns of genetic diversity in P. officinalis Molecular Ecology 11:675-684.

McMillan, W. O., A. Monteiro, and D. Kapan. (2002) Evolution and development on the wing. Trends in Ecology and Evolution, 17:125-133.

McMillan, W. O. and S. R. Palumbi. (1999) Color pattern evolution, mate preference and genetic differentiation in brightly colored butterflyfishes (Chaetodontidae). Evolution, 53: 247-260.

Davison, A., McMillan, W. O., Griffin, A. S., Jiggins, C., & Mallet, J. L. B. (1999) Behavioral and physiological differences between two parapatric Heliconius species. Biotropica, 31(4): 661-8.

Mallet, J., W. O. McMillan and C. D. Jiggins. (1998) Mate choice between a pair of Heliconius species in the wild. Evolution, 52:503-510.

Whitehouse, D. B., J. Tomkins, J. U. Lovegrove, D. A. Hopkinson, and W. O. McMillan. (1998) A phylogenetic approach to the identification of phosphoglucomutase genes. Molecular Biology and Evolution, 15:456-462.

Jiggins, C. D., W. O. McMillan, and J. Mallet. (1997) Host plant adaptation has not played a role in the recent speciation of Heliconius himera and H. erato. Ecological Entomology 22: 361-365.

Jiggins, C. D., W. O. McMillan, P. King and J. Mallet. (1997) The maintenance of species differences across a Heliconius hybrid zone. Heredity 79: 495-505.

Jiggins, C. J. and W. O. McMillan. (1997) The genetic basis of an adaptive radiation: mimicry in two Heliconius species. Proceedings of the Royal Society of London, B 264: 1168-1175.

McMillan, W. O. and S. R. Palumbi. (1997) Rapid rate of control region evolution in Pacific Butterflyfishes. Journal of Molecular Evolution 45: 473-484.

McMillan, W. O., C. D. Jiggins, and J. Mallet. (1997) What initiates speciation in passion-vine butterflies? Proceedings of the National Academy of Sciences USA 94: 8628-8633.

Mallet, J., C. D. Jiggins, and W. O. McMillan. (1996) Mimicry meets the mitochondrion. Current Biology 6 (8):937-940.

Jiggins, C. D., W. O. McMillan, W. Neuikirchen, and J. Mallet. (1996) What can hybrid zones tell us about speciation: a case in Heliconius butterflies. Biological Journal of the Linean Society 59: 221-242.

McMillan, W. O. and E. Bermingham. (1996) The phylogeographic patterning of mitochondrial DNA variation in Dall¹s porpoise (Phocoenoides dalli). Molecular Ecology 5: 47-61.

McMillan, W. O. and S. R. Palumbi. (1995) Concordant evolutionary patterns among Indo-West Pacific Butterflyfishes. Proceedings of the Royal Society of London, B 260: 229-236.

McMillan, W. O., R. A. Raff, and S. R. Palumbi. (1992) Population genetic consequences of developmental evolution and reduced dispersal in sea urchins (Genus Heliocidaris). Evolution 46: 1299-1312.

Book Chapters:

Mallet, J., W. O. McMillan and C. D. Jiggins. (1998) Mimicry and warning color at the boundary between microevolution and macroevolution. In Endless Forms: Species and Speciation, D. Howard and S. Berlocher, eds. Oxford University Press.

Hammond, R. L., I. J. Saccheri, C. Ciofi, T. Coote, S. M. Funk, W. O. McMillan, E. Taylor, and M. Bruford. (1997) Isolation of microsatellite markers in animals. In Molecular Tools for Screening Biodiversity, A. Karp, P. G. Isaac, and D. S. Ingram, eds. Chapman and Hall.

Palumbi, S. R., A. P. Martin, B. Kessing and W.O. McMillan. (1991) Detecting population structure using mitochondrial DNA. In Cetacean Genetics. International Whaling Commission. Cambridge, UK.