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Freeman, S., and J. C. Heron. 2001. Evolutionary analysis. 2d ed. Upper Sable River, NJ: Prentice Hall.
An excellent inquiry-based college-level textbook on evolution. It is somewhat more accessible than Futuyma's textbook.
Futuyma, D. J. 1998. Evolutionary biology. 3d ed. Sunderland, MA: Sinauer Press.
This is perhaps the most comprehensive textbook on evolutionary biology. It also provides an excellent entry into the primary literature of evolutionary biology.
Article
Hillis, D. M, J. P. Huelsenbeck, and C. W. Cunningham. 1994. Application and accuracy of molecular phylogenies. Science 264:671-77.
A technical review of the state of phylogenetic systematics as of the middle 1990s.
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