The methods of phylogenetic systematics are discussed in a number of sources. Key primary literature includes the classic work of Willi Hennig, published originally in German (Grundzüge einer Theorie der phylogenetischen Systematik [Berlin: Deutscher Zentralverlag, 1950]) and translated into English more than a decade later (Phylogenetic Systematics, trans. D. D. Davis and R. Zangerl [Urbana: University of Illinois Press, 1966]).
Methods of phylogenetic reconstruction, which form the basis for the chapter, are discussed in detail in P. Forey, ed., Cladistics: A Practical Course in Systematics (Oxford, Eng.: Clarendon Press, 1992); D. Hillis, C. Moritz, and B. Mable, eds., Molecular Systematics (Sunderland, Mass.: Sinauer Associates, 1996); R. DeSalle, G. Girbet, and W. Wheeler, Molecular Systematics and Evolution: Theory and Practice (Basel: BirkhauserVerlag, 2002).
A comprehensive treatment of the phenomenon of independent evolution of similar features is in M. Sanderson and L. Hufford, Homoplasy: The Recurrence of Similarity in Evolution (San Diego: Academic Press, 1996).
To see the tree of life and the different hypotheses for the relationships between living creatures, visit http://tolweb.org/tree/.
The notion that our evolutionary history has medical implications has been the subject of several good recent books. For comprehensive and well-referenced treatments, see N. Boaz, Evolving Health: The Origins of Illness and How the Modern World Is Making Us Sick (New York: Wiley, 2002); D. Mindell, The Evolving World: Evolution in Everyday Life (Cambridge, Mass.: Harvard University Press, 2006); R. M. Nesse and G. C. Williams, Why We Get Sick: The New Science of Darwinian Medicine (New York: Vintage, 1996); W. R. Trevathan, E. O. Smith, and J. J. McKenna, Evolutionary Medicine (New York: Oxford University Press, 1999).
The apnea example I derived from discussions with Nino Ramirez, chairman of the Department of Anatomy at the University of Chicago. The hiccup example is derived from Straus, C., et al. (2003) A phylogenetic hypothesis for the origin of hiccoughs, Bioessays 25:182-188. The human-bacterial gene switch used in the study of mitochondrial cardioencephalomyopathy was originally discussed in Lucioli, S., et al. (2006) Introducing a novel human mtDNA mutation into the Paracoccus denitriticans COX 1 gene explains functional deficits in a patient, Neurogenetics 7:51-57.
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