We have now seen several examples of evolution, in proteins and in genomes. These represent the extension to the molecular level of concerns that have occupied biologists since Darwin and even before. The basic principle is that the origin of similarity is common ancestry. Although there are many exceptions, arising from convergent evolution, the importance of this principle both for rationalizing contemporary observations and giving a window into the history of life cannot be overestimated.

The field of phylogeny has the goals of working out the relationships among species, populations, individuals, or genes. ^[3] Relationship is taken in the literal sense of kinship or genealogy, that is, assignment of a scheme of descendants of a common ancestor (see Box). The results are usually presented in the form of an evolutionary tree. The taxonomy of the ratites - large flightless birds - is a typical example (Fig. 4.7a). The ancestor of the ratites is believed to be a bird that could fly, probably related to the extant tinamous.

Figure 4.7: (a) Phylogenetic tree of ratites (large flightless birds) based on mitochondrial DNA sequences. The common ancestor is at the root of this tree. A surprising implication of these DNA sequences is that the moa and kiwi are not closest relatives, and therefore that New Zealand must have been colonized twice by ratites or their ancestors. (b) Unrooted tree of relationships among finches from the Galapagos and Cocos Islands. Darwin studied the Galapagos finches in 1835, noting...