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LET’S SUPPOSE that we are interested in studying the evolution of the squamates, the snakes and lizards. We know that if we track down the evolutionary tree of the squamates we find that they are lepidosauromorphs, and a sister group to the archosauromorphs. Ah-hah! The archosauromorphs diverged before the evolution of the lizards, so living archosauromorphs must preserve ancestral traits, we think. So we go forth and find an archosauromorph and sequence its genome. There are multiple species from which to choose, but we grab the closest one—the European starling. Since this is an archosauromorph and early diverging compared to the snakes and lizards that must mean that it is “primitive”.
Does this seem odd to you?
I RECENTLY READ a paleontology book that irked me by referring to the basal synapsids as “mammal-like reptiles”. This term pre-dates modern phylogenetics. It violates several rules of phylogenetics, the first being that all clades (groups of related organisms) should contain organisms sharing a single common ancestor in that clade, and the second being that clades should nest within each other, so that each more recent clade fits into its ancestors’ clades as well. In other words, clades should not be polyphyletic, but monophyletic. An example of a polyphyletic group is the pachydermata, an obsolete category containing elephants, hippopotami, rhinoceri, horses, tapirs, and pigs simply on the basis that these organisms have thick skin and hooves. Now these animals are placed into separate clades since they do not share a recent common ancestor. Polyphyletic groups are a great embarrassment to phylogenicists.