The reconstruction of phylogeny - Summary
• Phylogenetic relations are inferred using the shared characters of species. The best estimate of the phylogeny of a set of species is the one requiring the smallest number of evolutionary character changes. This is called the principle of parsimony.
• Phylogenies are often incompletely determined, in the form of an unrooted tree. An unrooted tree specifies the branching relations among species, but not the direction of evolution. The root can be identified if character polarities can be inferred.
• When different characters imply the same phylogeny, phylogenetic inference is easy; when they do not, methods are needed to unravel the disagreement.
• Homoplasies and ancestral homologies do not reliably indicate phylogenetic groups. Derived homologies do. Phylogenetic inference should rely on shared derived homologies.
• Character polarities can be inferred, with varying degrees of certainty, by outgroup comparison, the embryological criterion, and the fossil record.
• For molecular characters, the kinds of character analysis used with morphology are often inapplicable. Phylogenies are usually inferred by statistical techniques.
• The principle of parsimony can reconstruct an unrooted tree from a set of molecular sequences. The phylogeny can then be inferred provided that similarity is proportional to recency of common ancestry.
• When different classes of evidence, such as molecular and fossil evidence, indicate differing phylogenies, the evidence can all be re-scrutinized to find which is most reliable. No single class of evidence is universally more reliable than other classes.