Avian Molecular Systematics, 1970s to 1990s

We assessed the current state of avian molecular systematics by (i) considering some of the historical factors that have shaped the field in the last 20 years, (ii) reviewing the most commonly used molecular methods, and (iii) comparing higher-level phylogenies via congruence analysis. This three-pronged approach permitted us to identify strongly supported aspects of avian phylogeny and to propose technological and methodological explanations when congruence was low. We found, in general, that few areas of higher-level avian phylogeny are well supported and, hence, well understood. One main reason for this is that, despite a great deal of effort, few studies of higher-level avian phylogenetic relationships have been well planned and executed. Some investigations, for example, have gone astray because of preconceptions about rates of molecular evolution and monophyly, and others suffer from such problems as failure to find the shortest tree, lack of an outgroup, use of a nonmetric distance measure, and simple mistakes. This is not to say, however, that available techniques are incapable of reconstructing avian phylogeny. The extent of congruence that we found among branching patterns estimated by different methods, including carefully designed cladistic morphological analyses, indicates that when applied appropriately, a variety of methods provide useful insight into phylogeny.