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This study examines the genetic variation in 45 taxa of all tribes and most species of North American waterfowl (Anatidae) with a starch-gel electrophoretic survey of protein variation at 25 loci. Relationships were estimated using the resulting data from the patterns of allozyme variation and summarized in both phenetic and cladistic branching diagrams. The branching diagrams (phylogenetic trees) are employed to help compare and contrast phylogenetic relationships relative to other hypothesis. Although results of this study generally concur with classic phylogenetic trees and the taxonomic designations of the current American Ornithologists' Union (AOU) Check-list, exceptions are noted. Genetic data strongly contradict inclusion of Chen canagica (emperor goose) within the genus Chen. Clangula hyemalis (oldsquaw) and Melanitta nigra (black scoter) do not cluster on the branching diagrams as would be predicted from classical analysis. It is possible that they form a divergent group within the Tribe MERGINI.