Phylogenetic analysis of conservative nucleotide substitutions in 18 complete sequences of the mitochondrial cytochrome b gene of Phocidae (true seals), Odobenidae (walruses), and Otariidae (sea lions and fur seals), plus three ursid and three felid sequences, identified the pinnipeds as monophyletic with Otariidae and Odobenidae on a common evolutionary branch. Analysis of total nucleotide differences separated the evolutionary lineages of northern and southern phocids. Both lineages are distinct from the most ancestral phocid genus, Monachus (monk seals), represented by the Hawaiian monk seal. The inclusion of the Hawaiian monk seal in the subfamily Monachinae makes the subfamily paraphyletic. Among the northern phocids, the hooded seal (genus Cystophora, chromosome number 2n = 34) is sister taxon to the Phoca complex. The Phoca complex, which is characterized by the chromosome number 2n = 32, includes genus Phoca and the monotypic genus Halichoerus (grey seal). The comparison does not support a generic distinction of Halichoerus within the Phoca complex. The present data suggest that Cystophora and Phoca separated greater than or equal to 6 million years ago. Among the southern phocids the close molecular relationship of the Weddell and leopard seals relative to their morphological distinction exemplifies rapid adaptation to different ecological niches. This result stands in contrast to the limited morphological differentiation relative to the pronounced molecular distinctions that may occur within the Phoca complex.
