© 2004 The American Genetic Association
A Comprehensive and Validated Molecular Taxonomy of Beaked Whales, Family Ziphiidae
From the School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand (Dalebout and Baker); National Museum of Natural History, Mail Stop NHB 108, Smithsonian Institution, Washington, DC 20560 (Mead); Center for Dolphin Studies, Box 1856, Plettenberg Bay 6600, South Africa (Cockcroft); and National Science Museum, Tokyo, 3-23-1 Hyakunin-cho, Shinjuku-ku, Tokyo 169-0073, Japan (Yamada). M. L. Dalebout is currently at the Biology Department, Dalhousie University, Halifax, Nova Scotia B3H 4JI, Canada
Address correspondence to C. Scott Baker at the address above, or e-mail: cs.baker{at}auckland.ac.nz.
DNA sequences from orthologous loci can provide universal characters for taxonomic identification. Molecular taxonomy is of particular value for groups in which distinctive morphological features are difficult to observe or compare. To assist in species identification for the little known family Ziphiidae (beaked whales), we compiled a reference database of mitochondrial DNA (mtDNA) control region (437 bp) and cytochrome b (384 bp) sequences for all 21 described species in this group. This mtDNA database is complemented by a nuclear database of actin intron sequences (925 bp) for 17 of the 21 species. All reference sequences were derived from specimens validated by diagnostic skeletal material or other documentation, and included four holotypes. Phylogenetic analyses of mtDNA sequences confirmed the genetic distinctiveness of all beaked whale species currently recognized. Both mitochondrial loci were well suited for species identification, with reference sequences for all known ziphiids forming robust species-specific clades in phylogenetic reconstructions. The majority of species were also distinguished by nuclear alleles. Phylogenetic comparison of sequence data from "test" specimens to these reference databases resulted in three major taxonomic discoveries involving animals previously misclassified from morphology. Based on our experience with this family and the order Cetacea as a whole, we suggest that a molecular taxonomy should consider the following components: comprehensiveness, validation, locus sensitivity, genetic distinctiveness and exclusivity, concordance, and universal accessibility and curation.