The phylogenetic position of the zebrafish (Danio rerio), a model system in developmental biology: an invitation to the comparative method.

The zebrafish, Danio (Brachydanio) rerio, has become one of the most widely studied model systems in developmental biology. We present a DNA-based phylogeny of zebrafish and other species of the genus Danio, and the genera Rasbora, Puntius and Cyprinus. Homologous regions of the large (16S) mitochondrial ribosomal RNA gene were amplified by the polymerase chain reaction and directly sequenced. The phylogeny revealed: (i) the zebrafish, Danio (Brachydanio) rerio, is identical in its 16S sequence to its aquarium breeding morph, the leopard danio; (ii) the pearl danio (Danio albolineatus) is more closely related to the zebrafish than the giant danio (Danio aequipinnatus); and (iii) species of the genus Rasbora (hetermorpha, trilineata, elegans, pauciperforata, dorsiocellata) are more closely related to the danios than members of the genus Puntius (tetrazona, conchonius) and Cyprinus, the carp. All of these species are readily available in the aquarium trade, easily kept and bred in captivity, and amenable to developmental work. It is hoped that this molecular phylogeny will invite developmental biologists to use the comparative method to ask questions about function (e.g. cellular and genetic aspects) and evolution of zebrafish developmental biology in a phylogenetic context.