Comparative genomics provides evidence for an ancient genome duplication event in fish

There are approximately 25 000 species in the division Teleostei and most a rc believed to have arisen during a relatively short period of time ca. 200 Myr ago. The discovery of 'extra' Hox gene clusters in zebrafish (Danio re rio), medaka (Oryzias latipes), and pufferfish (Fugu rubripes), has led to the hypothesis that genome duplication provided the genetic raw material ne cessary for the telcost radiation. We identified 27 groups of orthologous g enes which included one gene from man, mouse and chicken, one or two genes from tetraploid Xenopus and two genes from zebrafish. A genome duplication in the ancestor of teleost fishes is the most parsimonious explanation for the observations that for 15 of these genes, the two zebrafish orthologues are sister sequences in phylogenies that otherwise match the expected organ ismal tree, the zebrafish gene pairs appear to have been formed at approxim ately the same time, and are unlinked. Phylogenies of nine genes differ a l ittle from the tree predicted by the fish-specific genome duplication hypot hesis: one tree shows a sister sequence relationship for the zebrafish gene s but differs slightly from the expected organismal tree and in eight trees , one zebrafish gene is the sister sequence to a clade which includes the s econd zebrafish gene and orthologues from Xenopus, chicken, mouse and man. For these nine gene trees, deviations from the predictions of the fish-spec ific genome duplication hypothesis are poorly supported. The two zebrafish orthologues for each of the three remaining genes are tightly linked and ar e, therefore, unlikely to have been formed during a genome duplication even t. We estimated that the unlinked duplicated zebrafish genes are between 30 0 and 450 Myr. Thus, genome duplication could have provided the genetic raw material for teleost radiation. Alternatively, the loss of different dupli cates in different populations (i.e. 'divergent resolution') may have promo ted speciation in ancient teleost populations.