Survey of Hox-like genes in the teleost Morone saxatilis: implications for evolution of the Hox gene family.

We used a PCR-based method to survey a defined subset of Hox-like genes in the genome of Morone saxatilis (striped bass) to determine their relationship to similar Hox genes in other vertebrates, to estimate Hox cluster number, and to gain additional information about vertebrate Hox gene evolution. We identified eight distinct striped bass Hox-like genes representing Hox clusters A, B, and C. Comparison of Hox gene evolutionary trees from striped bass, zebrafish, and mouse provided evidence consistent with current views of early evolutionary divergence of genes from the Hox 3' and central classes. However, estimates of Hox gene divergence based on nucleotide substitution frequencies among four fish species and the mouse were contrary to established vertebrate phylogenies according to either traditional or molecular taxonomic analyses.