The mitochondrial DNA control region is one of the most frequently utilized sequences for both intra- and interspecific genetic studies of fishes, yet a tenable divergence rate specifically for fish control regions has not been established. We attempted to establish a rate through a comparative study of control region sequences and those of a protein-coding mitochondrial gene region from geminate species of snook (Centropomus) assumed to have been separated by the emergence of the Isthmus of Panama 3.5 million years ago. The divergence rate suggested from the control region alignments between the geminates was markedly higher than rates currently applied in many studies, as was the rate suggested from the ND 5/6 protein coding region alignments. However, the suggested ND 5/6 rate when applied to alignments with the outgroup species was not concordant with the scant centropomid fossil record and therefore the assumed separation time of 3.5 million years seemed implausible. An average control region divergence rate was then estimated based on separation times of snook species derived assuming a divergence rate of 1% per million years for transversion substitutions at third codon positions in the ND 5/6 region. Using these separation times, a tenable average divergence rate for fish control regions of approximately 3.6% per million years +/- 0.46% SE was calculated.
Copyright 1999 Academic Press.