Intraspecific DNA sequence variation of the mitochondrial control region of white sturgeon (Acipenser transmontanus)

Intraspecific sequence variation in the D-loop region of mtDNA in whitesturgeon (Acipenser transmontanus), a relict North American fish species,was examined in 27 individuals from populations of the Columbia and Fraserrivers. Thirty-three varied nucleotide positions were present in a462-nucleotide D-loop sequence, amplified using the polymerase chainreaction. Bootstrapped neighbor-joining and maximum- parsimony trees ofsequences from 19 haplotypes suggest that the two populations have recentlydiverged. This is consistent with the hypothesis that the Columbia River, aPleistocene refugium habitat, was the source of founders for the FraserRiver after the last glacial recession. On the basis of a divergence timeof 10-12 thousand years ago, the estimated substitution rate of the whitesturgeon D-loop region is 1.1-1.3 x 10(-7) nucleotides/site/year, which iscomparable to rates for hypervariable sequences in the human D-loop region.Furthermore, the ratio of mean percent nucleotide differences in the D-loop (2.27%) to that in whole mtDNA (0.54%, as estimated fromrestriction-enzyme data) is 4.3, which is similar to the fourfold-to-fivefold-higher substitution rate estimated for the human D-loop. The highnucleotide substitution rate of the hypervariable region indicates that thevertebrate D-loop has potential as a genetic marker in molecular populationstudies.