How striped bass population structures can be confounded across generations by mitochondrial heteroplasmy

Heteroplasmy is the existence of multiple different genome sequences within a single organism and has been demonstrated to occur in striped bass as a series of tandem repeats of variable length.  These tandem repeats lie in the mitochondrial control region flanked by several restriction sites.  Scientists have taken advantage of the variable length of these repeats by performing RFLP mapping to determine the structure of wild striped bass populations.  While sequencing the complete mitochondrial genome of striped bass we discovered that the ND6 gene had been translocated from its ancestral position to a position directly adjacent these tandem repeats.  Using the ND6 gene as a priming site allowed us to selectively amplify and sequence the repeat region to test whether sequences of these tandem repeats could accurately reconstruct a population of F1 juveniles from known mothers.  Although the sequence data was more informative than the RFLP data, the juvenile’s sequences did not always match that of their mother.  However, a second experiment using single eggs from known mothers always reconstructed the correct phylogeny.  Here we discuss how heteroplasmy can explain this observed change in genotype during maturation and some implications for using heteroplasmic sites as population genetic markers.