Ancient three-spined stickleback (Gasterosteus aculeatus) mtDNA lineages are not associated with phenotypic or nuclear genetic variation

Historic population divergence can shape contemporary patterns of genetic variation, but the extent to which this happens in natural populations is unclear. We tested whether ancient mitochondrial DNA (mtDNA) divergence was associated with phenotypic and nuclear genetic variation in three-spined stickleback fish (Gasterosteus aculeatus) from two geographic regions in Alaska where individuals from ancient mitochondrial clades are found in sympatry. We tested the hypotheses that historic evolutionary divergence led to reproductive barriers that persist between fish carrying different mtDNA lineages in contemporary populations, or in the absence of such barriers, that epistatic interactions among loci in the mitochondrial and nuclear DNA created non-random associations between these genomes. We found no relationship between mtDNA lineage and armour and body shape traits. We also did not detect global nuclear genetic differentiation or genomically localized patterns of variation between fish with alternative mtDNA lineages. Thus, we find that the divergence that is still evident in the mtDNA of contemporary stickleback populations appears to have no residual influence on patterns of phenotypic or nuclear genetic variation at any scale.