The blue crab (Callinectes sapidus) is a widely distributed decapod which ranges from Nova Scotia to the northern Argentina coasts. It is one of the most abundant estuarine invertebrates, supporting both commercial and recreational fisheries along the Atlantic and Gulf coasts.

This thesis presents data clearly establishing the unprecedented hyper-variability in the mitochondrial genome of C. sapidus. This variation extended to multiple regions, including the cox1, nad2, and nad4 protein coding loci as well as ribosomal 12s RNA molecule. The haplotype diversity of the nad2 gene approached 1, with a nucleotide diversity approaching 1%. This hyper-variability in the mtDNA allows using a single mtDNA gene (nad2) to distinguish hatchery-produced crabs from wild crabs after release to the wild.

I found no dominant mtDNA haplotypes in wild populations but instead a distribution of a few low-frequency recurrent haplotypes with a large number of singletons. Because of this high diversity and extensive population mixing, the geographic structure in wild populations exhibits panmixia from the Atlantic to Gulf of Mexico.

Some of the high genetic diversity found seems to stem from the heteroplasmic nature of the blue crab mtDNA. By cloning high fidelity PCR products, I confirmed single individual crab and megalopa harbored dozens of copies of mitochondrial haplotypes. A copy number analysis indicates discovery of unique haplotypes was probably not saturated with the possibility of inadequate sampling. The heteroplasmy in the blue crab appears to be under maternal inheritance without paternal contribution. While minor haplotypes are represented in wild populations, other minor haplotypes contained stop codons and/or non-synonymous substitutions which may influence the viability of the mitochondria.

Given the blue crab inhabits a broad variety of environments and that the mtDNA genome appears to be under selective pressure, the potential for mtDNA functional correlates with this genetic diversity maybe at the basis for the robust physiological capability of the species.