mtDNA Genome Phylogeography of Atlantic Cod

(SM Carr & HD Marshall 2008. Genetics 108: 381-389)

    Atlantic Cod (Gadus morhua) spawn in a variety of inshore and offshore areas along the continental shelf of Newfoundland and Labrador, including populations in the "Northern Cod" stock complex on and off the Grand Banks, and at Flemish Cap, an offshore seamount. Populations numbers of Northern Cod have declined more than 99% since the 1970s. Despite closure of the fishery, numbers have not recovered.  An understanding of the spatial scale and magnitude of genetic differentiation among stock areas is crucial to management.

    On the basis of multiple complete mitochondrial DNA genome sequences, we describe the temporal phylogeography of Atlantic cod from four spawning aggregations from the northwest Atlantic and Norway. Every fish  has a unique mtDNA sequence. Phylogenetic analysis identifies six major haplogroups that range in age from 37 to 75 KYA. The widespread haplotype identified by previous single-locus analyses at the center of a ‘‘star phylogeny’’ is shown to be a paraphyletic assemblage of genome lineages. The coalescent that includes all cod occurs 162 KYA. The most basal clade comprises two fish from the western Atlantic. The most recent superclade that includes all fish examined from Norway dates to 128 KYA at the Sangamon / Würm interglacial, when ocean depths on continental shelves would have favored transcontinental movement. The pairwise mismatch distribution dates population expansion of this superclade to the middle of the Wisconsinan / Weichsel glaciation 59 KYA, rather than to a postglacial emergence from a marine refugium 12 KYA, or to more recent historic events.