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Population Genomics & Stock Structure of Atlantic Cod on (& off) the Flemish Cap:

insights from whole-mitochondrial-genome DNA sequences
H. Dawn Marshall, Kim A. Johnstone, Angela M. Pope, & Steven M. Carr*

"The Ecosystem of the Flemish Cap," 08 - 10 September 2004, Dartmouth NS

          ABSTRACT

    Genomics (the study of complete gene sets in organisms) and "genomic thinking" (the application of "massively parallel" biotechnologies to data collection and analysis) are now being applied to studies of biodiversity. We have begun to analyze the complete mitochondrial DNA genomes of animal species as a series of ordered, contiguous fragments, both among related species and for multiple individuals within speciesPhylogeographic analysis of completely-resolved intraspecific gene trees provides the detailed historical information and necessary statistical power to evaluate vicariance and dispersal phenomena at scales of interest to fisheries managers and population biologists.

    Atlantic Cod (Gadus morhua) spawn in a variety of inshore and offshore areas along the continental shelf of Newfoundland and Labrador, including populations on and off the Grand Banks, and at Flemish Cap, an offshore seamount. Analysis of complete mitochondrial DNA (mtDNA) genome sequences for fish from these populations has identified several hundred single-nucleotide polymorphisms (SNPs). Every individual fish has a unique mtDNA sequence: there are as many as 50 pairwise SNP differences among individuals, and these can be used to determine exact relationships among individual fish in a "family tree". Phylogeographic analysis shows evidence of extensive genetic variation and deep ancestral clades shared between the Barent's Sea and Flemish Cap (3M) populations, in contrast to relatively limited variation and close relationships among fish in shelf populations, including Hawke Channel (2J) and North Cape (3K). Alternative explanations include origin of continental shelf cod as a bottlenecked "founder population" from a marine refugium near Flemish Cap, or  continuing gene flow between Flemish Cap and the eastern Atlantic.

    [Contrasting patterns are seen in Greenland Halibut. Flemish Cap turbot are genetically indistinct. from other transatlantic populations.  Movements of flatfish occur at depths where shelf contours do not impede gene flow among geographic regions.]

New biotechnologies offer high-throughput, cost-effective assessment of genomic variation within species and species identification within ecosystems.

[Research supported by DFO / MUN Partnership Agreement, in cooperation with Drs. Pierre Pepin & John Brattey].
{Ray Bowering paid for the Turbot, Garry Stenson paid for the Seals}



All material ©2004 by Steven M. Carr