Genetic Structure of Fishery-Impacted Species in the Northwest Atlantic

Primary tabs

Project Type: 
Project Number: 
Inception Date: 
Completion Date: 
Theme Area: 
Fisheries Resources


Thomas Kocher UNH - Department of Biological Sciences Principal Investigator
Patricia Rosel UNH - Department of Biological Sciences Co-Principal Investigator

To determine population structure of three fishery-impacted species--harbor porpoise, Atlantic cod and winter flounder--in the Northwest Atlantic, through development of microsatellite DNA markers and through DNA sequencing of the highly variable mitochondrial DNA.


Microsatellite markers will be isolated for harbor porpoise and cod through enrichment of genomic DNA libraries. Candidate loci will be screened for variability using a subset of porpoise and cod samples. Fluorescently labeled primers and multiplexing will allow rapid genotyping of all samples on an automated sequencer. DNA sequencing of mt DNA will take place using an ABI373A automated sequencer.


Overexploitation of fish stocks in the northwest Atlantic has led to the near collapse of the groundfish industry. High by-catch rates of the federally protected harbor porpoise may result in it being listed as a threatened species. Accurate knowledge of population structure and exchange rates for harbor porpoise, cod and winter flounder will help the development of effective management plans.

Genetic structure of harbor porpoise
During this project the population structure of harbor porpoises in the Northwest Atlantic was examined by sequencing a portion of the mitochondrial DNA control region from 253 porpoises collected from the four putative sub-populations in the Northwest Atlantic. These DNA sequences were successfully collected and analyzed, and revealed that significant population subdivision does exist for this species in this region.
In addition, nuclear microsatellite markers specific for harbor porpoises were cloned, identified and evaluated. Six microsatellite loci proved highly polymorphic and were used to genotype 253 porpoises. Analysis of the nuclear markers did not reveal any population structure in the porpoises in the region, suggesting that male porpoises disperse more than females. This result is consistent with what has been found in other studies on harbor porpoises. This research provided significant insight into harbor porpoise population structure in the Northwest Atlantic.
The most significant finding from this research is that during the winter the mid-Atlantic states appear to be an area of mixing for different summer breeding populations of harbor porpoises in the Northwest Atlantic. This is significant because it raises considerable issues for management of this species in U.S. waters.
This work also provided the opportunity for a multinational collaborative effort between Dr. P. Rosel and two European researchers studying harbor porpoise population genetics in the Northeast Atlantic.
Genetic structure of Atlantic cod
We isolated new microsatellite markers from cod, and developed reliable multiplexed PCR assays for scoring population samples. Unfortunately, we ran out of funding before we were able to score significant numbers of animals from wild populations.


Available from the National Sea Grant Library (use NHU number to search) or NH Sea Grant

Journal Article

  • Rosel, P., R. Tiedermann and M. Walton (1999). Genetic evidence for limited trans-Atlantic movements of the harbor porpoise "Phocoena phocoena." Marine Biology 133:583-591.
  • Rosel, P., S. Frazier, J. Wang and T. Kocher (1999). Genetic structure of harbour porpoise "Phocoena phocoena" populations in the northwest Atlantic based on mitochondrial and nuclear markers. Molecular Ecology 8:S41-S54.