Using Genetic Biomarkers to Examine Population Structure of Spiny Dogfish, Squalus acanthias, in the Western North Atlantic

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Ana Verissimo Virginia Institue of Marine Science Co-Principal Investigator
Paul Tsang UNH - Department of Molecular, Cellular & Biomedical Sciences Principal Investigator
Wally Bubley UNH - Department of Molecular, Cellular & Biomedical Sciences Co-Principal Investigator
James Sulikowski University of New England Co-Principal Investigator
John Graves Virginia Institue of Marine Science Co-Principal Investigator

Introduction and Background

Because of a nearly ten-fold increase in landings from 1987 – 1996 (Northeast Fisheries Science Center 1998) and life history parameters (e.g., slow growth, extended gestation) that are not conducive to withstanding heavy fishing pressure, the Atlantic States Marine Fisheries Commission (ASMFC 2002) declared the spiny dogfish, Squalus acanthias, in the Western North Atlantic to be overfished. As a result, a Fisheries Management Plan was implemented, establishing quotas that have essentially ended any directed fishery. For a management plan to be effective, life history parameters such as age, growth and reproduction, must be accurate. Since previous dogfish life history studies were conducted prior to the recent stock population decline, we are currently conducting a comprehensive study funded by NH Sea Grant to develop and validate the use of vertebrae as the means to assess the age, growth and age at sexual maturity of spiny dogfish in the Gulf of Maine. Our goal is to provide updated information, which is necessary for sustainable management of the current spiny dogfish population, with the hope of re-establishing a profitable directed fishery once again in the Gulf of Maine.


While utilizing accurate and updated life history information in fisheries models is essential to successful management, it is equally important that these parameters be applied to models for the appropriate population. Currently, spiny dogfish are managed as a unit stock centering around a paradigm where the population spends the summer and fall months in more northerly waters off of Canada and New England and then migrates to waters south of Cape Cod, Mass., where they spend their winter and spring months. However, recent studies by Moore (1998) and Rulifson et al. (2001), using traditional tag and recapture methodology, suggest that there may be multiple dogfish populations along the Western Atlantic based on movement patterns. In addition, observations made from commercial fishing trip tickets and research trips conducted within the Gulf of Maine, suggest that a nearly year-round dogfish population exists in this region. Based on the aforementioned information, we believe that the current unit stock theory needs to be re-evaluated for spiny dogfish.

Microsatellites are molecular markers in genomic DNA that have been used to examine population structure in a variety of marine fishes (Feldheim et al. 2001). A microsatellite is a simple, tandem, bi- tri- or tetra-nucleotide repeats of DNA common in all organisms. It contains higher mutation rates than other regions of DNA (Weber and Wong 1993), and the differences in frequencies of these mutations between sampling locations can show separation of populations within a species. We intend to use this tool to compare the genomic information from spiny dogfish collected at six locations: North Carolina/Virginia, Delaware/New Jersey, New York/Rhode Island, the Gulf of Maine, and two locations between Nova Scotia and Labrador. These locations were chosen because they encompass the geographic range of this species in the Western North Atlantic. From these results, we hope to gain a greater understanding of spiny dogfish population structure along the Western North Atlantic. In the event that there are multiple dogfish populations in the Western North Atlantic, it would be imperative to change the present management strategy to successfully manage this fishery.

Our rationale for seeking NH Sea Grant Program Development funds is three-fold:

  1. We propose to use microsatellites as a method to determine population structure of the spiny dogfish. The results will complement our current NH Sea Grant project, providing significant new information towards a management plan for this species along the eastern coast of the United States and Canada. Also, because of our mutual interest with spiny dogfish, John Graves and Ana Verissimo of the Virginia Institute of Marine Science have agreed to collaborate. Although their main focus is the worldwide population structure and phylogeography of squaloid sharks, they will share their samples and the primers they have developed. The data generated from the Western North Atlantic in the present study will be included in a larger, global picture of dogfish population structure.
  1. The results obtained from the present study will form the basis for future grant applications to the NH Sea Grant Program and other extramural agencies to use pop-up satellites to characterize dogfish movement patterns, which will allow us to examine essential habitat use in the Western North Atlantic. Further, this will also enable us to determine the effects of movement patterns on structuring this population.
  1. We plan to present our findings to a national audience of our peers at the 2009 American Elasmobranch Society Annual Meeting in Portland, Oregon.

Fin clips have already been obtained from 75 sharks via opportunistic sampling from National Marine Fisheries Service (NMFS) bottom trawl surveys for each of the four different locations in U.S. waters along the Western North Atlantic. We also hope to obtain samples from two other locations in Canadian waters between Nova Scotia and Labrador, through contacts made by our research collaborator, James Sulikowski (University of New England).

DNA will be extracted from the fin clips and nine microsatellite loci will be amplified using polymerase chain reaction (PCR) with primers developed by McCauley et al. (2004) and Verissimo (Pers. Comm.) for spiny dogfish. The forward primers will be fluorescently labeled and the product of the amplification genotyped using an automated DNA sequencer. First, the loci will be characterized to determine if they are appropriate for the scope of this project. Tests will also be performed to ensure that there are no scoring errors, linkage, or null alleles which could affect the population analysis. Structure 2.2 will be used to analyze the data using a Markov Chain Monte Carlo simulation and Bayes Rule to determine the likelihood of differing numbers of populations. Genepop 3.4 will provide Fst and Rst values, as well as P-values and probabilities of differentiation between all sampling locations using Fisher’s exact tests.