Developing Genomic Tools for Identifying Atlantic Cod Population Structure and Management Units

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Adrienne Kovach UNH - Department of Natural Resources & the Environment Principal Investigator

The proposed funds will support the overarching goal of integrating modern and historical DNA analyses to characterize the biological stock structure of cod in the Gulf of Maine. The specific research aims are to:

1. Characterize the variation in neutral and adaptive genetic markers of remnant (nonspawning) cod in the eastern Gulf of Maine (GoM).

2. Compare the genetic variation of modern eastern GoM cod (from Obj. 1) with that of spatially proximate cod spawning aggregations, including the western GoM, the Bay of Fundy, and Georges Bank.

3. Characterize changes in genetic structure and diversity over time through genetic analyses of historical and archaeological GoM cod specimens from 16th-20th century.

Through working directly with fisheries scientists, managers, and the UNH Cooperative Extension, our research program has the following extension outreach objectives:

1. Provide fisheries scientists, managers and fishermen with an improved understanding of the biological structure of modern cod stocks, the extent to which they are influenced by local recruitment processes, and whether and how they have changed over time.

2. Develop biologically based management alternatives for cod that incorporate biological complexity and spatial-based management options.

Our proposed research program directly addresses priority needs for cod management identified by the Science and Statistical Committee of the New England Fishery Management Council in a recent Cod Stock Structure Workshop. Recent collapse of the Atlantic cod fishery and resulting economic hardships require changes in management to rebuild stocks in the Gulf of Maine (GoM). Biological knowledge of local populations is necessary for appropriate fisheries management and recovery of depleted stocks. By filling key knowledge gaps in cod stock structure and transferring these results to fisheries managers, our project will provide the biological information necessary for effective reevaluation of fisheries assessment and management. The proposed project goals also directly address Sustainable Fisheries & Aquaculture (SFA) goals of N.H. Sea Grant Strategic Plan 2014-2017. Specifically, we address SFA Goal 5: Integrated fisheries policy, science and management that allows sustainable management of marine fisheries and supports a healthy and resilient fishing community. By integrating modern stock identification techniques with historical marine ecology, our project utilizes innovative scientific approaches to improve the understanding of stock complexity, population dynamics, and the importance of spatial scale. To achieve these goals, our interdisciplinary team is comprised of marine historical ecologist Karen Alexander, (UNH/UMass Amherst), anthropologist Dr. Meghan Howe (UNH), fisheries scientist Dr. Steven Cadrin (UMass Dartmouth), and fisheries extension specialist Dr. Erik Chapman (UNH), who complement my expertise in population genetics.

If awarded, N.H. Sea Grant Development funds will be used specifically to develop an approach for the analysis of genome-wide SNP markers of Atlantic cod. We will conduct next generation Illumina sequencing, using a reduced representation approach (a highly efficient way of sampling polymorphism across the whole genome by sequencing a subset of short fragments distributed genome-wide). This work will be conducted at the UNH Hubbard Center for Genome Studies, with consultation by Dr. Kelley Thomas, who has expertise with this approach. This approach will yield thousands of polymorphisms for 96 individuals per sequencing run, from which population genetic analyses will identify both adaptive and neutral variation between populations. For this development phase, we will target two broad population complexes, the northern spring spawning complex and the southern spawning complex, shown in our previous work to be genetically distinct. We therefore anticipate the greatest functional differences will be found between these two population complexes, making them highly informative for developing our approach. Once developed, we will utilize these tools to extend our analyses to our full project goals (above), upon receipt of full project funding (proposal development ongoing). An additional advantage of this approach is that it will be highly suitable for working with degraded DNA that is typical of historical samples, thereby facilitating success of our proposed historical DNA analysis objectives.

2015 Accomplishment

Researchers in N.H. develop genetic approach for identifying cod stock structure

In 2015, N.H. Sea Grant-funded researchers developed a genomic approach for identifying cod stock structure and determined that winter and spring spawning Atlantic cod populations in Massachusetts Bay are genetically different from each other, which will help to inform management decisions about the species in the Gulf of Maine.
Relevance: Atlantic cod stocks in the Gulf of Maine are at an all-time low, and proper management of their population depends on accurate data about the species. Genomic data can help shed light on cod population structure and management units.
Response: With funding provided by N.H. Sea Grant, researchers conducted genomic analyses on cod fin clip samples in 2015 from two target cod populations — winter and spring spawning cod from Massachusetts and Ipswich Bays.
Results: Analyses of cod fin clip samples indicate that the winter and spring spawning populations from Massachusetts Bay were different from one another. The results confirm the fine-scale spatial and temporal differences in cod spawning populations in the Gulf of Maine, providing a proof of concept for a genome-wide approach to characterizing cod stock structure for improved management of the species.

2014 Accomplishment

N.H. Sea Grant researchers extract DNA samples for genetic testing of two cod populations in the Gulf of Maine
The recent collapse of the Atlantic cod fishery and resulting economic hardships require changes in management to rebuild stocks in the Gulf of Maine. The integration of modern and historical cod DNA analyses could help to characterize their stock structure for improved management of the species. In 2014, with funding provided by a NHSG development grant, researchers obtained cod fin clip samples from two target cod populations in the Gulf of Maine that are known to be the most distinct from each other. The DNA from those samples has been extracted for future genetic testing. These data will provide genomic tools for fishery scientists to more accurately identify Atlantic cod structure and management units for improved management of the cod populations.