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Research Project: Genetic Improvement of North American Atlantic Salmon and the Eastern Oyster for Aquaculture Production

Location: National Cold Water Marine Aquaculture Center

Title: Fine-scale environmentally associated spatial structure of Lumpfish (Cyclopterus lumpus) across the Northwest Atlantic

Author
item LANGILLE, BARBARA - DEPARTMENT OF FISHERIES AND OCEANS CANADA
item KESS, TONY - DEPARTMENT OF FISHERIES AND OCEANS CANADA
item BRACHMANN, MATTHEW - DEPARTMENT OF FISHERIES AND OCEANS CANADA
item NUGENT, CAMERON - DEPARTMENT OF FISHERIES AND OCEANS CANADA
item MESSMER, AMBER - DEPARTMENT OF FISHERIES AND OCEANS CANADA
item DUFFY, STEVEN - DEPARTMENT OF FISHERIES AND OCEANS CANADA
item HOLBORN, MELISSA - DEPARTMENT OF FISHERIES AND OCEANS CANADA
item VAN WYNGAARDEN, MALLORY - DEPARTMENT OF FISHERIES AND OCEANS CANADA
item KNUTSEN, TIM MARTIN - AQUAGEN
item KENT, MATTHEW - NORWEGIAN UNIVERSITY OF LIFE SCIENCES
item BOYCE, DANNY - MEMORIAL UNIVERSITY OF NEWFOUNLAND
item GREGORY, ROBERT - DEPARTMENT OF FISHERIES AND OCEANS CANADA
item GAUTHIER, JOHANNE - MAURICE-LAMONTAGNE INSTITUTE
item FAIRCHILD, ELIZABETH - UNIVERSITY OF NEW HAMPSHIRE
item Pietrak, Michael
item EDDY, STEPHEN - UNIVERSITY OF MAINE
item DE LEANIZ, CARLOS GARCIA - SWANSEA UNIVERSITY
item WHITTAKER, BEN - SWANSEA UNIVERSITY
item BENTZEN, PAUL - DALHOUSIE UNIVERSITY
item BRADBURY, IAN - DEPARTMENT OF FISHERIES AND OCEANS CANADA

Submitted to: Evolutionary Applications
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/15/2023
Publication Date: 9/6/2023
Citation: Langille, B.L., Kess, T., Brachmann, M., Nugent, C.M., Messmer, A., Duffy, S.J., Holborn, M.K., Van Wyngaarden, M., Knutsen, T., Kent, M., Boyce, D., Gregory, R.S., Gauthier, J., Fairchild, E.A., Pietrak, M.R., Eddy, S., De Leaniz, C., Whittaker, B., Bentzen, P., Bradbury, I.R. 2023. Fine-scale environmentally associated spatial structure of Lumpfish (Cyclopterus lumpus) across the Northwest Atlantic. Evolutionary Applications. https://doi.org/10.1111/eva.13590.
DOI: https://doi.org/10.1111/eva.13590

Interpretive Summary: Lumpfish have have gained significant recent interest as a means of eating sea lice off of farmed salmon both in Canadian and US salmon farms. Lumpfish are considered to be at risk in the wild. Little is known about the genetics of wild lumpfish. With efforts under way to culture and domesticate lumpfish for use in eating sea lice off of farmed salmon, scientist want to understand how any hatchery reared lumpfish put into salmon cages might impact wild populations if they escape. This study examined the genetics of fish from across the northwest Atlantic ocean. It found that two large scale genetic populations could be grouped by major environmental factors. There appeared to be a northern population in the areas of Newfoundland and the Gulf of St. Lawrence and a southern population in the Gulf of Maine and Bay of Fundy. The study will help to better define management areas to protect the wild lumpfish populations.

Technical Abstract: Lumpfish, Cyclopterus lumpus, have historically been harvested throughout Atlantic Canada and are increasingly in demand as a solution to controlling sea lice in Atlantic salmon farms – a process which involves both the domestication and the transfer of Lumpfish between geographic regions. At present little is known regarding population structure and diversity of wild Lumpfish in Atlantic Canada, limiting attempts to assess the potential impacts of escaped Lumpfish individuals from salmon cages/pens on currently at-risk wild populations. Here, we characterize the spatial structure of wild populations of Lumpfish throughout the Northwest Atlantic using both a 70K SNP array data and whole genome re-sequencing data (WGS). At broad spatial scales, our results reveal a large environmentally associated genetic break between the southern populations (Gulf of Maine and Bay of Fundy) and northern populations (Newfoundland and the Gulf of St. Lawrence), linked to variation in ocean temperature and ice cover. At finer spatial scales, evidence of further population structure was evident in a distinct coastal group in Newfoundland with significant isolation by distance across the northern region. Both evidence of consistent environmental associations and elevated genome-wide variation in FST values among these three regional groups supports their biological relevance. This study represents the first extensive description of population structure of Lumpfish in Atlantic Canada, revealing evidence of broad and fine geographic scale environmentally associated genomic diversity in this species. Our results will facilitate the commercial use of Lumpfish as a cleaner fish in Atlantic salmon aquaculture, the identification of Lumpfish escapees, and the delineation of conservation units of this at-risk species throughout Atlantic Canada.