Genome-wide analysis reveals regional patterns of drift, structure, and gene flow in longfin smelt (Spirinchus thaleichthys) in the northeastern Pacific

Autor: İsmail K. Sağlam, James A. Hobbs, Levi S. Lewis, Alyssa Benjamin, Randall D. Baxter, Amanda J. Finger
Přispěvatelé: Sağlam, İsmail Kudret (ORCID 0000-0003-3136-7334 & YÖK ID 168783), Hobbs, James, Baxter, Randall, Lewis, Levi S., Benjamin, Alyssa, Finger, Amanda J., College of Sciences, Department of Molecular Biology and Genetics
Rok vydání: 2021
Předmět:
Zdroj: Canadian Journal of Fisheries and Aquatic Sciences
ISSN: 1205-7533
0706-652X
DOI: 10.1139/cjfas-2021-0005
Popis: The southernmost stock of longfin smelt (Spirinchus thaleichthys) is approaching extirpation in the San Francisco Estuary (SFE); however, patterns of genetic structure, diversity and gene flow which are vital for management are poorly understood in this species. Here, we use genome-wide data to evaluate population structure of longfin smelt across a broad latitudinal scale across estuaries ranging from the SFE to Yakutat Bay and Lake Washington, and fine scale within the Fraser River and the SFE. Results indicate high genetic structure between major estuaries, fine-scale structure within the Fraser River, and low levels of structure within the SFE. Genetic structure was more pronounced between northern estuaries whereas southern estuaries showed shared ancestry and ongoing gene flow, most notably unidirectional northward migration out of the SFE. Furthermore, we detected signatures of local adaptation within the Fraser River and the Skeena River estuaries. Taken together, our results identify broad patterns of genetic diversity in longfin smelt shaped by co-ancestry, unidirectional migration and local adaptation. Results also suggest that the SFE population is genetically distinct from northernmost populations and an important source for maintaining nearby populations.
The authors thank Colin Grant (US Fish and Wildlife Service), who made many of the initial inquiries soliciting longfin smelt samples, and Josh Israel (US Bureau of Reclamation), who performed initial genetic analyses. The authors also thank the following individuals and agencies for help collecting samples: Hobbslab and staff -UC Davis; Matt Dekar and staff -US Fish and Wildlife Service; Kathy Hieb, Jennifer Giannetta, Jeremiah Bautista, Aaron Ng, Rebecca Garwood, James Ray, Justin Garwood, and Mike Wallace -California Department of Fish and Wildlife; Laurie Lloyd, Olaf Langness -Washington Department of Fish and Wildlife, Thomas Quinn, University of Washington; Eric Taylor -The University of British Columbia, John Kelson -Fish BiologistConsultant, Smithers, British Columbia; Mayumi Arimitsu -US Geological Survey, Alaska Science Center. Finally, the authors also thank a number of internal reviewers, Genomic Variation Lab Personnel, and other agency biologists who helped this project, including Matthew Campbell, Daphne Gille, Levi Lewis, Andrea Schreier, Josh Israel, and Alisha Goodbla. Funding for this project was generously provided by the California Department of Water Resources, Agreement Number 4600011196.
Databáze: OpenAIRE
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