An investigation into the genetic basis of migration timing in Chinook salmon (Oncorhynchus tshawytscha)

• Main Author: O'Malley, Kathleen G.
• Other Authors: Banks, Michael A., Kyriacou, Charalambos, Camara, Mark, Savage, Tom, Ford, Michael, Fisheries and Wildlife, Oregon State University. Graduate School
• Format: Doctoral or Postdoctoral Thesis
• Language: English; unknown
• Published: Oregon State University
• Subjects: Chinook salmon > Migration > New Zealand; Chinook salmon > New Zealand > Genetics; Circadian rhythms; Chinook salmon > California > Feather River Watershed > Genetics; Chinook salmon > Migration > California > Feather River Watershed; Salmo salar
• Online Access: https://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/5999n638d

The genetic basis of adaptation is complex as many fitness-related traits are quantitative and likely influenced by multiple genes with variable effects across different selective environments. One important adaptation for anadromous Chinook salmon (Oncorhynchus tshawytscha) is the time at which individuals return to natal breeding sites within a reproductive season. Here, I tested for adaptive genetic differentiation among temporally divergent migratory runs using candidate loci. First, I isolated and characterized two copies of the circadian rhythm gene, Clock, from Chinook salmon (OtsClock1a and OtsClock1b). Phylogenetic analysis revealed that these copies likely arose subsequent to the salmonid genome-wide duplication event. Each copy contains a polyglutamine repeat motif (PolyQ), an essential binding domain of this transcription factor. However, a 1200bp non-coding segment, showing >90% sequence identity to the Salmo salar Transferrin gene, is located downstream of the OtsClock1a PolyQ, yet absent from OtsClock1b providing evidence for nonhomologous recombination. Another candidate, Ots515NWFSC, shows sequence identity to three salmonid genes central to reproductive development: Gonadotropin-releasing hormone, CYP19b-I, and Ghrelin. I employed OtsClock1b and Ots515NWFSC to test for differentiation in two unique systems: Feather River, California; and Waitaki and Poulter Rivers, New Zealand. Based on length variation in these candidate genes, Feather River fall and spring run Chinook salmon are genetically differentiated. In contrast, these seasonal runs are genetically indistinguishable based on neutral microsatellite loci. Correspondingly, temporally divergent Chinook salmon runs in the Waitaki and Poulter Rivers show greater differentiation based on variation in OtsClock1b and Ots515NWFSC than microsatellite loci. Tests for selective neutrality indicate that OtsClock1b and Ots515NWFSC are likely under selection in both systems. In addition, I found evidence for a latitudinal cline in two OtsClock1b ...