RT Journal Article SR Electronic T1 Isolation-by-distance and population-size history inferences from the coho salmon (Oncorhynchus kisutch) genome JF bioRxiv FD Cold Spring Harbor Laboratory SP 2022.06.14.496192 DO 10.1101/2022.06.14.496192 A1 Eric B. Rondeau A1 Kris A. Christensen A1 David R. Minkley A1 Jong S. Leong A1 Michelle T.T. Chan A1 Cody A. Despins A1 Anita Mueller A1 Dionne Sakhrani A1 Carlo A. Biagi A1 Quentin Rougemont A1 Eric Normandeau A1 Steven J.M. Jones A1 Robert H. Devlin A1 Ruth E. Withler A1 Terry D. Beacham A1 Kerry A. Naish A1 José M. Yáñez A1 Roberto Neira A1 Louis Bernatchez A1 William S. Davidson A1 Ben F. Koop YR 2022 UL http://biorxiv.org/content/early/2022/06/17/2022.06.14.496192.abstract AB Coho salmon (Oncorhynchus kisutch) are a culturally and economically important species that return from multiyear ocean migrations to spawn in rivers that flow to the Northern Pacific Ocean. Southern stocks of coho salmon have significantly declined over the past quarter century, and unfortunately, conservation efforts have not reversed this trend. To assist in stock management and conservation efforts, we generated two chromosome-level genome assemblies and sequenced 24 RNA-seq libraries to better annotate the coho salmon genome assemblies. We also resequenced the genomes of 83 coho salmon across their North American range to identify nucleotide variants, characterize the broad effects of isolation-by-distance using a genome-wide association analysis approach, and understand the demographic histories of these salmon by modeling population size from genome-wide data. We observed that more than 13% of all SNPs were associated with latitude (before multiple test correction), likely an affect of isolation-by-distance. From demographic history modeling, we estimated that the SNP latitudinal gradient likely developed as recently as 8,000 years ago. In addition, we identified four genes each harboring multiple SNPs associated with latitude; all of these SNPs were also predicted to modify the function of the gene. Three of these genes have roles in cell junction maintenance and may be involved in osmoregulation. This signifies that ocean salinity may have been a factor influencing coho salmon recolonization after the last glaciation period – generating the current pattern of variation in these three genes.