PT  - JOURNAL ARTICLE
AU  - Eric B. Rondeau
AU  - Kris A. Christensen
AU  - David R. Minkley
AU  - Jong S. Leong
AU  - Michelle T.T. Chan
AU  - Cody A. Despins
AU  - Anita Mueller
AU  - Dionne Sakhrani
AU  - Carlo A. Biagi
AU  - Quentin Rougemont
AU  - Eric Normandeau
AU  - Steven J.M. Jones
AU  - Robert H. Devlin
AU  - Ruth E. Withler
AU  - Terry D. Beacham
AU  - Kerry A. Naish
AU  - José M. Yáñez
AU  - Roberto Neira
AU  - Louis Bernatchez
AU  - William S. Davidson
AU  - Ben F. Koop
TI  - Isolation-by-distance and population-size history inferences from the coho salmon (<em>Oncorhynchus kisutch</em>) genome
AID  - 10.1101/2022.06.14.496192
DP  - 2022 Jan 01
TA  - bioRxiv
PG  - 2022.06.14.496192
4099  - http://biorxiv.org/content/early/2022/06/17/2022.06.14.496192.short
4100  - http://biorxiv.org/content/early/2022/06/17/2022.06.14.496192.full
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.