The phenotypic, phenological, and genomic responses to the 2013-2015 marine heatwave in Pacific Coho salmon, Oncorhynchus kisutch

There is a significant knowledge gap in our understanding of how salmon populations respond and adapt to extreme estuarine and marine conditions during a marine heatwave (MHW). Our previous longitudinal study of the Inch Creek Hatchery Coho salmon detected a weak correspondence between low return and poor oceanographic indices in two generations. Of which, the 2012 brood years were also exposed to the 2013-2015 Pacific Northeast MHW, presenting an opportunity to characterize the adaptive response of a coho salmon population to a MHW. Using multiple sequencing and analytical approaches, I studied the genomes of surviving families across four generations (2006-2018) of Coho salmon from the Inch Creek Hatchery population to better understand the impacts of the 2013-2015 MHW on the dynamic interaction between genotype, phenotype, and phenology. The MHW significantly altered the population's fitness-related traits, phenology, and marine survival. The assessment of the influence of parental phenotypes, life history traits, and genetic diversities on the variation of survival in the offspring revealed an MHW-specific adaptation strategy in families with high marine survival. This was unique to the MHW generations and involved smaller body size, delayed run-timing, and altered life-history strategy (early sexual maturation, ESM). Signatures of positive selection further supported an MHW-unique adaptation strategy. I found an extended haplotype homozygosity hotspot on CHR5 linked to high marine survival during the MHW, which included intron variants in the master regulator of chromatin reprogramming, KDM5B, and several other genes involved in histone modification, transcriptional regulation, and formation of the spliceosomal complex. Lastly, I characterized and compared the genetic architecture of ESM in Coho and Chinook salmon and found limited conservation among the Salmo-Oncorhynchus lineage and sister species. The candidate loci identified in both species were linked to the sex-associated locus and the nutrient sensing, metabolism, and osmoregulation pathways. Overall, I have provided the first empirical evidence of the phenotypic, phenological and genetic response of a population of Coho salmon exposed to the 2013-2015 MHW, advancing our knowledge of the biological impact of MHWs on the Pacific salmonids.