Y-chromosome haplotypes drive variation in size and age at maturity in male Chinook salmon

ABSTRACT Variation in size and age at maturity is an important component of life history in salmon that is influenced both by environmental and genetic factors. Large size confers a direct reproductive advantage through increased fecundity and egg quality in females, while larger males gain a reproductive advantage by monopolizing access to females. In addition, variation in size and age at maturity in males can be associated with different reproductive strategies; younger smaller males may gain reproductive success by sneaking in among mating pairs. In both sexes there is a trade-off between older age and increased reproductive success and increased risk of mortality by delaying reproduction. We used RADseq data for 21 populations of Alaska Chinook salmon (Oncorhynchus tshawytscha) and identified four Y-chromosome haplotypes that showed regional and population-specific variation in frequency. These haplotypes exhibited associations with size at maturity in multiple populations suggesting that the lack of recombination between X and Y-chromosomes have allowed Y-chromosome haplotypes to capture different alleles that influence size at maturity. Ultimately, conservation of life history diversity in Chinook salmon may require conservation of Y-chromosome haplotype diversity.