Selection and Adaptation of Fitness-related traits in Coho Salmon

Abstract

Selection is the primary force driving phenotypic differentiation and adaptive evolution, and understanding how and to what extent selection drives adaptive evolution remains a key challenge in evolutionary biology. A number of commercially important species have been long exposed to deliberate, continuous selection focusing on the development or enhancement of desired traits, and the phenotypic characteristics of these species have been widely altered. Domesticated populations are excellent models to study the mechanism of adaptive evolution. In particular, such populations could be utilized to study the direct and indirect results of concerted selection on specific phenotypes, and to demonstrate how adaptive phenotypic differentiation following certain selective pressures are determined at specific sites in the genome. Such knowledge is useful as it provides insights into whether and how populations will evolve in response to natural and human-induced selection and how certain actions might mitigate or facilitate such changes. Here, I examined how selection acts on wild and domesticated coho salmon (Oncorhynchus kisutch) and investigated the genetic basis of adaptive evolution following domestication selection. This dissertation is two-fold and consists of four chapters. The aim of the first part of this dissertation (Chapter 1) was to investigate the temporal variation in selection by comparing the mode, direction and strength of selection on fitness related traits between two cohorts of wild coho salmon; specifically, I examined selection on date of return and body length using a constructed pedigree of the wild population at Big Beef Creek in Washington State, in order to illustrate how selection operates in wild and drives adaptive evolution over time. The aim of the second part of the dissertation (Chapter 2, 3, 4) was to construct a dense linkage map for this species, and to identify genomic regions that have responded to domestication selection in selectively bred salmon using this map. In Chapter 2, I investigated the relationship between chromosome arrangements and the retention of recently diverged or undifferentiated duplicated regions by deriving a linkage map for coho salmon and comparing this map with those of Chinook salmon, rainbow trout, and Atlantic salmon. Using this linkage map, I investigated the genetic architecture of growth-related traits, and examined the genetic basis for a tradeoff between age at sexual maturity and growth during crucial decision periods in coho salmon (Chapter 3). In Chapter 4, I determined whether there was evidence for selection at genomic regions linked with selectively bred traits in a domesticated population, and identified loci that played a role in driving adaptive phenotypic evolution in response to selective breeding. The work depicted herein demonstrated how phenotypic variation for important fitness-related traits might be maintained in wild, and provided insights into how phenotypic differentiation resulting from certain selective pressures was determined at specific sites in the genome.