Date of Award

Fall 2013

Degree Type


Degree Name

Doctor of Philosophy (PhD)


Biological Science

First Advisor

Krista Nichols

Committee Chair

Dennis Minchella

Committee Member 1

Krista Nichols

Committee Member 2

Richard Howard

Committee Member 3

Rebecca Doerge


Animal migrations play a critical role in the health and balance of ecological systems and in the evolution and diversification of species, and this is perhaps best displayed amongst salmonid fishes (salmon, trout, and char) who exhibit variation in the propensity to migrate both within and among species. Rainbow and steelhead trout (Oncorhynchus mykiss), members of the salmonid family of fishes, capture this variation throughout their native range. Some populations and ecotypes will remain resident in freshwater habitats throughout their life history; while others have the ability to embark on tremendous marine migrations. Those that migrate undergo a suite of behavioral, morphological, and physiological adaptations in a process called smoltification. And while much is known of the behavior, ecology, and physiology of the smoltification process and the migratory life history, little is known of the underlying genetic architecture modulating this adaptive tactic. Using quantitative and molecular genetic techniques I describe the genetic basis of the marine migratory life history in three focused research chapters.

In the first I conduct a quantitative trait locus (QTL) analysis, using an experimental cross, derived from wild resident rainbow and wild migratory steelhead trout from Southeast Alaska, and use high throughput restriction-site associated DNA (RAD) tag sequencing to identify the number, position, and relative contribution of genetic effects on a suite of 27 physiological and morphological traits associated with the migratory life history in this species. In total 37 QTL are localized to 19 unique QTL positions explaining 4 - 13.63 percent of the variation for 19 of the 27 migration related traits measured. Two chromosomal positions, one on chromosome Omy12 and the other on Omy14 each harbors seven QTL for migration related traits suggesting that these regions could harbor master genetic controls for the migratory life history tactic in this species. Another QTL region on Omy5 has been implicated in several studies of adaptive life histories within this species and could represent another important locus underlying the migratory life history. I also evaluate whether loci identified in this out-crossed QTL study co-localize to genomic positions previously identified for associations with migration-related traits in a doubled haploid mapping family.

In the second chapter I describe a quantitative genetic analysis of 22 growth, size, and morphological traits, in additional to overall life history classification (resident or migrant) over the temporal process of smoltification in a large multi-generation experimental pedigree (n=16,139) of migratory and resident rainbow trout derived from a wild population, which naturally segregates for migratory propensity. I identify significant additive genetic variance and genetic correlations among the suite of traits that make up a component of the migratory syndrome in this species. Additionally I identify high heritability estimates for the life history classifications and observe a strong negative genetic correlation between the migratory and precocious mature life history trajectories. Given the large heritability estimates of all of the traits that segregate between migratory and resident rainbow trout, I conclude that these traits can respond rapidly to selection. However, given the tremendous degree of genetic correlation between these traits, they do not evolve in isolation, but rather as a suite of correlated characters.

In the third chapter divergence in gene expression of 18 biological and positional candidate genes that underlie QTL for the smoltification process are investigated. Gene expression is reported in brain, gill, and liver tissue of migratory smolts, resident parr, and precocious mature male trout at the developmental stage of out-migration. This analysis reveals several genes differentially expressed between life history classes, and validates the candidate nature of several genes and implicates previously unexplored genes in the parr-smolt transformation including Clock1a, FSHb, GR, GH2, GHR1, GHR2, NDK7, p53, SC6a7, Taldo1, THRa, THRb, and Vdac2.