Selection and Differentiation Between Populations and Sexes in Brook Trout (Salvelinus fontinalis) and Rainbow Trout (Oncorhynchus mykiss)

Garrett Justin McKinney, Purdue University

Abstract

Many species of salmonids exhibit differences between populations in life history, phenotypes, and behaviors, however the varied habitats utilized by different populations as well as strong population structure leaves ample opportunity for both drift and selection to be driving divergence between populations. In the first chapter, genetic and morphological variation was compared between three populations of brook trout to determine if patterns of morphological divergence could be attributed to selection or were indistinguishable from drift. By temporally sampling, I was also able to examine if patterns of morphological divergence changed during ontogeny, and if there was evidence that selection for divergence changed during ontogeny. When all populations were combined, divergence in length and weight was attributed to selection at each of the three developmental stages while divergence in the remaining traits was consistent with expectations from genetic drift. Pairwise population analyses were done to determine if the patterns of divergence and selection between each population was concordant with the overall results. The results were largely found to be driven by divergence between the Assinica population relative to both the Iron River and Siskiwit populations. While the Iron River and Siskiwit populations did show divergence due in length and weight due to selection, this only occurred at the third developmental stage while divergence at earlier times was consistent with drift. In the second chapter, gene expression patterns throughout early development were examined using RNAseq in two populations of rainbow trout that share a recent coancestry but have diverged in life history phenotype. Differentially expressed genes in whole embryos or brain, depending on time point, were found throughout early development, from hatch until one year of age. The greatest number of genes was differentially expressed between males of each population at eight months of age. Genes previously associated with life history variation were differentially expressed and several were mapped to genomic regions associated with life history variation. In addition, differentially expressed genes that have not been previously associated with life history variation were mapped to genomic regions of interest and provide candidates for further study. Further analysis revealed changes in many biological functions and biological pathways, including pathways normally associated with vision but which may play a role in circadian rhythm regulation which is an important regulator for life history variation. In the third chapter, I examined patterns of differential gene expression in whole embryos and brain tissue between sexes from hatch until two years of age in two populations of rainbow trout. Few genes were differentially expressed between sexes throughout the first year of development in either population. The number of differentially expressed genes between sexes increased during the second year of development in both populations; however the migratory population showed a much greater increase in the number of differentially expressed genes between sexes. This pattern held even at the last time point where migrant and resident individuals were sequenced from each population, suggesting fundamental population level differences in gene expression between sexes that are independent of life history.

Degree

Ph.D.

Advisors

Howard, Purdue University.

Subject Area

Genetics|Evolution and Development|Bioinformatics

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