Population Structure of Lake Whitefish (Coregonus Clupeaformis) on Multiple Spatial Scales: Transitioning to a Genomics Approach

This thesis was undertaken to inform the recent transition from microsatellite DNA markers to single nucleotide polymorphisms (SNPs) in the field of molecular ecology, and to explore the population structure of important fish species. Microsatellite markers were the gold standard for two decades and were used to investigate the population structure of lake and round whitefish (Coregonus clupeaformis and Prosopium cylindraceum) in the vicinity of a nuclear power plant on Lake Huron. The analysis of over 200 individuals of each species revealed no fine scale population subdivision relevant to management. Microsatellites remain a valuable tool, but many molecular ecologists are transitioning to direct sequencing of thousands of single nucleotide polymorphisms in a subset of the genome based on reduced representation DNA libraries (RRL). These tools better represent evolutionary processes on a genomic level but molecular ecologists are now faced with many important and potentially complex decisions about study design. These factors greatly influence the cost of sequencing and quality of SNP data generated. Correspondingly, I investigated the influence of DNA quality, sequencing depth and genome coverage, and bioinformatics parameter settings on downstream analyses using RRLs and SNPs. Low to moderate levels of DNA degradation still resulted in adequate production of variable SNP loci, with higher sequencing depth (~12X) and larger numbers of polymorphic loci (~10,000) providing the best resolution of both broad and fine scale population differentiation analyses. Conservative bioinformatics parameters enabled retention of the largest number of informative loci with the best downstream population analyses. Finally, I used this new knowledge to investigate the population structure of lake whitefish across central Canada and the USA on multiple spatial scales using 10,000+ SNP loci. Hierarchical population subdivision was detected, with geographically isolated lakes across provincial boundaries resulting in larger amounts of genetic differentiation. Within provinces, lakes were differentiated based on watershed connectivity, and in Saskatchewan there was evidence for associations between environmental factors and particular SNP loci. My work provides valuable empirical data to guide the transition from microsatellites to SNPs, emphasizing how to best take advantage of the opportunities provided by RRLs and next generation DNA sequencing.

Name thesis:degree_name

Doctor of Philosophy (PhD)

Level thesis:degree_level

Doctoral -- first

Discipline thesis:degree_discipline

Biology

Grantor dc:publisher

Faculty of Graduate Studies and Research, University of Regina

Year dc:date.issued

2018

Author dc:creator

• Graham, Carly Florence

Advisor dc:contributor.advisor

• Somers, Christopher

Committee members dc:contributor.committeemember

• Stavrinides, John
• Manzon, Richard
• Butz, Cortney J.

Language dc:language.iso

en

DOI

https://doi.org/10.82465/3896

OAI identifier oai:identifier

oai:uregina.scholaris.ca:10294/8833