An Examination of the Utility of Large Genomic Datasets for Genetic Monitoring: An Atlantic Salmon (Salmo salar) Case Study

Abstract

Effective fisheries management requires an awareness of population demography and the spatial scale of population structuring, yet traditional approaches to quantifying both can be labour intensive and expensive. Here I explore the utility of large genomic datasets to characterize population structure, estimate effective population size, and monitor population status in Atlantic Salmon (Salmo salar) in Placentia Bay Newfoundland, Canada using a 220K SNP array. Population structure was linked to a temperature associated chromosomal polymorphism. Populations were small (N̂b < 350) and currently declining. Simulations suggested that large genomic datasets (≥ 100 microsatellites or ≥ 1000 SNPs) enabled accurate detection of population declines >30%. As such, I demonstrate that large genomic datasets allow the identification of fine-scale spatial structuring, the structuring forces involved, and provide a cost effective and accurate approach to monitor population status in the wild