Investigating population genomic structure of salmon lice (Lepeophtheirus salmonis) in northern Norway

Abstract

Salmon louse (Lepeophtheirus salmonis) is a parasitic copepod that causes significant damage to Atlantic salmon (Salmo salar) and incurs significant costs to the salmonid aquaculture industry. In Norway, the industry has been coping with salmon lice issues with various methods such as chemical treatments, but it has resulted in an acquisition of resistance in salmon lice towards the existing delousing treatments. In order to maximize the effectiveness of the treatments, it is important to understand population structuring of salmon lice, and factors that are driving the structure, since recent studies suggested that several Atlantic salmon lice populations are sharing genetic materials coding for resistance toward delousing treatments. The objective of this study was to investigate whether salmon lice in northern Norway display population structure and differentiation at small geographical scales. We identified 25,795 robustly supported SNPs among salmon lice from 8 different locations in northern Norway. While only very weak structure was observed based on the full SNP dataset (25,795 SNPs), relatively weak, but highly significant, population structure was observed using 303 important SNPs identified using a random forest classification approach. No significant correlation between genetic differentiation and geographical distance was observed. To our knowledge, it was the first study to reveal the significant population structure of salmon lice at such small spatial scales. Our results suggested that the observed population structure was a result of dispersal and mixing of salmon lice, as well as selective pressure such as delousing treatments and local environment. Our results are potentially helpful to make population specific delousing treatments, where the treatments are designed depending on the genetic characteristics of the targeted salmon lice population.