Whole genome sequencing reveals development of structured salmon lice (Lepeophtheirus salmonis, Krøyer, 1838) populations among aquaculture net pens through production

Abstract

Salmon louse, (Lepeophtheirus salmonis, Krøyer, 1838), is an ectoparasite that causes multiple health and economic problems in the farming of Atlantic salmon (Salmo salar L.), but also threatens wild salmonid species. The industry is struggling to identify proper measures for limiting lice infections, and to identify effective delousing treatments. One of the major production and management challenges, but interesting biological observations, is that each treatment, as seen for medicinal or chemical treatment, becomes less effective due to the development of resistance in salmon lice. This causes reduced fish health, large financial losses for the industry, and, so far, unsolvable challenges for the management of aquaculture. The current management regime assumes that salmon lice along the Norwegian coast is a panmictic population, despite it is known that delousing treatments act as strong selective agents that create phenotypes who display adaptive traits towards resistance. However, there is no prior research addressing the population genomics underlying this observation on smaller geographical scales through time. The objective of this study was to investigate within farm and among net pens genomic population structure of salmon lice within an aquaculture facility located in northern Norway through time. The results of the present study, based on whole genome sequencing, and analyses of 66,769 SNPs, revealed that a production of Atlantic salmon can be viewed as a continuum of genomic differentiation, where salmon lice colonize the hosts at the onset of production to developing weak, but significant, population structure among net pens and through time. The application of the random forest machine learning identified 107 SNPs and 260 SNPs discriminatory for genomic differences among net pens and timepoints, respectively. These two sets of SNPs increased significant differentiation among net pens, and significantly supported the development of genetic population differentiation over time of production. Overall, these findings show that salmon lice within aquaculture net pens evolve into genetically differentiated populations during production time.