Salmon lice, Lepeophtheirus salmonis, are naturally occurring parasites of salmon in sea water. Intensive salmon farming provides better conditions for parasite growth and transmission compared with natural conditions, creating problems for both the salmon farming industry and, under certain conditions, wild salmonids. Salmon lice originating from farms negatively impact wild stocks of salmonids, although the extent of the impact is a matter of debate. Estimates from Ireland and Norway indicate an odds ratio of 1.1:1-1.2:1 for sea lice treated Atlantic salmon smolt to survive sea migration compared to untreated smolts. This is considered to have a moderate population regulatory effect. The development of resistance against drugs most commonly used to treat salmon lice is a serious concern for both wild and farmed fish. Several large initiatives have been taken to encourage the development of new strategies, such as vaccines and novel drugs, for the treatment or removal of salmon lice from farmed fish. The newly sequenced salmon louse genome will be an important tool in this work. The use of cleaner fish has emerged as a robust method for controlling salmon lice, and aquaculture production of wrasse is important towards this aim. Salmon lice have large economic consequences for the salmon industry, both as direct costs for the prevention and treatment, but also indirectly through negative public opinion.

As part of an EU funded 7th Framework project, Prevent Escape, a programme of research was undertaken to document the extent, size and knowledge of the causes of escapes from marine fin fish farms in Europe over a three year period. Escape incidents were identified and assessed through questionnaires across the 6 countries (Ireland, UK, Norway, Spain, Greece, and Malta), and other data supplied by the Norwegian Fisheries Directorate and the Scottish Aquaculture Research Forum. A total of 8,922,863 fish were reported to have escaped from 242 incidents. Of these over 5 million occurred in two catastrophic escape incidents. Sea bream accounted for the highest number of escapes at 76.7% followed by Atlantic salmon at 9.2%. Of the 113 Atlantic salmon escape events, almost 75% were due to structure failure or operational error. Almost 50% of cod escape incidents were due to biological causes e.g. biting of nets. The nominal costs of escapes as calculated by value at point of first sale were very substantial, estimated at approximately €47.5 million per annum on average over the study period. Of this €42.8 million was for annual cost of losses of sea bass and sea bream in the Mediterranean and €4.7 million for losses of salmon in northern Europe.peer-reviewe

The reproductive output of Lepeophtheirus salmonis and Caligus elongatus was examined for one coastal area in Ireland. Size ranges of adult L. salmonis were examined in relation to reproductive output. The relative success of C. elongatus and L. salmonis as parasites of farmed salmonids is discussed. IntroductionTwo species of sea lice are found on farmed salmon off the Irish coast, Lepeophtheirus salmonis (Krqer, 1838) and Caligus elongatus ( N o r d m a~, 1832.) The life cycle of both species is similar with the eggs hatching to give non-feeding planktonic nauplii. There are two naupliar stages, the third moult giving rise to a copepodite which must find and attach to a host for further development to occur. Once established on a host, development proceeds through a series of chalimus stages, attached by a frontal filament, and preadult stages, which are mobile, to the adult. Detailed descriptions of development are given by Johannessen (1978) and Albright (1991a, 1991b) for L. salmonis and by Wooten et al. (1982) and Hogans and Trudeau (1989) for C. elongatus and L. salmonis.

Caligid sea lice represent a significant threat to salmonid aquaculture worldwide.Lepeophtheirus salmonis is the predominant species that occurs in the Northern Hemisphere.Dispersal of sea lice between marine aquaculture sites and geographic regions is thought to occur rapidly via planktonic transport of larvae. Population genetic analyses have consistently shown minimal population genetic structure in North Atlantic L. salmonis, frustrating efforts to track louse populations, improve targeted control measures and understand local adaption to environmental conditions. The aim of this study was to test the power of reduced representation library sequencing (IIb-RAD sequencing) coupled with random forest machine learning algorithms to define markers for fine-scale discrimination of louse populations. We identified 1286 robustly supported SNPs among four L. salmonis populations from Ireland (N=2, 27 individuals), Scotland (N=1, 11 individuals) and North Norway (N=1, 12 individuals). Weak global structure (FSC = 0.018, p<0.0001) and only one significant pairwise FST comparison was observed (Scotland vs Kenmare Bay, (FST = 0.018, p<0.0001)) using all 1286 SNPs. The application of a random forest machine-learning algorithm identified 98 discriminatory SNPs that dramatically improved population assignment (DAPC assignment probability = 1), increased global Fsc = 0.098, (p<0.0001) and resulted in pairwise comparisons that all showed highly significant Fst-values (range = 0.081 -0.096, p<0.0001). Out of 19 SNPs found to be under directional selection between populations, 12 corresponded to the discriminatory SNPs identified using random forest. Taken together our data suggest that L. salmonis SNP diversity exists with which it is possible to discriminate differences between nearby populations given suitable marker selection approaches, and that such differences might have an adaptive basis.We discuss these data in light of sea lice adaption to anthropogenic and environmental pressures as well as novel approaches to track and predict sea louse dispersal.

Background: Passive integrated transponder (PIT) tags are used to study the movement and behaviour in populations of a wide variety of fish species and for a number of different applications from fisheries to aquaculture. Before embarking on long-term studies, it is important to collect information on both short-and medium-term survival and tag retention for the species in question. In this study, 90 juvenile lumpfish (10-20 g, 30 fish per replicate tank) were implanted with 12.5-mm FDX PIT tags. Results: Tag retention, growth rates and survival were compared to those of fish subjected to handling only (90 fish, 30 per replicate tank). Overall survival was 100% during the 28-day monitoring period, and tag retention was 99%. Conclusions: Results indicate that retention rates of 12.5-mm PIT tags in juvenile lumpfish are high, and there is no significant effect on growth rates or survival in a hatchery environment.