Atlantic cod (Gadus morhua) is a large, cold-adapted teleost that sustains long-standing commercial fisheries and incipient aquaculture1,2. Here we present the genome sequence of Atlantic cod, showing evidence for complex thermal adaptations in its haemoglobin gene cluster and an unusual immune architecture compared to other sequenced vertebrates. The genome assembly was obtained exclusively by 454 sequencing of shotgun and paired-end libraries, and automated annotation identified 22,154 genes. The major histocompatibility complex (MHC) II is a conserved feature of the adaptive immune system of jawed vertebrates3,4, but we show that Atlantic cod has lost the genes for MHCII, CD4 and Ii that are essential for the function of this pathway. Nevertheless, Atlantic cod is not exceptionally susceptible to disease under natural conditions5. We find a highly expanded number of MHCI genes and a unique composition of its Toll-like receptor (TLR) families. This suggests how the Atlantic cod immune system has evolved compensatory mechanisms within both adaptive and innate immunity in the absence of MHCII. These observations affect fundamental assumptions about the evolution of the adaptive immune system and its components in vertebrates.

[1] Kongsfjorden and the West Spitsbergen Shelf is a region whose seasonal hydrography is dominated by the balance of Atlantic Water, Arctic waters, and glacial melt. Regional seasonality and the cross-shelf exchange processes have been investigated using conductivity-temperature-depth (CTD) observations from 2000-2003 and a 5-month mooring deployment through the spring and summer of 2002. Modeling of shelf-fjord dynamics was performed with the Bergen Ocean Model. Observations show a rapid and overwhelming intrusion of Atlantic Water across the shelf and into the fjord during midsummer giving rise to intense seasonality. Pockets of Atlantic Water, from the West Spitsbergen Current, form through barotropic instabilities at the shelf front. These leak onto the shelf and propagate as topographically steered features toward the fjord. Model results indicate that such cross-front exchange is enhanced by north winds. Normally, Atlantic Water penetration into the fjord is inhibited by a density front at the fjord mouth. This geostrophic control mechanism is found to be more important than the hydraulic control common to many fjords.

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.

Rates of ice mass loss at the calving margins of tidewater glaciers (frontal ablation rates) are a key uncertainty in sea level rise projections. Measurements are difficult because mass lost is replaced by ice flow at variable rates, and frontal ablation incorporates sub-aerial calving, and submarine melt and calving. Here we derive frontal ablation rates for three dynamically contrasting glaciers in Svalbard from an unusually dense series of satellite images. We combine ocean data, ice-front position and terminus velocity to investigate controls on frontal ablation. We find that frontal ablation is not dependent on ice dynamics, nor reduced by glacier surface freeze-up, but varies strongly with sub-surface water temperature. We conclude that calving proceeds by melt undercutting and ice-front collapse, a process that may dominate frontal ablation where submarine melt can outpace ice flow. Our findings illustrate the potential for deriving simple models of tidewater glacier response to oceanographic forcing.

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