Genome assembly, transcriptome and SNP database for chum salmon (Oncorhynchus keta)

Chum salmon (Oncorhynchus keta) is the species with the widest geographic range of the anadromous Pacific salmonids,. Chum salmon is the second largest of the Pacific salmon, behind Chinook salmon, and considered the most plentiful Pacific salmon by overall biomass. This species is of significant commercial and economic importance: on average the commercial chum salmon fishery has the second highest processed value of the Pacific salmon within British Columbia. The aim of this work was to establish genomic baseline resources for this species. Our first step to accomplish this goal was to generate a chum salmon reference genome assembly from a doubled-haploid chum salmon. Gene annotation of this genome was facilitated by an extensive RNA-seq database we were able to create from multiple tissues. Range-wide resequencing of chum salmon genomes allowed us to categorize genome-wide geographic variation, which in turn reinforced the idea that genetic differentiation was best described on a regional, rather than at a stock-specific, level. Within British Columbia, chum salmon regional groupings were described at the conservation unit (CU) level, and there may be substructure within particular CUs. Genome wide associations of phenotypic sex to SNP genetic markers identified two clear peaks, a very strong peak on Linkage Group 15, and another on Linkage Group 3. With these new resources, we were better able to characterize the sex-determining region and gain further insights into sex determination in chum salmon and the general biology of this species.

The pink salmon genome: Uncovering the genomic consequences of a two-year life cycle

Pink salmon (Oncorhynchus gorbuscha) adults are the smallest of the five Pacific salmon native to the western Pacific Ocean. Pink salmon are also the most abundant of these species and account for a large proportion of the commercial value of the salmon fishery worldwide. A two-year life history of pink salmon generates temporally isolated populations that spawn either in even-years or odd-years. To uncover the influence of this genetic isolation, reference genome assemblies were generated for each year-class and whole genome re-sequencing data was collected from salmon of both year-classes. The salmon were sampled from six Canadian rivers and one Japanese river. At multiple centromeres we identified peaks of Fst between year-classes that were millions of base-pairs long. The largest Fst peak was also associated with a million base-pair chromosomal polymorphism found in the odd-year genome near a centromere. These Fst peaks may be the result of a centromere drive or a combination of reduced recombination and genetic drift, and they could influence speciation. Other regions of the genome influenced by odd-year and even-year temporal isolation and tentatively under selection were mostly associated with genes related to immune function, organ development/maintenance, and behaviour.

Inuvialuit Knowledge of Pacific Salmon Range Expansion in the Western Canadian Arctic

Rapid climate change is altering Arctic ecosystems and significantly affecting the livelihoods and cultural traditions of Arctic Indigenous peoples. In the Inuvialuit Settlement Region (ISR), an increase in the harvest of Pacific salmon indicates largescale changes influencing Inuvialuit fisheries. In this project we recorded and synthesized Inuvialuit knowledge of Pacific salmon. We conducted 54 interviews with Inuvialuit fishers about the history of Pacific salmon harvest, how it has changed in recent decades, and concurrent changes to local environments and fish species. Our interviews show that historic, incidental salmon harvest in the ISR ranged from infrequent to common among western communities, but was rare or unprecedented among eastern communities. Participants in all six communities reported a recent increase in salmon harvest and attributed this shift to regional environmental change. Fishers were concerned that salmon would negatively affect their cultural traditions and preferred fish species. Given uncertainty about the effects of salmon on local fisheries, research on salmon diets in the Arctic, their subsidies to Arctic freshwater systems, and the likelihood of their establishment is vital.

ЛЕТНЕЕ ПИТАНИЕ СИВУЧА В ВОДАХ ДАЛЬНЕГО ВОСТОКА РОССИИ В 2004–2008 ГОДАХ

The diet of Steller sea lion Eumetopias jubatus was studied based on undigested food parts found in feces collected in the summer season on 20 rookeries in the Russian Far East. A total of 915 samples were analyzed between 2004 and 2008, in which 65 food items were identified. The frequency of occurrence of 11 diet items was greater than 5%, including Atka mackerel Pleurogrammus monopterygius (64.8%), Pollock Theragra chalcogramma (44.3%), Pacific salmon Salmonidae (20.5%), Irish lord Hemilepidotus sp. (20.4%), Pacific sand lance Ammodytes hexapterus (15.8%), Pacific herring Clupea pallasi (9.5%), Squid and Octopus Cephalopoda (8.4%), Pacific cod Gadus macrocephalus (5, 9%), Pacific sandfish Trichodon trichodon (5.9%), Flatfishes Pleuronectidae (5.8%), Threespine stickleback Gasterosteus aculaeatus (4.9%). Three regions with different diets were identified – the Sea of Okhotsk, the Kuril Islands, and Kamchatka with the Commander Islands. In the Sea of Okhotsk, Pollock and Herring (83.6% by frequency of occurrence) dominated among undigested food remains in feces. The diet at the Kuril Islands rookeries was variable within the region. The general pattern was a low diversity of diet at each Kuril Island sites and predominance of 1-3 food items, probably the most accessible near the sites (Pollock, Squid and Octopus, Atka mackerel, Pacific salmon). The diet pattern in Kamchatka and the Commander Islands in the summer season was characterized by a high diet diversity. In contrast to other regions, the diet includes in high proportion small non-commercial species – Sand lance, Irish lord, Pacific sandfish, Flatfishes, Threespine stickleback and others. The regional patterns of sea lion diets show the spatial distribution and areas of abundant biomass of the main food items. The diet patterns of sea lions from rookeries differed from haulouts in having a higher content of abundant food items. Long-term changes in diet structure were not statistically significant.

Diverse and changing use of the Salish Sea by Pacific salmon, trout, and char

Each year, juveniles of eight salmonid species enter the Salish Sea - the inland marine waters between northwestern Washington, USA and British Columbia, Canada. These species vary in the proportions remaining there and migrating to feed in the Pacific Ocean. Such differential migration affects their growth rates, and exposure to habitat alteration, predators, fisheries, and contaminants. We review these diverse migration patterns and present data from Puget Sound illustrating the variation in downstream migration timing, residency in the Salish Sea, and upriver return timing. Recreational catch records indicate that proportionally fewer remain in the Salish Sea than in past decades for several species, and the declines began after peaks in the late 1970s – early 1980s. These declines resist easy explanation because the factors controlling residency are poorly understood, and the Salish Sea has changed over the past decades. Regardless of the cause, the diversity of migration patterns is important to the ecology of the salmon and trout species, and to the humans and other members of the Salish Sea community with which they interact.

Glacier retreat creating new Pacific salmon habitat in western North America

Glacier retreat poses risks and benefits for species of cultural and economic importance. One example is Pacific salmon (Oncorhynchus spp.), supporting subsistence harvests, and commercial and recreational fisheries worth billions of dollars annually. Although decreases in summer streamflow and warming freshwater is reducing salmon habitat quality in parts of their range, glacier retreat is creating new streams and lakes that salmon can colonize. However, potential gains in future salmon habitat associated with glacier loss have yet to be quantified across the range of Pacific salmon. Here we project future gains in Pacific salmon freshwater habitat by linking a model of glacier mass change for 315 glaciers, forced by five different Global Climate Models, with a simple model of salmon stream habitat potential throughout the Pacific Mountain ranges of western North America. We project that by the year 2100 glacier retreat will create 6,146 (±1,619) km of new streams accessible for colonization by Pacific salmon, of which 1,930 (±569) km have the potential to be used for spawning and juvenile rearing, representing 0 to 27% gains within the 18 sub-regions we studied. These findings can inform proactive management and conservation of Pacific salmon in this era of rapid climate change.