scholarly journals The pink salmon genome: uncovering the genomic consequences of a strict two-year life-cycle

2021 ◽  
Author(s):  
Kris A. Christensen ◽  
Eric B. Rondeau ◽  
Dionne Sakhrani ◽  
Carlo A. Biagi ◽  
Hollie Johnson ◽  
...  
Keyword(s):  
Pacific Salmon ◽  
Pink Salmon ◽  
Chromosomal Polymorphism ◽  
Oncorhynchus Gorbuscha ◽  
Sequencing Data ◽  
Isolated Populations ◽  
Temporal Isolation ◽  
History Of ◽  
Genome Assemblies ◽  
Salmon Fishery

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 strict two-year life-history of most 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 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.

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

PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0255752
Author(s):  
Kris A. Christensen ◽  
Eric B. Rondeau ◽  
Dionne Sakhrani ◽  
Carlo A. Biagi ◽  
Hollie Johnson ◽  
...  
Keyword(s):  
Pacific Salmon ◽  
Pink Salmon ◽  
Chromosomal Polymorphism ◽  
Oncorhynchus Gorbuscha ◽  
Sequencing Data ◽  
Isolated Populations ◽  
Temporal Isolation ◽  
History Of ◽  
Genome Assemblies ◽  
Salmon Fishery

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.

scholarly journals Resources and fishery of Pacific salmon in Magadan region in the beginning of the 21st century

Trudy VNIRO ◽  
2020 ◽  
Vol 179 ◽  
pp. 90-102
Author(s):  
M. N. Gorokhov ◽  
V. V. Volobuev ◽  
I. S. Golovanov
Keyword(s):  
Chum Salmon ◽  
Coho Salmon ◽  
Pacific Salmon ◽  
Pink Salmon ◽  
Spawning Grounds ◽  
Magadan Region ◽  
Spawning Areas ◽  
Optimal Values ◽  
In The Beginning ◽  
Salmon Fishery

There are two main areas of pacific salmon fishing in the Magadan region: Shelikhova Gulf and Tauiskaya Bay. The main fishing species is pink salmon in the region. Its share of total salmon catch by odd-year returns reaches 85 %. Data on the dynamics of escapement to the spawning grounds of pink salmon of the Shelikhova Gulf and Tauiskaya Bay are presented. The displacement of the level of spawning returns of pink salmon into the Shelihova Gulf with the simultaneous reduction of its returns to the Tauiskaya Bay is shown. Data on the dynamics of the fishing indicators of pink salmon for the two main fishing areas are provided. The Tauiskaya Bay as the main pink salmon fishery area loses its importance is shown. Graphical data on the escapement of producers pink salmon to the spawning grounds are presented and the optimal values of spawning escapements are estimated. Chum salmon is the second largest and most fishing species. Information on the dynamics of the number of returns, catch and escapement to the spawning grounds of chum salmon is given. The indicators of escapement to the spawning areas and their compliance with the optimal passes of salmon producers are analyzed. The issues of the dynamics of returns number, catch and the escapement to the spawning grounds of coho salmon producers are considered. The level of the escapement to the spawning areas is shown and the ratio of actual to optimal values of passes is estimated. The role of coho salmon as an object of industrial fishing and amateur fishing is shown. The extent of fishing press on individual groups of salmon populations is discussed. It is concluded that it is necessary to remove the main salmon fishery from the Tauiskaya Bay to the Shelikhova Gulf.

Use of the stratified-Petersen estimator in fisheries management: estimating the number of pink salmon (Oncorhynchus gorbuscha) spawners in the Fraser River

1998 ◽  
Vol 55 (2) ◽  
pp. 281-296 ◽  
Author(s):  
Carl James Schwarz ◽  
Carolyn Gail Taylor
Keyword(s):  
Pacific Salmon ◽  
Pink Salmon ◽  
Oncorhynchus Gorbuscha ◽  
Fraser River ◽  
Differential Migration ◽  
Mark Recapture ◽  
Pink Salmon Oncorhynchus Gorbuscha ◽  
The Pacific ◽  
Recent Developments

The simple-Petersen estimator is a well-known mark-recapture method to estimate animal abundance. Two key assumptions are equal catchability in both samples and complete mixing of tagged and untagged animals. If these are violated, severe bias can occur. The stratified-Petersen estimator can be used to account for some of the heterogeneity in catchability or mixing. In this paper, we first review recent developments in the stratified-Petersen experiment for fisheries audiences and demonstrate some of the practical problems that can occur that have not been discussed in the theoretical literature. Second, we present a case study to estimate the gross escapement of Fraser River pink salmon (Oncorhynchus gorbuscha) in 1991. The motivation for this study is a discrepancy of over 5 million fish between the estimates as derived by the Pacific Salmon Commission (PSC) (7.5 million fish based on a hydroacoustic method) and the Department of Fisheries and Oceans (DFO), Canada (13.0 million fish based on a mark-recapture method). One hypothesis put forward was that the discrepancy may be due to the use of a pooled-Petersen estimator when there is differential migration over time. The stratified-Petersen model suggests that little of this discrepancy can be explained by differential migration.

The Skeena River Salmon Fishery, with Special Reference to Sockeye Salmon

1955 ◽  
Vol 12 (3) ◽  
pp. 451-485 ◽  
Author(s):  
D. J. Milne
Keyword(s):  
Special Reference ◽  
Sockeye Salmon ◽  
Coho Salmon ◽  
Pink Salmon ◽  
Relative Size ◽  
Accurate Data ◽  
Gill Net ◽  
History Of ◽  
Skeena River ◽  
Salmon Fishery

The general history of the Skeena River commercial salmon fishery is presented from 1877 to 1948. The changes in fishing areas, seasons and fishing methods are described, together with the trends in the catches obtained. The most accurate data pertain to the important sockeye salmon gill-net fishery. The sockeye catch attained a maximum of 187,000 cases in 1910 and since then has declined to a minimum of 28,000 cases in 1933 and 1943. In recent years the catches have tended to level off. The pink salmon catches declined markedly after 1930. The chum catches also appear to have declined in recent years. Whether or not the spring and coho salmon catches have declined is not known. The size of the sockeye catch appears to be the best available measure of the relative size of the population. An analysis of the age cycles in the catch of sockeye and pink salmon did not reveal a practical basis for prediction. Some possible changes in the fishing regulations are discussed and the need for more data on the fluctuations in the size of the stocks during the fresh water phase is stressed.

scholarly journals Climate and competition influence sockeye salmon population dynamics across the Northeast Pacific Ocean

2020 ◽  
Vol 77 (6) ◽  
pp. 943-949 ◽  
Author(s):  
Brendan Connors ◽  
Michael J. Malick ◽  
Gregory T. Ruggerone ◽  
Pete Rand ◽  
Milo Adkison ◽  
...  
Keyword(s):  
Sockeye Salmon ◽  
Large Scale ◽  
Pacific Salmon ◽  
Spatial Scales ◽  
Interspecific Interactions ◽  
Pink Salmon ◽  
Oncorhynchus Gorbuscha ◽  
Negative Effects ◽  
Positive Effects ◽  
The North

Pacific salmon productivity is influenced by ocean conditions and interspecific interactions, yet their combined effects are poorly understood. Using data from 47 North American sockeye salmon (Oncorhynchus nerka) populations, we present evidence that the magnitude and direction of climate and competition effects vary over large spatial scales. In the south, a warm ocean and abundant salmon competitors combined to strongly reduce sockeye productivity, whereas in the north, a warm ocean substantially increased productivity and offset the negative effects of competition at sea. From 2005 to 2015, the approximately 82 million adult pink salmon (Oncorhynchus gorbuscha) produced annually from hatcheries were estimated to have reduced the productivity of southern sockeye salmon by ∼15%, on average. In contrast, for sockeye at the northwestern end of their range, the same level of hatchery production was predicted to have reduced the positive effects of a warming ocean by ∼50% (from a ∼10% to a ∼5% increase in productivity, on average). These findings reveal spatially dependent effects of climate and competition on sockeye productivity and highlight the need for international discussions about large-scale hatchery production.

scholarly journals Response of the Sea Louse Lepeophtheirus salmonis Infestation Levels on Juvenile Wild Pink, Oncorhynchus gorbuscha, and Chum, O. keta, Salmon to Arrival of Parasitized Wild Adult Pink Salmon

2006 ◽  
Vol 120 (2) ◽  
pp. 199
Author(s):  
Alexandra Morton ◽  
Rob Williams
Keyword(s):  
Chum Salmon ◽  
Pacific Salmon ◽  
Pink Salmon ◽  
Primary Source ◽  
Sea Lice ◽  
Oncorhynchus Gorbuscha ◽  
Oncorhynchus Keta ◽  
Lepeophtheirus Salmonis ◽  
Louse Infestation ◽  
Age Cohorts

Recent recurring infestations of Sea Lice, Lepeophtheirus salmonis, on juvenile Pacific salmon (Oncorhynchus spp.) and subsequent annual declines of these stocks have made it imperative to identify the source of Sea Lice. While several studies now identify farm salmon populations as sources of Sea Louse larvae, it is unclear to what extent wild salmonid hosts also contribute Sea Lice. We measured Sea Louse numbers on adult Pink Salmon (Oncorhynchus gorbuscha) migrating inshore. We also measured Sea Louse numbers on wild juvenile Pink and Chum salmon (Oncorhynchus keta) migrating to sea before the adults returned, and as the two age cohorts mingled. Adult Pink Salmon carried an average of 9.89 (SE 0.90) gravid lice per fish, and thus were capable of infecting the adjacent juveniles. Salinity and temperature remained favourable to Sea Louse reproduction throughout the study. However, all accepted measures of Sea Louse infestation failed to show significant increase on the juvenile salmon, either in overall abundance of Sea Lice or of the initial infective-stage juvenile lice, while the adult wild salmon were present in the study area. This study suggests that even during periods of peak interaction, wild adult salmon are not the primary source of the recent and unprecedented infestations of Sea Lice on juvenile Pacific Pink and Chum salmon in the inshore waters of British Columbia.

Effect of incubation temperature on the development of five species of Pacific salmon (Oncorhynchus) embryos and alevins

1988 ◽  
Vol 66 (1) ◽  
pp. 266-273 ◽  
Author(s):  
C. B. Murray ◽  
J. D. McPhail
Keyword(s):  
Chinook Salmon ◽  
Sockeye Salmon ◽  
Coho Salmon ◽  
Incubation Temperature ◽  
Pacific Salmon ◽  
Pink Salmon ◽  
Oncorhynchus Gorbuscha ◽  
Embryo Survival ◽  
Salmon Fry ◽  
Incubation Temperatures

Embryo and alevin survival, time to hatching and emergence, and alevin and fry size of five species of Pacific salmon (Oncorhynchus) were observed at five incubation temperatures (2, 5, 8, 11, and 14 °C). No pink (Oncorhynchus gorbuscha) or chum (O. keta) salmon embryos survived to hatching at 2 °C. Coho (O. kisutch) and sockeye (O. nerka) salmon had higher embryo survival at 2 °C than chinook (O. tschawytscha) salmon. At 14 °C, chum, pink, and chinook salmon had higher embryo survival than coho or sockeye salmon. In all species, peaks of embryo mortality occurred at specific developmental stages (completion of epiboly, eye pigmentation, and hatching). Alevin survival to emergence was high for all species, except for coho and pink salmon at 14 °C. Hatching and emergence time varied inversely with incubation temperature, but coho salmon hatched and emerged sooner at all temperatures than the other species. Coho and sockeye salmon alevins were larger at 2 °C, pink, chum, and chinook salmon alevins were larger at 5 and 8 °C. Coho salmon fry were larger at 2 °C, chinook and chum salmon fry were larger at 5 °C, and sockeye and pink salmon fry were larger at 8 °C. High incubation temperatures reduced fry size in all species. Each species of Pacific salmon appears to be adapted to different spawning times and temperatures, and thus indirectly to specific incubation temperatures, to ensure maximum survival and size and to maintain emergence at the most favorable time each year.

Evaluation of a simple technique for recovering fish from capture stress: integrating physiology, biotelemetry, and social science to solve a conservation problem

2013 ◽  
Vol 70 (1) ◽  
pp. 90-100 ◽  
Author(s):  
M.R. Donaldson ◽  
G.D. Raby ◽  
V.N. Nguyen ◽  
S.G. Hinch ◽  
D.A. Patterson ◽  
...  
Keyword(s):  
Social Science ◽  
Sockeye Salmon ◽  
Pacific Salmon ◽  
Pink Salmon ◽  
Oncorhynchus Gorbuscha ◽  
Plasma Sodium ◽  
Low Velocity ◽  
Air Exposure ◽  
Positive Attitudes ◽  
Capture Stress

We evaluate the utility of an inexpensive, portable recovery bag designed to facilitate recovery of fish from capture stress by combining physiological assays, biotelemetry, and social science surveys. Adult migrating Pacific salmon (Oncorhynchus spp.) were used as a model, since some of their populations are threatened. While catch-and-release is common, there is a need to ensure that it is sustainable. A social science survey revealed that anglers generally have positive attitudes towards recovery bag use, particularly if research identifies that such techniques could be effective. Physiological assays on pink salmon (Oncorhynchus gorbuscha) revealed benefits of both high- and low-velocity recovery, but high velocity was most effective with reduced plasma cortisol concentrations and similar plasma sodium and chloride concentrations as those found in controls at all recovery durations. A biotelemetry study on sockeye salmon (Oncorhynchus nerka) captured by anglers and stressed by air exposure then placed in recovery bags had 20% higher, but not significantly different, survival than no-recovery salmon. The integration of natural science and social science provides an important step forward in developing methods for promoting recovery of fish from capture.

Detection and identification of Diphyllobothrium nihonkaiense plerocercoids from wild Pacific salmon (Oncorhynchus spp.) in Japan

2010 ◽  
Vol 84 (4) ◽  
pp. 434-440 ◽  
Author(s):  
J. Suzuki ◽  
R. Murata ◽  
K. Sadamasu ◽  
J. Araki
Keyword(s):  
Molecular Analysis ◽  
Detection Rate ◽  
Chum Salmon ◽  
Pacific Salmon ◽  
Pink Salmon ◽  
Oncorhynchus Gorbuscha ◽  
Oncorhynchus Keta ◽  
Oncorhynchus Masou ◽  
Detection Rates ◽  
Detection And Identification

AbstractWe investigated the risk of diphyllobothriasis from ingestion of wild Pacific salmon in Japan by surveying Diphyllobothrium plerocercoids in 182 salmon samples obtained from Japan. The plerocercoids were not detected in chum salmon (Oncorhynchus keta) (0/26), called Akizake in Japan, caught between September and November. However, the detection rate of plerocercoids in chum salmon, called Tokishirazu in Japan, caught between early April and June, was 51.1% (24/47) with an average of two plerocercoid larvae per fish. The detection rates of cherry salmon (Oncorhynchus masou) and pink salmon (Oncorhynchus gorbuscha) were 12.2% (10/82) and 18.5% (5/27), respectively, and the average number of plerocercoids per fish was 0.45 (37 larvae/82 fishes) and 0.22 larvae (6 larvae/27 fishes), respectively. Plerocercoids isolated from O. keta and O. masou were identified as Diphyllobothrium nihonkaiense on the basis of molecular analysis of the cox1 and nad3 genes. Moreover, four tapeworms (three from O. keta and one from O. masou) were obtained by infecting golden hamsters with plerocercoids. The morphological features of these tapeworms were similar to those of D. nihonkaiense isolated from humans. Therefore, we think that O. keta and not O. masou is the most important source of plerocercoid infections in Japan.

Consumption and distribution of salmon (Oncorhynchus spp.) nutrients and energy by terrestrial flies

2006 ◽  
Vol 63 (9) ◽  
pp. 2076-2086 ◽  
Author(s):  
Morgan D Hocking ◽  
Thomas E Reimchen
Keyword(s):  
Chum Salmon ◽  
Pacific Salmon ◽  
Pink Salmon ◽  
Isotope Analysis ◽  
Terrestrial Ecosystems ◽  
Oncorhynchus Gorbuscha ◽  
Oncorhynchus Keta ◽  
The North ◽  
Terrestrial Habitats ◽  
Salmon Carcasses

Anadromous Pacific salmon (Oncorhynchus spp.) subsidize terrestrial food webs with their nutrients and carcasses, a process driven largely by selective foraging by bears (Ursus spp.). We quantify wildlife transfer of salmon carcasses to riparian zones on two watersheds in coastal British Columbia and estimate total terrestrial fly production from remnant carcasses. Large-bodied chum salmon (Oncorhynchus keta) were transferred into the forest at a greater rate than were pink salmon (Oncorhynchus gorbuscha) (chum salmon mass = 6089–11 031 kg, 16%–48% of salmon run; pink salmon mass = 2266–2808 kg, 4%–6% of salmon run). Blow flies (genus Calliphora) and other Diptera dominated colonization (>90% of salmon carcasses). Between the two watersheds, 196 and 265 g of Calliphora larvae per metre of spawning length (4 and 7 million larvae for whole watersheds) were generated from salmon carcass transfer. Stable isotope analysis of δ15N and δ13C of spring-emerging adult Calliphora revealed that >80% of individuals had salmon-based signatures. Flies are a dominant consumer and vector of salmon nutrients in terrestrial habitats and supplement the diet of at least 16 vertebrate and 22 invertebrate species. Anticipated further declines of salmon in the North Pacific can be expected to further erode the complex associations coupling marine and terrestrial ecosystems.

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