scholarly journals Discriminating Among Pacific Salmon, Rainbow Trout, and Atlantic Salmon Species Using Common Genetic Screening Methods

2019 ◽  
Vol 10 (1) ◽  
pp. 228-240 ◽  
Author(s):  
Christopher Habicht ◽  
Christian T. Smith ◽  
Andrew Barclay ◽  
Heather A. Hoyt ◽  
Keith Turnquist ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Atlantic Salmon ◽  
Pacific Salmon ◽  
North Pacific Ocean ◽  
Genotyping By Sequencing ◽  
Population Monitoring ◽  
Common Species ◽  
Screening Methods ◽  
Life History Stage ◽  
The North

Abstract The five most common species of Pacific salmon, Rainbow Trout (steelhead) Oncorhynchus spp., and Atlantic Salmon Salmo salar intermingle in the North Pacific Ocean and its freshwater tributaries. Efficient morphological methods for distinguishing among these species are sometimes limited by condition of the specimen (degraded or missing morphology), life history stage, or training of the observer. Researchers have successfully applied various genetic methods to distinguish among these species when morphological analyses are not possible, but they cannot easily incorporate these methods into standard fish and wildlife population monitoring analysis workflows. Here we test five 5′–3′ exonuclease (TaqMan) assays developed from mitochondrial genes and provide novel methods that take advantage of TaqMan output to distinguish among these species. We found that combinations of as few as two of the five assays were adequate to distinguish all species. TaqMan chemistry is designed to interrogate a single nucleotide locus. We also explore the basis for the variation in the observed scatter plot distributions (variation in florescent signals) and show that this variation is due to nucleotide diversity in and near the probe site. Because the SNPs underlying the assays developed here are all physically close to one another along the mitochondrial genome, the potential exists to develop a single DNA sequence-based assay to discriminate among salmon species. This single assay can be added to a genotyping-by-sequencing panel to identify and exclude nontarget species from analyses.

Use of sequence data from rainbow trout and Atlantic salmon for SNP detection in Pacific salmon

2005 ◽  
Vol 14 (13) ◽  
pp. 4193-4203 ◽  
Author(s):  
CHRISTIAN T. SMITH ◽  
CARITA M. ELFSTROM ◽  
LISA W. SEEB ◽  
JAMES E. SEEB
Keyword(s):  
Rainbow Trout ◽  
Atlantic Salmon ◽  
Pacific Salmon ◽  
Sequence Data ◽  
Snp Detection

scholarly journals Pacific salmon abundance trends and climate change

2011 ◽  
Vol 68 (6) ◽  
pp. 1122-1130 ◽  
Author(s):  
James R. Irvine ◽  
Masa-aki Fukuwaka
Keyword(s):  
Climate Change ◽  
Pacific Ocean ◽  
North Pacific ◽  
Sockeye Salmon ◽  
Coho Salmon ◽  
Pacific Salmon ◽  
North Pacific Ocean ◽  
Pink Salmon ◽  
The North ◽  
Abundance Trends

Abstract Irvine, J. R., and Fukuwaka, M. 2011. Pacific salmon abundance trends and climate change. – ICES Journal of Marine Science, 68: 1122–1130. Understanding reasons for historical patterns in salmon abundance could help anticipate future climate-related changes. Recent salmon abundance in the northern North Pacific Ocean, as indexed by commercial catches, has been among the highest on record, with no indication of decline; the 2009 catch was the highest to date. Although the North Pacific Ocean continues to produce large quantities of Pacific salmon, temporal abundance patterns vary among species and areas. Currently, pink and chum salmon are very abundant overall and Chinook and coho salmon are less abundant than they were previously, whereas sockeye salmon abundance varies among areas. Analyses confirm climate-related shifts in abundance, associated with reported ecosystem regime shifts in approximately 1947, 1977, and 1989. We found little evidence to support a major shift after 1989. From 1990, generally favourable climate-related marine conditions in the western North Pacific Ocean, as well as expanding hatchery operations and improving hatchery technologies, are increasing abundances of chum and pink salmon. In the eastern North Pacific Ocean, climate-related changes are apparently playing a role in increasing chum and pink salmon abundances and declining numbers of coho and Chinook salmon.

The marine phase of the Atlantic salmon (Salmo salar) life cycle, with comparisons to Pacific salmon

1998 ◽  
Vol 55 (S1) ◽  
pp. 104-118 ◽  
Author(s):  
L P Hansen ◽  
T P Quinn
Keyword(s):  
Atlantic Salmon ◽  
Salmo Salar ◽  
Life Histories ◽  
North Atlantic Ocean ◽  
Pacific Salmon ◽  
Mortality Factor ◽  
Growth And Survival ◽  
Atlantic Salmon Salmo Salar ◽  
The North ◽  
Wide Range

Atlantic salmon (Salmo salar) are distributed over large areas in the north Atlantic Ocean. They usually move very quickly from freshwater to oceanic areas, whereas there is considerable variation among Pacific salmon in early marine movements. In some areas, Atlantic salmon of exploitable size are sufficiently abundant that commercial high seas fisheries have developed. Such areas are off west Greenland, where North American and European fish are harvested, and in the Norwegian Sea, north of the Faroe Islands, where mainly European fish are exploited. Atlantic salmon feed on a wide range of large crustaceans, pelagic fish, and squid in the marine environment, supporting the hypothesis that Atlantic salmon are opportunistic feeders. In the ocean the salmon grow relatively quickly and the sea age when they become sexually mature depends on both genetics and on growing conditions. Natural marine mortality of salmon is highest during the first few months at sea and the major mortality factor is probably predation. However, marine mortality of Atlantic salmon has increased in recent years, apparently correlated with a decline in sea surface temperatures. Similar relationships between environmental conditions and the growth and survival of Pacific salmon have been reported. Atlantic salmon life histories most closely mimic stream-type chinook salmon or steelhead trout among the Pacific species. Finally, Atlantic and Pacific salmon return to their home rivers with high precision and possible mechanisms controlling the oceanic homing migration are presented and discussed.

Influence of monsoon-driven hydrographic features on siphonophore assemblages in the Taiwan Strait, western North Pacific Ocean

2013 ◽  
Vol 64 (4) ◽  
pp. 348 ◽  
Author(s):  
Hung-Yen Hsieh ◽  
Shwu-Feng Yu ◽  
Wen-Tseng Lo
Keyword(s):  
Western North Pacific ◽  
North Pacific Ocean ◽  
Distribution Patterns ◽  
Common Species ◽  
Taiwan Strait ◽  
Zooplankton Biomass ◽  
Dynamic Nature ◽  
The North ◽  
Hydrographic Features ◽  
The Taiwan Strait

The spatial patterns of siphonophores were analysed in relation to local hydrographic features during two different monsoon seasons (the north-easterly monsoon in winter v. the south-westerly monsoon in summer) in the Taiwan Strait. Forty-eight species were identified, with five types of calycophoran siphonophores (Lensia subtiloides, Chelophyes appendiculata, Chelophyes contorta, Bassia bassensis, and Diphyes chamissonis) being most common in both seasons. Significantly higher abundances of four of the five common species were recorded in summer than in winter. Differences in the siphonophore species compositions were also observed between the northern and southern part of Taiwan Strait, with significantly higher diversity occurring in the southern waters. The distribution patterns of siphonophore assemblages were closely linked to the hydrographic features, influenced by the dynamic nature of the currents in the study area, with temperature, salinity and zooplankton biomass being the three most important factors.

scholarly journals Multiple introductions of salmonid alphavirus from a wild reservoir have caused independent and self-sustainable epizootics in aquaculture

2014 ◽  
Vol 95 (1) ◽  
pp. 52-59 ◽  
Author(s):  
Marius Karlsen ◽  
Britt Gjerset ◽  
Tove Hansen ◽  
Andrew Rambaut
Keyword(s):  
Rainbow Trout ◽  
Atlantic Salmon ◽  
Geographical Area ◽  
Farmed Fish ◽  
Multiple Introductions ◽  
The North ◽  
Geographical Distances ◽  
The North Sea ◽  
Phylogenetic Framework ◽  
Farmed Atlantic Salmon

Salmonid alphavirus (SAV) causes infections in farmed Atlantic salmon and rainbow trout in Europe. Genetic diversity exists among SAV strains from farmed fish and six subtypes have been proposed based on genetic distance. Here, we used six full-genome sequences and 71 partial sequences of the structural ORF to estimate the evolutionary rate of SAV. The rate, 2.13×10−4 nt substitutions per site per year, was further used to date evolutionary events in a Bayesian phylogenetic framework. The comparison of these dates with known historical events suggested that all six subtypes diverged prior to the twentieth century, earlier than the first attempts to introduce and farm rainbow trout in Europe. The subtypes must therefore have existed in a wild reservoir, as yet unidentified. The strains of each subtype, with the exception of subtype 2, have a common ancestor that existed after the 1970s – the start of modern farming of Atlantic salmon. These ancestors are likely to represent the independent introductions to farmed fish populations from the wild reservoir. The subtypes have developed subsequently into self-sustainable epizootics. The most parsimonious phylogeographic reconstruction suggested that the location of the wild reservoir is in or around the North Sea. After the initial introductions to aquaculture, further transmission of SAV was likely related to the industry infrastructure. This was exemplified by the finding of genetically identical subtype 2 and 3 strains separated by large geographical distances, as well as genetically distinct co-circulating lineages within the same geographical area.

THE IDENTITY OF THE SPECIES OF LEPEOPHTHEIRUS (COPEPODA) PARASITIC ON PACIFIC SALMON (GENUS ONCORHYNCHUS) AND ATLANTIC SALMON (SALMO SALAR)

1958 ◽  
Vol 36 (6) ◽  
pp. 889-892 ◽  
Author(s):  
L. Margolis
Keyword(s):  
Atlantic Salmon ◽  
Salmo Salar ◽  
North American ◽  
North Pacific ◽  
Pacific Salmon ◽  
Distinct Species ◽  
Atlantic Salmon Salmo Salar ◽  
The North ◽  
Wide Range ◽  
The North Pacific

A review of existing descriptions of Lepeophtheirus from salmonids, based on specimens collected mainly from Salmo salar in the European and North American Atlantic and from Oncorhynchus spp. in the Asiatic and North American Pacific, coupled with observations by the author on material from S. salar from England and from Oncorhynchus spp. from a wide range of localities in the North Pacific, suggest that L. salmonis (Krøyer, 1838) is the only species found on salmonids from both oceans. The differentiation of L. uenoi Yamaguti, 1939 as a distinct species on Pacific salmon seems to be the result of incorrect or inadequate early descriptions of L. salmonis.

scholarly journals An overview of monitoring for raptors in Finland

Acrocephalus ◽  
2012 ◽  
Vol 33 (154-155) ◽  
pp. 203-215 ◽  
Author(s):  
Pertti Saurola
Keyword(s):  
Population Monitoring ◽  
Common Species ◽  
Population Fluctuations ◽  
National Board ◽  
Nest Sites ◽  
The North ◽  
Economic Support ◽  
Annual Population ◽  
Occupied Territories ◽  
Population Indices

Abstract In Finland, population monitoring for both diurnal and nocturnal raptors has been almost entirely based on fieldwork carried out by voluntary raptor ringers. Responsible organisations include the Finnish Museum of Natural History, with economic support for administration from the Ministry of Environment, “Metsahallitus” (former National Board of Forestry) and WWF Finland. Since the early 1970s, numbers and productivity of four endangered species, the White-tailed Eagle Haliaeetus albicilla, Golden Eagle Aquila chrysaetos, Osprey Pandion haliaetus and Peregrine Falcon Falco peregrinus have been monitored by country-wide Comprehensive Surveys, with the aim of checking all known nest sites of these species every year. The Gyrfalcon F. rusticolus was included in this group in the late 1990s. Data for monitoring the populations of the other raptor species have been gathered by the Raptor Grid and Raptor Questionnaire projects. The Raptor Grid project produces annual population indices, which are calculated from the data collected from 10 × 10 km study plots (n = ca. 130/year) and quite well reflect the annual population fluctuations and longterm trends of seven common species of diurnal and six species of nocturnal raptors breeding in the southern part of Finland. For the rest of the species, which are either rare all over Finland or breed mostly in the north, outside the good coverage of the distribution of Raptor Grid study plots, conclusions on population changes are based on the total numbers of occupied territories and active nests reported annually by the Raptor Questionnaires

Sequence of Sockeye Salmon Type 1 and 2 Growth Hormone Genes and the Relationship of Rainbow Trout with Atlantic and Pacific Salmon

1993 ◽  
Vol 50 (8) ◽  
pp. 1738-1748 ◽  
Author(s):  
Robert H. Devlin
Keyword(s):  
Growth Hormone ◽  
Rainbow Trout ◽  
Gene Duplication ◽  
Atlantic Salmon ◽  
Sockeye Salmon ◽  
Pacific Salmon ◽  
Duplication Event ◽  
Breeding Population ◽  
Gene Duplication Event ◽  
Relationship Of

Two types of growth hormone genes have been isolated from sockeye salmon (Oncorhynchus nerka) and their complete nucleotide sequence determined. The genes encode proteins of 210 amino acids and show considerable similarity to growth hormones characterized in other salmonids and fishes. The two genes presumably arose from a gene duplication event that generated the tetraploid condition in salmonids and are highly conserved in their coding regions. The sequences have diverged approximately 18% in noncoding regions since the gene duplication event and show numerous deletions and/or insertions. Isolation of these two genes from a Pacific salmon allows comparison of their sequences to growth hormone genes characterized from rainbow trout and from Atlantic salmon. The results indicate that rainbow trout is more similar to Pacific than to Atlantic salmon and suggest that Atlantic salmon diverged from Pacific salmonids at a time when sockeye and rainbow trout were part of a common breeding population. These results support the recent reclassification of rainbow trout from the genus Salmo to Oncorhynchus.

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