Interannual variability in the effects of physical habitat and parentage on Chinook salmon egg-to-fry survival

2016 ◽  
Vol 73 (7) ◽  
pp. 1047-1059 ◽  
Author(s):  
Philip Roni ◽  
Christopher Johnson ◽  
Trenton De Boer ◽  
George Pess ◽  
Andrew Dittman ◽  
...  
Keyword(s):  
Developmental Stage ◽  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Developmental Stages ◽  
Field Measurements ◽  
Physical Habitat ◽  
Median Particle ◽  
River Reach ◽  
High Flows ◽  
Major Factors

Mortality during incubation is believed to be a major factor limiting the recovery of many salmon populations, though direct field measurements of egg-to-fry survival are rare or small in scale. To determine the effects of physical habitat (river reach, fine sediment intrusion, scour), parentage (mating, source of gametes) on Chinook salmon (Oncorhynchus tshawytscha) egg-to-fry survival and developmental stage at emergence across a basin, we constructed 324 artificial redds in nine reaches over 4 years in the Yakima River Basin, Washington, USA. Mean egg-to-fry survival ranged from 49% to 69% annually from 2009 to 2012 brood years. Survival was significantly different among reaches in 2010, but not in 2009, 2011, or 2012, while mating was a significant factor in all years but 2010. In contrast, developmental stage differed significantly among reaches and matings in all 4 years. Percentage of fines, days-in-gravel, and median particle size explained only small (<10%) additional amount of variation in survival or developmental stages. Our results suggest that parentage and reach within a basin are major factors influencing egg-to-fry survival, but their relative influence varies annually, presumably depending on the magnitude of high flows and scour during incubation.

Relationship between chinook salmon (Oncorhynchus tshawytscha) redd densities and PHABSIM-predicted habitat in the Merced and Lower American rivers, California

1999 ◽  
Vol 56 (4) ◽  
pp. 570-577 ◽  
Author(s):  
Sean P Gallagher ◽  
Mark F Gard
Keyword(s):  
Fisheries Management ◽  
Chinook Salmon ◽  
Significant Relationship ◽  
Oncorhynchus Tshawytscha ◽  
Simulation System ◽  
Physical Habitat ◽  
Instream Flow ◽  
Spawning Habitat ◽  
Habitat Simulation

An index of chinook salmon (Oncorhynchus tshawytscha) spawning habitat predicted using the physical habitat simulation system (PHABSIM) component of the instream flow incremental methodology was compared with redd densities and locations for sites in the Merced River, California, during 1996 and with redd numbers in sites in the Merced and Lower American rivers, California, from 1989 through 1996. Predicted weighted useable area (WUA) was significantly correlated with chinook salmon spawning density and location at five of seven sites in the Merced River. At the microhabitat level, in the Merced River during 1996, there was a significant relationship between chinook salmon redd location and predicted WUA. Cells with more WUA in the Merced River tended to have more redds. At the mesohabitat level, there was a significant relationship between redd density and predicted WUA in both rivers. Transect areas in the Merced River with higher predicted WUA had more redds. Sites with higher numbers of redds had more predicted WUA. Significant correlations between predicted WUA and spawning locations increase confidence in the use of PHABSIM modeling results for fisheries management in the Merced and Lower American rivers as well as in other rivers.

scholarly journals Generalisation of physical habitat-discharge relationships

2007 ◽  
Vol 11 (1) ◽  
pp. 141-157 ◽  
Author(s):  
D. J. Booker ◽  
M. C. Acreman
Keyword(s):  
Data Collection ◽  
Field Measurements ◽  
Physical Habitat ◽  
Major Drawback ◽  
Channel Form ◽  
River Hydraulics ◽  
Habitat Simulation ◽  
River Reach ◽  
The Uk ◽  
A Site

Abstract. Physical habitat is increasingly used worldwide as a measure of river ecosystem health when assessing changes to river flows, such as those caused by abstraction. The major drawback with this approach is that defining precisely the relationships between physical habitat and flow for a given river reach requires considerable data collection and analysis. Consequently, widely used models such as the Physical Habitat Simulation (PHABSIM) system are expensive to apply. There is, thus, a demand for rapid methods for defining habitat-discharge relationships from simple field measurements. This paper reports the analysis of data from 63 sites in the UK where PHABSIM has been applied. The results demonstrate that there are strong relationships between single measurements of channel form and river hydraulics and the habitat available for target species. The results can form the basis of a method to estimate sensitivity of physical habitat to flow change by visiting a site at only one flow. Furthermore, the uncertainty in estimates reduces as more information is collected. This allows the user to select the level of investment in data collection appropriate for the desired confidence in the estimates. The method is demonstrated using habitat indicators for different life stages of Atlantic salmon, brown trout, roach and dace.

Ceratomyxa shasta (Myxozoa: Myxosporea) in juvenile chinook salmon (Oncorhynchus tshawytscha): experimental transmission and natural infections in the Fraser River, British Columbia

1985 ◽  
Vol 63 (7) ◽  
pp. 1737-1740 ◽  
Author(s):  
Susan M. Bower
Keyword(s):  
Chinook Salmon ◽  
Sockeye Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Developmental Stages ◽  
River Estuary ◽  
Fraser River ◽  
Experimental Transmission ◽  
Juvenile Chinook Salmon ◽  
Juvenile Chinook ◽  
Intraperitoneal Inoculation

Ceratomyxa shasta (mainly trophozoites) from the intestinal tract of a naturally infected juvenile chinook salmon (Oncorhynchus tshawytscha) developed in the coelom of laboratory-reared chinook salmon when inoculated intraperitoneally. All developmental stages were observed. Successful subpassages were accomplished by intraperitoneal inoculation of trophozoites and sporoblasts, but an infection did not develop when these stages were pipetted into the esophagus of susceptible fish. Heavy infections, including the presence of C. shasta sporoblasts or spores, were observed in 2 of 28 feral juvenile chinook salmon seined from the Fraser River estuary in late July and early August. Trophozoite-like cells were observed in six other chinook salmon from this group. No C. shasta were observed in 15 juvenile sockeye salmon (Oncorhynchus nerka) caught in the estuary along with the chinook salmon.

Systematic hexamitid (Protozoa: Diplomonadida) Infection in seawater pen-reared Chinook salmon Oncorhynchus tshawytscha

1992 ◽  
Vol 14 ◽  
pp. 81-89 ◽  
Author(s):  
ML Kent ◽  
J Ellis ◽  
JW Fournie ◽  
SC Dawe ◽  
JW Bagshaw ◽  
...  
Keyword(s):  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha

scholarly journals Spatio-temporal selection of reference genes in the two congeneric species of Glycyrrhiza

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yuping Li ◽  
Xiaoju Liang ◽  
Xuguo Zhou ◽  
Yu An ◽  
Ming Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Developmental Stage ◽  
Reference Genes ◽  
Developmental Stages ◽  
Individual Factors ◽  
Congeneric Species ◽  
Spatio Temporal ◽  
The Stability ◽  
Different Tissues ◽  
Selection Of

AbstractGlycyrrhiza, a genus of perennial medicinal herbs, has been traditionally used to treat human diseases, including respiratory disorders. Functional analysis of genes involved in the synthesis, accumulation, and degradation of bioactive compounds in these medicinal plants requires accurate measurement of their expression profiles. Reverse transcription quantitative real-time PCR (RT-qPCR) is a primary tool, which requires stably expressed reference genes to serve as the internal references to normalize the target gene expression. In this study, the stability of 14 candidate reference genes from the two congeneric species G. uralensis and G. inflata, including ACT, CAC, CYP, DNAJ, DREB, EF1, RAN, TIF1, TUB, UBC2, ABCC2, COPS3, CS, R3HDM2, were evaluated across different tissues and throughout various developmental stages. More importantly, we investigated the impact of interactions between tissue and developmental stage on the performance of candidate reference genes. Four algorithms, including geNorm, NormFinder, BestKeeper, and Delta Ct, were used to analyze the expression stability and RefFinder, a comprehensive software, provided the final recommendation. Based on previous research and our preliminary data, we hypothesized that internal references for spatio-temporal gene expression are different from the reference genes suited for individual factors. In G. uralensis, the top three most stable reference genes across different tissues were R3HDM2, CAC and TUB, while CAC, CYP and ABCC2 were most suited for different developmental stages. CAC is the only candidate recommended for both biotic factors, which is reflected in the stability ranking for the spatio (tissue)-temporal (developmental stage) interactions (CAC, R3HDM2 and DNAJ). Similarly, in G. inflata, COPS3, R3HDM2 and DREB were selected for tissues, while RAN, COPS3 and CS were recommended for developmental stages. For the tissue-developmental stage interactions, COPS3, DREB and ABCC2 were the most suited reference genes. In both species, only one of the top three candidates was shared between the individual factors and their interactions, specifically, CAC in G. uralensis and COPS3 in G. inflata, which supports our overarching hypothesis. In summary, spatio-temporal selection of reference genes not only lays the foundation for functional genomics research in Glycyrrhiza, but also facilitates these traditional medicinal herbs to reach/maximize their pharmaceutical potential.

scholarly journals Transcriptome analysis identifies differentially expressed genes in the progenies of a cross between two low phytic acid soybean mutants

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hangxia Jin ◽  
Xiaomin Yu ◽  
Qinghua Yang ◽  
Xujun Fu ◽  
Fengjie Yuan
Keyword(s):  
Developmental Stage ◽  
Phytic Acid ◽  
Differentially Expressed Genes ◽  
Transcriptome Analysis ◽  
Defense Mechanisms ◽  
Developmental Stages ◽  
Sucrose Metabolism ◽  
Differentially Expressed ◽  
Sequencing Analysis ◽  
Seed Developmental Stage

AbstractPhytic acid (PA) is a major antinutrient that cannot be digested by monogastric animals, but it can decrease the bioavailability of micronutrients (e.g., Zn and Fe). Lowering the PA content of crop seeds will lead to enhanced nutritional traits. Low-PA mutant crop lines carrying more than one mutated gene (lpa) have lower PA contents than mutants with a single lpa mutant gene. However, little is known about the link between PA pathway intermediates and downstream regulatory activities following the mutation of these genes in soybean. Consequently, we performed a comparative transcriptome analysis using an advanced generation recombinant inbred line with low PA levels [2mlpa (mips1/ipk1)] and a sibling line with homozygous non-mutant alleles and normal PA contents [2MWT (MIPS1/IPK1)]. An RNA sequencing analysis of five seed developmental stages revealed 7945 differentially expressed genes (DEGs) between the 2mlpa and 2MWT seeds. Moreover, 3316 DEGs were associated with 128 metabolic and signal transduction pathways and 4980 DEGs were annotated with 345 Gene Ontology terms related to biological processes. Genes associated with PA metabolism, photosynthesis, starch and sucrose metabolism, and defense mechanisms were among the DEGs in 2mlpa. Of these genes, 36 contributed to PA metabolism, including 22 genes possibly mediating the low-PA phenotype of 2mlpa. The expression of most of the genes associated with photosynthesis (81 of 117) was down-regulated in 2mlpa at the late seed developmental stage. In contrast, the expression of three genes involved in sucrose metabolism was up-regulated at the late seed developmental stage, which might explain the high sucrose content of 2mlpa soybeans. Furthermore, 604 genes related to defense mechanisms were differentially expressed between 2mlpa and 2MWT. In this study, we detected a low PA content as well as changes to multiple metabolites in the 2mlpa mutant. These results may help elucidate the regulation of metabolic events in 2mlpa. Many genes involved in PA metabolism may contribute to the substantial decrease in the PA content and the moderate accumulation of InsP3–InsP5 in the 2mlpa mutant. The other regulated genes related to photosynthesis, starch and sucrose metabolism, and defense mechanisms may provide additional insights into the nutritional and agronomic performance of 2mlpa seeds.

scholarly journals Managed Wetlands Can Benefit Juvenile Chinook Salmon in a Tidal Marsh

2021 ◽  
Author(s):  
Nicole M. Aha ◽  
Peter B. Moyle ◽  
Nann A. Fangue ◽  
Andrew L. Rypel ◽  
John R. Durand
Keyword(s):  
San Francisco ◽  
Growth Rates ◽  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Nursery Habitat ◽  
San Francisco Estuary ◽  
Rice Fields ◽  
Fish Growth ◽  
Juvenile Chinook Salmon ◽  
Juvenile Chinook

AbstractLoss of estuarine and coastal habitats worldwide has reduced nursery habitat and function for diverse fishes, including juvenile Chinook salmon (Oncorhynchus tshawytscha). Underutilized off-channel habitats such as flooded rice fields and managed ponds present opportunities for improving rearing conditions and increasing habitat diversity along migratory corridors. While experiments in rice fields have shown enhanced growth rates of juvenile fishes, managed ponds are less studied. To evaluate the potential of these ponds as a nursery habitat, juvenile Chinook salmon (~ 2.8 g, 63 mm FL) were reared in cages in four contrasting locations within Suisun Marsh, a large wetland in the San Francisco Estuary. The locations included a natural tidal slough, a leveed tidal slough, and the inlet and outlet of a tidally muted managed pond established for waterfowl hunting. Fish growth rates differed significantly among locations, with the fastest growth occurring near the outlet in the managed pond. High zooplankton biomass at the managed pond outlet was the best correlate of salmon growth. Water temperatures in the managed pond were also cooler and less variable compared to sloughs, reducing thermal stress. The stress of low dissolved oxygen concentrations within the managed pond was likely mediated by high concentrations of zooplankton and favorable temperatures. Our findings suggest that muted tidal habitats in the San Francisco Estuary and elsewhere could be managed to promote growth and survival of juvenile salmon and other native fishes.

Analysis of straying variation in Alaskan hatchery chinook salmon (Oncorhynchus tshawytscha) following transplantation

1999 ◽  
Vol 56 (4) ◽  
pp. 578-589 ◽  
Author(s):  
Jeffrey J Hard ◽  
William R Heard
Keyword(s):  
British Columbia ◽  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Release Site ◽  
Substantial Variation

In 1976 chinook salmon (Oncorhynchus tshawytscha) gametes from the Chickamin and Unuk rivers in southeastern Alaska were transplanted 250 km to establish hatchery runs at Little Port Walter (LPW), Baranof Island. From 1977 to 1989, 1 862 058 marked smolts from 12 broods were released from LPW. Homing and straying were estimated from adult recoveries at 25 locations in Alaska and British Columbia between 1981 and 1989. Of 22 198 LPW fish recovered over this period, 21 934 (98.8%) were collected at LPW. Of 264 fish recovered elsewhere, 38.3% were within 7 km of LPW; 64.4% were within 25 km of LPW. No LPW fish were recovered from the ancestral rivers, but nine fish were recovered from rivers supporting wild chinook salmon. Straying declined with distance from the release site but varied between hatcheries and streams. Straying declined with increasing age and run size. Straying was similar between the populations but varied among broods, and analysis of straying in experimental groups provided evidence for a heritable component. Males strayed more often than females. Population, gender, run size, and recovery age interacted to produce substantial variation in straying, indicating that run composition can produce complex straying responses.

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