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730 results for “Trout”
Migration-related phenotypic divergence is associated with epigenetic variation in rainbow trout
GEO Series GSE62195. Oncorhynchus mykiss. 18 samples. Type: Methylation profiling by high throughput sequencing.
Effects of sustained swimming on the red and white muscle transcriptome of rainbow trout (Oncorhynchus mykiss) fed a carbohydrate-rich diet
GEO Series GSE47141. Oncorhynchus mykiss. 4 samples. Type: Expression profiling by array.
Characterizing alternative feeds for rainbow trout (O. mykiss) by 1H-NMR metabolomics
<p>The CPMG NMR representative spectra of alternative feeds used in the manuscript draft entiteld:</p> <p><strong>Characterizing alternative feeds for rainbow trout </strong><strong>(<em>O. mykiss</em>) by <sup>1</sup>H-NMR metabolomics</strong></p> <p>Simon Roques<sup>1,2,3</sup>, Catherine Deborde<sup>3,4</sup>, Nadège Richard<sup>2</sup>, Luce Sergent<sup>5</sup>, Francis Kurz<sup>6</sup>, Sandrine Skiba-Cassy<sup>1</sup>, Benoît Fauconneau<sup>1</sup>, Annick Moing<sup>3,4</sup></p> <p> </p> <p><sup>1</sup> INRA, Univ Pau & Pays Adour, E2S UPPA, UMR 1419, Nutrition Métabolisme, Aquaculture, Saint Pée sur Nivelle, F-64310, France</p> <p><sup>2</sup> Phileo Lesaffre Animal Care, 59700 Marcq-en-Baroeul, France</p> <p><sup>3</sup> Bordeaux Metabolome Facility, MetaboHUB, CGFB, Centre INRA de Nouvelle Aquitaine Bordeaux, 33140 Villenave d’Ornon, France</p> <p><sup>4</sup> INRA, Univ. Bordeaux, UMR 1332 Fruit Biology and Pathology, Centre INRA de Nouvelle Aquitaine Bordeaux, 33140 Villenave d’Ornon, France</p> <p><sup>5</sup> Copalis Industrie, 62480 Le Portel, France</p> <p><sup>6</sup> Algae Natural Food, 67400 Illkirch-Graffenstaden, France</p> <p> </p> <p><em>Corresponding author: </em>simon.roques@inra.fr<em> </em></p>
Data from: Investigating the extent of parallelism in morphological and genomic divergence among lake trout ecotypes in Lake Superior
Understanding the emergence of species through the process of ecological speciation is a central question in evolutionary biology which also has implications for conservation and management. Lake Trout (Salvelinus namaycush) is renowned for the occurrence of different ecotypes linked to resource and habitat use throughout North America. We aimed to unravel the fine genetic structure of the four Lake Trout ecotypes in Lake Superior. A total of 486 individuals from four sites were genotyped at 6822 filtered SNPs using RADseq technology. Our results revealed different extent of morphological and genetic differentiation within the different sites. Overall, genetic differentiation was weak but significant and was on average three times higher between sites (Mean FST = 0.016) than between ecotypes within sites (Mean FST = 0.005) indicating higher level of gene flow or a more recent shared ancestor between ecotypes within each site than between populations of the same ecotype. Evidence of divergent selection was also found between ecotypes and/or in association with morphological variation. Outlier loci found in genes related to lipid metabolism and visual acuity were of particular interest in this context of ecotypic divergence. However, we did not find clear indication of parallelism at the genomic level, despite the presence of phenotypic parallelism among some ecotypes from different sampling sites. Overall, the occurrence of different levels of both genomic and phenotypic differentiation between ecotypes within each site with several differentiated loci linked to relevant biological functions support the presence of a continuum of divergence in Lake Trout.
Figure 1 from: Turan D, Bayçelebi E, Aksu S, Oral M (2024) The trouts of the Marmara and Aegean Sea drainages in Türkiye, with the description of a new species (Teleostei, Salmonidae). Zoosystematics and Evolution 100(1): 87-99. https://doi.org/10.3897/zse.100.112557
Figure 1 Distributions of Salmo in Marmara and Aegean Sea basins.
Figure 3 from: Küçük F, Kalaycı G, Güçlü SS, Oral M, Turan D (2024) A new species of trout from the Köprüçay River, a drainage of Mediterranean Sea, Türkiye (Salmoniformes, Salmonidae). Zoosystematics and Evolution 100(2): 391-403. https://doi.org/10.3897/zse.100.121174
Figure 3 Salmo ekmekciae, IFC-ESUF 02-0022, paratype, 150 mm SL, female; Türkiye: Köprüçay River.
Figure 2 from: Küçük F, Kalaycı G, Güçlü SS, Oral M, Turan D (2024) A new species of trout from the Köprüçay River, a drainage of Mediterranean Sea, Türkiye (Salmoniformes, Salmonidae). Zoosystematics and Evolution 100(2): 391-403. https://doi.org/10.3897/zse.100.121174
Figure 2 Salmo ekmekciae, IFC ESUF 02-0029, holotype, 216 mm SL, male; Türkiye: Köprüçay River.
Figure 5 from: Küçük F, Kalaycı G, Güçlü SS, Oral M, Turan D (2024) A new species of trout from the Köprüçay River, a drainage of Mediterranean Sea, Türkiye (Salmoniformes, Salmonidae). Zoosystematics and Evolution 100(2): 391-403. https://doi.org/10.3897/zse.100.121174
Figure 5 Type localties of Salmo species in the Türkiye.
Figure 4 from: Küçük F, Kalaycı G, Güçlü SS, Oral M, Turan D (2024) A new species of trout from the Köprüçay River, a drainage of Mediterranean Sea, Türkiye (Salmoniformes, Salmonidae). Zoosystematics and Evolution 100(2): 391-403. https://doi.org/10.3897/zse.100.121174
Figure 4 Salmo ekmekciae, IFC-ESUF 02-0022, paratype, 84 mm SL, juvenile; Türkiye: Köprüçay River.
Figure 1 from: Turan D, Aksu İ, Oral M, Kaya C, Bayçelebi E (2021) Contribution to the trout of Euphrates River, with description of a new species, and range extension of Salmo munzuricus (Salmoniformes, Salmonidae). Zoosystematics and Evolution 97(2): 471-482. https://doi.org/10.3897/zse.97.72181
Figure 1 Distribution of Salmo species in the Euphrates River basin.
Figure 3 in Feeding habit of Brown trout (Salmo trutta fario) in upper parts of river Swat, Pakistan
Figure 3. Relationship between feeding intensity and length groups.
Data from: Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing
Rapid and inexpensive methods for genomewide single nucleotide polymorphism (SNP) discovery and genotyping are urgently needed for population management and conservation. In hybridized populations, genomic techniques that can identify and genotype thousands of species-diagnostic markers would allow precise estimates of population- and individual-level admixture as well as identification of 'super invasive' alleles, which show elevated rates of introgression above the genomewide background (likely due to natural selection). Techniques like restriction-site-associated DNA (RAD) sequencing can discover and genotype large numbers of SNPs, but they have been limited by the length of continuous sequence data they produce with Illumina short-read sequencing. We present a novel approach, overlapping paired-end RAD sequencing, to generate RAD contigs of >300–400 bp. These contigs provide sufficient flanking sequence for design of high-throughput SNP genotyping arrays and strict filtering to identify duplicate paralogous loci. We applied this approach in five populations of native westslope cutthroat trout that previously showed varying (low) levels of admixture from introduced rainbow trout (RBT). We produced 77 141 RAD contigs and used these data to filter and genotype 3180 previously identified species-diagnostic SNP loci. Our population-level and individual-level estimates of admixture were generally consistent with previous microsatellite-based estimates from the same individuals. However, we observed slightly lower admixture estimates from genomewide markers, which might result from natural selection against certain genome regions, different genomic locations for microsatellites vs. RAD-derived SNPs and/or sampling error from the small number of microsatellite loci (n = 7). We also identified candidate adaptive super invasive alleles from RBT that had excessively high admixture proportions in hybridized cutthroat trout populations.
Effects of visual environmental enrichment on the welfare of farmed rainbow trout (Oncorhynchus mykiss)
<p>Dataset for manuscript of the same name. Submitted to <em>The Journal of Applied Animal Welfare Science.</em></p>
Disease Risk Reduction and Omega-3 Rich Rainbow Trout (Fish for Health)
ClinicalTrials.gov study NCT02204709. IPD Sharing: NO. Countries: 1. Publications: 0.
The Effects of Trout Fed With a Vegetable Based Feed on Cardiovascular Risk Markers and Plasma Proteome
ClinicalTrials.gov study NCT00445614. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Toxic effects of dietary methylmercury (MeHg) on rainbow trout and zebrafish
GEO Series GSE32431. Oncorhynchus mykiss; Salmo salar; Oncorhynchus tshawytscha; Osmerus mordax; Danio rerio; Coregonus clupeaformis. 28 samples. Type: Expression profiling by array.
Toxicity of atrazine and nonylphenol in juvenile rainbow trout (Oncorhynchus mykiss): Effects on general health, disease susceptibility and gene expression
GEO Series GSE38726. Oncorhynchus mykiss; Salmo salar. 24 samples. Type: Expression profiling by array.
Juvenile rainbow trout exposed in situ at site receiving different concentrations of municipal wastewater effluent (MWWE) and an upstream reference site
GEO Series GSE23613. Oncorhynchus mykiss. 16 samples. Type: Expression profiling by array.
Transcriptomic profiles of wild brown trout chronically exposed to metals using RNA-seq in a Illumina GAII platform
GEO Series GSE45637. Salmo trutta. 8 samples. Type: Expression profiling by high throughput sequencing.
Data from: Genetic monitoring reveals temporal stability over 30 years in a small, lake resident brown trout population
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