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96 results for “salmonidae”
Fig. 1 in Global systematic diversity, range distributions, conservation and taxonomic assessments of graylings (Teleostei: Salmonidae; Thymallus spp.)
Fig. 1 Map showing the global distribution range of Thymallus species. Information on sampling sites and species is given in Table S1. Numbers in the map refer to known contact zones of the following species: 1 = T. arcticus s.l. and T. baicalensis in the lower Enisei River; 2 = T. arcticus s.l. and T. baicalolenensis in the lower Lena River; 3 = T. nikolskyi and T. baicalensis in tributaries of the upper Ob River; 4 = T. baicalolenensis and T. baicalensis in tributaries of Lake Baikal; 5 = T. grubii, T. tugarinae
Data from: A synthesis of the coast-wide decline in survival of west coast Chinook salmon (Oncorhynchus tshawytscha, Salmonidae)
<p>We collated smolt-to-adult return rate (SAR) data for Chinook salmon from all available regions of the Pacific coast of North America to examine the large-scale patterns of salmon survival. For consistency, our analyses primarily used coded wire tag-based (CWT) SAR estimates. Survival collapsed over the past half century by roughly a factor of three to ca. 1% for many regions. Within the Columbia River, the SARs of Snake River populations, often singled out as exemplars of poor survival, are unexceptional and in fact higher than estimates reported from many other regions of the west coast lacking dams. Given the seemingly congruent decline in SARs to similar levels, the notion that contemporary survival is driven primarily by broader oceanic factors rather than local factors should be considered. Ambitious Columbia River rebuilding targets may be unachievable because other regions with nearly pristine freshwater conditions, such as SE Alaska and northern BC, also largely fail to reach these levels. Passive integrated transponder (PIT) tag-based SAR estimates available for Columbia River basin populations are generally consistent with CWT findings; however, PIT tag-based SARs are not adjusted for harvest which compromises their intended use because harvest rates are large and variable. More attention is needed on how SARs should be quantified and how rebuilding targets are defined. We call for a systematic review by funding agencies to assess consistency and comparability of the SAR data generated and to further assess the implications of survival falling to similar levels in most regions of the west coast.</p>
Concordant patterns of morphological, stable isotope, and genetic variation in a recent ecological radiation (Salmonidae:Coregonus spp.)
<p>Groups of sympatric taxa with low inter-specific genetic differentiation, but considerable ecological differences, offer great opportunities to study the dynamics of divergence and speciation. This is the case of ciscoes (<em>Coregonus</em> spp.) in the Laurentian Great Lakes, which are characterized by a complex evolutionary history and are commonly described as having undergone an adaptive radiation. In this study, morphometrics, stable isotopes and transcriptome sequencing were used to study the relationships within the <em>Coregonus artedi</em> complex in western Lake Superior. We observed general concordance for morphological, ecological and genomic variation, but the latter was more taxonomically informative as it showed less overlap among species in multivariate space. Low levels of genetic differentiation were observed between individuals morphologically identified as <em>C. hoyi</em> and <em>C. zenithicus</em>, which could be evidence of incomplete lineage sorting or recent hybridization between the two groups. Transcriptome-based single nucleotide polymorphisms exhibited significant divergence for genes associated with vision, development, metabolism and immunity among species that occupy different habitats. This study highlights the importance of using an integrative approach when studying groups of taxa with a complex evolutionary history, as individual-level analyses of multiple independent datasets can provide a clearer picture of the patterns and processes associated with the origins of biodiversity.</p>
Concordant patterns of morphological, stable isotope, and genetic variation in a recent ecological radiation (Salmonidae:Coregonus spp.)
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Data from: A synthesis of the coast-wide decline in survival of west coast Chinook salmon (Oncorhynchus tshawytscha, Salmonidae)
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Data from: Genetic correlations and little genetic variance for reaction norms may limit potential for adaptation to pollution by ionic and nanoparticulate silver in a whitefish (Salmonidae)
For natural populations to adapt to anthropogenic threats, heritable variation must persist in tolerance traits. Silver nanoparticles, the most widely used engineered nanoparticles, are expected to increase in concentrations in freshwaters. Little is known about how these particles affect wild populations, and whether genetic variation persists in tolerance to permit rapid evolutionary responses. We sampled wild adult whitefish and crossed them in vitro full factorially. In total, 2896 singly raised embryos of 48 families were exposed to two concentrations (0.5 μg/L; 100 μg/L) of differently sized silver nanoparticles or ions (silver nitrate). These doses were not lethal; yet higher concentrations prompted embryos to hatch earlier and at a smaller size. The induced hatching did not vary with nanoparticle size and was stronger in the silver nitrate group. Additive genetic variation for hatching time was significant across all treatments, with no apparent environmental dependencies. No genetic variation was found for hatching plasticity. We found some treatment-dependent heritable variation for larval length and yolk volume, and one instance of additive genetic variation for the reaction norm on length at hatching. Our assessment suggests that the effects of silver exposure on additive genetic variation vary according to trait and silver source. While the long-term fitness consequences of low-level silver exposure on whitefish embryos must be further investigated to determine whether it is, in fact, detrimental, our results suggest that the evolutionary potential for adaptation to these types of pollutants may be low.
Data from: Phylogeny of salmonids (salmoniformes: Salmonidae) and its molecular dating: analysis of mtDNA data
Phylogenetic relationships among 41 species of salmonid fish and some aspects of their diversification-time history were studied using the GenBank and original mtDNA data. The position of the root of the Salmonidae phylogenetic tree was uncertain. Among the possible variants, the most reasonable seems to be that in which thymallins are grouped into the same clade as coregonins and the lineage of salmonins occupied a basal position relative to this clade. The genera of Salmoninae formed two distinct clades, i.e., (Brachymystax, Hucho) and (Salmo, Parahucho, (Salvelinus, (Parasalmo, Oncorhynchus)). Furthermore, the genera Parasalmo and Oncorhynchus were reciprocally monophyletic. The congruence of Salmonidae phylogenetic trees obtained using different types of phylogenetic markers is discussed. According to Bayesian dating, ancestral lineages of salmonids and their sister esocoids diverged about 106 million years ago. Sometime after, probably 100–70 million years ago, the salmonid-specific whole genome duplication took place. The divergence of salmonid lineages on the genus level occurred much later, within the time interval of 42–20 million years ago. The main wave of the diversification of salmonids at the species level occurred during the last 12 million years. The possible effect of genome duplication on the Salmonidae diversification pattern is discussed.
Data from: MHC class I expression dependent on bacterial infection and parental factors in whitefish embryos (Salmonidae)
Ecological conditions can influence not only the expression of a phenotype, but also the heritability of a trait. As such, heritable variation for a trait needs to be studied across environments. We have investigated how pathogen challenge affects the expression of MHC genes in embryos of the lake whitefish Coregonus palaea. In order to experimentally separate paternal (i.e. genetic) from maternal and environmental effects, and determine whether and how stress affects the heritable variation for MHC expression, embryos were produced in full-factorial in vitro fertilizations, reared singly, and exposed at 208 degree days (late-eyed stage) to either one of two strains of Pseudomonas fluorescens that differ in their virulence characteristics (one increased mortality, while both delayed hatching time). Gene expression was assessed 48 h postinoculation, and virulence effects of the bacterial infection were monitored until hatching. We found no evidence of MHC class II expression at this stage of development. MHC class I expression was markedly down-regulated in reaction to both pseudomonads. While MHC expression could not be linked to embryo survival, the less the gene was expressed, the earlier the embryos hatched within each treatment group, possibly due to trade-offs between immune function and developmental rate or further factors that affect both hatching timing and MHC expression. We found significant additive genetic variance for MHC class I expression in some treatments. That is, changes in pathogen pressures could induce rapid evolution in MHC class I expression. However, we found no additive genetic variance in reaction norms in our study population.
Data from: The transcriptomics of sympatric dwarf and normal lake whitefish (Coregonus clupeaformis spp., Salmonidae) divergence as revealed by next-generation sequencing
Gene expression divergence is one of the mechanisms thought to be involved in the emergence of incipient species. Next-generation sequencing has become an extremely valuable tool for the study of this process by allowing whole transcriptome sequencing, or RNA-Seq. We have conducted a 454 GS-FLX pyrosequencing experiment in order to refine our understanding of adaptive divergence between dwarf and normal lake whitefish species (Coregonus clupeaformis spp.). The objectives were to: (1) investigate transcriptomic divergence as measured by liver RNA-Seq; (2) test the correlation between divergence in expression and sequence polymorphism and (3) investigate the extent of allelic imbalance. We also compared the results of RNA-seq with those of a previous microarray study performed on the same fish. Following de novo assembly, results showed that normal whitefish over-expressed more contigs associated with protein synthesis while dwarf fish over-expressed more contigs related to energy metabolism, immunity and DNA replication and repair. Moreover, 63 SNPs showed significant allelic imbalance, and this phenomenon prevailed in the recently diverged dwarf whitefish. Results also showed an absence of correlation between gene expression divergence as measured by RNA-Seq and either polymorphism rate or sequence divergence between normal and dwarf whitefish. This study reiterates an important role for gene expression divergence, and provides evidence for allele-specific expression divergence as well as evolutionary decoupling of regulatory and coding sequences in the adaptive divergence of normal and dwarf whitefish. It also demonstrates how next-generation sequencing can lead to a more comprehensive understanding of transcriptomic divergence in a young species pair.
FIGURE 4 in Salmo tigridis, a new species of trout from the Tigris River, Turkey (Teleostei: Salmonidae)
FIGURE 4. Scatter plot of scores of first two principal components (PC 1, PC 2) for 132 specimens of seven Salmo species in Anatolia based on 5 meristic characters.
FIGURE 3 in Salmo tigridis, a new species of trout from the Tigris River, Turkey (Teleostei: Salmonidae)
FIGURE 3. Scatter plot of scores of first two principal components (PC 1, PC 2) for 136 males of seven Salmo species in Anatolia based on 28 morphometric characters.
FIGURE 1 in Salmo tigridis, a new species of trout from the Tigris River, Turkey (Teleostei: Salmonidae)
FIGURE 1. Salmo tigridis; Turkey: Van Prov.: Çatak stream; a, FFR 1253, paratype, 136 mm SL, juvenile; b, FFR 1253, paratype, 165 mm SL, female; c, FFR 1250, holotype, 220 mm SL, male.
FIGURE 8 in Revalidation and redescription of Brachymystax tsinlingensis Li, 1966 (Salmoniformes: Salmonidae) from China
FIGURE 8. Neighbor-Joining tree obtained as a result of analysis of mtDNA data on species of Brachymystax and Hucho. Figures above branches are bootstrap confidence values (% of 1000 bootstrap replicates). Numbers in brackets refer to GeneBank Accession numbers. [HALF COLUMN]
FIGURE 6 in Revalidation and redescription of Brachymystax tsinlingensis Li, 1966 (Salmoniformes: Salmonidae) from China
FIGURE 6. Number of lateral-line scales in (a) Brachymystax tsinlingensis and B. lenok, and in (b) B. tsinlingensis and B. tumensis.
FIGURE 5 in Revalidation and redescription of Brachymystax tsinlingensis Li, 1966 (Salmoniformes: Salmonidae) from China
FIGURE 5. Comparison of spots on opercles of (a) Brachymystax tsinlingensis, (b) B. tumensis, and (c) B. lenok.
FIGURE 4 in Revalidation and redescription of Brachymystax tsinlingensis Li, 1966 (Salmoniformes: Salmonidae) from China
FIGURE 4. Distribution of Brachymystax in China and neighbor areas, above: Distribution; below: Collect locality of B. tsinlingens. (Dot, B. tsinlingens; triangle, B. lenok; diamond, B. savinovi; cross, B. tumensis; square, Brachymystax sp.). [HALF COLUMN]
FIGURE 1 in Revalidation and redescription of Brachymystax tsinlingensis Li, 1966 (Salmoniformes: Salmonidae) from China
FIGURE 1. Principal measurements taken on species of Brachymystax. Drawing of B. tsinlingensis. Standard length (SL), from tip of snout to posterior end of last half-centrum (A-H); body depth, from insertion of dorsal fin to ventral midline (U-T); predorsal length, from tip of snout to insertion of dorsal fin (A–D); posterior edge of head to dorsal-fin origin (dorsal scales start here) (C–D); dorsal-fin length, from insertion of dorsal fin to tip of longest ray (D–F); dorsal-fin base length, from anterior to posterior end of dorsal-fin base (D–E); preanal length, from tip of snout to insertion of anal fin (A–K); anal-fin length, from insertion of anal fin to tip of longest ray (K–L); anal-fin base length, from anterior to posterior end of anal-fin base (K–J); prepectoral length, from tip of snout to base of pectoral-fin origin (A–Q); pectoral-fin length, from base of anterior pectoral-fin ray to tip of longest ray (Q-R); pectoral-fin base length, from anterior to posterior end of pectoral-fin base (Q-P); prepelvic length, from tip of snout to base of anterior pelvic-fin ray (A–N); pelvic-fin length, from base of anterior pelvic-fin ray to tip of longest ray (N–O); pelvic-fin base length, from anterior to posterior end of pelvic-fin base (N–M); caudal-peduncle length, from end of anal-fin base to posterior end of last half-centrum (J–H); caudal-peduncle depth, at middle of caudal peduncle (G– I); head length, from tip of snout to most posterior point of operculum (not including skin flap, 1; A–S); head depth, from nape vertically to ventral midline (C–B); head width, distance between most posterior margins of opercule; snout length, from tip of snout to anterior margin of circumorbital series (2); eye diameter, from anterior to posterior margins of circumorbital series (3), pressing slightly to find firm points; interorbital width, shortest distance between orbits across top of head; rictal barbel length, from anterior to posterior end of rictal barbel. [HALF COLUMN]
FIGURE 7 in The trouts of the upper Kura and Aras rivers in Turkey, with description of three new species (Teleostei: Salmonidae)
FIGURE 7. Salmo cf. ciscaucasicus; FSJF 1576, Russia: Dagestan Province: Tyurkidagunchay Stream: Samur River drainage; a, 194 mm SL, male; b, 182 mm SL, male; c, 145 mm SL, female.
FIGURE 6 in The trouts of the upper Kura and Aras rivers in Turkey, with description of three new species (Teleostei: Salmonidae)
FIGURE 6. Salmo araxensis; FFR 3144, paratype, 265 mm SL, male; Turkey: Kars Prov.: İncilipınar Stream.
FIGURE 5 in The trouts of the upper Kura and Aras rivers in Turkey, with description of three new species (Teleostei: Salmonidae)
FIGURE 5. Salmo araxensis; Turkey: Kars Prov.: Kırkpınar Stream; a, FFR 3224, holotype, 259 mm SL, male; b, FFR 3122, paratype, 220 mm SL, female; c, FFR 3122, paratype, 145 mm SL, juvenile.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.