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730 results for “Trout”
Individual genotypes of 1 416 brook trout genotyped at 14 779 high-quality SNPs for studying local adaptation and maladaptation in small populations
<p><span><span><span><span><span><span><span><span><span><span><span>Investigating the relative importance of neutral <i>versus</i> selective processes governing the accumulation of genetic variants is a key goal in both evolutionary and conservation biology. This is particularly true in the context of small populations, where genetic drift can counteract the effect of selection. Using Brook Charr (<i>Salvelinus fontinalis</i>) from Québec, Canada as a case study, we investigated the importance of demographic <i>versus</i> selective processes governing the accumulation of both adaptive and maladaptive mutations in closed <i>versus</i> open and connected populations to assess gene flow effect. This was achieved by using 14 779 high-quality filtered SNPs genotyped among 1 416 fish representing 50 populations from three life history types: lacustrine (closed populations), riverine and anadromous (connected populations). Using the Provean algorithm, we observed a considerable accumulation of putative deleterious mutations across populations. The absence of correlation between the occurrence of putatively beneficial or deleterious mutations and local recombination rate supports the hypothesis that genetic drift might be the main driver of the accumulation of such variants. However, despite a lower genetic diversity observed in lacustrine than in riverine or anadromous populations, lacustrine populations do not exhibit more deleterious mutations than the two other history types, suggesting that the negative effect of genetic drift in lacustrine populations may be mitigated by that of relaxed purifying selection. Moreover, we also identified genomic regions associated with anadromy, as well as an overrepresentation of transposable elements associated with variation in environmental variables, thus supporting the importance of transposable elements in adaptation. </span></span></span></span></span></span></span></span></span></span></span></p>
Bull trout concealment experimental data
<p>Bull trout (<i>Salvelinus confluentus) </i>are challenging to detect as a result of the species cryptic behavior and coloration, relatively low densities in complex habitats, and affinity for cold, high clarity, low conductivity waters. Bull trout are also closely associated with the stream bed, frequently conceal in substrate, and this concealment behavior is poorly understood. Consequently, population assessments are problematic and biologists and managers often lack quantitative information to accurately describe bull trout distributions, estimate abundance, and assess status and trends; particularly for stream-dwelling populations. During controlled laboratory trials, we recorded concealment, resting, and swimming behavior of juvenile wild bull trout in response to: (1) constant and fluctuating water temperature, (2) presence or absence of light, and (3) substrate size. Light level had the strongest influence on wild fish concealment and more fish concealed as light levels increased from darkness to daylight. Wild fish were 14.5 times less likely to conceal in constant darkness and 4.1 times more likely to conceal in 12 h light x 12 h darkness compared to constant light. Wild fish were 6.2 times less likely to conceal in small (26-51 mm) substrate compared to larger (52-102 mm) substrate. As water temperature increased, fewer wild fish concealed. Knowledge of wild bull trout concealment will improve field sampling protocols and increase detection efficiencies. These data also enhance knowledge of bull trout niche requirements which informs conservation and restoration efforts.</p>
Data from: Experimental test of genetic rescue in isolated populations of brook trout
Genetic rescue is an increasingly considered conservation measure to address genetic erosion associated with habitat loss and fragmentation. The resulting gene flow from facilitating migration may improve fitness and adaptive potential, but is not without risks (e.g., outbreeding depression). Here, we conducted a test of genetic rescue by translocating ten (five of each sex) brook trout (Salvelinus fontinalis) from a single source to four nearby and isolated stream populations. To control for the demographic contribution of translocated individuals, ten resident individuals (five of each sex) were removed from each recipient population. Prior to the introduction of translocated individuals, the two smallest above-barrier populations had substantially lower genetic diversity, and all populations had reduced effective number of breeders relative to adjacent below-barrier populations. In the first reproductive bout following translocation, 31 of 40 (78%) translocated individuals reproduced successfully. Translocated individuals contributed to more families than expected under random mating and generally produced larger full-sibling families. We observed relatively high (>20%) introgression in three of the four recipient populations. The translocations increased genetic diversity of recipient populations by 45% in allelic richness and 25% in expected heterozygosity. Additionally, strong evidence of hybrid vigour was observed through significantly larger body sizes of hybrid offspring relative to resident offspring in all recipient populations. Continued monitoring of these populations will test for negative fitness effects beyond the first generation. However, these results provide much-needed experimental data to inform the potential effectiveness of genetic rescue-motivated translocations.
Data from: Temporal constraints on the potential role of fry odors as cues of past reproductive success for spawning lake trout
Deciding where to reproduce is a major challenge for most animals. Many select habitats based upon cues of successful reproduction by conspecifics, such as the presence of offspring from past reproductive events. For example, some fishes select spawning habitat following odors released by juveniles whose rearing habitat overlaps with spawning habitat. However, juveniles may emigrate before adults begin to search for spawning habitat; hence, the efficacy of juvenile cues could be constrained by degradation or dissipation rates. In lake trout (Salvelinus namaycush), odors deposited by the previous year's offspring have been hypothesized to guide adults to spawning reefs. However, in most extant populations, lake trout fry emigrate from spawning reefs during the spring and adults spawn during the fall. Therefore, we postulated that the role of fry odors in guiding habitat selection might be constrained by the time between fry emigration and adult spawning. Time course chemical, physiological, and behavioral assays indicated that the odors deposited by fry likely degrade or dissipate before adults select spawning habitats. Furthermore, fry feces did not attract wild lake trout to constructed spawning reefs in Lake Huron. Taken together, our results indicate fry odors are unlikely to act as cues for lake trout searching for spawning reefs in populations whose juveniles emigrate before the spawning season, and underscore the importance of environmental constraints on social cues.
Data from: Development and evaluation of 200 novel SNP assays for population genetic studies of westslope cutthroat trout and genetic identification of related taxa
DNA sequence data were collected and screened for single nucleotide polymorphisms (SNPs) in westslope cutthroat trout (Oncorhynchus clarki lewisi) and also for substitutions that could be used to genetically discriminate rainbow trout (O. mykiss) and cutthroat trout, as well as several cutthroat trout subspecies. In total, 260 expressed sequence tag-derived loci were sequenced and allelic discrimination genotyping assays developed from 217 of the variable sites. Another 50 putative SNPs in westslope cutthroat trout were identified by restriction-site-associated DNA sequencing, and seven of these were developed into assays. Twelve O. mykiss SNP assays that were variable within westslope cutthroat trout and 12 previously published SNP assays were also included in downstream testing. A total of 241 assays were tested on six westslope cutthroat trout populations (N = 32 per population), as well as collections of four other cutthroat trout subspecies and a population of rainbow trout. All assays were evaluated for reliability and deviation from Hardy–Weinberg and linkage equilibria. Poorly performing and duplicate assays were removed from the data set, and the remaining 200 assays were used in tests of population differentiation. The remaining markers easily distinguished the various subspecies tested, as evidenced by mean GST of 0.74. A smaller subset of the markers (N = 86; average GST = 0.40) was useful for distinguishing the six populations of westslope cutthroat trout. This study increases by an order of magnitude the number of genetic markers available for the study of westslope cutthroat trout and closely related taxa and includes many markers in genes (developed from ESTs).
Data from: Evidence of neutral and adaptive genetic divergence between European trout populations sampled along altitudinal gradients
Species with a wide geographical distribution are often composed of distinct subgroups which may be adapted to their local environment. European trout (Salmo trutta species complex) provide an example of such a complex consisting of several genetically and ecologically distinct forms. However, trout populations are strongly influenced by human activities, and it is unclear to what extent neutral and adaptive genetic differences have persisted. We sampled 30 Swiss trout populations from heterogeneous environments along replicated altitudinal gradients in three major European drainages. More than 850 individuals were genotyped at 18 microsatellite loci which included loci diagnostic for evolutionary lineages and candidate markers associated with temperature tolerance, reproductive timing and immune defence. We find that the phylogeographic structure of Swiss trout populations has not been completely erased by stocking. Distinct genetic clusters corresponding to the different drainages could be identified, although nonindigenous alleles were clearly present, especially in the two Mediterranean drainages. We also still detected neutral genetic differentiation within rivers which was often associated with the geographical distance between populations. Five loci showed evidence of divergent selection between populations with several drainage-specific patterns. Lineage-diagnostic markers, a marker linked to a quantitative trait locus for upper temperature tolerance in other salmonids and a marker linked to the major histocompatibility class I gene were implicated in local adaptation and some patterns were associated with altitude. In contrast, tentative evidence suggests a signal of balancing selection at a second immune relevant gene (TAP2). Our results confirm the persistence of both neutral and potentially adaptive genetic differences between trout populations in the face of massive human-mediated dispersal.
FIGURE 2 in Salmo tigridis, a new species of trout from the Tigris River, Turkey (Teleostei: Salmonidae)
FIGURE 2. Distribution of named Salmo species in Anatolia.
Supplementary material 2 from: Schallenberg LA, Thomson-Laing G, Kelly D, Pearman JK, Howarth JD, Vandergoes MJ, Puddick J, Fitzsimons S, Rees A, Wood SA (2023) Insights into the ecological impact of trout introduction in an oligotrophic lake using sedimentary environmental DNA. Metabarcoding and Metagenomics 7: e111467. https://doi.org/10.3897/mbmg.7.111467
Supplementary data 2
Supplementary material 1 from: Schallenberg LA, Thomson-Laing G, Kelly D, Pearman JK, Howarth JD, Vandergoes MJ, Puddick J, Fitzsimons S, Rees A, Wood SA (2023) Insights into the ecological impact of trout introduction in an oligotrophic lake using sedimentary environmental DNA. Metabarcoding and Metagenomics 7: e111467. https://doi.org/10.3897/mbmg.7.111467
Supplementary data 1
Figure 6 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 6 Principal Component Analysis (PCA) plot using 187,385 unlinked SNPs. Rectangular symbols represent the Danubian (DA) lineage reference, whereas circles indicate trout specimens used in the study. Colors represent the Salmo coruhensis and S. duhani specimens.
Figure 3 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 3 Salmo brunoi, from top: FFR 3216, paratypes, 137 mm SL, male; 105 mm SL, female; Türkiye: stream Aras, a tributary of Nilüfer River.
Figure 5 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 5 Bar plots of the individuals ancestry generated by ADMIXTURE v.1.3.0 using 187,385 unlinked SNPs. Vertical lines represent each individual and color-code defines the ancestry origin with k= 9 groups. Reference trout specimens are: Adriatic (AD), Atlantic (AT) and Danubian (DA) lineage (originates from two different locations), Salmo marmaratus and S. obtusirostris.
Figure 2 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 2 Salmo brunoi, FFR 3243, holotype, 175 mm SL, male; Türkiye: stream Aras, a tributary of Nilüfer River.
Figure 4 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 4 Salmo brunoi, from top: not preserved, ~145 mm SL, male; not preserved, ~150 mm SL, female; Türkiye: stream Aras, a tributary of Nilüfer River.
F I G U R E 3 in Differences in growth between offspring of anadromous and freshwater brown trout Salmo trutta
F I G U R E 3 Temperature from fertilization on 9 November 2018 to hatching (1) and start of feeding (2) of Salmo trutta eggs incubated in cold (solid line) and hot (broken line) water
Supplementary material 1 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
Pairwise distance values (p distance model) based on cytochrome b sequences of Salmo species
Figure 1 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 1 Maximum likelihood (ML) tree based on mitochondrial cytochrome b gene sequences of Salmo species. Bayesian inference and ML analyses resulted in congruent trees. Bootstrap and posterior probability values are shown above nodes on tree if 50% or higher.
Figure 8 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 8 Bayesian inference (BI) phylogenetic tree based on Cyt b sequences of Salmo species. ML and BI methods generated the similar topologies and therefore only the BI tree is shown. The bootstrap values of ML and posterior probability values of BI are indicated on nodes (ML/BI).
Figure 7 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 7 a. Stream Sinek, Murat River, Turkey; type locality of Salmo baliki: b. Stream Alakoçlu; c. Stream Mengel, Murat River Turkey, two new localities of S. munzuricus.
Figure 6 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 6 Salmo okumusi, FFR 3157, 260 mm SL, male; Turkey: stream Gökpınar, a tributary of Tohma River.
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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.
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DANDI Archive for NWB datasets
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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.