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54 results for “Char”
Data from: Assembly ASM291031v2 (Genbank: GCA_002910315.2) identified as assembly of the Northern Dolly Varden (Salvelinus malma malma) genome, and not the Arctic char (S. alpinus) genome
<p>Here is the data that is a supplementary to the preprint: Shedko S.V. 2019. Assembly ASM291031v2 (Genbank: GCA_002910315.2) identified as assembly of the Northern Dolly Varden (Salvelinus malma malma) genome, and not the Arctic char (S. alpinus) genome // arXiv:1912.02474 <a href="https://arxiv.org/abs/1912.02474">https://arxiv.org/abs/1912.02474</a></p>
Data from: Male lake char release taurocholic acid as part of a mating pheromone
<p>The evolutionary origins of sexual preferences for chemical signals remain poorly understood, due, in part, to scant information on the molecules involved. In the current study, we identified a male pheromone in lake char (<em>Salvelinus namaycush</em>) to evaluate the hypothesis that it exploits a nonsexual preference for juvenile odour. In anadromous char species, the odour of stream-resident juveniles guides migratory adults into spawning streams. Lake char are also attracted to juvenile odour but have lost the anadromous phenotype and spawn on nearshore reefs, where juvenile odour does not persist long enough to act as a cue for spawning site selection by adults. Previous behavioural data raised the possibility that males release a pheromone that includes components of juvenile odour. Using metabolomics, we found that the most abundant molecule released by males was also released by juveniles but not females. Tandem mass spectrometry and nuclear magnetic resonance were used to identify the molecule as taurocholic acid (TCA), which was previously implicated as a component of juvenile odour. Additional chemical analyses revealed that males release TCA at high rates via their urine during the spawning season. Finally, picomolar concentrations of TCA attracted prespawning and spawning females but not males. Taken together, our results indicate male lake char release TCA, a mating pheromone, and support the hypothesis that the pheromone is a partial match of juvenile odour.</p> <p><span> </span></p>
Data from: Full-factorial breeding experiment with lake char (lake Geneva, winter 2018/2019)
<p><span>The 'good genes' hypotheses of sexual selection predict that females prefer males with strong ornaments because they are in good health and vigor and can afford the costs of the ornaments. A key assumption of this concept is that male health and vigor are useful predictors of genetic quality and hence offspring performance. We tested this prediction in wild-caught lake char (<em>Salvelinus umbla</em>) whose breeding coloration is known to reveal aspects of male health. We first reanalyzed results from sperm competition trials in which embryos of known parenthood had been raised singly in either a stress- or non-stress environment. Paternal coloration did not correlate with any measures of offspring performance. However, offspring growth was reduced with higher kinship coefficients between the parents. To test the robustness of these first observations, we collected a new sample of wild males and females, used their gametes in a full-factorial <em>in vitro</em> breeding experiment, and singly raised about 3,000 embryos in either a stress- or non-stress environment (stress induced by microbes). Again, paternal coloration did not predict offspring performance, while offspring growth was reduced with higher kinship between the parents. We conclude that, in lake char, the genetic benefits of mate choice would be strongest if females could recognize and avoid genetically related males, while male breeding colors may be more relevant in intra-sexual selection.</span></p>
Fig. 1 in Salmincola markewitschi (Copepoda: Lernaeopodidae) Parasitic on Whitespotted Char, Salvelinus leucomaenis, in a Mountain Stream of Honshu Island, Central Japan
Fig. 1. Salmincola markewitschi, female, NSMT-Cr 28337, from whitespotted char, Salvelinus leucomaenis, from the Zako River, a tributary of the upper Nakatsu River, Nagano Prefecture, central Honshu Island, Japan. A, habitus, lateral view; B, habitus, dorsal view; C, cephalothorax, second maxillae and bulla, anterior view; D, first antenna, dorsal view; E, second antenna, anterolateral view; F, exopod of second antenna, lateral view; G, H, mandibles, lateral view; I, first maxilla, lateral view; J, maxilliped, dorsolateral view; K, maxilliped, palp, dorsolateral view. Abbreviations: h1, hook 1; p, palp; p4, process 4; p5, process 5; s2, spine 2; t3, tubercle 3. Scale bars: A–C, 1 mm; D, 20 µm; E, 50 µm; F–H, 20 µm; I, 30 µm; J, 100 µm; K, 20 µm.
Full-factorial breeding experiment with lake char (Lake Geneva, winter 2017/2018)
<p>We sampled 16 wild lake char (<em>Salvelinus umbla</em>) and used their gametes to investigate the genetic consequences of different mating scenarios. A full-factorial breeding was used to separate additive genetic from maternal environmental effects, and embryos were raised singly after sublethal exposures to a pathogen, a common pollutant, or water only. In all treatment groups, embryo development was strongly reduced with increased genetic relatedness between the parents. Contrary to predictions of 'good genes' sexual selection, pathogen tolerance of offspring declined with increasing coloration of their fathers.</p> <p>Determination of inbreeding and kinship coefficients: All 10 males and 4 of the 6 females were used in a parallel study that included sperm competition experiments (Nusbaumer et a. 2021). These 14 parents had been prepared in one library for ddRAD sequencing on 2 lanes on an Illumina HIseq 2500 (see de Guttry et al. 2022 for the corresponding 14 gzipped .fastq of these individuals). The remaining 2 females were later genotyped in a different library but again on an Illumina HIseq 2500. After demultiplexing, the 16 individuals were processed together using stacks 2.53, and with the resulting filtered VCF file estimations of kinship and inbreeding have been done. For each individual, the fastq files of the 2 sequencings lanes (2018/2019), or of the replicates within the same library (2021), were merged after demultiplexing using process_radtags (Stacks 2.53). The bash and R scripts are provided. There are no legal or ethical considerations regarding the above-mentioned data.</p>
Text-fig. 4. Charred grass from diatomite of Saint-Bauzile. a: Overview of diatomite slab with one larger specimen of charred grass (left) and several smaller, lath-shaped charcoal fragments; SM.B 22260; scale bar = 1 cm. b: Detail of vein exhibited on split grass blade, with stomata oriented parallel to vein. c: Stomata oriented in rows and bands parallel to veins exposed on split grass blade. d: Surface of grass leaf with rectangular, elongated cells with strongly undulating margins in an intercostal area. in Evidence For Wildfires During Deposition Of The Late Miocene Diatomites Of The Konservat-Lagerstätte Lake Saint-Bauzile (Ardèche, France) - Preliminary Results
Text-fig. 4. Charred grass from diatomite of Saint-Bauzile. a: Overview of diatomite slab with one larger specimen of charred grass (left) and several smaller, lath-shaped charcoal fragments; SM.B 22260; scale bar = 1 cm. b: Detail of vein exhibited on split grass blade, with stomata oriented parallel to vein. c: Stomata oriented in rows and bands parallel to veins exposed on split grass blade. d: Surface of grass leaf with rectangular, elongated cells with strongly undulating margins in an intercostal area.
Text-fig. 2. Charred fern from diatomite of Saint-Bauzile. a: Overview of diatomite slab with large fragment of charred fern; SM.B 22258; scale bar = 1 cm. b: SEM overview image of charred fern pinnule. c: Enlargement of (b) showing details of undulating anticlinal walls of the epidermis. in Evidence For Wildfires During Deposition Of The Late Miocene Diatomites Of The Konservat-Lagerstätte Lake Saint-Bauzile (Ardèche, France) - Preliminary Results
Text-fig. 2. Charred fern from diatomite of Saint-Bauzile. a: Overview of diatomite slab with large fragment of charred fern; SM.B 22258; scale bar = 1 cm. b: SEM overview image of charred fern pinnule. c: Enlargement of (b) showing details of undulating anticlinal walls of the epidermis.
Variations in microscopic properties of biomass char: Implications for biochar characterization
<p><strong>Submitted data was used to write an article:</strong> <span>Mastalerz, M., Drobniak, A., Briggs, D., Bradburn, J., 2023, Variations in microscopic properties of biomass char: Implications for biochar characterization. International Journal of Coal Geology 271, 104235. https://doi.org/10.1016/j.coal.2023.104235</span></p> <p> </p> <p><strong>Funding acknowledgments:</strong> The project is co-financed by the Polish National Agency for Academic Exchange within the Polish Returns Programme (BPN/PPO/2021/1/00005/DEC/1), the National Science Center, Poland (2022/01/1/ST10/00024), and the research activities co-financed by the funds granted under the Research Excellence Initiative of the University of Silesia in Katowice, Poland. </p> <p> </p> <p><strong>Article Abstract</strong>: Biochar, a carbon-rich material produced during the thermochemical conversion of biomass, is considered to be an important material for environmental applications and sustainable agriculture. With interest in its use growing, it is essential to understand how pyrolysis parameters control biochar properties and, subsequently, which analytical methods can be applied effectively in characterizing biochar. While various methods are already in use, the potential of reflected light microscopy analysis has not yet been widely explored. This paper focuses on examining the microscopic properties of various biochars by implementing reflected light microscopy and assessing whether this technique has the potential to deliver quick, reliable, and essential information for biochar characterization. To support microscopic observations, selected physical (density and surface area) and chemical parameters (carbon and sulfur content, functional group distribution) of biochar samples were also determined. Megascopically and microscopically there is a considerable difference among biochars of different feeds including their size and shape, porosity, ratio of the abundance of cellular to non-cellular pores, inorganic matter content, the ratio of thick-walled to thin-walled inertinite, or the ratio between high-reflectance inertinite to low reflectance inertinite and their reactivity. The biochars studied also showed variations in the oxygenated groups contribution, a wide range of carbon content (14.7 to 98.8%), density (1.45 to 2.47 g/cm3), and surface areas (from <1 to 363.6 m2/g). Our results demonstrate that microscopic characteristics and reflectance of biochar can provide crucial diagnostic value for predicting biochar properties and, in combination with other physical and chemical properties, help to enhance information about the biomass conversion process and potential practical use of biochar.</p>
Fig. 3 in Two Copepods Salmincola edwardsii and Salmincola markewitschi (Lernaeopodidae) Parasitic on Chars (Salvelinus spp.) Reared in a Salmon Museum, Northern Japan
Fig. 3. Salmincola markewitschi, female, NSMT-Cr 28446, from whitespotted char, Salvelinus leucomaenis, reared in the Sapporo Salmon Museum, Hokkaido, Japan. Formalin-fixed and preserved specimen. A, Habitus, ventrolateral view; B, second antenna, distal half, ventral view; C, mandible, lateral view; D, first maxilla, lateral view; E, maxilliped, lateral view; F, palp of maxilliped. Abbreviations: ex, exopod; h1, hook 1; p, palp; pap, papilla; p4, process 4; p5, process 5; s2, spine 2; t3, tubercle 3. Scale bars: A, 1 mm; B, 50 µm; C, 20 µm; D, 30 µm; E, 100 µm; F, 20 µm.
Fig. 2 in Two Copepods Salmincola edwardsii and Salmincola markewitschi (Lernaeopodidae) Parasitic on Chars (Salvelinus spp.) Reared in a Salmon Museum, Northern Japan
Fig. 2. Salmincola edwardsii, female, NSMT-Cr 28445, from southern Asian Dolly Varden, Salvelinus malma krascheninnikova, reared in the Sapporo Salmon Museum, Hokkaido, Japan. Formalin-fixed and preserved specimen. A, Habitus, lateral view; B, second antenna, distal half, ventral view; C, mandible, lateral view; D, first maxilla, lateral view; E, maxilliped, lateral view; F, palp of maxilliped. Abbreviations: ex, exopod; h1, hook 1; p, palp; pap, papilla; p4, process 4; p5, process 5; s2, spine 2. Scale bars: A, 1 mm; B, 50 µm; C, 20 µm; D, 50 µm; E, 100 µm; F, 20 µm.
Fig. 1 in Two Copepods Salmincola edwardsii and Salmincola markewitschi (Lernaeopodidae) Parasitic on Chars (Salvelinus spp.) Reared in a Salmon Museum, Northern Japan
Fig. 1. Salmincola edwardsii (A), female, NSMT-Cr 28445, and Salmincola markewitschi (B–D), females, NSMT-Cr 28446–28448, from chars reared in the Sapporo Salmon Museum, Hokkaido, Japan. Formalin-fixed and preserved specimens (A–C) and ethanol-fixed and preserved specimen (D), lateral views. A, From southern Asian Dolly Varden, Salvelinus malma krascheninnikova; B, from whitespotted char, Salvelinus leucomaenis; C, from Nikko char, Salvelinus leucomaenis pluvius; D, from brook trout, Salvelinus fontinalis. Scale bars: A, D, 1 mm; B, C, 2 mm.
Effects of Charring on Squash (Cucurbita L ) Seed Morphology and Compression Strength: Implications for Paleoethnobotany Metric Data
<p>Metric data resulting from a series of charring experiments on seeds from three species of squash: <em>Cucurbita pepo</em>, <em>Cucurbita moschata</em>, and <em>Cucurbita maxima</em>.</p>
Full-factorial breeding experiment with lake char (Lake Geneva, winter 2017/2018)
Open the record for dataset details and reuse information.
Data from: Male lake char release taurocholic acid as part of a mating pheromone
Open the record for dataset details and reuse information.
Data from: Full-factorial breeding experiment with lake char (lake Geneva, winter 2018/2019)
Open the record for dataset details and reuse information.
Sperm competition experiment with lake char (Lake Geneva 2017/18)
<p><span>Male and female wild lake char (</span><em>Salvelinus umbla</em>) <span>were sampled from Lake Geneva in December 2017 and December 2018. Male size and colouration (all samples, N = 34) were compared to milt characteristics. For the 2017 samples, m</span><span>ilt characteristics were also determined after sperm activation in diluted ovarian fluid or </span><span>water only, and the gametes were used in sperm competition trials:</span><span> Equal numbers of sperm competed for fertilization in the presence or absence of ovarian fluids. The resulting embryos were raised singly in an environment that supports symbiotic microbes (sublethal stress) or in a clean environment, and microsatellite markers were used to assign in total 1,464 embryos (from 70 experimental trials) to their fathers. Overall, the sperm of more colourful males were faster and reached higher fertilization success than the sperm of pale males. These differences were enhanced by the presence of ovarian fluids. The primary sex ratio did not differ among families and was about 1:1. Female embryos hatched on average later and showed lower stress tolerance than male embryos. There were significant parental effects on offspring growth and mortality, but the sex differences in embryo performance were not family-specific. Offspring of yellow males seemed less stress-tolerant than those of pale males, and embryo development was slowed down with increasing genetic similarity between the parents.</span></p>
Investigating the morphological and genetic divergence of arctic char (Salvelinus alpinus) populations in lakes of arctic Alaska
<p>Polymorphism facilitates coexistence of divergent morphs (e.g., phenotypes) of the same species by minimizing intraspecific competition, especially when resources are limiting. Arctic char (<i>Salvelinus</i> <i>sp</i>.) are a Holarctic fish often forming morphologically, and sometimes genetically, divergent morphs. In this study, we assessed the morphological and genetic diversity and divergence of 263 individuals from seven populations of arctic char with varying length-frequency distributions across two distinct groups of lakes in northern Alaska. Despite close geographic proximity, each lake group occurs on landscapes with different glacial ages and surface water connectivity, and thus were likely colonized by fishes at different times. Across lakes, a continuum of physical (e.g., lake area, maximum depth) and biological characteristics (e.g., primary productivity, fish density) exists, likely contributing to characteristics of present-day char populations. Although some lakes exhibit bimodal size distributions, using model-based clustering of morphometric traits corrected for allometry, we did not detect morphological differences within and across char populations. Genomic analyses using 15,934 SNPs obtained from genotyping-by-sequencing demonstrated differences among lake groups related to historical biogeography, but within lake groups and within individual lakes, genetic differentiation was not related to total body length. We used PERMANOVA to identify environmental and biological factors related to observed char size structure. Significant predictors included water transparency (i.e., a primary productivity proxy), char density (fish·ha<sup>-1</sup>), and lake group. Larger char occurred in lakes with greater primary production and lower char densities, suggesting less intraspecific competition and resource limitation. Thus, char populations in more productive and connected lakes may prove more stable to environmental changes, relative to food-limited and closed lakes, if lake productivity increases concomitantly. Our findings provide some of the first descriptions of genomic characteristics of char populations in arctic Alaska, and offer important consideration for the persistence of these populations for subsistence and conservation.</p>
Morphometric trait measurements of Arctic char in foothill lakes of arctic Alaska
<p class="CxSpFirst">Polymorphism facilitates coexistence of divergent morphs (e.g., phenotypes) of the same species by minimizing intraspecific competition, especially when resources are limiting. Arctic char <i>(Salvelinus sp</i>.) are a Holarctic fish often forming morphologically, and sometimes genetically, divergent morphs. In this study, we assessed the morphological and genetic diversity and divergence of 263 individuals from seven populations of arctic char with varying length-frequency distributions across two distinct groups of lakes in northern Alaska. Despite close geographic proximity, each lake group occurs on landscapes with different glacial ages and surface water connectivity, and thus were likely colonized by fishes at different times. Across lakes, a continuum of physical (e.g., lake area, maximum depth) and biological characteristics (e.g., primary productivity, fish density) exists, likely contributing to characteristics of present-day char populations. Although some lakes exhibit bimodal size distributions, using model-based clustering of morphometric traits corrected for allometry, we did not detect morphological differences within and across char populations. Genomic analyses using 15,934 SNPs obtained from genotyping-by-sequencing demonstrated differences among lake groups related to historical biogeography, but within lake groups and within individual lakes, genetic differentiation was not related to total body length. We used PERMANOVA to identify environmental and biological factors related to observed char size structure. Significant predictors included water transparency (i.e., a primary productivity proxy), char density (fish·ha<sup>-1</sup>), and lake group. Larger char occurred in lakes with greater primary production and lower char densities, suggesting less intraspecific competition and resource limitation. Thus, char populations in more productive and connected lakes may prove more stable to environmental changes, relative to food-limited and closed lakes, if lake productivity increases concomitantly. Our findings provide some of the first descriptions of genomic characteristics of char populations in arctic Alaska, and offer important consideration for the persistence of these populations for subsistence and conservation.</p>
Inbreeding and kinship coefficients of parents of sperm competition experiment with lake char (Lake Geneva 2017/18)
<p>A total of 14 lake char (<em>Salvelinus umbla</em>) were genotyped in the same library using ddRADsequencing. The data includes 14 gzipped .fastq files generated using 2 lanes of sequencing on an Illumina HIseq 2500 and the final dataset with the final estimates of kinship and inbreeding. For each individual, the fastq files of the 2 sequencings lanes were merged after demultiplexing using <em>process_radtags</em> (Stacks 1.48). We provide the bash and R scripts that we used. There are no legal or ethical considerations regarding the above-mentioned data.</p>
Climate change vulnerability of Arctic char across Scandinavia
<p>Data and code for the paper "Climate change vulnerability of Arctic char across Scandinavia" by Muhlfeld et al. (2024) accepted in the journal <em>Global Change Biology</em>. This an extensive fish community and environmental dataset for 1,762 lakes sampled across Scandinavia (mid-1990s) that were used to model the climate vulnerability of Arctic char (<em>Salvelinus alpinus</em>) under baseline (1990s) and future climate warming scenarios (2050s and 2080s). </p>
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