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2,331 results for “Polymorphic”
Data from: Association genetics of growth and adaptive traits in loblolly pine (Pinus taeda L.) using whole-exome-discovered polymorphisms
In the United States, forest genetics research began over 100 years ago and loblolly pine breeding programs were established in the 1950s. However, the genetics underlying complex traits of loblolly pine remains to be discovered. To address this, adaptive and growth traits were measured and analyzed in a clonally tested loblolly pine (Pinus taeda L.) population. Over 2.8 million single nucleotide polymorphism (SNP) markers detected from exome sequencing were used to test for single locus associations, SNP-SNP interactions and correlation of individual heterozygosity with phenotypic traits. A total of 36 SNP-trait associations were found for specific leaf area (5 SNPs), branch angle (2), crown width (3), stem diameter (4), total height (9), carbon isotope discrimination (4), nitrogen concentration (2), and pitch canker resistance traits (7). Eleven SNP-SNP interactions were found to be associated with branch angle (1 SNP-SNP interaction), crown width (2), total height (2), carbon isotope discrimination (2), nitrogen concentration (1), and pitch canker resistance (3). Non-additive effects imposed by dominance and epistasis account for a large fraction of the genetic variance for the quantitative traits. Genes that contain the identified SNPs have a wide spectrum of functions. Individual heterozygosity positively correlated with water use efficiency and nitrogen concentration. In conclusion, multiple effects identified in this study influence the performance of loblolly pines, provide resources for understanding the genetic control of complex traits, and have potential value for assessing with breeding through marker assisted selection and genomic selection.
Orthology guided transcriptome assembly of Italian ryegrass and meadow fescue for single nucleotide polymorphisms discovery (data set)
<p>Transcriptome sequencing was performed on ten samples (corresponding to six genotypes) of <em>Festuca pratensis</em> and ten samples (corresponding to six genotypes) of <em>Lolium multiflorum</em> and fourteen samples of<em> Lolium perenne</em> (corresponding to fourteen genotypes). Using the OGA approach, 18,952 non-redundant <em>F. pratensis</em> transcripts were assembled by combining the contigs of all six genotypes based on orthology with the <em>Brachypodium distachyon </em>proteome. Similarly, <em>19,036</em> non-redundant<em> L. multiflorum</em> transcripts were assembled and annotated. In total, 17,455 orthologous transcripts were shared between the transcriptomes of the two species. Out of these, 16,613 orthologous transcripts overlap with the previously published<em> L. perenne</em> transcriptome containing 19,279 non-redundant transcripts(fasta files). We identified SNPs, the following criteria were used to classify it as one of following three classes (1) intraspecific SNPs (INTRA), (2) interspecific SNPs in two-way comparison (INTER-2W) and (3) interspecific SNPs in three-way comparison (INTER-3W) (GFF files).</p>
FIGURE 5 in Sponge epizoism in the Caribbean and the discovery of new Plakortis and Haliclona species, and polymorphism of Xestospongia deweerdtae (Porifera)
FIGURE 5 Haliclona plakophila sp. nov. (A-B) holotype (USNM 1254650) growing on Plakortis symbiotica sp. nov. (brown), encrusting (A) and papillated (B); (C) tangential section of the ectosome (LM); (D) perpendicular section through the ectosome and choanosome (LM); (E) close-up of a perpendicular section of the choanosome (LM); (F) oxeas (SEM).
FIGURE 4 in Sponge epizoism in the Caribbean and the discovery of new Plakortis and Haliclona species, and polymorphism of Xestospongia deweerdtae (Porifera)
FIGURE 4 Maximum likelihood topology generated from partial sequences of cytochrome b oxidase (cob) (A) and cytochrome c oxidase subunit I (cox 1) (B) of the Homoscleromorpha of this study and from sequences downloaded from GenBank. Topology for both trees is rooted on the sponge Ectyoplasia ferox (Duchassaing & Michelloti, 1864) EU 23748.1 (Class Demospongiae, Order Axinellida). Bootstrap values less than 50 % were omitted from the trees. Coding following the species names refers to the museum catalogue number or collection location (PA-Panama, PR- Puerto Rico, BH-Bahamas) followed by lifestyle (AS-associated, FL-free-living). Species highlighted in bold represented sequences provided by this study.
FIGURE 2 in Sponge epizoism in the Caribbean and the discovery of new Plakortis and Haliclona species, and polymorphism of Xestospongia deweerdtae (Porifera)
FIGURE 2. Plakortis deweerdtaephila sp. nov. (A) holotype (USNM 1254645) (basibiont-brown) fully overgrown by Xestospongia deweerdtae (epibiont-pink) in Panama; the specimen has been uplifted from the bottom to show the basibiont; oscules directed downwards are visible; (B) Bahamas USNM 1254647 (brown) partially overgrown by X. deweerdtae (pink); (C) tangential section of the ectosome (LM); (D) perpendicular section through the ectosome and choanosome (LM); (E) closeup of a perpendicular section through the choanosome (LM); (F) diods from specimens from Panama (SEM); (G-H) diods from specimens collected in the Bahamas (SEM); (I) triods from specimens from Panama (SEM).
FIGURE 1 in Sponge epizoism in the Caribbean and the discovery of new Plakortis and Haliclona species, and polymorphism of Xestospongia deweerdtae (Porifera)
FIGURE 1. Collection sites of Plakortis deweerdtaephila sp. nov., Plakortis symbiotica sp. nov., Haliclona plakophila and Xestospongia deweerdtae in the Caribbean. (A) Detailed map of sponge species and sponge pair locations for the Bahamas (Little San Salvador, San Salvador, Hogsty Reef, Acklins, Mayaguana, Mira Por Voz, Plana Cays, Little Inagua, Great Inagua) (B), Mexico (Cozumel, Banco Chinchorro) (C), Puerto Rico (Mona, Desecheo, La Parguera) (D), and Panama (Bocas del Toro Province) (E). A list of sponge species and their lifestyle are indicated in the legend on panel B. The Plakortis symbiotica and Haliclona plakophila pair has been found only on the south coast of Puerto Rico.
FIGURE 3 in Sponge epizoism in the Caribbean and the discovery of new Plakortis and Haliclona species, and polymorphism of Xestospongia deweerdtae (Porifera)
FIGURE 3 Plakortis symbiotica sp. nov. (A) holotype (USNM 1254650) (brown) being overgrown by Xestospongia deweerdtae (pink) with zoanthids (red) in situ; (B) tangential section of the ectosome (LM); (C) perpendicular section through the ectosome and choanosome (LM); (D) close-up of a perpendicular section through the choanosome (LM); (E-F) diods (SEM); (G) triods (SEM).
Comparing photoelectrochemical water oxidation, recombination kinetics and charge trapping in the three polymorphs of TiO2
<p>Please find the TA data sets and the model calculation of rutile attached. Note that the data is normalised to the amplitude at 100 us.</p>
Data from: Ontogeny of color development in two green-brown polymorphic grasshopper species
<p class="MsoNormal">Many insects, including several orthopterans, undergo dramatic changes in body coloration during ontogeny. This variation is particularly intriguing in gomphocerine grasshoppers, where the green and brown morphs appear to be genetically determined (Schielzeth & Dieker, 2020; Winter, Varma, & Schielzeth, 2021). A better understanding of how these color morphs develop during ontogeny can provide valuable insights into the evolution and ecology of such a widespread color polymorphism. Here, we focus on the color development of two green-brown polymorphic species, the club-legged grasshopper <em>Gomphocerus sibiricus </em>and the steppe grasshopper <em>Chorthippus</em> <em>dorsatus</em>. By following the color development of individuals from hatching to adulthood, we found that color morph differences begin to develop during the second nymphal stage,<span> are clearly defined by the third nymphal stage,</span> and remain stable throughout the life of an individual. Interestingly, we also observed that <span>shed skins of late nymphal stages are identifiable by color morphs based on their yellowish coloration, rather than the green that marks green body parts. </span>Furthermore, by assessing how these colors are perceived by different visual systems, we found that certain potential predators can chromatically discriminate between morphs, while others may not. These results suggest that the putative genes controlling color morph are active during the early stages of ontogeny, and that green color is likely composed of two components, one present in the cuticle and one not. In addition, the effectiveness of camouflage appears to vary depending on the specific predator involved.</p>
Germline CpG methylation signatures in the human population inferred from genetic polymorphism
<p>This repository contains data released accompanying the manuscript "Germline CpG methylation signatures in the human population inferred from genetic polymorphism". </p>
Preferential cannibalism as a key stabilizing mechanism of intraguild predation systems with trophic polymorphic predators
<p><span>Theory predicts intraguild predation (IGP) to be unstable despite its ubiquity in nature, prompting exploration of stabilizing mechanisms of IGP. One of the many ways IGP manifests is through inducible trophic polymorphisms in the intraguild (IG) predator, where a resource-eating predator morph competes with the intraguild (IG) prey for the shared resource while a top predator morph consumes the IG prey. Cannibalism is common in this type of system due to the top predator morph's specialization on the trophic level below it, which includes the resource-eating predator morph. Here, we explore the consequences of inducible trophic polymorphisms in cannibal predators for IGP stability using an IGP model with and without cannibalism. We employ linear stability analysis and identify regions of coexistence based on the top predator morph's preference for conspecifics vs. heterospecifics and the IG prey's competitive ability relative to the resource-eating morph. Our findings reveal preferential cannibalism (i.e. the preferential consumption of conspecifics) stabilizes the system when the IG prey and resource-eating morph have similar competitive abilities for the shared resource. Though original IGP theory finds the IG prey must be a superior resource competitor as a general criterion for coexistence, this is not typically the case when the predator has an inducible trophic polymorphism and the resource-eating morph is specialized in resource acquisition. Preferential cannibalism may therefore be a key stabilizing mechanism in IGP systems with a cannibalistic, trophic polymorphic IG predators, providing further insight into what general mechanisms stabilize the pervasive IGP interaction.</span></p>
Data from: Exploring polymorphism in a palatable prey: Predation risk and frequency-dependence in relation to distinct levels of conspicuousness
<p>Camouflage and warning signals are different anti-predator strategies, which offer an excellent opportunity to study the evolutionary forces acting on prey appearance. Edible prey often escape detection via camouflage, which usually leads to apostatic selection favoring rare morphs. By contrast, defended prey often display conspicuous coloration acting as warning signals to predators, which usually leads to positive frequency-dependence and signal uniformity. However, when two morphs of the same species vary greatly in conspicuousness, the maintenance of both cryptic and conspicuous forms in profitable prey populations remains enigmatic. Using the white and melanic morphs of the invasive box tree moth (<em>Cydalima perspectalis</em>) presented at three different frequencies, we investigate a) the palatability of caterpillars and adult moths to birds, b) predation rates on the less conspicuous melanic morph, and c) the role of frequency-dependence in balancing morph frequencies. Our results show that caterpillars are distasteful for birds but not adult moths, which are fully palatable. We found that the less conspicuous, melanic morph, benefits from reduced predation due to its lower detectability. The more conspicuous, white morph, instead, is more predated and is best off when common, suggesting positive-frequency dependence. These results offer new insights into the evolution of color polymorphism and prey defenses in a polymorphic moth species. Further investigation is required to understand the role of different predation regimes on the maintenance of the polymorphism in this species, and test if additional selection pressures operate in natural populations.</p>
Elucidating the Polymorphism of Xanthone: A Crystallization and Characterization Study
<p>Dataset related to the publication: "Elucidating the Polymorphism of Xanthone: A Crystallization and Characterization Study". Accepted in Crystal Growth and Design on February 9th, 2024.</p> <p>Abstract: The aim of this work is to shed light on the polymorphism of xanthones, a class of oxygenated molecules well known for their bioactivity, including antioxidant, anticancer, and anti-inflammatory effects. Understanding the polymorphism of xanthones can enable the design of novel solid products for pharmaceutical, nutraceutical, and agrochemical applications. Prior to this work, two entries accounting for different space groups were deposited for 9-xanthone in the Cambridge Structure Database (CSD): an orthorhombic P212121 and a monoclinic P21 structure solved at room and low temperatures, respectively. However, the very high similarity between these two structures and the lack of clear differences in the physical properties (e.g., thermal behavior) suggested the possibility of the existence of only one crystal structure. In fact, the differences shown in the literature data might be related to the chosen operating parameters, as well as the instrumental resolution of the single-crystal X-ray diffraction experiments. In the work presented here, the ambiguity in the polymorphism of xanthone is investigated using thermal analysis, powder and synchrotron single-crystal XRD, and optical microscopy. Additionally, a workflow for the correct identification of twinned crystal structures, which can be applied to other polymorphic systems, is presented. Such workflow combines the collection of a large data set of high-resolution diffraction patterns using synchrotron radiation with the use of principal component analysis, a dimensionality reduction technique, for a quick and effective identification of phase transitions happening during the data collection. Crystallization experiments were designed to promote the formation of different crystal structures of xanthone that were recrystallized based on past literature and beyond.</p>
F I G U R E 3 A in A low-density single nucleotide polymorphism panel for brown trout (Salmo trutta L.) suitable for exploring genetic diversity at a range of spatial scales
F I G U R E 3 A priori discriminant analysis of principal components (DAPC) plot of Camel trout. Each point represents the genotype of an individual fish, with centroids for each site labelled. Discriminant function 1 (DF1) is represented by the x axis, and discriminant function 2 (DF2) by the y-axis
F I G U R E 1 in A low-density single nucleotide polymorphism panel for brown trout (Salmo trutta L.) suitable for exploring genetic diversity at a range of spatial scales
F I G U R E 1 Map showing the location of rivers sampled for brown trout within the UK, France and Ireland. The left panel shows the rivers used to assess the performance of the single nucleotide polymorphisms (SNP) panel at characterising genetic parameters within and outside the target region. The top right (blue) panel shows the locations of the four sampled rivers in Mount's Bay, Cornwall (Case Study 1). The bottom right (red) panel shows the location of the sample locations in the Camel catchment (Case Study 2). The red box within the bottom right panel gives the position of the impassable De Lank quarry site
F I G U R E 2 A in A low-density single nucleotide polymorphism panel for brown trout (Salmo trutta L.) suitable for exploring genetic diversity at a range of spatial scales
F I G U R E 2 A priori discriminant analysis of principal components (DAPC) of trout genotypes from rivers flowing into Mount's Bay, Cornwall. Individuals are represented by individual points, with centroids for each river labelled. Discriminant function 1 (DF1) is represented by the x axis, and discriminant function 2 (DF2) by the y-axis
F I G U R E 4 in A low-density single nucleotide polymorphism panel for brown trout (Salmo trutta L.) suitable for exploring genetic diversity at a range of spatial scales
F I G U R E 4 Correlation between geographic distance (km) against genetic distance (linear FST) for the trout samples from the River Camel. The red points represent those between the De Lank and all other sites, the black points for all pair-wise comparisons excluding the De Lank. Linear regression for all sites including the De Lank is given by the red line (r2 = 0.321, P = 0.231), and linear regression for all pair-wise sites excluding the De Lank is given by the black line (r2 = 0.658, P = 0.0671)
Single nucleotide polymorphism (SNPs) data for Scurria scurra, Scurria variabilis, Scurria ceciliana and Scurria araucana
<p>The distribution of genetic diversity is often heterogeneous in space, and it usually correlates with environmental transitions or historical processes that affect demography. The coast of Chile encompasses two biogeographic provinces and spans a broad environmental gradient together with oceanographic processes linked to coastal topography that can affect species' genetic diversity. Here, we evaluated the genetic connectivity and historical demography of four <em>Scurria</em> limpets, <em>S. scurra, S. variabilis, S. ceciliana</em> and <em>S. araucana</em>, between ca. 19° S and 53° S in the Chilean coast using genome-wide SNPs markers. Genetic structure varied among species which was evidenced by species-specific breaks together with two shared breaks. One of the shared breaks was located at 22–25° S and was observed in <em>S. araucana</em> and <em>S. variabilis</em>, while the second break around 31–34° S was shared by three <em>Scurria</em> species. Interestingly, the identified genetic breaks are also shared with other low-disperser invertebrates. Demographic histories show bottlenecks in <em>S. scurra</em> and <em>S. araucana</em> populations and recent population expansion in all species. The shared genetic breaks can be linked to oceanographic features acting as soft barriers to dispersal and also to historical climate, evidencing the utility of comparing multiple and sympatric species to understand the influence of a particular seascape on genetic diversity.</p>
Supplemental data for: Structural polymorphism and diversity of human segmental duplications
<p>Data used for figure generation and analysis in: Structural polymorphism and diversity of human segmental duplications</p> <p> </p> <p>Code used for data analysis is on https://github.com/hrrsjeong/pangenome_SD</p>
Genetic polymorphisms in COMT and BDNF influence synchronization dynamics of human neuronal oscillations
<p>Neuronal oscillations, their inter-areal synchronization, and scale-free dynamics constitute fundamental mechanisms for cognition by regulating communication in neuronal networks. These oscillatory dynamics have large inter-individual variability that is partly heritable. We hypothesized that this variability could be partially explained by genetic polymorphism in neuromodulatory genes. We recorded resting-state magnetoencephalography (MEG) from 82 healthy participants and investigated whether oscillation dynamics were influenced by genetic polymorphisms in Catechol-O-methyltransferase (COMT) Val<sup>158</sup>Met and brain-derived neurotrophic factor (BDNF) Val<sup>66</sup>Met. Both COMT and BDNF polymorphisms influenced local oscillation amplitudes and their long-range temporal correlations (LRTCs), while only BDNF polymorphism affected the strength of large-scale synchronization. Our findings demonstrate that COMT and BDNF genetic polymorphisms contribute to inter-individual variability in neuronal oscillation dynamics. Comparison of these results to computational modeling of near-critical synchronization dynamics further suggested that COMT and BDNF polymorphisms influenced local oscillations by modulating the excitation-inhibition balance according to the brain criticality framework.</p>
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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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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.